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Conserved domains on  [gi|124358955|ref|NP_849211|]
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protein SON isoform 1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 2387-2437 3.85e-28

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380699  Cd Length: 75  Bit Score: 109.29  E-value: 3.85e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124358955 2387 GKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPYQPNC 2437
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSV 51
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 2323-2367 6.00e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


:

Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 76.39  E-value: 6.00e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 124358955  2323 TGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2367
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
rne super family cl35953
ribonuclease E; Reviewed
 1323-1501 1.65e-10

ribonuclease E; Reviewed


The actual alignment was detected with superfamily member PRK10811:

Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 66.99  E-value: 1.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1323 PAVTISQPAENSLELPSMTVPAPstmTTTESPVVAVTEippVAVPEPPIMAVPELPTMAVVKTPAVAVPEPLVAAPEPPT 1402
Cdd:PRK10811  846 PVVRPQDVQVEEQREAEEVQVQP---VVAEVPVAAAVE---PVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEV 919

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1403 MATPelcslsvseppvaVSELPALADPEHAITAVSGVSSLEPSVPILEPAVSVLQPV----MIVSEPSVPVQEPTVAVSE 1478
Cdd:PRK10811  920 IAAP-------------VTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAetaeVVVAEPEVVAQPAAPVVAE 986

                         170       180
                  ....*....|....*....|...
gi 124358955 1479 PAVIVSEHtqiTSPEMAVESSPV 1501
Cdd:PRK10811  987 VAAEVETV---TAVEPEVAPAQV 1006
PspC_subgroup_2 super family cl41463
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 173-456 1.12e-08

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


The actual alignment was detected with superfamily member NF033839:

Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 60.55  E-value: 1.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  173 GLSEASETALVLEPPVVSMEVQESHVLETLKPATKAA---ELSVVSTSVISEQSEQPMPGmLEPSMTKILDSFTaaPVPM 249
Cdd:NF033839  146 DSSSSSSSGSSTKPETPQPENPEHQKPTTPAPDTKPSpqpEGKKPSVPDINQEKEKAKLA-VATYMSKILDDIQ--KHHL 222

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  250 STAALKSPEPVVTMSVEYQKSVLKSLETMPPETSKTTLVELPIAKV--VEPSETLTIVSETPTE-VHPEPS---PSTMDF 323
Cdd:NF033839  223 QKEKHRQIVALIKELDELKKQALSEIDNVNTKVEIENTVHKIFADMdaVVTKFKKGLTQDTPKEpGNKKPSapkPGMQPS 302

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  324 PESSTTDVQRLPEQPVEAPSEIADSSMTRPQESLELPKTTA---VELQESTVASALELPGPPATSILELQGPPVTPVPEL 400
Cdd:NF033839  303 PQPEKKEVKPEPETPKPEVKPQLEKPKPEVKPQPEKPKPEVkpqLETPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPET 382

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 124358955  401 PGPSATPVPELSGPLSTPVPELPGPPATVVPELPGPSVTPVPQLSQE--LPGPPAPSM 456
Cdd:NF033839  383 PKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPevKPQPEKPKP 440
PHA03379 super family cl33730
EBNA-3A; Provisional
 333-641 2.26e-05

EBNA-3A; Provisional


The actual alignment was detected with superfamily member PHA03379:

Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 50.06  E-value: 2.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  333 RLPEQPVEAPSEIADSSMTRPQESLELPKTTAVE-LQESTVASALELPGPPATSILElQGP---------------PVTP 396
Cdd:PHA03379  396 KLTERAREALEKASEPTYGTPRPPVEKPRPEVPQsLETATSHGSAQVPEPPPVHDLE-PGPlhdqhsmapcpvaqlPPGP 474

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  397 VP------ELPG------PSATPVPELSGPLSTP----VPELPG-PPATVVPE-LPGPSVtPVPQLSQELPGPPAPSMGL 458
Cdd:PHA03379  475 LQdlepgdQLPGvvqdgrPACAPVPAPAGPIVRPweasLSQVPGvAFAPVMPQpMPVEPV-PVPTVALERPVCPAPPLIA 553

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  459 EPPQEVPEPPVMAQELSGVPAVS-------AAIELTGQPA----------VTVAMELTEQPVTTTE--FEQPVAMTTVEH 519
Cdd:PHA03379  554 MQGPGETSGIVRVRERWRPAPWTpnpprspSQMSVRDRLArlraeaqpyqASVEVQPPQLTQVSPQqpMEYPLEPEQQMF 633

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  520 PGHP-----EVTTATGL--LGQPEAAMVLELP---GQPVATTALELSGQPSVTG-------VPELSGLPSATRALELSGQ 582
Cdd:PHA03379  634 PGSPfsqvaDVMRAGGVpaMQPQYFDLPLQQPisqGAPLAPLRASMGPVPPVPAtqpqyfdIPLTEPINQGASAAHFLPQ 713

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 124358955  583 SVATGALeLPGQLMATGALEFSGQSGAAGALELLGQPLATGVLElpGQPGAPELPGQPV 641
Cdd:PHA03379  714 QPMEGPL-VPERWMFQGATLSQSVRPGVAQSQYFDLPLTQPINH--GAPAAHFLHQPPM 769
rne super family cl35953
ribonuclease E; Reviewed
 1191-1393 1.82e-04

ribonuclease E; Reviewed


The actual alignment was detected with superfamily member PRK10811:

Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 46.96  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1191 TEVTLSTGESLSQPEPPVSQSEISEPMAVPAnysmsesETSMLASEAVMTVPEPAREPEssVTSAPVESAVVAEHEMVPE 1270
Cdd:PRK10811  848 VRPQDVQVEEQREAEEVQVQPVVAEVPVAAA-------VEPVVSAPVVEAVAEVVEEPV--VVAEPQPEEVVVVETTHPE 918

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1271 rpmtymVSETTMSVEPAVLT-SEASVISETSETydsmrpsGHAISEVtmsllEPAVTISQPAENSLElpsMTVPAPSTMT 1349
Cdd:PRK10811  919 ------VIAAPVTEQPQVITeSDVAVAQEVAEH-------AEPVVEP-----QDETADIEEAAETAE---VVVAEPEVVA 977

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 124358955 1350 TTESPVVAVTEIPPVAVPEPPIMAVPELPTMAVV----------KTPAVA-VPEP 1393
Cdd:PRK10811  978 QPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVehnhatapmtRAPAPEyVPEA 1032
 
Name Accession Description Interval E-value
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 2387-2437 3.85e-28

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 109.29  E-value: 3.85e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124358955 2387 GKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPYQPNC 2437
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSV 51
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 2323-2367 6.00e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 76.39  E-value: 6.00e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 124358955  2323 TGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2367
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 2321-2367 2.35e-15

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 71.81  E-value: 2.35e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 124358955   2321 PVTGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2367
Cdd:smart00443    1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
rne PRK10811
ribonuclease E; Reviewed
 1323-1501 1.65e-10

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 66.99  E-value: 1.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1323 PAVTISQPAENSLELPSMTVPAPstmTTTESPVVAVTEippVAVPEPPIMAVPELPTMAVVKTPAVAVPEPLVAAPEPPT 1402
Cdd:PRK10811  846 PVVRPQDVQVEEQREAEEVQVQP---VVAEVPVAAAVE---PVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEV 919

