A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 309 GLVNLGNSCYLAATMQIVFSTHSFISRYFShqsLKMAFEMAPADPTLDLNMQLTKLGHGLLSGKYSMPATQKDatTGDPR 388
Cdd:cd02658   1 GLRNLGNSCYLNSVLQVLFSIPSFQWRYDD---LENKFPSDVVDPANDLNCQLIKLADGLLSGRYSKPASLKS--ENDPY 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 389 QEGIPPRMFKNVIAASHAEFSSMRQQDALDFFLHLVGKVERASNTTPDLDPSRSFKFGIEEKILCPS-GKVGYNKREDCI 467
Cdd:cd02658  76 QVGIKPSMFKALIGKGHPEFSTMRQQDALEFLLHLIDKLDRESFKNLGLNPNDLFKFMIEDRLECLScKKVKYTSELSEI 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 468 LSLNIPLHEATNKDEleafhkqkagkgleendmrssDEIVRPRVPLEACLANFASSEPIEDYYSSaLKGMTTAIKTTGLT 547
Cdd:cd02658 156 LSLPVPKDEATEKEE---------------------GELVYEPVPLEDCLKAYFAPETIEDFCST-CKEKTTATKTTGFK 213

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 548 SFPDYLVLHMRKFVMEEGWVPKKLDVYIDVPDVIdishmrskglqpgeellpdgvpeevmesaqpvaneeivaqlvsmgf 627
Cdd:cd02658 214 TFPDYLVINMKRFQLLENWVPKKLDVPIDVPEEL---------------------------------------------- 247

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 628 sqlhcqkaaintsnagveeamnwllshmddpdidapishqtsdidqssvdtllsfgfaedvarkalkasggdiekatdwv 707
Cdd:cd02658     --------------------------------------------------------------------------------

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 708 fnnpnasvsdmdvsssnsaqtpaqsglpdGGGKYKLFGIVSHMGTSVHCGHYVAHILK----EGRWVIFNDDKVGISTDP 783
Cdd:cd02658 248 -----------------------------GPGKYELIAFISHKGTSVHSGHYVAHIKKeidgEGKWVLFNDEKVVASQDP 298

                       490
                ....*....|...
gi 22331218 784 P--KDMGYVYFFQ 794
Cdd:cd02658 299 PemKKLGYIYFYQ 311

Zn-finger in ubiquitin-hydrolases and other protein;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 22331218   180 CSKCDKTENLWLNLTDGMILCGRKNwdgtggNNHAVEHYKETAYPLAVKLGTITadleaadVYSYPEDDSVLDPLL 255
Cdd:pfam02148   1 CSLCGNTSNLWLCLTCGHVGCGRYQ------NSHALEHYEETGHPLAVNLSTLT-------VYCYPCDDYVHDPSL 63

UBA2 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins; atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant development. It can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. atUBP14 contains two ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain which show a high level of sequence similarity with mammalian ubiquitin-associated and SH3 domain-containing protein A (UBS3A).

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 22331218 674 SSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNP 711
Cdd:cd14388   1 SSVDTLVSFGFAADVARKALKATGGDIERAAEWIFNNS 38

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 309 GLVNLGNSCYLAATMQIVFSTHSFISRYFShqsLKMAFEMAPADPTLDLNMQLTKLGHGLLSGKYSMPATQKDatTGDPR 388
Cdd:cd02658   1 GLRNLGNSCYLNSVLQVLFSIPSFQWRYDD---LENKFPSDVVDPANDLNCQLIKLADGLLSGRYSKPASLKS--ENDPY 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 389 QEGIPPRMFKNVIAASHAEFSSMRQQDALDFFLHLVGKVERASNTTPDLDPSRSFKFGIEEKILCPS-GKVGYNKREDCI 467
Cdd:cd02658  76 QVGIKPSMFKALIGKGHPEFSTMRQQDALEFLLHLIDKLDRESFKNLGLNPNDLFKFMIEDRLECLScKKVKYTSELSEI 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 468 LSLNIPLHEATNKDEleafhkqkagkgleendmrssDEIVRPRVPLEACLANFASSEPIEDYYSSaLKGMTTAIKTTGLT 547
Cdd:cd02658 156 LSLPVPKDEATEKEE---------------------GELVYEPVPLEDCLKAYFAPETIEDFCST-CKEKTTATKTTGFK 213

