Citrus Sinensis ID: 018828

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350
Protein Sequence
MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAFKGSDSSLSSPHHSPSHGLRGSAYFHTSSDVRTAPGSGSRSRRGL
Secondary Structure (PSIPRED)
cccccccccEEEEEcccccccccccccccHHHHHHHHHccccEEEEEEEEEEccccccccEEEEEEEcccccccccccccEEEccccccccccccHHHcHHHHHHHcccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHccccEEEEEEEcccccccEccccccHHHHHHHHHccccEEEEEEEEEEcccccccEEEEEEEEEcccccccccEEEEEEEcccccEEEEcccccccccccccccccccccccccccccHHHHcccccccccccccccEEEcccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccEEEEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mtvltgrtTRVIGwyhshphitvlpshvDVRTQAMYQLLDTGFIGLIFSCFsedankvgRIQVIAFqssdgkqnhiskpiallpvnkstvidlesslssseslsarsgnvlaenpeqdtgdskivagswkgggrtselggffanvdanhperartggnyqtgdlsnaigdidpmdmsESMQEAMHRsnldmsgaeyvrkeiplhvlptssllkldspltsfTDLQRVLYEEERAAYNQAIMQnmsdgkvhpltyiHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLeseafkgsdsslssphhspshglrgsayfhtssdvrtapgsgsrsrrgl
Flexible Loop (DISEMBL)
MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFqssdgkqnhiskPIALLPVNKSTVIDLESSLSSSESLSARSGNVlaenpeqdtgdskiVAGSWKGGGRTSELGGFFANVDANHperartggnyqtgdLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVlptssllkldspLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAFKGSDSSLSSPHHSPSHGLRGSAYFhtssdvrtapgsgsrsrrgl
Low Complexity Region (SEG)
MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPIALLPVNKSTVIDlesslssseslsARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAFKgsdsslssphhspshglrgsAYFHTSSDVRTAPGSGSRSRRGL
Disordered region (IsUnstruct)
***LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQS**********PIALLPVN***************************************************LGGFFAN***************************************************YVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRL***********************************************************
Disordered Region (DISOPRED)
********TRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAF***********************************************N****TG**KIVAGSWKGGGRTSELGGFFA********************************************************EIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAY**************PLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENE**************************************************************
Disordered Region (DISEMBL)
MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPIALLPVNKSTVID***************GNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKS***********************LRGSAYFHTSSD***************
Disordered Region (DISPRO)
*****GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLES***************************************TSELGGFFANVDANHPE**R****************I*P*DMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESE**********************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAxxxxxxxxxxxxxxxxxxxxxxxxxxxxAFKGSDSSLSSPHHSPSHGLRGSAYFHTSSDVRTAPGSGSRSRRGL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	350	2.2.26 [Sep-21-2011]
Q4VA72	261	Lys-63-specific deubiquit	yes	no	0.268	0.360	0.565	2e-26
Q66GV6	261	Lys-63-specific deubiquit	N/A	no	0.268	0.360	0.565	3e-26
B5X8M4	260	Lys-63-specific deubiquit	N/A	no	0.268	0.361	0.555	1e-25
P46737	291	Lys-63-specific deubiquit	yes	no	0.231	0.278	0.616	2e-25
B2RYM5	291	Lys-63-specific deubiquit	yes	no	0.268	0.323	0.555	2e-25
Q5R9L6	247	Lys-63-specific deubiquit	yes	no	0.202	0.287	0.680	1e-24
B0KWU8	316	Lys-63-specific deubiquit	no	no	0.202	0.224	0.680	1e-24
P46736	316	Lys-63-specific deubiquit	no	no	0.202	0.224	0.680	1e-24
A5PJP6	316	Lys-63-specific deubiquit	no	no	0.202	0.224	0.680	2e-24
Q7M757	291	Lys-63-specific deubiquit	no	no	0.265	0.319	0.510	2e-23

>sp|Q4VA72|BRCC3_XENTR Lys-63-specific deubiquitinase BRCC36 OS=Xenopus tropicalis GN=brcc3 PE=2 SV=1

 Score =  120 bits (300), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/99 (56%), Positives = 70/99 (70%), Gaps = 5/99 (5%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           +TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GRI 
Sbjct: 80  ITGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDVGFVGLIFSCFIEDKNTKTGRIL 139

Query: 63  VIAFQSSDGKQN----HISKPIALLPVNKSTVIDLESSL 97
              FQS   +++     I  P+ ++P N    + LES++
Sbjct: 140 YTCFQSVQAQKSSEYERIEVPLHVVPHNTIRKVCLESAV 178

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the brca1-bard1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the rnf8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.
Xenopus tropicalis (taxid: 8364)
EC: 3EC: .EC: 4EC: .EC: 1EC: 9EC: .EC: -

>sp|Q66GV6|BRCC3_XENLA Lys-63-specific deubiquitinase BRCC36 OS=Xenopus laevis GN=brcc3 PE=2 SV=1

 Score =  119 bits (299), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 56/99 (56%), Positives = 70/99 (70%), Gaps = 5/99 (5%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           +TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GRI 
Sbjct: 80  ITGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDVGFVGLIFSCFIEDKNTKTGRIL 139

Query: 63  VIAFQSSDGKQN----HISKPIALLPVNKSTVIDLESSL 97
              FQS   +++     I  P+ ++P N    + LES++
Sbjct: 140 YTCFQSVQAQKSSEYERIEVPLHVVPHNTIRKVCLESAV 178

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the brca1-bard1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the rnf8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|B5X8M4|BRCC3_SALSA Lys-63-specific deubiquitinase BRCC36 OS=Salmo salar GN=brcc3 PE=2 SV=1

 Score =  117 bits (293), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 55/99 (55%), Positives = 68/99 (68%), Gaps = 5/99 (5%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           +TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct: 80  MTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 139

Query: 63  VIAFQSSDGKQ----NHISKPIALLPVNKSTVIDLESSL 97
              FQS   ++      I  PI ++P      + LES++
Sbjct: 140 YTCFQSVQAQKGSEYERIEIPIHVVPHEAIGKVCLESAV 178

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the brca1-bard1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the rnf8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.

Salmo salar (taxid: 8030)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|P46737|BRCC3_MOUSE Lys-63-specific deubiquitinase BRCC36 OS=Mus musculus GN=Brcc3 PE=2 SV=1

 Score =  117 bits (292), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 53/86 (61%), Positives = 63/86 (73%), Gaps = 5/86 (5%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct: 110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query: 63  VIAFQSSDGKQN----HISKPIALLP 84
              FQS   +++     I  PI ++P
Sbjct: 170 YTCFQSIQAQKSSEYERIEIPIHIVP 195

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the RNF8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|B2RYM5|BRCC3_RAT Lys-63-specific deubiquitinase BRCC36 OS=Rattus norvegicus GN=Brcc3 PE=2 SV=1

 Score =  116 bits (291), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 55/99 (55%), Positives = 69/99 (69%), Gaps = 5/99 (5%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct: 110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query: 63  VIAFQSSDGKQN----HISKPIALLPVNKSTVIDLESSL 97
              FQS   +++     I  P+ ++P      + LES++
Sbjct: 170 YTCFQSVQAQKSSDYERIEIPVHVVPHVTIGKVCLESAV 208

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the RNF8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q5R9L6|BRCC3_PONAB Lys-63-specific deubiquitinase BRCC36 OS=Pongo abelii GN=BRCC3 PE=2 SV=1

 Score =  114 bits (285), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 49/72 (68%), Positives = 57/72 (79%), Gaps = 1/72 (1%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct: 110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query: 63  VIAFQSSDGKQN 74
              FQS   +++
Sbjct: 170 YTCFQSIQAQKS 181

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the RNF8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|B0KWU8|BRCC3_CALJA Lys-63-specific deubiquitinase BRCC36 OS=Callithrix jacchus GN=BRCC3 PE=3 SV=2

 Score =  114 bits (284), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 49/72 (68%), Positives = 57/72 (79%), Gaps = 1/72 (1%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct: 110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query: 63  VIAFQSSDGKQN 74
              FQS   +++
Sbjct: 170 YTCFQSIQAQKS 181

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the RNF8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.