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1403 MATPelcslsvseppvaVSELPALADPEHAITAVSGVSSLEPSVPILEPAVSVLQPV----MIVSEPSVPVQEPTVAVSE 1478
Cdd:PRK10811  920 IAAP-------------VTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAetaeVVVAEPEVVAQPAAPVVAE 986

                         170       180
                  ....*....|....*....|...
gi 124358955 1479 PAVIVSEHtqiTSPEMAVESSPV 1501
Cdd:PRK10811  987 VAAEVETV---TAVEPEVAPAQV 1006
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 173-456 1.12e-08

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 60.55  E-value: 1.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  173 GLSEASETALVLEPPVVSMEVQESHVLETLKPATKAA---ELSVVSTSVISEQSEQPMPGmLEPSMTKILDSFTaaPVPM 249
Cdd:NF033839  146 DSSSSSSSGSSTKPETPQPENPEHQKPTTPAPDTKPSpqpEGKKPSVPDINQEKEKAKLA-VATYMSKILDDIQ--KHHL 222

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  250 STAALKSPEPVVTMSVEYQKSVLKSLETMPPETSKTTLVELPIAKV--VEPSETLTIVSETPTE-VHPEPS---PSTMDF 323
Cdd:NF033839  223 QKEKHRQIVALIKELDELKKQALSEIDNVNTKVEIENTVHKIFADMdaVVTKFKKGLTQDTPKEpGNKKPSapkPGMQPS 302

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  324 PESSTTDVQRLPEQPVEAPSEIADSSMTRPQESLELPKTTA---VELQESTVASALELPGPPATSILELQGPPVTPVPEL 400
Cdd:NF033839  303 PQPEKKEVKPEPETPKPEVKPQLEKPKPEVKPQPEKPKPEVkpqLETPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPET 382

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 124358955  401 PGPSATPVPELSGPLSTPVPELPGPPATVVPELPGPSVTPVPQLSQE--LPGPPAPSM 456
Cdd:NF033839  383 PKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPevKPQPEKPKP 440
DSRM smart00358
Double-stranded RNA binding motif;
2390-2433 2.43e-07

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.95  E-value: 2.43e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 124358955   2390 PVSALMEICNKRRWqPPEFLLVHDSGPDHRKHFLFRVLRNGSPY 2433
Cdd:smart00358    1 PKSLLQELAQKRKL-PPEYELVKEEGPDHAPRFTVTVKVGGKRT 43
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
 2390-2441 3.27e-07

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 405408  Cd Length: 80  Bit Score: 50.03  E-value: 3.27e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 124358955  2390 PVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNG--SPYQPNCMFFL 2441
Cdd:pfam14709    3 AVSHLEELCQKNKWGSPVYELHSTAGPDGKQLFTYKVVIPGieTPFPGVIWIFM 56
PHA03247 PHA03247
large tegument protein UL36; Provisional
 233-482 5.25e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 55.71  E-value: 5.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  233 PSMTKILDSFTAAPVPMSTAALKSPEPVVTMSVEYQKSVlksleTMPPETSKTTLVELPIAKVVEPSETLTIVSETPTEV 312
Cdd:PHA03247 2760 PPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESL-----PSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSA 2834

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  313 HPEPSPSTMDFPESSTT---------DVQRLP--EQPV---EAPSEIADSSMTRPQeslelpkttaveLQESTVASALEL 378
Cdd:PHA03247 2835 QPTAPPPPPGPPPPSLPlggsvapggDVRRRPpsRSPAakpAAPARPPVRRLARPA------------VSRSTESFALPP 2902

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  379 PGPPATSILELQGPPVTPVPELPGPSATPVPElsgplSTPVPELPGPPATVVPELPGPS-VTPVPQLSQELPG------- 450
Cdd:PHA03247 2903 DQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP-----PPPRPQPPLAPTTDPAGAGEPSgAVPQPWLGALVPGrvavprf 2977

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 124358955  451 ---PPAPSMgleppqEVPEPPVMAQELSGVPAVSA 482
Cdd:PHA03247 2978 rvpQPAPSR------EAPASSTPPLTGHSLSRVSS 3006
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 209-454 6.22e-06

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 51.69  E-value: 6.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  209 AELSVVSTSVISEQSEQPMPGMLEPSMTKILDSFTA-APVPMSTAALKSPEPVVTMSVEYQKSVLKSlETMPPETSKTTL 287
Cdd:NF033839  246 SEIDNVNTKVEIENTVHKIFADMDAVVTKFKKGLTQdTPKEPGNKKPSAPKPGMQPSPQPEKKEVKP-EPETPKPEVKPQ 324

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  288 VELPIAKVVEPSETltivseTPTEVHPE---PSPSTMDFPESSTTDVQRLPEQPVEAPSEIADSSMTRPQESLELPK--- 361
Cdd:NF033839  325 LEKPKPEVKPQPEK------PKPEVKPQletPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKpev 398

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  362 TTAVELQESTVASALELPGPPATSILELQGPPVTPVPELPGPSATPVPELSGPLSTPVPELPGPPATVVPELPGPSVTPV 441
Cdd:NF033839  399 KPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQ 478

                         250
                  ....*....|...
gi 124358955  442 PQLSQELPGPPAP 454
Cdd:NF033839  479 PEKPKPDNSKPQA 491
PHA03379 PHA03379
EBNA-3A; Provisional
 333-641 2.26e-05

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 50.06  E-value: 2.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  333 RLPEQPVEAPSEIADSSMTRPQESLELPKTTAVE-LQESTVASALELPGPPATSILElQGP---------------PVTP 396
Cdd:PHA03379  396 KLTERAREALEKASEPTYGTPRPPVEKPRPEVPQsLETATSHGSAQVPEPPPVHDLE-PGPlhdqhsmapcpvaqlPPGP 474

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  397 VP------ELPG------PSATPVPELSGPLSTP----VPELPG-PPATVVPE-LPGPSVtPVPQLSQELPGPPAPSMGL 458
Cdd:PHA03379  475 LQdlepgdQLPGvvqdgrPACAPVPAPAGPIVRPweasLSQVPGvAFAPVMPQpMPVEPV-PVPTVALERPVCPAPPLIA 553

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  459 EPPQEVPEPPVMAQELSGVPAVS-------AAIELTGQPA----------VTVAMELTEQPVTTTE--FEQPVAMTTVEH 519
Cdd:PHA03379  554 MQGPGETSGIVRVRERWRPAPWTpnpprspSQMSVRDRLArlraeaqpyqASVEVQPPQLTQVSPQqpMEYPLEPEQQMF 633

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  520 PGHP-----EVTTATGL--LGQPEAAMVLELP---GQPVATTALELSGQPSVTG-------VPELSGLPSATRALELSGQ 582
Cdd:PHA03379  634 PGSPfsqvaDVMRAGGVpaMQPQYFDLPLQQPisqGAPLAPLRASMGPVPPVPAtqpqyfdIPLTEPINQGASAAHFLPQ 713

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 124358955  583 SVATGALeLPGQLMATGALEFSGQSGAAGALELLGQPLATGVLElpGQPGAPELPGQPV 641
Cdd:PHA03379  714 QPMEGPL-VPERWMFQGATLSQSVRPGVAQSQYFDLPLTQPINH--GAPAAHFLHQPPM 769
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1272-1511 7.10e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 48.37  E-value: 7.10e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1272 PMTYMVSETTMSVEPAVLTSEASVISETSETYDSMRPSGHAISEVTMSLlePAVT-----ISQPAEN--SLELPSMTVPA 1344
Cdd:pfam05109  400 PKTLIITRTATNATTTTHKVIFSKAPESTTTSPTLNTTGFAAPNTTTGL--PSSThvptnLTAPASTgpTVSTADVTSPT 477