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 548 SFPDYLVLHMRKFVMEEGWVPKKLDVYIDVPDVIdishmrskglqpgeellpdgvpeevmesaqpvaneeivaqlvsmgf 627
Cdd:cd02658 214 TFPDYLVINMKRFQLLENWVPKKLDVPIDVPEEL---------------------------------------------- 247

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 628 sqlhcqkaaintsnagveeamnwllshmddpdidapishqtsdidqssvdtllsfgfaedvarkalkasggdiekatdwv 707
Cdd:cd02658     --------------------------------------------------------------------------------

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 708 fnnpnasvsdmdvsssnsaqtpaqsglpdGGGKYKLFGIVSHMGTSVHCGHYVAHILK----EGRWVIFNDDKVGISTDP 783
Cdd:cd02658 248 -----------------------------GPGKYELIAFISHKGTSVHSGHYVAHIKKeidgEGKWVLFNDEKVVASQDP 298

                       490
                ....*....|...
gi 22331218 784 P--KDMGYVYFFQ 794
Cdd:cd02658 299 PemKKLGYIYFYQ 311

Variant UBP zinc finger; This domain is found in ubiquitin C-terminal hydrolase enzymes and is related to the pfam02148 domain. However, it has an altered pattern of zinc binding residues.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22331218    11 VQIPEPTHRIYKHECCISFDTPRSEGGLFVDMNSFLAFGKDYVSWNYEKTGNPVYLHIKQTRK 73
Cdd:pfam17807   1 VRVPSASDRVYKDECIFCFDTPESEGGLFVCLKCFLGFCKKHAQLHFERTGHPVYLNIKRTKK 63

UBA1 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins; atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant development. It can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. atUBP14 contains two ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 22331218 615 NEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPD 659
Cdd:cd14295   1 DQELVAQLMEMGFPKVRAEKALFFTQNKGLEEAMEWLEEHSEDAD 45

Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 22331218    179 KCSKCDKTENLWLNLTDGMILCGRKnwdgtgGNNHAVEHYKETAYPLAVKLGTIT 233
Cdd:smart00290   1 RCSVCGTIENLWLCLTCGQVGCGRY------QNGHALEHFEETGHPLVVKLGTQR 49

Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 306 GYTGLVNLGNSCYLAATMQIVFSTHSfISRYFSHQSLKMafemapadptlDLNMQLTKLGHGLLSGKYSMPATQkdatTG 385
Cdd:COG5560 264 GTCGLRNLGNTCYMNSALQCLMHTWE-LRDYFLSDEYEE-----------SINEENPLGMHGSVASAYADLIKQ----LY 327

                        90       100       110
                ....*....|....*....|....*....|....
gi 22331218 386 DPRQEGIPPRMFKNVIAASHAEFSSMRQQDALDF 419
Cdd:COG5560 328 DGNLHAFTPSGFKKTIGSFNEEFSGYDQQDSQEF 361

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 22331218   615 NEEIVAQLVSMGFSQLHCQKAAINTSNaGVEEAMNWL 651
Cdd:pfam00627   2 DEEAIQRLVEMGFDREQVREALRATGN-NVERAAEYL 37

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 309 GLVNLGNSCYLAATMQIVFSTHSFISRYFShqsLKMAFEMAPADPTLDLNMQLTKLGHGLLSGKYSMPATQKDatTGDPR 388
Cdd:cd02658   1 GLRNLGNSCYLNSVLQVLFSIPSFQWRYDD---LENKFPSDVVDPANDLNCQLIKLADGLLSGRYSKPASLKS--ENDPY 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 389 QEGIPPRMFKNVIAASHAEFSSMRQQDALDFFLHLVGKVERASNTTPDLDPSRSFKFGIEEKILCPS-GKVGYNKREDCI 467
Cdd:cd02658  76 QVGIKPSMFKALIGKGHPEFSTMRQQDALEFLLHLIDKLDRESFKNLGLNPNDLFKFMIEDRLECLScKKVKYTSELSEI 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 468 LSLNIPLHEATNKDEleafhkqkagkgleendmrssDEIVRPRVPLEACLANFASSEPIEDYYSSaLKGMTTAIKTTGLT 547
Cdd:cd02658 156 LSLPVPKDEATEKEE---------------------GELVYEPVPLEDCLKAYFAPETIEDFCST-CKEKTTATKTTGFK 213