Callithrix jacchus (taxid: 9483)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|P46736|BRCC3_HUMAN Lys-63-specific deubiquitinase BRCC36 OS=Homo sapiens GN=BRCC3 PE=1 SV=2

 Score =  114 bits (284), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 49/72 (68%), Positives = 57/72 (79%), Gaps = 1/72 (1%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct: 110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query: 63  VIAFQSSDGKQN 74
              FQS   +++
Sbjct: 170 YTCFQSIQAQKS 181

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the RNF8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|A5PJP6|BRCC3_BOVIN Lys-63-specific deubiquitinase BRCC36 OS=Bos taurus GN=BRCC3 PE=2 SV=1

 Score =  114 bits (284), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 49/72 (68%), Positives = 57/72 (79%), Gaps = 1/72 (1%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
           LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct: 110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query: 63  VIAFQSSDGKQN 74
              FQS   +++
Sbjct: 170 YTCFQSIQAQKS 181

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not have activity toward 'Lys-48'-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX, antagonizing the RNF8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates. Mediates the specific 'Lys-63'-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q7M757|BRC3L_MOUSE Lys-63-specific deubiquitinase BRCC36-like OS=Mus musculus GN=C6.1al PE=2 SV=1

 Score =  110 bits (275), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 50/98 (51%), Positives = 65/98 (66%), Gaps = 5/98 (5%)

Query: 5   TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDA-NKVGRIQV 63
           TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D  F+GLIF+CF ED   K+GR+  
Sbjct: 111 TGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQSFVGLIFACFIEDKPTKIGRVLY 170

Query: 64  IAFQSSDGKQN----HISKPIALLPVNKSTVIDLESSL 97
             FQS    ++     +  PI ++P      + L S++
Sbjct: 171 TCFQSVQASKSSEYERLEIPIHIVPRTTIGTVCLRSAI 208

Metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	350
225442853	437	PREDICTED: uncharacterized protein LOC10	0.997	0.798	0.75	1e-155
297743401	357	unnamed protein product [Vitis vinifera]	0.997	0.977	0.75	1e-154
449469008	436	PREDICTED: uncharacterized protein LOC10	0.994	0.798	0.701	1e-138
358248516	436	uncharacterized protein LOC100784991 [Gl	0.991	0.795	0.708	1e-137
224058695	434	predicted protein [Populus trichocarpa]	0.962	0.776	0.702	1e-136
356550598	436	PREDICTED: uncharacterized protein LOC10	0.991	0.795	0.697	1e-135
357455111	443	Lys-63-specific deubiquitinase BRCC36 [M	0.96	0.758	0.673	1e-129
449532194	359	PREDICTED: LOW QUALITY PROTEIN: lys-63-s	0.945	0.922	0.664	1e-121
145337792	406	BRCA1/BRCA2-containing complex subunit 3	0.874	0.753	0.712	1e-121
297833458	413	hypothetical protein ARALYDRAFT_478001 [	0.891	0.755	0.663	1e-117

>gi|225442853|ref|XP_002285369.1| PREDICTED: uncharacterized protein LOC100253140 [Vitis vinifera]

 Score =  553 bits (1425), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 267/356 (75%), Positives = 307/356 (86%), Gaps = 7/356 (1%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
           MTV TG+TTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSCFSEDA KVGR
Sbjct: 81  MTVATGKTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCFSEDAQKVGR 140

Query: 61  IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTG 120
           IQVIAFQS+DGKQ+++S+PI+L PV++S++ID+ESS SSSE+  A+SG    E+ EQDTG
Sbjct: 141 IQVIAFQSTDGKQSNMSRPISLSPVHRSSIIDVESSFSSSENAPAKSGPARVESSEQDTG 200

Query: 121 DSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESM 180
           DS+ +A   KGGGR+S+LGGFFAN DAN+  R + GGNY T +  NA+ D+DPMDMSESM
Sbjct: 201 DSRTMALVNKGGGRSSDLGGFFANADANYLGRDKMGGNYHTNNSENAVVDVDPMDMSESM 260

Query: 181 QEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 240
           QEAMHRSNLDMSGAEYVRKE+PL V PT SLLKLDSPLTSFTDLQRVLYEEERAAYNQAI
Sbjct: 261 QEAMHRSNLDMSGAEYVRKEVPLLVFPTLSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 320

Query: 241 MQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKS 300
           +QNM DGKVHPL +IHHTSTYQASMCKL+EYCLSPAI+ALQDRLKENEIRLA+LTDEA++
Sbjct: 321 VQNMRDGKVHPLAFIHHTSTYQASMCKLMEYCLSPAINALQDRLKENEIRLAILTDEART 380

Query: 301 LESEAFKGSDSSLSSPHHSPSHGLRGSAYF-------HTSSDVRTAPGSGSRSRRG 349
           LE+EAFKGS+SS  SP +  SHG+RGSA F         S ++R+  G GSRSRRG
Sbjct: 381 LETEAFKGSESSSGSPRNFQSHGIRGSASFGHRDLYPAESINLRSVAGPGSRSRRG 436

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743401|emb|CBI36268.3| unnamed protein product [Vitis vinifera]

 Score =  552 bits (1422), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 267/356 (75%), Positives = 307/356 (86%), Gaps = 7/356 (1%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
           MTV TG+TTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSCFSEDA KVGR
Sbjct: 1   MTVATGKTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCFSEDAQKVGR 60

Query: 61  IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTG 120
           IQVIAFQS+DGKQ+++S+PI+L PV++S++ID+ESS SSSE+  A+SG    E+ EQDTG
Sbjct: 61  IQVIAFQSTDGKQSNMSRPISLSPVHRSSIIDVESSFSSSENAPAKSGPARVESSEQDTG 120

Query: 121 DSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESM 180
           DS+ +A   KGGGR+S+LGGFFAN DAN+  R + GGNY T +  NA+ D+DPMDMSESM
Sbjct: 121 DSRTMALVNKGGGRSSDLGGFFANADANYLGRDKMGGNYHTNNSENAVVDVDPMDMSESM 180

Query: 181 QEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 240
           QEAMHRSNLDMSGAEYVRKE+PL V PT SLLKLDSPLTSFTDLQRVLYEEERAAYNQAI
Sbjct: 181 QEAMHRSNLDMSGAEYVRKEVPLLVFPTLSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 240

Query: 241 MQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKS 300
           +QNM DGKVHPL +IHHTSTYQASMCKL+EYCLSPAI+ALQDRLKENEIRLA+LTDEA++
Sbjct: 241 VQNMRDGKVHPLAFIHHTSTYQASMCKLMEYCLSPAINALQDRLKENEIRLAILTDEART 300

Query: 301 LESEAFKGSDSSLSSPHHSPSHGLRGSAYF-------HTSSDVRTAPGSGSRSRRG 349
           LE+EAFKGS+SS  SP +  SHG+RGSA F         S ++R+  G GSRSRRG
Sbjct: 301 LETEAFKGSESSSGSPRNFQSHGIRGSASFGHRDLYPAESINLRSVAGPGSRSRRG 356

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449469008|ref|XP_004152213.1| PREDICTED: uncharacterized protein LOC101217628 [Cucumis sativus]

 Score =  497 bits (1280), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 251/358 (70%), Positives = 295/358 (82%), Gaps = 10/358 (2%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
           MT +TGRTTRVIGWYHSHPHITVLPSHVDVRTQ  YQLLD+GFIGLIFSCFSEDANKVGR
Sbjct: 81  MTAMTGRTTRVIGWYHSHPHITVLPSHVDVRTQGTYQLLDSGFIGLIFSCFSEDANKVGR 140

Query: 61  IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTG 120
           IQVIAFQSSDGKQNH+S+PI+L PV +++VID+ESSLSSS+++S   G    ENPEQDTG
Sbjct: 141 IQVIAFQSSDGKQNHLSRPISLSPVYRNSVIDVESSLSSSDNVSGNVGYGPGENPEQDTG 200

Query: 121 DSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESM 180
           DS ++AG+ KG GR+SELG FFAN D N+  + + GG+Y   + ++ I DIDPMD+SESM
Sbjct: 201 DS-MIAGALKGTGRSSELGYFFANADTNYQGKEKIGGSYLINNTNSGITDIDPMDLSESM 259

Query: 181 QEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 240
           QEAMHRSN++MS AE+ RKEIPLHV+PT+SL+KLDSPLTSFTDLQ VL+EEER+AYNQAI
Sbjct: 260 QEAMHRSNIEMSAAEFSRKEIPLHVMPTASLIKLDSPLTSFTDLQHVLFEEERSAYNQAI 319

Query: 241 MQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKS 300
             NM DGKVHPLT+IHHTSTYQASMCKLIEYCLSPAISALQDR+KENEIRLA+L +EA++
Sbjct: 320 SNNMKDGKVHPLTFIHHTSTYQASMCKLIEYCLSPAISALQDRVKENEIRLALLAEEARN 379

Query: 301 LESEAFKGSDSSLSSPHHSPSHGLRGSA-------YFHTSS-DVRTAPGSGSRSRRGL 350
           LE EA K ++S   SPH   +HG R SA       Y  T+S   R+   S  RSR+GL
Sbjct: 380 LEVEAAKANESVPGSPHQV-THGSRASASPTHRDLYPSTASVGARSGGSSMYRSRKGL 436

