CTLH/CRA C-terminal to LisH motif domain; RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined. This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720  95 PFLELNRILEALHEQDLGPALEWAVSHRQRLLELNSSLEFKLHRLHFIRLLAGGpaKQLEALSYAR-HFQPFARLHQREI 173
Cdd:pfam10607   1 VFKERNRILEAILNGDITEAIEWCNENKPELLKINSNLEFELRLQQFIELIRSG--KILEALEYAReNLAPFNEEHLKEL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034645720 174 QVMMGSLVYLRLgLEKSPYCHLLDSSHWAEICETFTRDACSLLGLSVESPLSVSFASGCVALPVLM 239
Cdd:pfam10607  79 EKLMGLLAFPDP-TDSSPYKSLLSPSRWEKLASEFNRAILKLLGLSSESPLEILLKAGLSALKTLS 143

Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.

                           10        20        30
                   ....*....|....*....|....*....|...
gi 1034645720   56 QQQILQMAIVEHLYQQGMLSVAEELCQESTLNV 88
Cdd:smart00667   2 SRSELNRLILEYLLRNGYEETAETLQKESGLSL 34

CTLH/CRA C-terminal to LisH motif domain; RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined. This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720  95 PFLELNRILEALHEQDLGPALEWAVSHRQRLLELNSSLEFKLHRLHFIRLLAGGpaKQLEALSYAR-HFQPFARLHQREI 173
Cdd:pfam10607   1 VFKERNRILEAILNGDITEAIEWCNENKPELLKINSNLEFELRLQQFIELIRSG--KILEALEYAReNLAPFNEEHLKEL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034645720 174 QVMMGSLVYLRLgLEKSPYCHLLDSSHWAEICETFTRDACSLLGLSVESPLSVSFASGCVALPVLM 239
Cdd:pfam10607  79 EKLMGLLAFPDP-TDSSPYKSLLSPSRWEKLASEFNRAILKLLGLSSESPLEILLKAGLSALKTLS 143

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720   2 SQCCRKIKDTVQKLASDHKDIHSSVSRVGKAIDR--NFDSEICGVVSDAVWDAREqqqqiLQMAIVEHLYQQGMLSVAEE 79
Cdd:COG5109    48 SALSLKNGQEFDTLSHAEADLVGSWKSLLKEDCRpaNFDVQVGNQIYPFSTQTVT-----YLVVYYLLENNCADVVERHI 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720  80 LCQESTLNVDLDFKQPFLELNRILEALHEQDLGPALEWAvSHRQRLLELNSSLEFKLHRLHFIRLLAGGPAkQLEALSYA 159
Cdd:COG5109   123 SETKDGKDEIIKIRDGFVKLKKVISGISEKSTFLLIEFL-QIEGYLSKGDTESELELYLVSHESLLLIHKR-YDEALRLC 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720 160 R-HFQPFARLHQREIQVMMGSLVYLRLGLEKSPYCHLLDSSH---------------------WAEICETFTRDACSLLG 217
Cdd:COG5109   201 FtKLASFVPKHIQDVKPLLRFLVNAPTDCFRHREKELMQNIQealkksligqpiedidkvnksRKKLIELFKSEYCAANG 280

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720 218 LSVESPLSVSFASGCVALPVLMNIKAVIEQRQCTgvWNHKDELPIEIELGMKCWYHSVFACPILRQQTSDSNPPIKLICG 297
Cdd:COG5109   281 MPNRSPLRELVETGTIAFLQLSKSGSILFDKHVD--WTDDSELPMEIKLPKGRHFHSLFICPVLKELCTDENPPVMLECG 358

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 1034645720 298 HVISRDALNKLINGGKL--KCPYCPMEQNPADGKRIIF 333
Cdd:COG5109   359 HVISKEALSVLSQNGVLsfKCPYCPEMSKYENILRVRF 396

Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.

                           10        20        30
                   ....*....|....*....|....*....|...
gi 1034645720   56 QQQILQMAIVEHLYQQGMLSVAEELCQESTLNV 88
Cdd:smart00667   2 SRSELNRLILEYLLRNGYEETAETLQKESGLSL 34

CTLH/CRA C-terminal to LisH motif domain; RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined. This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720  95 PFLELNRILEALHEQDLGPALEWAVSHRQRLLELNSSLEFKLHRLHFIRLLAGGpaKQLEALSYAR-HFQPFARLHQREI 173
Cdd:pfam10607   1 VFKERNRILEAILNGDITEAIEWCNENKPELLKINSNLEFELRLQQFIELIRSG--KILEALEYAReNLAPFNEEHLKEL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034645720 174 QVMMGSLVYLRLgLEKSPYCHLLDSSHWAEICETFTRDACSLLGLSVESPLSVSFASGCVALPVLM 239
Cdd:pfam10607  79 EKLMGLLAFPDP-TDSSPYKSLLSPSRWEKLASEFNRAILKLLGLSSESPLEILLKAGLSALKTLS 143