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 548 SFPDYLVLHMRKFVMEEGWVPKKLDVYIDVPDVIdishmrskglqpgeellpdgvpeevmesaqpvaneeivaqlvsmgf 627
Cdd:cd02658 214 TFPDYLVINMKRFQLLENWVPKKLDVPIDVPEEL---------------------------------------------- 247

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 628 sqlhcqkaaintsnagveeamnwllshmddpdidapishqtsdidqssvdtllsfgfaedvarkalkasggdiekatdwv 707
Cdd:cd02658     --------------------------------------------------------------------------------

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 708 fnnpnasvsdmdvsssnsaqtpaqsglpdGGGKYKLFGIVSHMGTSVHCGHYVAHILK----EGRWVIFNDDKVGISTDP 783
Cdd:cd02658 248 -----------------------------GPGKYELIAFISHKGTSVHSGHYVAHIKKeidgEGKWVLFNDEKVVASQDP 298

                       490
                ....*....|...
gi 22331218 784 P--KDMGYVYFFQ 794
Cdd:cd02658 299 PemKKLGYIYFYQ 311

Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 410 SMRQQDALDFFLHLVGKVERASNTTPDLDPSRS---------FKFGIEEKILCPS-GKVGYNKREDCILSLNIPLHEATN 479
Cdd:cd02257  19 FSEQQDAHEFLLFLLDKLHEELKKSSKRTSDSSslkslihdlFGGKLESTIVCLEcGHESVSTEPELFLSLPLPVKGLPQ 98

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 480 KDeleafhkqkagkgleendmrssdeivrprvpLEACLANFASSEPIEDY--YSSALKGMTTAIKTTGLTSFPDYLVLHM 557
Cdd:cd02257  99 VS-------------------------------LEDCLEKFFKEEILEGDncYKCEKKKKQEATKRLKIKKLPPVLIIHL 147

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 558 RKFVMEEGWVPKKLDVYIDVPDVIDISHMRSKGLQPGEEllpdgvpeevmesaqpvaneeivaqlvsmgfsqlhcqkaai 637
Cdd:cd02257 148 KRFSFNEDGTKEKLNTKVSFPLELDLSPYLSEGEKDSDS----------------------------------------- 186

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 638 ntsnagveeamnwllshmddpdidapishqtsdidqssvdtllsfgfaedvarkalkasggdiekatdwvfnnpnasvsd 717
Cdd:cd02257     --------------------------------------------------------------------------------

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 718 mdvsssnsaqtpaqsglPDGGGKYKLFGIVSHMGTSVHCGHYVAHILK--EGRWVIFNDDKV-------GISTDPPKDMG 788
Cdd:cd02257 187 -----------------DNGSYKYELVAVVVHSGTSADSGHYVAYVKDpsDGKWYKFNDDKVtevseeeVLEFGSLSSSA 249

                ....*.
gi 22331218 789 YVYFFQ 794
Cdd:cd02257 250 YILFYE 255

Zn-finger in ubiquitin-hydrolases and other protein;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 22331218   180 CSKCDKTENLWLNLTDGMILCGRKNwdgtggNNHAVEHYKETAYPLAVKLGTITadleaadVYSYPEDDSVLDPLL 255
Cdd:pfam02148   1 CSLCGNTSNLWLCLTCGHVGCGRYQ------NSHALEHYEETGHPLAVNLSTLT-------VYCYPCDDYVHDPSL 63

UBA1 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 22331218 615 NEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPDID 661
Cdd:cd14385   1 NAEALAQLLGMGFPEVRCKKALLATGNSDAEAAMNWLFEHMDDPDID 47

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase UBP5, UBP13 and similar proteins; UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13, is an ortholog of UBP5. It has similar domain architecture, but functions differently from USP5 in cellular deubiquitination processes. It exhibits a weak deubiquitinating activity preferring to Lys63-linked polyubiquitin in a non-activation manner. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA1 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 22331218 616 EEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPD 659
Cdd:cd14294   1 EAVVSQLAEMGFPLEACRKAVYHTNNSGLEAAMNWIMEHMDDPD 44