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248516|ref|NP_001240150.1| uncharacterized protein LOC100784991 [Glycine max] gi|255635958|gb|ACU18325.1| unknown [Glycine max]

 Score =  495 bits (1275), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 253/357 (70%), Positives = 291/357 (81%), Gaps = 10/357 (2%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
           MT  TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSC+SED NKVGR
Sbjct: 81  MTTSTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCYSEDVNKVGR 140

Query: 61  IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTG 120
           IQVIAFQSSDGKQNH S+PI L PVN+S VID++SS SSSE++S + G   AEN EQDTG
Sbjct: 141 IQVIAFQSSDGKQNHRSRPIPLSPVNRSPVIDIDSSPSSSENVSTKPGYFEAENAEQDTG 200

Query: 121 DSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESM 180
           DS+ V  S K GGR S+LG FFAN DAN+  R ++GGNY   +    I D+DPMDMSESM
Sbjct: 201 DSRSVVVS-KDGGR-SDLGNFFANADANYLGRDKSGGNYHPNNSDTNIVDVDPMDMSESM 258

Query: 181 QEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 240
           QEAMHRSNLDMSGAE+VRKEIPL+VLP  SL+ LDSPL+S+TDLQ VL+EEE+ AYNQAI
Sbjct: 259 QEAMHRSNLDMSGAEFVRKEIPLYVLPALSLINLDSPLSSYTDLQHVLFEEEQNAYNQAI 318

Query: 241 MQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKS 300
           +QNM DGKVHPLT+IHHTSTYQAS+CKLIEYCLSPAI+ALQDRL+ENEIRLA+L++EAKS
Sbjct: 319 LQNMRDGKVHPLTFIHHTSTYQASLCKLIEYCLSPAINALQDRLRENEIRLAVLSEEAKS 378

Query: 301 LESEAFKGSDSSLSSPHH--SPSH------GLRGSAYFHTSSDVRTAPGSGSRSRRG 349
           LE+EA++GS++S+ SP    SP H      GLR       S   R     GSRSR+G
Sbjct: 379 LEAEAYRGSEASVGSPRRVASPVHRGGSSPGLRNLHDSPESLGSRNVASPGSRSRKG 435

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224058695|ref|XP_002299607.1| predicted protein [Populus trichocarpa] gi|222846865|gb|EEE84412.1| predicted protein [Populus trichocarpa]

 Score =  489 bits (1260), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 253/360 (70%), Positives = 280/360 (77%), Gaps = 23/360 (6%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
           MT  TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD GFIGLIFSCF+ED NKVGR
Sbjct: 81  MTASTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDPGFIGLIFSCFNEDVNKVGR 140

Query: 61  IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTG 120
           IQVIAFQSSDGKQN++ +P++ LPVNKS++I+L+SS S   SL         E PE DT 
Sbjct: 141 IQVIAFQSSDGKQNNMLRPVSALPVNKSSIIELDSSSSDIASL---------EGPELDTA 191

Query: 121 DSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESM 180
           DS+  AGS KGG R+  LG FFAN DAN+  R R GGNY + +  + I DIDPMDMSESM
Sbjct: 192 DSR-AAGSSKGGARSLGLGDFFANADANYVGRERIGGNYYSSNSGDKITDIDPMDMSESM 250

Query: 181 QEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 240
           QEAMHRSNLDMSGAEY R+EIPLHVLPT SLLKLDSPL SF DLQRVLYEEER AYNQAI
Sbjct: 251 QEAMHRSNLDMSGAEYSRREIPLHVLPTCSLLKLDSPLMSFGDLQRVLYEEERGAYNQAI 310

Query: 241 MQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKS 300
           +QNM +GKVHPLT+IHHT+TYQASMCKLIEYCLSPAI+ALQ RL+EN+IRLA L DEAK 
Sbjct: 311 LQNMRNGKVHPLTFIHHTATYQASMCKLIEYCLSPAINALQGRLRENDIRLATLADEAKM 370

Query: 301 LESEAFKGSDSSL-----SSPHHSPSHGLRGSAY-----FHTSSD---VRTAPGSGSRSR 347
           LE E  KGS+  +      SP   PS GLRGSA      FH SS+    RT    GSRSR
Sbjct: 371 LEMETAKGSELQISPSSSRSPRQVPSPGLRGSALSGQRDFHGSSESLSSRTVASPGSRSR 430

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550598|ref|XP_003543672.1| PREDICTED: uncharacterized protein LOC100781761 [Glycine max]

 Score =  489 bits (1258), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 249/357 (69%), Positives = 288/357 (80%), Gaps = 10/357 (2%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
           MT  TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSC+SED NKVGR
Sbjct: 81  MTTSTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCYSEDVNKVGR 140

Query: 61  IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTG 120
           IQVIAFQSSDGK NH+S+P+ L PVN+S VID++SS SSSE++S R G   AEN EQDTG
Sbjct: 141 IQVIAFQSSDGKHNHMSRPVPLSPVNRSPVIDIDSSPSSSENVSTRPGYFKAENAEQDTG 200

Query: 121 DSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESM 180
           DS+ V  S K GGR S+LG FFAN DAN+  R ++GGNY   +    I D+D MDMSESM
Sbjct: 201 DSRSVVVS-KDGGR-SDLGNFFANADANYLGRDKSGGNYHPNNSDTNIVDVDAMDMSESM 258

Query: 181 QEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 240
           QEAMHRSNLDMSGAE+VRKEIPL+VLP  SL+ +DSPL+S+TDLQ VL+EEER AYNQAI
Sbjct: 259 QEAMHRSNLDMSGAEFVRKEIPLYVLPALSLINIDSPLSSYTDLQHVLFEEERNAYNQAI 318

Query: 241 MQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKS 300
           +QN  DGKVHPLT+IHHTSTYQAS+CKLIEYCLSPAI+ALQDRL+ENEIRLA+L +EAKS
Sbjct: 319 LQNKRDGKVHPLTFIHHTSTYQASLCKLIEYCLSPAINALQDRLRENEIRLAVLREEAKS 378

Query: 301 LESEAFKGSDSSLSSPHH--SPSH------GLRGSAYFHTSSDVRTAPGSGSRSRRG 349
           LE+EA++GS++S+ +P    SP H      GLR       S   R     GSRSR+G
Sbjct: 379 LEAEAYRGSEASVGTPRRVASPVHRGGSSPGLRNLHDSPESLGSRNVASPGSRSRKG 435

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357455111|ref|XP_003597836.1| Lys-63-specific deubiquitinase BRCC36 [Medicago truncatula] gi|355486884|gb|AES68087.1| Lys-63-specific deubiquitinase BRCC36 [Medicago truncatula]

 Score =  466 bits (1199), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 239/355 (67%), Positives = 280/355 (78%), Gaps = 19/355 (5%)

Query: 12  IGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG 71
           IGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSC++EDANK+G+IQVIAFQSSDG
Sbjct: 91  IGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCYNEDANKIGKIQVIAFQSSDG 150

Query: 72  KQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKG 131
           KQN +S+PI L PVNKS++I ++SS SSSE+L+ RSG    ++PEQDTGDS+  AG+ KG
Sbjct: 151 KQNSMSRPIPLSPVNKSSIIHIDSSPSSSENLTTRSGYFKGDSPEQDTGDSR-SAGASKG 209

Query: 132 GGRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDM 191
           GGR+SELG FFAN DAN+    + G NY   + S+ I   DPMDMSESMQEAMHRSNLDM
Sbjct: 210 GGRSSELGNFFANADANYLGSVKDGENYHLNN-SDIIAVDDPMDMSESMQEAMHRSNLDM 268

Query: 192 SGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMS-DGKVH 250
           SGAEYVRKEIPLHVLP+ S + LDSPL+S+TDLQ VL+EEER AYNQAI+QN   DGKVH
Sbjct: 269 SGAEYVRKEIPLHVLPSLSFINLDSPLSSYTDLQHVLFEEERTAYNQAILQNTRWDGKVH 328

Query: 251 PLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEA--FKG 308
           PLT+IHHTSTYQAS+CKLIEYCLSPAI+ALQDRL+ENEIRLA+L++EAKSLE+EA   +G
Sbjct: 329 PLTFIHHTSTYQASLCKLIEYCLSPAINALQDRLRENEIRLAVLSEEAKSLEAEASTSRG 388

Query: 309 SDSSLSSPHHSPSHGLRGSAYFHTSSDVR--------------TAPGSGSRSRRG 349
           S++SL SP    S     S     SS  R              +    GSRSR+G
Sbjct: 389 SEASLGSPRQVASPRQVASPIHRGSSSPRQRNSQSSSESLGSKSVASPGSRSRKG 443

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449532194|ref|XP_004173067.1| PREDICTED: LOW QUALITY PROTEIN: lys-63-specific deubiquitinase BRCC36-like, partial [Cucumis sativus]