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1345 PSTMTTTESPVVAvteiPPVAVPEPPIMAVPEL--PTMAVVK-TPAVAVPEPLVAAPEP----PTMATPELCSLSVSEPP 1417
Cdd:pfam05109  478 PAGTTSGASPVTP----SPSPRDNGTESKAPDMtsPTSAVTTpTPNATSPTPAVTTPTPnatsPTLGKTSPTSAVTTPTP 553

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1418 VAVSELPALADPEhaitavsgvsslePSVPIlePAVSVLQPVMIVSEPSVPVQEPTVAVSEPAVIVSEHT-QITSPEMAV 1496
Cdd:pfam05109  554 NATSPTPAVTTPT-------------PNATI--PTLGKTSPTSAVTTPTPNATSPTVGETSPQANTTNHTlGGTSSTPVV 618

                          250
                   ....*....|....*
gi 124358955  1497 ESSPVIVDSSVMSSQ 1511
Cdd:pfam05109  619 TSPPKNATSAVTTGQ 633
rne PRK10811
ribonuclease E; Reviewed
 1191-1393 1.82e-04

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 46.96  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1191 TEVTLSTGESLSQPEPPVSQSEISEPMAVPAnysmsesETSMLASEAVMTVPEPAREPEssVTSAPVESAVVAEHEMVPE 1270
Cdd:PRK10811  848 VRPQDVQVEEQREAEEVQVQPVVAEVPVAAA-------VEPVVSAPVVEAVAEVVEEPV--VVAEPQPEEVVVVETTHPE 918

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1271 rpmtymVSETTMSVEPAVLT-SEASVISETSETydsmrpsGHAISEVtmsllEPAVTISQPAENSLElpsMTVPAPSTMT 1349
Cdd:PRK10811  919 ------VIAAPVTEQPQVITeSDVAVAQEVAEH-------AEPVVEP-----QDETADIEEAAETAE---VVVAEPEVVA 977

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 124358955 1350 TTESPVVAVTEIPPVAVPEPPIMAVPELPTMAVV----------KTPAVA-VPEP 1393
Cdd:PRK10811  978 QPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVehnhatapmtRAPAPEyVPEA 1032
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 82-574 3.26e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 3.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955    82 DLKEASRKSRCVSV--QTDPTDEVPTKKSKKHKKHKNKKKKKKKEKEKKYKRQPEESE--SKLKSHHDGNLESDSFLKFD 157
Cdd:pfam03154   38 DLRSSGRNSPSAAStsSNDSKAESMKKSSKKIKEEAPSPLKSAKRQREKGASDTEEPEraTAKKSKTQEISRPNSPSEGE 117

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   158 SEPSAAALEHPVRAFGLSEASETALVLEPPVVSMEVQESHvletlkpATKAAELSVVSTSVISEQSEQPMPGMLEPSMTK 237
Cdd:pfam03154  118 GESSDGRSVNDEGSSDPKDIDQDNRSTSPSIPSPQDNESD-------SDSSAQQQILQTQPPVLQAQSGAASPPSPPPPG 190

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   238 ILDSFTAAPVPMSTAALKSPEPVVTMSVEYQKSvlksleTMPPETSKTTLVELPIAKVVEPSETLTIV------SETPTE 311
Cdd:pfam03154  191 TTQAATAGPTPSAPSVPPQGSPATSQPPNQTQS------TAAPHTLIQQTPTLHPQRLPSPHPPLQPMtqppppSQVSPQ 264

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   312 VHPEPSPSTMDFP-----ESSTTDVQR-LPEQPVEAPSEIADS------SMTRPQESLELPKTTAVELQESTVASALELP 379
Cdd:pfam03154  265 PLPQPSLHGQMPPmphslQTGPSHMQHpVPPQPFPLTPQSSQSqvppgpSPAAPGQSQQRIHTPPSQSQLQSQQPPREQP 344

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   380 GPPA-TSILELQGPPVTPVPELPGPSATPVP-ELSGPLSTPVP-ELPGPPA----TVVPELPGPSVTPVP-QL---SQEL 448
Cdd:pfam03154  345 LPPApLSMPHIKPPPTTPIPQLPNPQSHKHPpHLSGPSPFQMNsNLPPPPAlkplSSLSTHHPPSAHPPPlQLmpqSQQL 424

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   449 PGPPAPSMGLEPPQEVPEPPVMAQELSGVPAVSAAIELTGQPAVTVAMELTEQPvTTTEFEQPVAMTTVEHPGHPEVTTA 528
Cdd:pfam03154  425 PPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPITPP-SGPPTSTSSAMPGIQPPSSASVSSS 503

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*.
gi 124358955   529 TGLLGQPEAAmvleLPGQPVATTALELSGQPSVTGVPELSGLPSAT 574
Cdd:pfam03154  504 GPVPAAVSCP----LPPVQIKEEALDEAEEPESPPPPPRSPSPEPT 545
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
2380-2433 3.11e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 41.62  E-value: 3.11e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 124358955 2380 AAMKDLSGKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPY 2433
Cdd:COG0571   149 EIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVL 202
 
Name Accession Description Interval E-value
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 2387-2437 3.85e-28

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 109.29  E-value: 3.85e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124358955 2387 GKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPYQPNC 2437
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSV 51
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 2323-2367 6.00e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 76.39  E-value: 6.00e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 124358955  2323 TGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2367
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 2321-2367 2.35e-15

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 71.81  E-value: 2.35e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 124358955   2321 PVTGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2367
Cdd:smart00443    1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
rne PRK10811
ribonuclease E; Reviewed
 1323-1501 1.65e-10

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 66.99  E-value: 1.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1323 PAVTISQPAENSLELPSMTVPAPstmTTTESPVVAVTEippVAVPEPPIMAVPELPTMAVVKTPAVAVPEPLVAAPEPPT 1402
Cdd:PRK10811  846 PVVRPQDVQVEEQREAEEVQVQP---VVAEVPVAAAVE---PVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEV 919

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1403 MATPelcslsvseppvaVSELPALADPEHAITAVSGVSSLEPSVPILEPAVSVLQPV----MIVSEPSVPVQEPTVAVSE 1478
Cdd:PRK10811  920 IAAP-------------VTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAetaeVVVAEPEVVAQPAAPVVAE 986

                         170       180
                  ....*....|....*....|...
gi 124358955 1479 PAVIVSEHtqiTSPEMAVESSPV 1501
Cdd:PRK10811  987 VAAEVETV---TAVEPEVAPAQV 1006
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 173-456 1.12e-08

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 60.55  E-value: 1.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  173 GLSEASETALVLEPPVVSMEVQESHVLETLKPATKAA---ELSVVSTSVISEQSEQPMPGmLEPSMTKILDSFTaaPVPM 249
Cdd:NF033839  146 DSSSSSSSGSSTKPETPQPENPEHQKPTTPAPDTKPSpqpEGKKPSVPDINQEKEKAKLA-VATYMSKILDDIQ--KHHL 222