UBA domain found in ubiquitin-associated and SH3 domain-containing protein A (UBS3A) and similar proteins; UBS3A, also called Cbl-interacting protein 4 (CLIP4), suppressor of T-cell receptor signaling 2 (Sts-2), or T-cell ubiquitin ligand 1 (TULA-1), is a lymphoid protein only detected in thymus, spleen, and bone marrow. UBS3A exhibits extremely low phosphatase activity, but is capable of promoting T-cell apoptosis independent of either T cell receptor (TCR)/CD3-mediated signaling or caspase activity. It functions as a negative regulator of TCR signaling. UBS3A can also inhibit HIV-1 biogenesis through the binding of ATP-binding cassette protein family E member 1 (ABCE-1), a host factor of HIV-1 assembly. Moreover, UBS3A acts as the Cbl- and ubiquitin-interacting protein that can inhibit endocytosis and downregulation of ligand-activated epidermal growth factor receptor (EGFR) by impairing Cbl-induced ubiquitination, as well as inhibit clathrin-dependent endocytosis in general. This family also includes Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and some uncharacterized AAA-type ATPase-like proteins found in plants.

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 22331218 676 VDTLLSFGFAEDVARKALKASGGD-IEKATDWVFNN 710
Cdd:cd14300   1 LETLLAMGFPEDVARKALKATGGKsIEKATDWLLSH 36

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA1 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 22331218 613 VANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPD 659
Cdd:cd14383   1 MLDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDPD 47

UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain.

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 22331218 676 VDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNP 711
Cdd:cd14297   4 VKQLVDMGFTEAQARKALRKTNNNVERAVDWLFEGP 39

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 309 GLVNLGNSCYLAATMQIVFSTHSFISryfshqslkmafemapadptldlnmqltklghgLLSGKysmpatqkdattgdpr 388
Cdd:cd02667   1 GLSNLGNTCFFNAVMQNLSQTPALRE---------------------------------LLSET---------------- 31

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 389 qegipPRMFKNVIAASHAEFSSMRQQDALDFFLHLvgkverasnttpdLDPSRSFK---FGIE--EKILCPSGKvGYNKR 463
Cdd:cd02667  32 -----PKELFSQVCRKAPQFKGYQQQDSHELLRYL-------------LDGLRTFIdsiFGGEltSTIMCESCG-TVSLV 92

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 464 EDCILSLNIPlheatnkdeleafhkqkagkgleendmrSSDEIVRPrVPLEACLANFASSEPIEDYYSSALKGMTTAIKT 543
Cdd:cd02667  93 YEPFLDLSLP----------------------------RSDEIKSE-CSIESCLKQFTEVEILEGNNKFACENCTKAKKQ 143

                       250       260       270       280
                ....*....|....*....|....*....|....*....|.
gi 22331218 544 TGLTSFPDYLVLHMRKFVMEEGWVPKKLDVYIDVPDVIDIS 584
Cdd:cd02667 144 YLISKLPPVLVIHLKRFQQPRSANLRKVSRHVSFPEILDLA 184

UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA2 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 22331218 671 IDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNP 711
Cdd:cd14386   1 VPEEAVAMLVSMGFTRDQAIKALKATDNNVERAADWIFSHP 41

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 22331218   671 IDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDW 706
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEY 36

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 22331218 741 YKLFGIVSHMGTSVHCGHYVAHILKE--GRWVIFNDDKV 777
Cdd:cd02668 246 YELSGVLIHQGVSAYSGHYIAHIKDEqtGEWYKFNDEDV 284

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 22331218    672 DQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVF 708
Cdd:smart00165   1 DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37

UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins; The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ubiquitin-associated (UBA) domain and a C-terminal HECT domain. UBA domain may be involved in ubiquitin metabolism. HECT domain is necessary and sufficient for their E3 catalytic activity, but requires ATP, E1 and an E2 of the Arabidopsis UBC8 family to ubiquitinate proteins.