 Score =  441 bits (1135), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 228/343 (66%), Positives = 276/343 (80%), Gaps = 12/343 (3%)

Query: 16  HSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNH 75
           ++ P + +L +  DVRTQ  YQLLD+GFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNH
Sbjct: 21  NNFPFMEILLA--DVRTQGTYQLLDSGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNH 78

Query: 76  ISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRT 135
           +S+PI+L PV +++VID+ESSLSSS+++S   G  L ENPEQDTGDS ++AG+ KG GR+
Sbjct: 79  LSRPISLSPVYRNSVIDVESSLSSSDNVSGNVGYGLGENPEQDTGDS-MIAGALKGTGRS 137

Query: 136 SELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAE 195
           SELG FFAN D N+  + + GG+Y   + ++ I DIDPMD+SESMQEAMHRSN++MS AE
Sbjct: 138 SELGXFFANADTNYQGKEKIGGSYLINNTNSGITDIDPMDLSESMQEAMHRSNIEMSAAE 197

Query: 196 YVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYI 255
           + RKEIPLHV+PT+SL+KLDSPLTSFTDLQ VL+EEER+AYNQAI  NM DGKVHPLT+I
Sbjct: 198 FSRKEIPLHVMPTASLIKLDSPLTSFTDLQHVLFEEERSAYNQAISNNMKDGKVHPLTFI 257

Query: 256 HHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAFKGSDSSLSS 315
           HHTSTYQASMCKLIEYCLSPAISALQDR+KENEIRLA+L +EA++LE EA K ++S   S
Sbjct: 258 HHTSTYQASMCKLIEYCLSPAISALQDRVKENEIRLALLAEEARNLEVEAAKANESVPGS 317

Query: 316 PHHSPSHGLRGSA-------YFHTSS-DVRTAPGSGSRSRRGL 350
           PH   +HG R SA       Y  T+S   R+   S  RSR+GL
Sbjct: 318 PHQV-THGSRASASPTHRDLYPSTASVGARSGGSSMYRSRKGL 359

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145337792|ref|NP_178138.2| BRCA1/BRCA2-containing complex subunit 3 [Arabidopsis thaliana] gi|20147355|gb|AAM10390.1| At1g80210/F18B13_28 [Arabidopsis thaliana] gi|25090323|gb|AAN72276.1| At1g80210/F18B13_28 [Arabidopsis thaliana] gi|332198249|gb|AEE36370.1| BRCA1/BRCA2-containing complex subunit 3 [Arabidopsis thaliana]

 Score =  441 bits (1133), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 223/313 (71%), Positives = 258/313 (82%), Gaps = 7/313 (2%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
           MT+ TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSCFSEDANKVGR
Sbjct: 82  MTISTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCFSEDANKVGR 141

Query: 61  IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTG 120
           IQVIAFQSSDGK N I K ++L+  NK +VIDLESS SSS+S+  RS +   +NPE DT 
Sbjct: 142 IQVIAFQSSDGKPNSIPKSMSLVLANKDSVIDLESSFSSSDSIYQRSSSARGDNPELDTS 201

Query: 121 DSKIVAGSWKGGGRTSELGGFFAN-VDANHPERARTGGNYQTGDLSNAIGDIDPMDMSES 179
           D+   +GS KGGGR S+   FF N  +AN+  R  T GNY     S AI +ID MDMSES
Sbjct: 202 DTATTSGS-KGGGRVSDFEAFFVNNTEANNTRRDGTSGNYS----STAI-EIDSMDMSES 255

Query: 180 MQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQA 239
           MQEAMHRSNL+ SG  YVRKE+PLHVLPTSSLL+L+SPL SF  LQRVLYEEERAAY+Q+
Sbjct: 256 MQEAMHRSNLETSGVGYVRKEVPLHVLPTSSLLQLNSPLASFKSLQRVLYEEERAAYHQS 315

Query: 240 IMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAK 299
           + Q+  DG+VHPL +IH+TSTYQASMCKLIEYCLSPAI+ALQDRLKEN+IRLAML DEA+
Sbjct: 316 VQQSKRDGRVHPLAFIHNTSTYQASMCKLIEYCLSPAINALQDRLKENKIRLAMLMDEAE 375

Query: 300 SLESEAFKGSDSS 312
            LE++  KG+++S
Sbjct: 376 VLEAQKLKGAETS 388

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297833458|ref|XP_002884611.1| hypothetical protein ARALYDRAFT_478001 [Arabidopsis lyrata subsp. lyrata] gi|297330451|gb|EFH60870.1| hypothetical protein ARALYDRAFT_478001 [Arabidopsis lyrata subsp. lyrata]

 Score =  429 bits (1102), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 221/333 (66%), Positives = 259/333 (77%), Gaps = 21/333 (6%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
           MT+ TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSCFSEDANKVGR
Sbjct: 63  MTISTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCFSEDANKVGR 122

Query: 61  IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTG 120
           IQVIAFQSSDGK N I K ++L+  NK +VIDLESS SSS+S+  RS +   +NPE DT 
Sbjct: 123 IQVIAFQSSDGKPNSIPKSMSLVLANKDSVIDLESSFSSSDSIYQRSSSARGDNPELDTT 182

Query: 121 DS------KIVAG--------------SWKGGGRTSELGGFFA-NVDANHPERARTGGNY 159
            +      K++                +  GGGR S+ G FF  N +AN   R  T GNY
Sbjct: 183 IAFYSSLMKVLTNYNFCIIQLIIQILKTIMGGGRVSDFGAFFVNNTEANITGRDGTSGNY 242

Query: 160 QTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLT 219
            +G+LS+   +ID MDMSESMQEAM RSNL+ SG  YVRKE+PLHVLPTSSLL+L+SPL 
Sbjct: 243 SSGNLSSTAIEIDSMDMSESMQEAMLRSNLETSGVGYVRKEVPLHVLPTSSLLQLNSPLA 302

Query: 220 SFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISA 279
           SF  LQRVLYEEERAAY+Q++ Q+M DG+VHPL +IH+TSTYQASMCKLIEYCLSPAI+A
Sbjct: 303 SFKSLQRVLYEEERAAYHQSVQQSMRDGRVHPLAFIHNTSTYQASMCKLIEYCLSPAINA 362

Query: 280 LQDRLKENEIRLAMLTDEAKSLESEAFKGSDSS 312
           LQDRLKEN+IRLAML DEA+ LE++  KG ++S
Sbjct: 363 LQDRLKENKIRLAMLMDEAEVLEAQKLKGPETS 395

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	350
TAIR|locus:2016279	406	BRCC36A "AT1G80210" [Arabidops	0.86	0.741	0.691	1.3e-109
TAIR|locus:2083318	405	BRCC36B "AT3G06820" [Arabidops	0.857	0.740	0.685	9.2e-107
UNIPROTKB|Q4VA72	261	brcc3 "Lys-63-specific deubiqu	0.237	0.318	0.602	9.3e-38
UNIPROTKB|Q66GV6	261	brcc3 "Lys-63-specific deubiqu	0.237	0.318	0.602	1.5e-37
UNIPROTKB|B5X8M4	260	brcc3 "Lys-63-specific deubiqu	0.231	0.311	0.604	1.3e-36
MGI|MGI:2389572	291	Brcc3 "BRCA1/BRCA2-containing	0.231	0.278	0.616	2.7e-36
UNIPROTKB|F1RZ41	291	BRCC36 "Uncharacterized protei	0.231	0.278	0.616	3.5e-36
RGD|1588543	291	Brcc3 "BRCA1/BRCA2-containing	0.231	0.278	0.604	1.2e-35
UNIPROTKB|F1P4L2	226	BRCC3 "Uncharacterized protein	0.214	0.331	0.662	1.5e-35
UNIPROTKB|P46736	316	BRCC3 "Lys-63-specific deubiqu	0.202	0.224	0.680	3.9e-35

TAIR|locus:2016279 BRCC36A "AT1G80210" [Arabidopsis thaliana (taxid:3702)]

 Score = 1062 (378.9 bits), Expect = 1.3e-109, Sum P(2) = 1.3e-109
 Identities = 213/308 (69%), Positives = 243/308 (78%)

Query:     1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
             MT+ TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSCFSEDANKVGR
Sbjct:    82 MTISTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCFSEDANKVGR 141

Query:    61 IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDXXXXXXXXXXXXARSGNVLAENPEQDTG 120
             IQVIAFQSSDGK N I K ++L+  NK +VID             RS +   +NPE DT 
Sbjct:   142 IQVIAFQSSDGKPNSIPKSMSLVLANKDSVIDLESSFSSSDSIYQRSSSARGDNPELDTS 201