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  250 STAALKSPEPVVTMSVEYQKSVLKSLETMPPETSKTTLVELPIAKV--VEPSETLTIVSETPTE-VHPEPS---PSTMDF 323
Cdd:NF033839  223 QKEKHRQIVALIKELDELKKQALSEIDNVNTKVEIENTVHKIFADMdaVVTKFKKGLTQDTPKEpGNKKPSapkPGMQPS 302

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  324 PESSTTDVQRLPEQPVEAPSEIADSSMTRPQESLELPKTTA---VELQESTVASALELPGPPATSILELQGPPVTPVPEL 400
Cdd:NF033839  303 PQPEKKEVKPEPETPKPEVKPQLEKPKPEVKPQPEKPKPEVkpqLETPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPET 382

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 124358955  401 PGPSATPVPELSGPLSTPVPELPGPPATVVPELPGPSVTPVPQLSQE--LPGPPAPSM 456
Cdd:NF033839  383 PKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPevKPQPEKPKP 440
DSRM smart00358
Double-stranded RNA binding motif;
2390-2433 2.43e-07

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.95  E-value: 2.43e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 124358955   2390 PVSALMEICNKRRWqPPEFLLVHDSGPDHRKHFLFRVLRNGSPY 2433
Cdd:smart00358    1 PKSLLQELAQKRKL-PPEYELVKEEGPDHAPRFTVTVKVGGKRT 43
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
 2390-2441 3.27e-07

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 405408  Cd Length: 80  Bit Score: 50.03  E-value: 3.27e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 124358955  2390 PVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNG--SPYQPNCMFFL 2441
Cdd:pfam14709    3 AVSHLEELCQKNKWGSPVYELHSTAGPDGKQLFTYKVVIPGieTPFPGVIWIFM 56
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 2388-2433 4.07e-07

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 49.03  E-value: 4.07e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 124358955 2388 KHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPY 2433
Cdd:cd10845     1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVI 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 233-482 5.25e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 55.71  E-value: 5.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  233 PSMTKILDSFTAAPVPMSTAALKSPEPVVTMSVEYQKSVlksleTMPPETSKTTLVELPIAKVVEPSETLTIVSETPTEV 312
Cdd:PHA03247 2760 PPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESL-----PSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSA 2834

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  313 HPEPSPSTMDFPESSTT---------DVQRLP--EQPV---EAPSEIADSSMTRPQeslelpkttaveLQESTVASALEL 378
Cdd:PHA03247 2835 QPTAPPPPPGPPPPSLPlggsvapggDVRRRPpsRSPAakpAAPARPPVRRLARPA------------VSRSTESFALPP 2902

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  379 PGPPATSILELQGPPVTPVPELPGPSATPVPElsgplSTPVPELPGPPATVVPELPGPS-VTPVPQLSQELPG------- 450
Cdd:PHA03247 2903 DQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP-----PPPRPQPPLAPTTDPAGAGEPSgAVPQPWLGALVPGrvavprf 2977

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 124358955  451 ---PPAPSMgleppqEVPEPPVMAQELSGVPAVSA 482
Cdd:PHA03247 2978 rvpQPAPSR------EAPASSTPPLTGHSLSRVSS 3006
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 2389-2422 2.63e-06

second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380692  Cd Length: 67  Bit Score: 46.99  E-value: 2.63e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 124358955 2389 HPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHF 2422
Cdd:cd19863     1 NPVGILQELCVQRRWRLPEYEVEQESGPPHEKEF 34
G-patch_2 pfam12656
G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ...
 2319-2364 2.95e-06

G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.


Pssm-ID: 432700 [Multi-domain]  Cd Length: 61  Bit Score: 46.50  E-value: 2.95e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 124358955  2319 AAPVtGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGL 2364
Cdd:pfam12656   11 KVPV-EEFGAAMLRGMGWKPGQGIGKNKKGDVKPKEYKRRPGGLGL 55
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 1299-1502 5.15e-06

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 52.39  E-value: 5.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1299 TSETYDSMRP--SGHAISEvTMSLLEPAVTISQPAENSLELPSMTVPAPSTMTTTESPVVAVTEIPPVAVPEPPIMAVPE 1376
Cdd:PRK10263  300 TQPEYDEYDPllNGAPITE-PVAVAAAATTATQSWAAPVEPVTQTPPVASVDVPPAQPTVAWQPVPGPQTGEPVIAPAPE 378

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1377 -LPTMAVVKTPAVAVPEPLvAAPEPPTMATPELCSLSVSEPPVAVSELPALADPEHAITAVSGVSSLEPSVPilEPAVSV 1455
Cdd:PRK10263  379 gYPQQSQYAQPAVQYNEPL-QQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQA--EEQQST 455

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 124358955 1456 LQPvmivsepsVPVQEPTVAVSEPAVIVSEHT--QITSPEMAVESSPVI 1502
Cdd:PRK10263  456 FAP--------QSTYQTEQTYQQPAAQEPLYQqpQPVEQQPVVEPEPVV 496
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 2396-2426 6.11e-06

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380698  Cd Length: 70  Bit Score: 45.82  E-value: 6.11e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 124358955 2396 EICNKRRWQPPEFLLVHDSGPDHRKHFLFRV 2426
Cdd:cd19869     2 EICLKRRWPMPVYRCVEEEGPAHAKRFTYMV 32
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 209-454 6.22e-06

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 51.69  E-value: 6.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  209 AELSVVSTSVISEQSEQPMPGMLEPSMTKILDSFTA-APVPMSTAALKSPEPVVTMSVEYQKSVLKSlETMPPETSKTTL 287
Cdd:NF033839  246 SEIDNVNTKVEIENTVHKIFADMDAVVTKFKKGLTQdTPKEPGNKKPSAPKPGMQPSPQPEKKEVKP-EPETPKPEVKPQ 324

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  288 VELPIAKVVEPSETltivseTPTEVHPE---PSPSTMDFPESSTTDVQRLPEQPVEAPSEIADSSMTRPQESLELPK--- 361
Cdd:NF033839  325 LEKPKPEVKPQPEK------PKPEVKPQletPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKpev 398

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  362 TTAVELQESTVASALELPGPPATSILELQGPPVTPVPELPGPSATPVPELSGPLSTPVPELPGPPATVVPELPGPSVTPV 441
Cdd:NF033839  399 KPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQ 478

                         250
                  ....*....|...
gi 124358955  442 PQLSQELPGPPAP 454
Cdd:NF033839  479 PEKPKPDNSKPQA 491
PRK07994 PRK07994
DNA polymerase III subunits gamma and tau; Validated
 1318-1495 1.57e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236138 [Multi-domain]  Cd Length: 647  Bit Score: 50.25  E-value: 1.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1318 MSLL-----EPAVTISQPAENSLELPSMTVPAPSTMTTTESPVVAVTEIPPVAVPEPPIMAVPelptmavvktPAVAVPE 1392
Cdd:PRK07994  351 MTLLrmlafHPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAV----------PLPETTS 420

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1393 PLVAAPEPPTMATPELcSLSVSEPPVAVSELPAlADPEHAITAVSGVSSLEPSVPILEPAVSVlqpvmivsEPSVPVQEP 1472
Cdd:PRK07994  421 QLLAARQQLQRAQGAT-KAKKSEPAAASRARPV-NSALERLASVRPAPSALEKAPAKKEAYRW--------KATNPVEVK 490

