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 571031354  155 PFLELNRILEALHEQDLGPALEWAVSHRQRLLELNSSLEFKLHRLHFIRLLAGGpaKQLEALSYAR-HFQPFARLHQREI 233
Cdd:pfam10607   1 VFKERNRILEAILNGDITEAIEWCNENKPELLKINSNLEFELRLQQFIELIRSG--KILEALEYAReNLAPFNEEHLKEL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571031354  234 QVMMGSLVYLRLgLEKSPYCHLLDSSHWAEICETFTRDACSLLGLSVESPLSVSFASGCVALPVLM 299
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 571031354   116 QQQILQMAIVEHLYQQGMLSVAEELCQESTLNV 148
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 571031354  155 PFLELNRILEALHEQDLGPALEWAVSHRQRLLELNSSLEFKLHRLHFIRLLAGGpaKQLEALSYAR-HFQPFARLHQREI 233
Cdd:pfam10607   1 VFKERNRILEAILNGDITEAIEWCNENKPELLKINSNLEFELRLQQFIELIRSG--KILEALEYAReNLAPFNEEHLKEL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571031354  234 QVMMGSLVYLRLgLEKSPYCHLLDSSHWAEICETFTRDACSLLGLSVESPLSVSFASGCVALPVLM 299
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 571031354  60 VMSQCCRKIKDTVQKLASDHKDIHSSVSRVGKAIDR--NFDSEICGVVSDAVWDAREqqqqiLQMAIVEHLYQQGMLSVA 137
Cdd:COG5109   46 IRSALSLKNGQEFDTLSHAEADLVGSWKSLLKEDCRpaNFDVQVGNQIYPFSTQTVT-----YLVVYYLLENNCADVVER 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571031354 138 EELCQESTLNVDLDFKQPFLELNRILEALHEQDLGPALEWAvSHRQRLLELNSSLEFKLHRLHFIRLLAGGPAkQLEALS 217
Cdd:COG5109  121 HISETKDGKDEIIKIRDGFVKLKKVISGISEKSTFLLIEFL-QIEGYLSKGDTESELELYLVSHESLLLIHKR-YDEALR 198

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571031354 218 YAR-HFQPFARLHQREIQVMMGSLVYLRLGLEKSPYCHLLDSSH---------------------WAEICETFTRDACSL 275
Cdd:COG5109  199 LCFtKLASFVPKHIQDVKPLLRFLVNAPTDCFRHREKELMQNIQealkksligqpiedidkvnksRKKLIELFKSEYCAA 278

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571031354 276 LGLSVESPLSVSFASGCVALPVLMNIKAVIEQRQCTgvWNHKDELPIEIELGMKCWYHSVFACPILRQQTSDSNPPIKLI 355
Cdd:COG5109  279 NGMPNRSPLRELVETGTIAFLQLSKSGSILFDKHVD--WTDDSELPMEIKLPKGRHFHSLFICPVLKELCTDENPPVMLE 356

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 571031354 356 CGHVISRDALNKLINGGKL--KCPYCPMEQNPADGKRIIF 393
Cdd:COG5109  357 CGHVISKEALSVLSQNGVLsfKCPYCPEMSKYENILRVRF 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 571031354   116 QQQILQMAIVEHLYQQGMLSVAEELCQESTLNV 148
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 571031354  155 PFLELNRILEALHEQDLGPALEWAVSHRQRLLELNSSLEFKLHRLHFIRLLAGGpaKQLEALSYAR-HFQPFARLHQREI 233
Cdd:pfam10607   1 VFKERNRILEAILNGDITEAIEWCNENKPELLKINSNLEFELRLQQFIELIRSG--KILEALEYAReNLAPFNEEHLKEL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571031354  234 QVMMGSLVYLRLgLEKSPYCHLLDSSHWAEICETFTRDACSLLGLSVESPLSVSFASGCVALPVLM 299
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 571031354  60 VMSQCCRKIKDTVQKLASDHKDIHSSVSRVGKAIDR--NFDSEICGVVSDAVWDAREqqqqiLQMAIVEHLYQQGMLSVA 137
Cdd:COG5109   46 IRSALSLKNGQEFDTLSHAEADLVGSWKSLLKEDCRpaNFDVQVGNQIYPFSTQTVT-----YLVVYYLLENNCADVVER 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571031354 138 EELCQESTLNVDLDFKQPFLELNRILEALHEQDLGPALEWAvSHRQRLLELNSSLEFKLHRLHFIRLLAGGPAkQLEALS 217
Cdd:COG5109  121 HISETKDGKDEIIKIRDGFVKLKKVISGISEKSTFLLIEFL-QIEGYLSKGDTESELELYLVSHESLLLIHKR-YDEALR 198

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571031354 218 YAR-HFQPFARLHQREIQVMMGSLVYLRLGLEKSPYCHLLDSSH---------------------WAEICETFTRDACSL 275
Cdd:COG5109  199 LCFtKLASFVPKHIQDVKPLLRFLVNAPTDCFRHREKELMQNIQealkksligqpiedidkvnksRKKLIELFKSEYCAA 278

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571031354 276 LGLSVESPLSVSFASGCVALPVLMNIKAVIEQRQCTgvWNHKDELPIEIELGMKCWYHSVFACPILRQQTSDSNPPIKLI 355
Cdd:COG5109  279 NGMPNRSPLRELVETGTIAFLQLSKSGSILFDKHVD--WTDDSELPMEIKLPKGRHFHSLFICPVLKELCTDENPPVMLE 356

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 571031354 356 CGHVISRDALNKLINGGKL--KCPYCPMEQNPADGKRIIF 393
Cdd:COG5109  357 CGHVISKEALSVLSQNGVLsfKCPYCPEMSKYENILRVRF 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 571031354 336 FACPILRQQTSDSNPPIKLICGHVISRDALNKLI--NGGKLKCPYCPME 382
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 571031354 338 CPILRQQTSDSNPPIKLICGHVISRDALNKLINGGKLKCPYC 379
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 571031354 334 SVFACPILRQQTSDSNPPIKLICGHVISRDALNKL--INGGKLKCPY 378
Cdd:cd16659    1 SRLVCRITGEVMNEHNPPLALPNGYVYSEKALEEMaeKNDGKVVCPR 47