Query:   121 DSKIVAGSWKGGGRTSELGGFFAN-VDANHPERARTGGNYQTGDLSNAIGDIDPMDMSES 179
             D+   +GS KGGGR S+   FF N  +AN+  R  T GNY     S AI +ID MDMSES
Sbjct:   202 DTATTSGS-KGGGRVSDFEAFFVNNTEANNTRRDGTSGNYS----STAI-EIDSMDMSES 255

Query:   180 MQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQA 239
             MQEAMHRSNL+ SG  YVRKE+PLHVLPTSSLL+L+SPL SF  LQRVLYEEERAAY+Q+
Sbjct:   256 MQEAMHRSNLETSGVGYVRKEVPLHVLPTSSLLQLNSPLASFKSLQRVLYEEERAAYHQS 315

Query:   240 IMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAK 299
             + Q+  DG+VHPL +IH+TSTYQASMCKLIEYCLSPAI+ALQDRLKEN+IRLAML DEA+
Sbjct:   316 VQQSKRDGRVHPLAFIHNTSTYQASMCKLIEYCLSPAINALQDRLKENKIRLAMLMDEAE 375

Query:   300 SLESEAFK 307
              LE++  K
Sbjct:   376 VLEAQKLK 383

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006281 "DNA repair" evidence=IMP

GO:0006310 "DNA recombination" evidence=IMP

TAIR|locus:2083318 BRCC36B "AT3G06820" [Arabidopsis thaliana (taxid:3702)]

 Score = 1031 (368.0 bits), Expect = 9.2e-107, Sum P(2) = 9.2e-107
 Identities = 211/308 (68%), Positives = 241/308 (78%)

Query:     1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
             MT+ TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD+GFIGLIFSCFSEDANKVGR
Sbjct:    82 MTISTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDSGFIGLIFSCFSEDANKVGR 141

Query:    61 IQVIAFQSSDGKQNHISKPIALLPVNKSTVIDXXXXXXXXXXXXARSGNVLAENPEQDTG 120
             IQVIAFQSSDGK N I K ++L+  NK +VID             RS +     PE DT 
Sbjct:   142 IQVIAFQSSDGKPNSIPKSMSLVLANKDSVIDIESSSSSSDSIYQRSSS---SKPELDTI 198

Query:   121 DSKIVAGSWKGGGRTSELGGFFAN-VDANHPERARTGGNYQTGDLSNAIGDIDPMDMSES 179
             D+   +GS KGGGR S+ G FF N ++AN   R  T   +++G+LS+    ID MDMSES
Sbjct:   199 DTATTSGS-KGGGRVSDFGPFFTNNIEANITGRDET---HKSGNLSSTTIGIDSMDMSES 254

Query:   180 MQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQA 239
             MQEAM RSNLD SGA YVRKE+PLHVLPTSSLL ++SPL SF  LQRVLYEEERAAY Q+
Sbjct:   255 MQEAMLRSNLDTSGAGYVRKEVPLHVLPTSSLLPVNSPLASFKSLQRVLYEEERAAYYQS 314

Query:   240 IMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAK 299
             + QNM DG+VHPL +IH+TSTYQASMCKLIEYCLSPAI+ALQDR KEN+IRLAML DEA+
Sbjct:   315 VQQNMRDGRVHPLAFIHNTSTYQASMCKLIEYCLSPAINALQDRQKENKIRLAMLMDEAE 374

Query:   300 SLESEAFK 307
              LE++  K
Sbjct:   375 VLEAQKLK 382

GO:0003674 "molecular_function" evidence=ND

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=ISS

GO:0006281 "DNA repair" evidence=IMP

UNIPROTKB|Q4VA72 brcc3 "Lys-63-specific deubiquitinase BRCC36" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 274 (101.5 bits), Expect = 9.3e-38, Sum P(2) = 9.3e-38
 Identities = 53/88 (60%), Positives = 64/88 (72%)

Query:     4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
             +TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GRI 
Sbjct:    80 ITGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDVGFVGLIFSCFIEDKNTKTGRIL 139

Query:    63 VIAFQSSDGKQN----HISKPIALLPVN 86
                FQS   +++     I  P+ ++P N
Sbjct:   140 YTCFQSVQAQKSSEYERIEVPLHVVPHN 167

GO:0004221 "ubiquitin thiolesterase activity" evidence=ISS

GO:0004843 "ubiquitin-specific protease activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0008237 "metallopeptidase activity" evidence=ISS

GO:0010212 "response to ionizing radiation" evidence=ISS

GO:0031572 "G2 DNA damage checkpoint" evidence=ISS

GO:0031593 "polyubiquitin binding" evidence=ISS

GO:0045739 "positive regulation of DNA repair" evidence=ISS

GO:0070531 "BRCA1-A complex" evidence=ISS

GO:0070536 "protein K63-linked deubiquitination" evidence=ISS

GO:0070537 "histone H2A K63-linked deubiquitination" evidence=ISS

GO:0070552 "BRISC complex" evidence=ISS

UNIPROTKB|Q66GV6 brcc3 "Lys-63-specific deubiquitinase BRCC36" [Xenopus laevis (taxid:8355)]

 Score = 274 (101.5 bits), Expect = 1.5e-37, Sum P(2) = 1.5e-37
 Identities = 53/88 (60%), Positives = 64/88 (72%)

Query:     4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
             +TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GRI 
Sbjct:    80 ITGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDVGFVGLIFSCFIEDKNTKTGRIL 139

Query:    63 VIAFQSSDGKQN----HISKPIALLPVN 86
                FQS   +++     I  P+ ++P N
Sbjct:   140 YTCFQSVQAQKSSEYERIEVPLHVVPHN 167

GO:0004221 "ubiquitin thiolesterase activity" evidence=ISS

GO:0004843 "ubiquitin-specific protease activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0008237 "metallopeptidase activity" evidence=ISS

GO:0010212 "response to ionizing radiation" evidence=ISS

GO:0031572 "G2 DNA damage checkpoint" evidence=ISS

GO:0031593 "polyubiquitin binding" evidence=ISS

GO:0045739 "positive regulation of DNA repair" evidence=ISS

GO:0070531 "BRCA1-A complex" evidence=ISS

GO:0070536 "protein K63-linked deubiquitination" evidence=ISS

GO:0070537 "histone H2A K63-linked deubiquitination" evidence=ISS

GO:0070552 "BRISC complex" evidence=ISS

UNIPROTKB|B5X8M4 brcc3 "Lys-63-specific deubiquitinase BRCC36" [Salmo salar (taxid:8030)]

 Score = 269 (99.8 bits), Expect = 1.3e-36, Sum P(2) = 1.3e-36
 Identities = 52/86 (60%), Positives = 62/86 (72%)

Query:     4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
             +TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct:    80 MTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 139

Query:    63 VIAFQSSDGKQN----HISKPIALLP 84
                FQS   ++      I  PI ++P
Sbjct:   140 YTCFQSVQAQKGSEYERIEIPIHVVP 165

GO:0004221 "ubiquitin thiolesterase activity" evidence=ISS

GO:0004843 "ubiquitin-specific protease activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0008237 "metallopeptidase activity" evidence=ISS

GO:0010212 "response to ionizing radiation" evidence=ISS

GO:0031572 "G2 DNA damage checkpoint" evidence=ISS

GO:0031593 "polyubiquitin binding" evidence=ISS

GO:0045739 "positive regulation of DNA repair" evidence=ISS

GO:0070531 "BRCA1-A complex" evidence=ISS

GO:0070536 "protein K63-linked deubiquitination" evidence=ISS

GO:0070537 "histone H2A K63-linked deubiquitination" evidence=ISS

GO:0070552 "BRISC complex" evidence=ISS

MGI|MGI:2389572 Brcc3 "BRCA1/BRCA2-containing complex, subunit 3" [Mus musculus (taxid:10090)]

 Score = 273 (101.2 bits), Expect = 2.7e-36, Sum P(2) = 2.7e-36
 Identities = 53/86 (61%), Positives = 63/86 (73%)

Query:     4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
             LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct:   110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query:    63 VIAFQSSDGKQN----HISKPIALLP 84
                FQS   +++     I  PI ++P
Sbjct:   170 YTCFQSIQAQKSSEYERIEIPIHIVP 195

GO:0000151 "ubiquitin ligase complex" evidence=ISO

GO:0000152 "nuclear ubiquitin ligase complex" evidence=ISO

GO:0004221 "ubiquitin thiolesterase activity" evidence=ISO

GO:0004843 "ubiquitin-specific protease activity" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

GO:0006302 "double-strand break repair" evidence=ISO

GO:0006508 "proteolysis" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0008237 "metallopeptidase activity" evidence=ISO

GO:0010165 "response to X-ray" evidence=ISO

GO:0010212 "response to ionizing radiation" evidence=ISO

GO:0016568 "chromatin modification" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0030234 "enzyme regulator activity" evidence=ISO