                         170       180
                  ....*....|....*....|...
gi 124358955 1473 TVAVSEPAVIVSEHTQITSPEMA 1495
Cdd:PRK07994  491 KEPVATPKALKKALEHEKTPELA 513
rne PRK10811
ribonuclease E; Reviewed
 1311-1492 1.66e-05

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 50.42  E-value: 1.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1311 HAISEVTMSLLEPAVTISQPAEnsleLPSMTVPAPSTMTTTESPVVAVTEIPPVAVPEPPIMAV-PELPTMAVVKTPAVA 1389
Cdd:PRK10811  856 EEQREAEEVQVQPVVAEVPVAA----AVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETThPEVIAAPVTEQPQVI 931

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1390 VPEPLVAAPEPPTMATPelcslsVSEPPVAVSELPALADPEHAITAVSGVSSLEPSVPILEPAVSVLQPvmivsepsvPV 1469
Cdd:PRK10811  932 TESDVAVAQEVAEHAEP------VVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETV---------TA 996

                         170       180
                  ....*....|....*....|...
gi 124358955 1470 QEPTVAVSEPAVIVSEHTQITSP 1492
Cdd:PRK10811  997 VEPEVAPAQVPEATVEHNHATAP 1019
PHA03247 PHA03247
large tegument protein UL36; Provisional
 203-456 1.82e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.71  E-value: 1.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  203 KPATKAAELSVVSTSVISEQSEQPMPGMLEPSMTKildsfTAAPVPMSTAALKSPEPVVTmsveyqksvlksLETMPPET 282
Cdd:PHA03247 2682 RPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALV-----SATPLPPGPAAARQASPALP------------AAPAPPAV 2744

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  283 SKTTLVELPIAKVVEPSETLTIVSETPTEVHPEPSPSTMDFPESSTTDVQR--LPEQPVEAPSEIADSSMTRPQESLELP 360
Cdd:PHA03247 2745 PAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESResLPSPWDPADPPAAVLAPAAALPPAASP 2824

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  361 KTTAVELQESTVASALELPGPPATSI-----------LELQGPPVTPVPELPGPSATPVPELSGPLSTPVPELPGPPATV 429
Cdd:PHA03247 2825 AGPLPPPTSAQPTAPPPPPGPPPPSLplggsvapggdVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQ 2904

                         250       260
                  ....*....|....*....|....*..
gi 124358955  430 VPELPGPSVTPVPQLSQELPGPPAPSM 456
Cdd:PHA03247 2905 PERPPQPQAPPPPQPQPQPPPPPQPQP 2931
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 1363-1481 2.20e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 49.71  E-value: 2.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1363 PVAVPEPPIMAVPELPTMAVVKTPAvAVPEPLVAAPEPPTMATPELCSLSVSEPPVAVSE---LPALADPEHAITAVSGV 1439
Cdd:PRK14951  366 PAAAAEAAAPAEKKTPARPEAAAPA-AAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPApvaAPAAAAPAAAPAAAPAA 444

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 124358955 1440 SSLEPSVPILEPAVSVLQPVMIVSEPSVPVQEPTVAVSEPAV 1481
Cdd:PRK14951  445 VALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAA 486
PHA03379 PHA03379
EBNA-3A; Provisional
 333-641 2.26e-05

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 50.06  E-value: 2.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  333 RLPEQPVEAPSEIADSSMTRPQESLELPKTTAVE-LQESTVASALELPGPPATSILElQGP---------------PVTP 396
Cdd:PHA03379  396 KLTERAREALEKASEPTYGTPRPPVEKPRPEVPQsLETATSHGSAQVPEPPPVHDLE-PGPlhdqhsmapcpvaqlPPGP 474

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  397 VP------ELPG------PSATPVPELSGPLSTP----VPELPG-PPATVVPE-LPGPSVtPVPQLSQELPGPPAPSMGL 458
Cdd:PHA03379  475 LQdlepgdQLPGvvqdgrPACAPVPAPAGPIVRPweasLSQVPGvAFAPVMPQpMPVEPV-PVPTVALERPVCPAPPLIA 553

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  459 EPPQEVPEPPVMAQELSGVPAVS-------AAIELTGQPA----------VTVAMELTEQPVTTTE--FEQPVAMTTVEH 519
Cdd:PHA03379  554 MQGPGETSGIVRVRERWRPAPWTpnpprspSQMSVRDRLArlraeaqpyqASVEVQPPQLTQVSPQqpMEYPLEPEQQMF 633

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  520 PGHP-----EVTTATGL--LGQPEAAMVLELP---GQPVATTALELSGQPSVTG-------VPELSGLPSATRALELSGQ 582
Cdd:PHA03379  634 PGSPfsqvaDVMRAGGVpaMQPQYFDLPLQQPisqGAPLAPLRASMGPVPPVPAtqpqyfdIPLTEPINQGASAAHFLPQ 713

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 124358955  583 SVATGALeLPGQLMATGALEFSGQSGAAGALELLGQPLATGVLElpGQPGAPELPGQPV 641
Cdd:PHA03379  714 QPMEGPL-VPERWMFQGATLSQSVRPGVAQSQYFDLPLTQPINH--GAPAAHFLHQPPM 769
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 315-672 3.35e-05

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 49.40  E-value: 3.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  315 EPSPSTMDFPESSTTDVQRLPeQPVEAPSEIADSSMTRPQESL---ELPKTTAVELQESTVASALELP-GPPATSILELQ 390
Cdd:PHA03307    2 DNAPDLYDLIEAAAEGGEFFP-RPPATPGDAADDLLSGSQGQLvsdSAELAAVTVVAGAAACDRFEPPtGPPPGPGTEAP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  391 GPPVTPVPELPGPSATPVPELSGPLSTP--VPELPGPPATVVPELPGPSvtPVPQLSQELPGPPAPSmgleppqeVPEPP 468
Cdd:PHA03307   81 ANESRSTPTWSLSTLAPASPAREGSPTPpgPSSPDPPPPTPPPASPPPS--PAPDLSEMLRPVGSPG--------PPPAA 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  469 VMAQELSGVPAVSAAIELTGQPAVTVAM-ELTEQPVTTTEFEQPVAMTTVEHPGHPEVttatglLGQPEAAMVLELPGQP 547
Cdd:PHA03307  151 SPPAAGASPAAVASDAASSRQAALPLSSpEETARAPSSPPAEPPPSTPPAAASPRPPR------RSSPISASASSPAPAP 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  548 VATTALELSGQPSVTGVPELSGLPSATRAlELSGQSVATGALELPGQLMATGALEFSG---QSGAAGALELLGQPlatgv 624
Cdd:PHA03307  225 GRSAADDAGASSSDSSSSESSGCGWGPEN-ECPLPRPAPITLPTRIWEASGWNGPSSRpgpASSSSSPRERSPSP----- 298

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 124358955  625 leLPGQPGAPELPGQPVAtVALEISVQSVVTTSELSTMTVSQSLEVPS 672
Cdd:PHA03307  299 --SPSSPGSGPAPSSPRA-SSSSSSSRESSSSSTSSSSESSRGAAVSP 343
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1272-1511 7.10e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 48.37  E-value: 7.10e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1272 PMTYMVSETTMSVEPAVLTSEASVISETSETYDSMRPSGHAISEVTMSLlePAVT-----ISQPAEN--SLELPSMTVPA 1344
Cdd:pfam05109  400 PKTLIITRTATNATTTTHKVIFSKAPESTTTSPTLNTTGFAAPNTTTGL--PSSThvptnLTAPASTgpTVSTADVTSPT 477