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 22331218 617 EIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSH 654
Cdd:cd14327   1 EAVAQLVEMGFSRERAEEALRAVGTNSVELAMEWLFTN 38

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13); UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13, is an ortholog of UBP5 implicated in catalyzing hydrolysis of various ubiquitin (Ub)-chains. It contains a zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. Due to the non-activating catalysis for K63-polyubiquitin chains, UBP13 may function differently from USP5 in cellular deubiquitination processes. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA1 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 22331218 615 NEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPD 659
Cdd:cd14384   3 DESSVMQLAEMGFPLEACRKAVYYTGNMGAEVAFNWIIAHMEEPD 47

UBA domain found in plant PNGase/UBA or UBX (PUB) domain-containing proteins; This family includes some uncharacterized hypothetical proteins found in plants. Although their biological function remain unclear, all family members contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal PUB domain. UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 22331218 615 NEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPDID 661
Cdd:cd14290   3 NADLLKELEAMGFPRARAVRALHHTGNTSVEAAVNWIVEHENDPDID 49

UBA domain found in ubiquitin-associated and SH3 domain-containing protein B (UBS3B) and similar proteins; UBS3B, or Cbl-interacting protein p70, suppressor of T-cell receptor signaling 1 (Sts-1), T-cell ubiquitin ligand 2 (TULA-2), or tyrosine-protein phosphatase STS1/TULA2, is ubiquitously expressed in mammalian tissues in a variety of cell types. It exhibits high phosphatase activity, but demonstrates no proapoptotic activity. It negatively regulates the tyrosine kinase Zap-70 activation and T cell receptor (TCR) signaling pathways that modulate T cell activation. Moreover, UBS3B acts as a Cbl- and ubiquitin-interacting protein that inhibits endocytosis of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor.

                        10        20        30
                ....*....|....*....|....*....|...
gi 22331218 622 LVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSH 654
Cdd:cd14301   6 LLSMGFPKHRAEKALAATGGRSVQLASDWLLSH 38

UBA domain found in eukaryotic E3 ubiquitin-protein ligase HUWE1 and similar proteins; HUWE1, also called ARF-binding protein 1 (ARF-BP1), HECT, UBA and WWE domain-containing protein 1, homologous to E6AP carboxyl terminus homologs protein 9 (HectH9), large structure of UREB1 (LASU1), Mcl-1 ubiquitin ligase E3 (Mule), upstream regulatory element-binding protein 1 (URE-B1), or URE-binding protein 1, may function as a ubiquitin-protein ligase that involves in the ubiquitination cascade that targets specific substrate proteins in proteolysis. It can ubiquitylate DNA polymerase beta (Pol beta), the major BER DNA polymerase and modulates base excision repair (BER). HUWE1 also acts as a critical mediator of both the p53-independent and p53-dependent tumor suppressor functions of ARF tumor suppressor in p53 regulation. Moreover, HUWE1 is both required and sufficient for the polyubiquitination of Mcl-1, an anti-apoptotic Bcl-2 family member involving in DNA damage-induced apoptosis. Furthermore, HUWE1 plays an important role in the regulation of Cdc6 stability after DNA damage. In addition, HUWE1 works as a partner of N-Myc oncoprotein in neural cells. It ubiquitinates N-Myc and primes it for proteasomal-mediated degradation. HUWE1 contains a ubiquitin-associated (UBA) domain, a WWE domain, and a Bcl-2 homology region 3 (BH3) domain at the N-terminus and a HECT domain at the C-terminus. WWE domain plays a role in the regulation of specific protein-protein interactions in a ubiquitin conjugation system. BH3 domain is responsible for the specific binding to Mcl-1. HECT domain involves in the inhibition of the transcriptional activity of p53 via a ubiquitin-dependent degradation pathway. It also controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 22331218 615 NEEIVAQLVSMGFSQLHCQKAAINTSNagVEEAMNWLLSH 654
Cdd:cd14288   2 NEAHLQQLMDMGFTREHALEALLHTST--LEQATEYLLTH 39

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 22331218 739 GKYKLFGIVSHMGTSVHCGHYVAHILKE--GRWVIFNDDKVGISTD 782
Cdd:cd02657 239 GYYELVAVITHQGRSADSGHYVAWVRRKndGKWIKFDDDKVSEVTE 284