GO:0031572 "G2 DNA damage checkpoint" evidence=ISO

GO:0031593 "polyubiquitin binding" evidence=ISO

GO:0045739 "positive regulation of DNA repair" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0050790 "regulation of catalytic activity" evidence=ISO

GO:0070531 "BRCA1-A complex" evidence=ISO

GO:0070536 "protein K63-linked deubiquitination" evidence=ISO

GO:0070537 "histone H2A K63-linked deubiquitination" evidence=ISO

GO:0070552 "BRISC complex" evidence=ISO

UNIPROTKB|F1RZ41 BRCC36 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 272 (100.8 bits), Expect = 3.5e-36, Sum P(2) = 3.5e-36
 Identities = 53/86 (61%), Positives = 63/86 (73%)

Query:     4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
             LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct:   110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query:    63 VIAFQSSDGKQN----HISKPIALLP 84
                FQS   +++     I  PI ++P
Sbjct:   170 YTCFQSIQAQKSSEYERIEIPIHVVP 195

GO:0070552 "BRISC complex" evidence=IEA

GO:0070537 "histone H2A K63-linked deubiquitination" evidence=IEA

GO:0070531 "BRCA1-A complex" evidence=IEA

GO:0045739 "positive regulation of DNA repair" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0031572 "G2 DNA damage checkpoint" evidence=IEA

GO:0030234 "enzyme regulator activity" evidence=IEA

GO:0010165 "response to X-ray" evidence=IEA

GO:0008237 "metallopeptidase activity" evidence=IEA

GO:0006302 "double-strand break repair" evidence=IEA

GO:0004843 "ubiquitin-specific protease activity" evidence=IEA

GO:0004221 "ubiquitin thiolesterase activity" evidence=IEA

GO:0000152 "nuclear ubiquitin ligase complex" evidence=IEA

RGD|1588543 Brcc3 "BRCA1/BRCA2-containing complex, subunit 3" [Rattus norvegicus (taxid:10116)]

 Score = 271 (100.5 bits), Expect = 1.2e-35, Sum P(2) = 1.2e-35
 Identities = 52/86 (60%), Positives = 63/86 (73%)

Query:     4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
             LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct:   110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query:    63 VIAFQSSDGKQN----HISKPIALLP 84
                FQS   +++     I  P+ ++P
Sbjct:   170 YTCFQSVQAQKSSDYERIEIPVHVVP 195

GO:0000151 "ubiquitin ligase complex" evidence=ISO

GO:0000152 "nuclear ubiquitin ligase complex" evidence=IEA;ISO

GO:0004221 "ubiquitin thiolesterase activity" evidence=ISO;ISS

GO:0004843 "ubiquitin-specific protease activity" evidence=ISO;ISS

GO:0005634 "nucleus" evidence=ISO;ISS

GO:0006302 "double-strand break repair" evidence=ISO;ISS

GO:0006508 "proteolysis" evidence=IEA

GO:0008237 "metallopeptidase activity" evidence=ISO;ISS

GO:0010165 "response to X-ray" evidence=IEA;ISO

GO:0010212 "response to ionizing radiation" evidence=ISO;ISS

GO:0030234 "enzyme regulator activity" evidence=IEA;ISO

GO:0031572 "G2 DNA damage checkpoint" evidence=ISO;ISS

GO:0031593 "polyubiquitin binding" evidence=ISO;ISS

GO:0045739 "positive regulation of DNA repair" evidence=ISO;ISS

GO:0046872 "metal ion binding" evidence=IEA

GO:0050790 "regulation of catalytic activity" evidence=ISO

GO:0070531 "BRCA1-A complex" evidence=ISO;ISS

GO:0070536 "protein K63-linked deubiquitination" evidence=ISO;ISS

GO:0070537 "histone H2A K63-linked deubiquitination" evidence=ISO;ISS

GO:0070552 "BRISC complex" evidence=ISO;ISS

UNIPROTKB|F1P4L2 BRCC3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 269 (99.8 bits), Expect = 1.5e-35, Sum P(2) = 1.5e-35
 Identities = 51/77 (66%), Positives = 58/77 (75%)

Query:     4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
             +TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GRI 
Sbjct:    24 MTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRIL 83

Query:    63 VIAFQSSDG-KQNHISK 78
                FQS    K + + K
Sbjct:    84 YTCFQSIQAQKSSEVQK 100

GO:0000152 "nuclear ubiquitin ligase complex" evidence=IEA

GO:0004221 "ubiquitin thiolesterase activity" evidence=IEA

GO:0004843 "ubiquitin-specific protease activity" evidence=IEA

GO:0006302 "double-strand break repair" evidence=IEA

GO:0008237 "metallopeptidase activity" evidence=IEA

GO:0010165 "response to X-ray" evidence=IEA

GO:0030234 "enzyme regulator activity" evidence=IEA

GO:0031572 "G2 DNA damage checkpoint" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0045739 "positive regulation of DNA repair" evidence=IEA

GO:0070531 "BRCA1-A complex" evidence=IEA

GO:0070537 "histone H2A K63-linked deubiquitination" evidence=IEA

GO:0070552 "BRISC complex" evidence=IEA

UNIPROTKB|P46736 BRCC3 "Lys-63-specific deubiquitinase BRCC36" [Homo sapiens (taxid:9606)]

 Score = 268 (99.4 bits), Expect = 3.9e-35, Sum P(2) = 3.9e-35
 Identities = 49/72 (68%), Positives = 57/72 (79%)

Query:     4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVGRIQ 62
             LTGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D GF+GLIFSCF ED N K GR+ 
Sbjct:   110 LTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVL 169

Query:    63 VIAFQSSDGKQN 74
                FQS   +++
Sbjct:   170 YTCFQSIQAQKS 181

GO:0006508 "proteolysis" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0010212 "response to ionizing radiation" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0000152 "nuclear ubiquitin ligase complex" evidence=IDA

GO:0070552 "BRISC complex" evidence=IDA

GO:0006302 "double-strand break repair" evidence=IMP

GO:0031572 "G2 DNA damage checkpoint" evidence=IMP

GO:0070531 "BRCA1-A complex" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0070537 "histone H2A K63-linked deubiquitination" evidence=IMP;IDA

GO:0070536 "protein K63-linked deubiquitination" evidence=IDA

GO:0004221 "ubiquitin thiolesterase activity" evidence=IMP

GO:0004843 "ubiquitin-specific protease activity" evidence=IMP

GO:0008237 "metallopeptidase activity" evidence=IMP

GO:0045739 "positive regulation of DNA repair" evidence=IMP

GO:0031593 "polyubiquitin binding" evidence=IDA

GO:0000151 "ubiquitin ligase complex" evidence=IDA

GO:0010165 "response to X-ray" evidence=IDA

GO:0030234 "enzyme regulator activity" evidence=IDA

GO:0050790 "regulation of catalytic activity" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00034568001 SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (357 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	350
cd08068	244	cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC3	6e-44
cd08068	244	cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC3	3e-26
cd08058	119	cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN)	1e-22
pfam01398	117	pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin pro	3e-10
smart00232	135	smart00232, JAB_MPN, JAB/MPN domain	4e-09
cd08067	187	cd08067, MPN_2A_DUB, Mov34/MPN/PAD-1 family: Histo	7e-08
cd08069	268	cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: p	1e-06
COG1310	134	COG1310, COG1310, Predicted metal-dependent protea	0.003

>gnl|CDD|163699 cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex

 Score =  151 bits (383), Expect = 6e-44
 Identities = 53/91 (58%), Positives = 68/91 (74%), Gaps = 5/91 (5%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDAN-KVG 59
           +T  TGR  RV+GWYHSHPHITV PSHVDVRTQAMYQ++D+GF+GLIFSCF+ED + K+G
Sbjct: 81  LTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMG 140

Query: 60  RIQVIAFQSSDGKQN----HISKPIALLPVN 86
            +QV  FQS  G +      I  P+ ++P +
Sbjct: 141 EVQVTCFQSVQGNKAGQYERIEVPLEIVPTS 171

BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-containing complex and is essential for the integrity of the complex. There are studies suggesting that MERIT40/NBA1 ties BRCA1 complex integrity, DSB recognition, and ubiquitin chain activities to the DNA damage response. It has also been shown that BRCA1-containing complex resembles the lid complex of the 26S proteasome. Length = 244

>gnl|CDD|163699 cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex

 Score =  104 bits (261), Expect = 3e-26
 Identities = 46/141 (32%), Positives = 71/141 (50%), Gaps = 13/141 (9%)

Query: 154 RTGGNYQTGDLSNAIGDI------DPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLP 207
           RT   YQ  D S  +G I      D       +Q    +S       +Y R E+PL ++P
Sbjct: 111 RTQAMYQMMD-SGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGNKAGQYERIEVPLEIVP 169