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1345 PSTMTTTESPVVAvteiPPVAVPEPPIMAVPEL--PTMAVVK-TPAVAVPEPLVAAPEP----PTMATPELCSLSVSEPP 1417
Cdd:pfam05109  478 PAGTTSGASPVTP----SPSPRDNGTESKAPDMtsPTSAVTTpTPNATSPTPAVTTPTPnatsPTLGKTSPTSAVTTPTP 553

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1418 VAVSELPALADPEhaitavsgvsslePSVPIlePAVSVLQPVMIVSEPSVPVQEPTVAVSEPAVIVSEHT-QITSPEMAV 1496
Cdd:pfam05109  554 NATSPTPAVTTPT-------------PNATI--PTLGKTSPTSAVTTPTPNATSPTVGETSPQANTTNHTlGGTSSTPVV 618

                          250
                   ....*....|....*
gi 124358955  1497 ESSPVIVDSSVMSSQ 1511
Cdd:pfam05109  619 TSPPKNATSAVTTGQ 633
PHA03247 PHA03247
large tegument protein UL36; Provisional
 247-516 7.41e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.40  E-value: 7.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  247 VPMSTAALKSPEPVVTmsveyqksvlkSLETMPPETSKTTLVELPIAKVVEPSETLTIVSETPTEVHPEPSPSTMDFPES 326
Cdd:PHA03247 2568 VPPPRPAPRPSEPAVT-----------SRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAAN 2636

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  327 STTDVQRLPEQPVEAPSEIADSSMTRPqeslelPKTTAVELQESTVASALELPGPPAT-----SILELQGPPVTPVPELP 401
Cdd:PHA03247 2637 EPDPHPPPTVPPPERPRDDPAPGRVSR------PRRARRLGRAAQASSPPQRPRRRAArptvgSLTSLADPPPPPPTPEP 2710

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  402 GP----SATPVPELSG------------PLSTPVPELPG----------PPATVVPELPGPSVTPVPQLSQELPGPPAPS 455
Cdd:PHA03247 2711 APhalvSATPLPPGPAaarqaspalpaaPAPPAVPAGPAtpggparparPPTTAGPPAPAPPAAPAAGPPRRLTRPAVAS 2790

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124358955  456 MGLEPPQEVPEPPVmAQELSGVPAVSAAIELTGQPAVTVAMELTEQPVTTTEFEQPVAMTT 516
Cdd:PHA03247 2791 LSESRESLPSPWDP-ADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSL 2850
rne PRK10811
ribonuclease E; Reviewed
 1354-1503 9.58e-05

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 48.11  E-value: 9.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1354 PVVAVTEIPPVAVPEPPimavpelptmAVVKTPAVAVPEPLVAAPEPPTMATPELCSLSVSEPPVAVSELPALADP-EHA 1432
Cdd:PRK10811  846 PVVRPQDVQVEEQREAE----------EVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVvETT 915

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358955 1433 ITAVSGVSSLEPSVPILEPAVSVLQPVMIVSEPSVPVQEPTVAVSEPA----VIVSEHTQITSPEMAVESSPVIV 1503
Cdd:PRK10811  916 HPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAetaeVVVAEPEVVAQPAAPVVAEVAAE 990
DSRM_A1CF cd19900
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF) and similar ...
 2388-2436 1.24e-04

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF) and similar proteins; A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. It contains three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380729  Cd Length: 81  Bit Score: 42.46  E-value: 1.24e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 124358955 2388 KHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRV--------LRNGSPYQPN 2436
Cdd:cd19900     1 KSPPQILEEICQKNNWGQPVYQLHSTIGPDQRQLFLYKVtipalasqYPNITPFQPN 57
rne PRK10811
ribonuclease E; Reviewed
 1191-1393 1.82e-04

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 46.96  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1191 TEVTLSTGESLSQPEPPVSQSEISEPMAVPAnysmsesETSMLASEAVMTVPEPAREPEssVTSAPVESAVVAEHEMVPE 1270
Cdd:PRK10811  848 VRPQDVQVEEQREAEEVQVQPVVAEVPVAAA-------VEPVVSAPVVEAVAEVVEEPV--VVAEPQPEEVVVVETTHPE 918

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1271 rpmtymVSETTMSVEPAVLT-SEASVISETSETydsmrpsGHAISEVtmsllEPAVTISQPAENSLElpsMTVPAPSTMT 1349
Cdd:PRK10811  919 ------VIAAPVTEQPQVITeSDVAVAQEVAEH-------AEPVVEP-----QDETADIEEAAETAE---VVVAEPEVVA 977

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 124358955 1350 TTESPVVAVTEIPPVAVPEPPIMAVPELPTMAVV----------KTPAVA-VPEP 1393
Cdd:PRK10811  978 QPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVehnhatapmtRAPAPEyVPEA 1032
rne PRK10811
ribonuclease E; Reviewed
 1213-1418 2.46e-04

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 46.57  E-value: 2.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1213 ISEPMAVPANYSMSESETSMLASEAVMTVPEPAREPESSVTSAPVESAVVAehemVPERPMTymVSETTMSVEPAVLTSE 1292
Cdd:PRK10811  843 IRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAE----VVEEPVV--VAEPQPEEVVVVETTH 916

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1293 ASVISETSETydsmrpSGHAISEVTMSLLEPAVTISQPAEnslelpsmtvpapsTMTTTESPVVAVTEIPPVAVPEPPim 1372
Cdd:PRK10811  917 PEVIAAPVTE------QPQVITESDVAVAQEVAEHAEPVV--------------EPQDETADIEEAAETAEVVVAEPE-- 974

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 124358955 1373 avpelptmAVVKTPAVAVPEPLVAAPEPPTmATPELCSLSVSEPPV 1418
Cdd:PRK10811  975 --------VVAQPAAPVVAEVAAEVETVTA-VEPEVAPAQVPEATV 1011
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 2388-2426 3.11e-04

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 41.09  E-value: 3.11e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 124358955 2388 KHPVSALMEICNKRRWqPPEFLLVHDSGPDHRKHFLFRV 2426
Cdd:cd19862     1 KTPISVLQELCAKRGI-TPKYELISSEGAVHEPTFTFRV 38
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 82-574 3.26e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 3.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955    82 DLKEASRKSRCVSV--QTDPTDEVPTKKSKKHKKHKNKKKKKKKEKEKKYKRQPEESE--SKLKSHHDGNLESDSFLKFD 157
Cdd:pfam03154   38 DLRSSGRNSPSAAStsSNDSKAESMKKSSKKIKEEAPSPLKSAKRQREKGASDTEEPEraTAKKSKTQEISRPNSPSEGE 117

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   158 SEPSAAALEHPVRAFGLSEASETALVLEPPVVSMEVQESHvletlkpATKAAELSVVSTSVISEQSEQPMPGMLEPSMTK 237
Cdd:pfam03154  118 GESSDGRSVNDEGSSDPKDIDQDNRSTSPSIPSPQDNESD-------SDSSAQQQILQTQPPVLQAQSGAASPPSPPPPG 190