UBA domain found in ubiquitin-associated and SH3 domain-containing protein B (UBS3B) and similar proteins; UBS3B, or Cbl-interacting protein p70, suppressor of T-cell receptor signaling 1 (Sts-1), T-cell ubiquitin ligand 2 (TULA-2), or tyrosine-protein phosphatase STS1/TULA2, is ubiquitously expressed in mammalian tissues in a variety of cell types. It exhibits high phosphatase activity, but demonstrates no proapoptotic activity. It negatively regulates the tyrosine kinase Zap-70 activation and T cell receptor (TCR) signaling pathways that modulate T cell activation. Moreover, UBS3B acts as a Cbl- and ubiquitin-interacting protein that inhibits endocytosis of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 22331218 674 SSVDTLLSFGFAEDVARKALKASGG-DIEKATDWVFN 709
Cdd:cd14301   1 SALEVLLSMGFPKHRAEKALAATGGrSVQLASDWLLS 37

UBA domain found in plant AAA-type ATPase-like proteins; This family includes some uncharacterized AAA-type ATPase-like proteins found in plant. The AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. Members in this family contains an N-terminal ubiquitin-association (UBA) domain, a AAA-type ATPase domain and a C-terminal MgsA AAA+ ATPase domain. This model corresponds to the UBA domain which show a high level of sequence similarity with mammalian ubiquitin-associated and SH3 domain-containing protein A (UBS3A).

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 22331218 676 VDTLLSFGFAEDVARKALKASGGD-IEKATDWVFNN 710
Cdd:cd14389   1 MEQLVDMGFSSDLAAEALAATGGKsTQKATEWILSH 36

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 309 GLVNLGNSCYLAATMQIVFSTHSFisryfsHQSLKmafEMAPADPTLDLNMqltklgHGLLSgkysmpATQKDATTGDPR 388
Cdd:cd02657   1 GLTNLGNTCYLNSTLQCLRSVPEL------RDALK---NYNPARRGANQSS------DNLTN------ALRDLFDTMDKK 59

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 389 QEGIPPRMFKNVIAASHAEFSSM------RQQDALDFFLHLVgKVERASNTTPDLDPS---RSFKFGIEEKILCPSGKVG 459
Cdd:cd02657  60 QEPVPPIEFLQLLRMAFPQFAEKqnqggyAQQDAEECWSQLL-SVLSQKLPGAGSKGSfidQLFGIELETKMKCTESPDE 138

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22331218 460 YNKREDCILSLNIPLHEATNKDELEAfhkqKAGKGLEENDMRSSDEIVRPRVPleaclanfassepiedyyssalkgmtt 539
Cdd:cd02657 139 EEVSTESEYKLQCHISITTEVNYLQD----GLKKGLEEEIEKHSPTLGRDAIY--------------------------- 187

                       250       260
                ....*....|....*....|.
gi 22331218 540 aIKTTGLTSFPDYLVLHMRKF 560
Cdd:cd02657 188 -TKTSRISRLPKYLTVQFVRF 207

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 22331218 724 NSAQTPAQSGLPDGGGKYKLFGIVSHMGTsVHCGHYVAHI-LKEGRWVIFNDDKV 777
Cdd:cd02660 256 SSIGDTQDSNSLDPDYTYDLFAVVVHKGT-LDTGHYTAYCrQGDGQWFKFDDAMI 309

A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22331218 737 GGGKYKLFGIVSHMGtSVHCGHYVAHILKE--GRWVIFNDDKV--GISTDPPKDMGYVYFFQ 794
Cdd:cd02674 170 GPFKYDLYAVVNHYG-SLNGGHYTAYCKNNetNDWYKFDDSRVtkVSESSVVSSSAYILFYE 230

UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.

                        10        20
                ....*....|....*....|....*...
gi 22331218 683 GFAEDVARKALKASGGDIEKATDWVFNN 710
Cdd:cd14306   8 GFPEEDCIRALRACGGNVEEAANWLLEN 35

UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins; scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been identified as a K29-linked polyubiquitin binding protein as well. It is involved in K29-linked polyubiquitin metabolism by binding to the 29-linked Ub4 resin and serving as an internal positive control in budding yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.