Query: 208 TSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCK 267
           TS++ +  + L S  +L  +LY+EE  AYN+A+     D    PLT IH+ S Y  S+C 
Sbjct: 170 TSTISE--ACLESLVELPEILYQEEEDAYNKALQSCDLD----PLTKIHNGSVYTKSLCH 223

Query: 268 LIEYCLSPAISALQDRLKENE 288
           ++E    P +  L+ RL++N+
Sbjct: 224 ILETISGPLLQLLEARLEQNK 244

BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-containing complex and is essential for the integrity of the complex. There are studies suggesting that MERIT40/NBA1 ties BRCA1 complex integrity, DSB recognition, and ubiquitin chain activities to the DNA damage response. It has also been shown that BRCA1-containing complex resembles the lid complex of the 26S proteasome. Length = 244

>gnl|CDD|163689 cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic

 Score = 91.1 bits (226), Expect = 1e-22
 Identities = 25/64 (39%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
             V TGR   V+GWYHSHP  T   S VD+ TQA YQL+    I ++ S    +    G 
Sbjct: 57  FNVQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRN-KDTGI 115

Query: 61  IQVI 64
            ++ 
Sbjct: 116 FRLT 119

This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor proteins, including p53, p27, and Smad4. Over-expression of CSN5 has been implicated in cancer initiation and progression. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. It is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity; it is targeted to DNA damage foci after irradiation. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. It is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene and serves as a marker in prostate tumors. Length = 119

>gnl|CDD|216478 pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin protease

 Score = 57.0 bits (138), Expect = 3e-10
 Identities = 17/36 (47%), Positives = 20/36 (55%)

Query: 5   TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD 40
             R   V+GWYHSHP      S VDV TQ +YQ + 
Sbjct: 80  VNRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMI 115

Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain and PAD-1-like domain, JABP1 domain or JAMM domain. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are predicted to have a similar role. Length = 117

>gnl|CDD|214573 smart00232, JAB_MPN, JAB/MPN domain

 Score = 53.9 bits (130), Expect = 4e-09
 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 10  RVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS 69
            ++GWYHSHP  +  PS VDV T   YQ      + LI        +  GR+ + AF+ +
Sbjct: 77  EIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLI---VDPIKSFQGRLSLRAFRLT 133

Query: 70  D 70
            
Sbjct: 134 P 134

Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function. Length = 135

>gnl|CDD|163698 cd08067, MPN_2A_DUB, Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase

 Score = 51.5 bits (124), Expect = 7e-08
 Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 7/53 (13%)

Query: 11  VIGWYHSHPHITVLPSHVDVRTQAMYQLLDTG-------FIGLIFSCFSEDAN 56
           V+GWYHSHP     PS  D+ TQ  YQ++  G        +GLI S +    +
Sbjct: 81  VVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNS 133

This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it participates in transcriptional regulation events in androgen receptor-dependent gene activation. In prostate tumors, the levels of uH2A are dramatically decreased, thus 2A-DUB serving as a cancer-related marker. Length = 187

>gnl|CDD|163700 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5

 Score = 48.8 bits (117), Expect = 1e-06
 Identities = 19/42 (45%), Positives = 24/42 (57%)

Query: 5   TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGL 46
           TGR   V+GWYHSHP      S +DV TQ + Q L   F+ +
Sbjct: 83  TGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAV 124

This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations in Rpn11 cause cell cycle and mitochondrial defects, temperature sensitivity and sensitivity to DNA damaging reagents such as UV. It has been shown that the C-terminal region of Rpn11 is involved in the regulation of the mitochondrial fission and tubulation processes. CSN5, one of the eight subunits of CSN, is critical for nuclear export and the degradation of several tumor suppressor proteins, including p53, p27, and Smad4. Its MPN+ domain is critical for the physical interaction of RUNX3 and Jab1. It has been suggested that the direct interaction of CSN5/JAB1 with p27 provides p27 with a leucine-rich nuclear export signal (NES), which is required for binding to chromosomal region maintenance 1 (CRM1), and facilitates nuclear export. The over-expression of CSN5/JAB1 also has been implicated in cancer initiation and progression, including cancer of the lung, pancreas, mouth, thyroid, and breast, suggesting that the oncogenic activity of CSN5 is associated with the down-regulation of RUNX3. Length = 268

>gnl|CDD|224229 COG1310, COG1310, Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]

 Score = 37.1 bits (86), Expect = 0.003
 Identities = 13/28 (46%), Positives = 15/28 (53%)

Query: 11 VIGWYHSHPHITVLPSHVDVRTQAMYQL 38
          V+GWYHSHP     PS  D R   +  L
Sbjct: 71 VVGWYHSHPGGPPYPSEADRRLSKLGPL 98

Length = 134

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	350
cd08068	244	MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subun	100.0
KOG1554	347	consensus COP9 signalosome, subunit CSN5 [Posttran	100.0
KOG1555	316	consensus 26S proteasome regulatory complex, subun	100.0
cd08069	268	MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal	99.96
cd08067	187	MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deu	99.84
cd08058	119	MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains w	99.75
cd08066	173	MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associ	99.57
smart00232	135	JAB_MPN JAB/MPN domain. Domain in Jun kinase activ	99.42
cd08065	266	MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains wi	99.35
cd07767	116	MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (al	99.3
PF01398	114	JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; Inte	99.25
KOG2880	424	consensus SMAD6 interacting protein AMSH, contains	99.06
cd08070	128	MPN_like Mpr1p, Pad1p N-terminal (MPN) domains wit	98.89
COG1310	134	Predicted metal-dependent protease of the PAD1/JAB	98.86
cd08057	157	MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domai	98.71
cd08062	280	MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains w	98.35
cd08064	265	MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains wi	98.14
cd08056	252	MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains wit	98.14
PF14464	104	Prok-JAB: Prokaryotic homologs of the JAB domain;	98.08
cd08072	117	MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1	97.96
KOG1555	316	consensus 26S proteasome regulatory complex, subun	97.55
KOG1560	339	consensus Translation initiation factor 3, subunit	97.37
cd08073	108	MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains	97.36
cd08063	288	MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains wit	96.95
cd08059	101	MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains	96.58
cd08061	274	MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein l	96.22
TIGR02256	131	ICE_VC0181 integrative and conjugative element pro	96.15
PLN03246	303	26S proteasome regulatory subunit; Provisional	95.58
TIGR03735	192	PRTRC_A PRTRC system protein A. A novel genetic sy	94.02
KOG1556	309	consensus 26S proteasome regulatory complex, subun	93.41
cd08060	182	MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family	93.08
PF05021	306	NPL4: NPL4 family; InterPro: IPR007717 The HRD4 ge	88.81

>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex

Probab=100.00  E-value=9e-52  Score=386.49  Aligned_cols=163  Identities=52%  Similarity=0.917  Sum_probs=151.5

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccc-cccCceEEEEEEeeCCCCccccCC
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDA-NKVGRIQVIAFQSSDGKQNHISKP   79 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~-~s~Gkv~i~AFR~~~~~~~~~~rp   79 (350)
                      |++.+||++.+||||||||+++||||.+|++||..||+++++||+|||||++.+. +..|+++++|||+.++++      
T Consensus        81 ~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g~~------  154 (244)
T cd08068          81 LTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGNK------  154 (244)
T ss_pred             HHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCCCC------
Confidence            5678899999999999999999999999999999999999999999999998663 456899999999988532      


Q ss_pred             cccccCCCcchhcccccCCccccccccccccccCCccccccccccccccccCCCccccCCCccccccCCccccccCCCCc
Q 018828           80 IALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNY  159 (350)
Q Consensus        80 ~~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~N~~~~~~~~~~~  159 (350)
                                                                                                      
T Consensus       155 --------------------------------------------------------------------------------  154 (244)
T cd08068         155 --------------------------------------------------------------------------------  154 (244)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCCcCCCCCCCcchHHHHHhhhccccCCCCceeeeeeeeeeecCCCcccCCCcchhHHHHhHHHHHHHHHHHHHH
Q 018828          160 QTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQA  239 (350)
Q Consensus       160 ~~~~~~~~~~~~~~~d~s~~~qea~hrs~ld~sg~~y~rkEvpl~v~p~~~~~~~~~~l~s~~~Lq~iL~~EE~~ay~qa  239 (350)
                                                       |++|+|+||||+|+|+.++.++  ||+++++||+||++||++||++|
T Consensus       155 ---------------------------------~~~~~~~e~pl~i~~~~~~~~~--~~~~~~~l~~~l~~e~~~a~~~~  199 (244)
T cd08068         155 ---------------------------------AGQYERIEVPLEIVPTSTISEA--CLESLVELPEILYQEEEDAYNKA  199 (244)
T ss_pred             ---------------------------------CCcceEEEeeeEEecCcccccc--CHHHHHHHHHHHHHHHHHHHHHH
Confidence                                             5889999999999999999997  59999999999999999999999