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   238 ILDSFTAAPVPMSTAALKSPEPVVTMSVEYQKSvlksleTMPPETSKTTLVELPIAKVVEPSETLTIV------SETPTE 311
Cdd:pfam03154  191 TTQAATAGPTPSAPSVPPQGSPATSQPPNQTQS------TAAPHTLIQQTPTLHPQRLPSPHPPLQPMtqppppSQVSPQ 264

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   312 VHPEPSPSTMDFP-----ESSTTDVQR-LPEQPVEAPSEIADS------SMTRPQESLELPKTTAVELQESTVASALELP 379
Cdd:pfam03154  265 PLPQPSLHGQMPPmphslQTGPSHMQHpVPPQPFPLTPQSSQSqvppgpSPAAPGQSQQRIHTPPSQSQLQSQQPPREQP 344

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   380 GPPA-TSILELQGPPVTPVPELPGPSATPVP-ELSGPLSTPVP-ELPGPPA----TVVPELPGPSVTPVP-QL---SQEL 448
Cdd:pfam03154  345 LPPApLSMPHIKPPPTTPIPQLPNPQSHKHPpHLSGPSPFQMNsNLPPPPAlkplSSLSTHHPPSAHPPPlQLmpqSQQL 424

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955   449 PGPPAPSMGLEPPQEVPEPPVMAQELSGVPAVSAAIELTGQPAVTVAMELTEQPvTTTEFEQPVAMTTVEHPGHPEVTTA 528
Cdd:pfam03154  425 PPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPITPP-SGPPTSTSSAMPGIQPPSSASVSSS 503

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*.
gi 124358955   529 TGLLGQPEAAmvleLPGQPVATTALELSGQPSVTGVPELSGLPSAT 574
Cdd:pfam03154  504 GPVPAAVSCP----LPPVQIKEEALDEAEEPESPPPPPRSPSPEPT 545
DSRM_A1CF-like cd19872
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ...
 2389-2436 4.09e-04

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380701  Cd Length: 75  Bit Score: 41.12  E-value: 4.09e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124358955 2389 HPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPYQPN 2436
Cdd:cd19872     1 NPVQILEEICQKNGWGEPVYQLLSTSSNNEVQLFIYKVTIPNLPNGRL 48
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
1317-1500 5.49e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 45.23  E-value: 5.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1317 TMSLL-----EPAVTI-SQPAENSLELPSMTVPAPSTMTTTESPVVAVTEIPPVAVPePPIMAVPE--LPTMAVVKTPAV 1388
Cdd:PRK07003  349 TMTLLrmlafEPAVTGgGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGA-AGAALAPKaaAAAAATRAEAPP 427

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1389 AVPEPLVAAPEPPTMATPELCSLSVSEPPVAVSELPALAD--PEHAITAVSGVSSLEPSVPILEPAVSVLQPVMIVSEPS 1466
Cdd:PRK07003  428 AAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDaqPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAV 507

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 124358955 1467 VPVQEPTVA--VSEPAVIVSEHTQITSPEMAVESSP 1500
Cdd:PRK07003  508 PDARAPAAAsrEDAPAAAAPPAPEARPPTPAAAAPA 543
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 2388-2433 1.17e-03

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 39.58  E-value: 1.17e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 124358955 2388 KHPVSALMEICNKRRwQPPEFLLVHDSGPDHRKHFLFRVLRNGSPY 2433
Cdd:cd19902     1 KNPVSALMEYAQSRG-VTAEIEVLSQSGPPHNPRFKAAVFVGGRRF 45
rne PRK10811
ribonuclease E; Reviewed
 1254-1439 1.47e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 43.87  E-value: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1254 SAPVesAVVAEHEMVPERPmtymvsETTMSVEPAVLTSEASVISETSETYDSMRpsghaisEVTMSLLEPAVTISQPAEN 1333
Cdd:PRK10811  844 RYPV--VRPQDVQVEEQRE------AEEVQVQPVVAEVPVAAAVEPVVSAPVVE-------AVAEVVEEPVVVAEPQPEE 908

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1334 SLELPSMTVPAPSTMTTTESPVVAVTEIPPVAVPEPPIMAVPELPTMAVVKTPAVAVPEPLVAAPEPPTMATPElcslSV 1413
Cdd:PRK10811  909 VVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAP----VV 984

                         170       180
                  ....*....|....*....|....*.
gi 124358955 1414 SEPPVAVSELPALADPEHAITAVSGV 1439
Cdd:PRK10811  985 AEVAAEVETVTAVEPEVAPAQVPEAT 1010
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 2388-2437 1.60e-03

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 39.17  E-value: 1.60e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 124358955 2388 KHPVSALMEICNKRRwQPPEFLLVhDSGPDHRKHFLFRVLRNGSPYQPNC 2437
Cdd:cd19875     1 KNPVSALNEYCQKRG-LSLEFVDV-SVGPDHCPGFTASATIDGIVFASAT 48
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 1314-1481 2.04e-03

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 43.41  E-value: 2.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1314 SEVTMSLLEPAVTISQPAENSLELPSMTVPAPSTMTTTESPVVAVTEipPVAVPEPPIMAVpELPTMAVVKTPAVAVPEP 1393
Cdd:pfam17823   84 TEVTAEHTPHGTDLSEPATREGAADGAASRALAAAASSSPSSAAQSL--PAAIAALPSEAF-SAPRAAACRANASAAPRA 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1394 LVAAPEPPTMATPELCSlSVSEPPVAVSELPALADPEHAitAVSGVSSLEPSVPILEPAVSVLQPVMIVSEPSVPVQEPT 1473
Cdd:pfam17823  161 AIAAASAPHAASPAPRT-AASSTTAASSTTAASSAPTTA--ASSAPATLTPARGISTAATATGHPAAGTALAAVGNSSPA 237


                   ....*...
gi 124358955  1474 VAVSEPAV 1481
Cdd:pfam17823  238 AGTVTAAV 245
DSRM_DRADA_rpt1 cd19913
first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 2388-2435 2.33e-03

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA); DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380742  Cd Length: 71  Bit Score: 38.70  E-value: 2.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124358955 2388 KHPVSALMEICnKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPYQP 2435
Cdd:cd19913     1 KNPVSGLMEYA-QFLGQTCEFLLLEQSGPSHDPRFKFQAVIDGRRFPP 47
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 1176-1512 3.10e-03

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 42.64  E-value: 3.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1176 LSTEQSALTADNTWSTEVTLSTGESLSQPeppvsqsEISEPMAVPANYSMSESETSMLASEAVMTVPEPAREPESSVTSA 1255
Cdd:pfam17823   72 LTKGTSAAHLNSTEVTAEHTPHGTDLSEP-------ATREGAADGAASRALAAAASSSPSSAAQSLPAAIAALPSEAFSA 144

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1256 PVESAVVAEHEMVPERPMTYMVSETTMSvePAVLTSEASVISETSETYDSMRPSGHAISevTMSLLEPAVTISQPAensl 1335
Cdd:pfam17823  145 PRAAACRANASAAPRAAIAAASAPHAAS--PAPRTAASSTTAASSTTAASSAPTTAASS--APATLTPARGISTAA---- 216

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1336 elpsmtvpapsTMTTTESPVVAVTEIPPVAVPEPPIMAVPELPTMAVVKTPAVAVpEPLVAAPEPPTMATPELCSLSVSE 1415
Cdd:pfam17823  217 -----------TATGHPAAGTALAAVGNSSPAAGTVTAAVGTVTPAALATLAAAA-GTVASAAGTINMGDPHARRLSPAK 284