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720   2 SQCCRKIKDTVQKLASDHKDIHSSVSRVGKAIDR--NFDSEICGVVSDAVWDAREqqqqiLQMAIVEHLYQQGMLSVAEE 79
Cdd:COG5109    48 SALSLKNGQEFDTLSHAEADLVGSWKSLLKEDCRpaNFDVQVGNQIYPFSTQTVT-----YLVVYYLLENNCADVVERHI 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720  80 LCQESTLNVDLDFKQPFLELNRILEALHEQDLGPALEWAvSHRQRLLELNSSLEFKLHRLHFIRLLAGGPAkQLEALSYA 159
Cdd:COG5109   123 SETKDGKDEIIKIRDGFVKLKKVISGISEKSTFLLIEFL-QIEGYLSKGDTESELELYLVSHESLLLIHKR-YDEALRLC 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720 160 R-HFQPFARLHQREIQVMMGSLVYLRLGLEKSPYCHLLDSSH---------------------WAEICETFTRDACSLLG 217
Cdd:COG5109   201 FtKLASFVPKHIQDVKPLLRFLVNAPTDCFRHREKELMQNIQealkksligqpiedidkvnksRKKLIELFKSEYCAANG 280

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034645720 218 LSVESPLSVSFASGCVALPVLMNIKAVIEQRQCTgvWNHKDELPIEIELGMKCWYHSVFACPILRQQTSDSNPPIKLICG 297
Cdd:COG5109   281 MPNRSPLRELVETGTIAFLQLSKSGSILFDKHVD--WTDDSELPMEIKLPKGRHFHSLFICPVLKELCTDENPPVMLECG 358

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 1034645720 298 HVISRDALNKLINGGKL--KCPYCPMEQNPADGKRIIF 333
Cdd:COG5109   359 HVISKEALSVLSQNGVLsfKCPYCPEMSKYENILRVRF 396

Degenerated RING (dRING) finger found in Saccharomyces cerevisiae required for meiotic nuclear division protein 5 (Rmd5p) and similar proteins; Rmd5p, also known as glucose-induced degradation protein 2 (Gid2) or sporulation protein RMD5, is an E3 ubiquitin ligase containing a Lissencephaly type-1-like homology motif (LisH), a C-terminal to LisH motif (CTLH) domain, and a degenerated RING finger that is characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues compared with the classic C3H2C3-/C3HC4-type RING fingers. It forms the heterodimeric E3 ligase unit of the glucose induced degradation deficient (GID) complex with Gid9 (also known as Fyv10), which has a degenerated RING finger as well. The GID complex triggers polyubiquitylation and subsequent proteasomal degradation of the gluconeogenic enzymes fructose-1, 6-bisphosphate by fructose-1, 6-bisphosphatase (FBPase), phosphoenolpyruvate carboxykinase (PEPCK), and cytoplasmic malate dehydrogenase (c-MDH). Moreover, Rmd5p can form the GID complex with the other six Gid proteins, including Gid1/Vid30, Gid4/Vid24, Gid5/Vid28, Gid7, Gid8, and Gid9/Fyv10. The GID complex in which the seven Gid proteins reside functions as a novel ubiquitin ligase (E3) involved in the regulation of carbohydrate metabolism.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1034645720 276 FACPILRQQTSDSNPPIKLICGHVISRDALNKLI--NGGKLKCPYCPME 322
Cdd:cd16652     1 FACPVSREQSTEENPPMRLPCGHVISKDSLKKLSknNGNKFKCPYCPVE 49

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1034645720 278 CPILRQQTSDSNPPIKLICGHVISRDALNKLINGGKLKCPYC 319
Cdd:cd00162     1 CPICREEMNDRRPVVLLSCGHTFSRSAIARWLEGSKQKCPFC 42

U-box domain, a modified RING finger, found in erythroblast macrophage protein (Emp) and similar proteins; Emp, also known as cell proliferation-inducing gene 5 protein or macrophage erythroblast attacher (MAEA), is a key protein which functions in normal differentiation of erythroid cells and macrophages. It is a potential biomarker for hematopoietic evaluation of Hematopoietic stem cell transplantation (HSCT) patients. Emp was initially identified as a heparin-binding protein involved in the association of erythroblasts with macrophages. It promotes erythroid proliferation and maturation. It also plays an important role in erythroblastic island formation. Absence of Emp leads to failure of erythroblast nuclear extrusion. It is required in definitive erythropoiesis and plays a cell intrinsic role in the erythroid lineage. Emp contains a Lissencephaly type-1-like homology (LisH) motif, a C-terminal to LisH (CTLH) domain, and a RING-like U-box domain at the C-terminus.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1034645720 274 SVFACPILRQQTSDSNPPIKLICGHVISRDALNKL--INGGKLKCPY 318
Cdd:cd16659     1 SRLVCRITGEVMNEHNPPLALPNGYVYSEKALEEMaeKNDGKVVCPR 47