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  1416 --PPVAVSELPALADPEHAITAVSGVSSLEPSVPIL-EPAVSvlqPVMIVSEPSVPvqePTVAVSEPAVIVSEHTQITSP 1492
Cdd:pfam17823  285 hmPSDTMARNPAAPMGAQAQGPIIQVSTDQPVHNTAgEPTPS---PSNTTLEPNTP---KSVASTNLAVVTTTKAQAKEP 358

                          330       340
                   ....*....|....*....|
gi 124358955  1493 emavESSPVIVDSSVMSSQI 1512
Cdd:pfam17823  359 ----SASPVPVLHTSMIPEV 374
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
2380-2433 3.11e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 41.62  E-value: 3.11e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 124358955 2380 AAMKDLSGKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPY 2433
Cdd:COG0571   149 EIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVL 202
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 246-458 4.31e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 42.22  E-value: 4.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  246 PVPMSTAALKSPEPVVTMSVEYQKSVLKSLETmPPEtskttlvelPIAKVVEPSETLTIVSETPTEVHPEPSPSTMDFPE 325
Cdd:PLN03209  328 VPPKESDAADGPKPVPTKPVTPEAPSPPIEEE-PPQ---------PKAVVPRPLSPYTAYEDLKPPTSPIPTPPSSSPAS 397

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  326 SSTTDVQRLPEQPVEAPSeiADSSMTRPQ-ESLELPKTTAVELQESTVASALELP-----------GPPATSILELQGPP 393
Cdd:PLN03209  398 SKSVDAVAKPAEPDVVPS--PGSASNVPEvEPAQVEAKKTRPLSPYARYEDLKPPtspsptaptgvSPSVSSTSSVPAVP 475

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124358955  394 VTPVPELPGPSATPVPELSGPLST-PVPELPGPPATVVPELPGPSVTPVPQLSQELPGPPAPSMGL 458
Cdd:PLN03209  476 DTAPATAATDAAAPPPANMRPLSPyAVYDDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTAL 541
PRK07994 PRK07994
DNA polymerase III subunits gamma and tau; Validated
 382-553 4.62e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236138 [Multi-domain]  Cd Length: 647  Bit Score: 42.16  E-value: 4.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  382 PATSILELQGPPVTPVPeLPGPSATPVPELSGPLSTPVPELPGPPATVVPELPGPSVTPVPQLSQELPGPPAPSMGLEPP 461
Cdd:PRK07994  361 PAAPLPEPEVPPQSAAP-AASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQGATKAK 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  462 QEVPEPPVMAQELSGV-----PAVSAAIELTGQPAVTVAMELTEQP---VTTTEFEQPVAMT-TVEHPGHPEVTTATGLL 532
Cdd:PRK07994  440 KSEPAAASRARPVNSAlerlaSVRPAPSALEKAPAKKEAYRWKATNpveVKKEPVATPKALKkALEHEKTPELAAKLAAE 519

                         170       180
                  ....*....|....*....|....*.
gi 124358955  533 GQPE---AAMV--LELPGqPVATTAL 553
Cdd:PRK07994  520 AIERdpwAALVsqLGLPG-LVEQLAL 544
PLN02983 PLN02983
biotin carboxyl carrier protein of acetyl-CoA carboxylase
 375-455 4.74e-03

biotin carboxyl carrier protein of acetyl-CoA carboxylase


Pssm-ID: 215533 [Multi-domain]  Cd Length: 274  Bit Score: 41.36  E-value: 4.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  375 ALELPGPPAtSILELQGPPVTPVPELPGPSATPVPELSGPLSTPVPELPGPPATVVPELPgPSVTPVPQLSQELPGPPAP 454
Cdd:PLN02983  140 ALPQPPPPA-PVVMMQPPPPHAMPPASPPAAQPAPSAPASSPPPTPASPPPAKAPKSSHP-PLKSPMAGTFYRSPAPGEP 217


                  .
gi 124358955  455 S 455
Cdd:PLN02983  218 P 218
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 2388-2426 5.31e-03

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380743  Cd Length: 71  Bit Score: 37.52  E-value: 5.31e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 124358955 2388 KHPVSALMEiCNKRRWQPPEFLLVHDSGPDHRKHFLFRV 2426
Cdd:cd19914     1 KNPISVLME-HSQKSGNMCEFQLLSQEGPPHDPKFTYCV 38
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 1342-1445 6.07e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 42.01  E-value: 6.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1342 VPAPSTMTTTESPVVAVTEIPPVAVPEPPIMAVPELPTMAVVKTPAVA-VPEPLVAAPEPPTMATPElcslsVSEPPVAV 1420
Cdd:PRK14951  392 APVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAaAPAAVALAPAPPAQAAPE-----TVAIPVRV 466

                          90       100
                  ....*....|....*....|....*
gi 124358955 1421 SELPALADPEHAITAVSGVSSLEPS 1445
Cdd:PRK14951  467 APEPAVASAAPAPAAAPAAARLTPT 491
rne PRK10811
ribonuclease E; Reviewed
 243-423 9.83e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 41.18  E-value: 9.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  243 TAAPVPMSTAAlKSPE----------PVVTmsVEYQKSVLKSLETMPPETskTTLVELPIAKVVEPSETLTIVSETPTEV 312
Cdd:PRK10811  821 TQSPMPLTVAC-ASPEmasgkvwiryPVVR--PQDVQVEEQREAEEVQVQ--PVVAEVPVAAAVEPVVSAPVVEAVAEVV 895

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955  313 HPEP---SPSTMDFPESSTTDVQRLPEQPVEAPSEIADSSMTRPQESLELPK-TTAVELQESTVASALELPGPPATSILE 388
Cdd:PRK10811  896 EEPVvvaEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEpVVEPQDETADIEEAAETAEVVVAEPEV 975

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 124358955  389 LQGPPVTPVPELPGPSATPVPELSGPLSTPVPELP 423
Cdd:PRK10811  976 VAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEAT 1010
PHA02682 PHA02682
ORF080 virion core protein; Provisional
 1307-1447 9.87e-03

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 40.61  E-value: 9.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358955 1307 RPSGHaisevtmSLLEPAVTISQPAENSlelPSMTVPAPSTMTTTESPVVAVTEIPPVAVPEPPIMAVPELPTMAVVKTP 1386
Cdd:PHA02682   75 RPSGQ-------SPLAPSPACAAPAPAC---PACAPAAPAPAVTCPAPAPACPPATAPTCPPPAVCPAPARPAPACPPST 144

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124358955 1387 AVAVPEPLVAAPEPPTMATPELCSLSVSEPPVAVSELPALAdpehaiTAVSGVSSLEPSVP 1447
Cdd:PHA02682  145 RQCPPAPPLPTPKPAPAAKPIFLHNQLPPPDYPAASCPTIE------TAPAASPVLEPRIP 199
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 2390-2422 9.90e-03

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380681  Cd Length: 67  Bit Score: 37.01  E-value: 9.90e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 124358955 2390 PVSALMEICNKRRWQPPEFLLVHDSGPDHRKHF 2422
Cdd:cd10844     2 PVGALQELVVQKGWRLPEYTVTQESGPAHRKEF 34
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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