Q ss_pred             HHhhcCCCCCCccceeehhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 018828          240 IMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENE  288 (350)
Q Consensus       240 ~~q~~~~~~~hpLt~iHh~sty~~slc~l~e~~l~P~~~~l~drl~~n~  288 (350)
                      +.|+.+    ||||+|||++|||++||+|||+|++|++++||+||++|+
T Consensus       200 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~  244 (244)
T cd08068         200 LQSCDL----DPLTKIHNGSVYTKSLCHILETISGPLLQLLEARLEQNK  244 (244)
T ss_pred             Hhcccc----hHHHHHHhhHHHHHHHHHHHHHHHhhHHHHHHHHHHhcC
Confidence            987654    499999999999999999999999999999999999985

BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai

>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=100.00  E-value=2e-40  Score=316.44  Aligned_cols=134  Identities=21%  Similarity=0.250  Sum_probs=123.2

Q ss_pred             ccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccc---cC
Q 018828            2 TVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHI---SK   78 (350)
Q Consensus         2 ~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~---~r   78 (350)
                      .+..||.++|||||||||+|+||+|+|||.||+++|++++||||||+||.+  +.++|++.|+|||++|.++.+.   +.
T Consensus       124 ~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~R--tlsagkv~iGAFRTyp~gyk~~d~~~s  201 (347)
T KOG1554|consen  124 AKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTR--TLSAGKVNIGAFRTYPKGYKPPDEPPS  201 (347)
T ss_pred             HHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCcc--ccccCceeeceeecccCCCCCCCCCch
Confidence            567899999999999999999999999999999999999999999999986  5678999999999999988654   33


Q ss_pred             CcccccCCCcchhcccccCCcccc-ccccccccccCCccccccccccccccccCCCccccCCCccccccC
Q 018828           79 PIALLPVNKSTVIDLESSLSSSES-LSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDA  147 (350)
Q Consensus        79 p~~~~pl~k~siid~~~~~g~~~~-YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~  147 (350)
                      .++..|++|      |++||.||+ ||+|+|+||++.+|.+.++    .||+|||++|+++++++.|.|-
T Consensus       202 eyqtipl~k------ied~gvHck~yysl~isyfks~ld~kll~----~Lwnkywv~Tlsss~ll~N~dy  261 (347)
T KOG1554|consen  202 EYQTIPLNK------IEDFGVHCKQYYSLEISYFKSSLDMKLLE----LLWNKYWVRTLSSSPLLKNIDY  261 (347)
T ss_pred             hhhccchhh------hhhcccceEEeeccchhhhhhhhhHHHHH----HHHhhhhhcccccccccccchh
Confidence            477778887      799999998 9999999999999999999    9999999999999999998763

>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=4.9e-37  Score=295.85  Aligned_cols=192  Identities=35%  Similarity=0.500  Sum_probs=158.4

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccccCCc
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPI   80 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~~rp~   80 (350)
                      |++++||++.|||||||||+|+||||++||+||+.||++.+..++++++|..   +..|++.++|||++.+.....    
T Consensus       107 ~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~---S~~g~vv~d~f~~In~~~~~~----  179 (316)
T KOG1555|consen  107 LLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQ---SPYGKVVPDAFSSINPQWISP----  179 (316)
T ss_pred             HHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeeccc---CCCCCccCChhhhcCcccccC----
Confidence            5789999999999999999999999999999999999998888888888743   456899999999988654211    


Q ss_pred             ccccCCCcchhcccccCCccccccccccccccCCccccccccccccccccCCCccccCCCccccccCCccccccCCCCcC
Q 018828           81 ALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQ  160 (350)
Q Consensus        81 ~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~N~~~~~~~~~~~~  160 (350)
                                                                                                      
T Consensus       180 --------------------------------------------------------------------------------  179 (316)
T KOG1555|consen  180 --------------------------------------------------------------------------------  179 (316)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCcCCCCCCCcchHHHHHhhhccccCCCCceeeeeeeeeeecCCCcccCCCcchhHHHHhHHHHHHHHHHHHHHH
Q 018828          161 TGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI  240 (350)
Q Consensus       161 ~~~~~~~~~~~~~~d~s~~~qea~hrs~ld~sg~~y~rkEvpl~v~p~~~~~~~~~~l~s~~~Lq~iL~~EE~~ay~qa~  240 (350)
                      +++-+.....+++|||+++|||++|++|      .|.|+|||++|.|......++-|+.++.++|+++|+||+++|.+..
T Consensus       180 ~~eprqtts~~~~m~~~~s~q~~~~g~n------~y~~~ei~~~v~~~~~~~~~nv~~~s~~~~~~~~y~e~~k~~~~~~  253 (316)
T KOG1555|consen  180 GGEPRQTTSNGGHMDMQESLQEDIHGLN------RYYRIEIPLHVLPYEQLMLLNVPLKSWKSLQDVLYEEKLKAYLQSV  253 (316)
T ss_pred             CCCCccccccccccccchhHHhHhhccC------ceEEEEeeEEechhhhhchhccchhhhhhcchhhHHHHHHHhhhhh
Confidence            0122334456789999999999999999      6999999999999777777777899999999999999999999766


Q ss_pred             HhhcCCCCCCccceeehhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 018828          241 MQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAFKGSDSS  312 (350)
Q Consensus       241 ~q~~~~~~~hpLt~iHh~sty~~slc~l~e~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~~~~~~~~  312 (350)
                      .+...                           |+++++++.++.++++.++.+++++.++..++-.++....
T Consensus       254 ~~~~s---------------------------L~~~~N~~~~~~k~~~~~~~~i~d~~~~~~kq~l~~~v~~  298 (316)
T KOG1555|consen  254 PSMKS---------------------------LSKVYNKVCDVCKQMSDFLLMIEDVGEQNPKQHLKEAVTE  298 (316)
T ss_pred             hHHHh---------------------------HHHHHHHHHHHHhhccHHHHHHHHhhhhhHHHHhHHHhhh
Confidence            54321                           7778888888888888888888888888866655544443

>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5

Probab=99.96  E-value=5.3e-31  Score=247.89  Aligned_cols=134  Identities=20%  Similarity=0.220  Sum_probs=115.9

Q ss_pred             ccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCcc---ccC
Q 018828            2 TVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNH---ISK   78 (350)
Q Consensus         2 ~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~---~~r   78 (350)
                      ++.+++++++||||||||+++||||.+||.||..||++.+|+|+|||||..  +.+.|++.++|||+++.....   -..
T Consensus        80 ~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~--t~~~g~~~i~Afr~~~~~~~~~~~~~~  157 (268)
T cd08069          80 LKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIR--SLVKGKVVIGAFRTIPPGYKPLEPRQT  157 (268)
T ss_pred             HHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCc--cccCCcceeeEEEEECccccccCcccC
Confidence            467899999999999999999999999999999999999999999999975  236789999999999988653   123


Q ss_pred             CcccccCCCcchhcccccCCcccc-ccccccccccCCccccccccccccccccCCCccccCCCccccc
Q 018828           79 PIALLPVNKSTVIDLESSLSSSES-LSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANV  145 (350)
Q Consensus        79 p~~~~pl~k~siid~~~~~g~~~~-YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~  145 (350)
                      ..+.+.+.+++++    .++.+++ ||+|+|.||++.+|+.+|.    .||+|+|+++|.+++|++|+
T Consensus       158 ~s~~~~~~~~~~~----~~~~~~~~y~~l~i~~~~s~l~~~~L~----~l~~~~w~~~l~~~~~~~~~  217 (268)
T cd08069         158 TSNIGHLPKPKIE----DFGGHNKQYYSLPIEYFKSSLDRKLLL----NLWNKYWVNTLSLSPLLENS  217 (268)
T ss_pred             ccccCccCcHHHH----HhCchhcEEEEeeeEEecCHHHHHHHH----HHHHHhHHHHhhCCchhhhh
Confidence            3555666665444    5566665 9999999999999999999    99999999999999999998

This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i

>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase

Probab=99.84  E-value=3.1e-21  Score=174.26  Aligned_cols=69  Identities=33%  Similarity=0.525  Sum_probs=60.5

Q ss_pred             cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCc-------CceEEEeccccccccccCceEEEEEEeeCCCCc
Q 018828            5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT-------GFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQN   74 (350)
Q Consensus         5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~-------pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~   74 (350)
                      ..+++++||||||||.++||||.+||+||..||.+.+       ||||||||||+++.. ..+++|+|||+.++..+
T Consensus        75 ~~~gl~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~-~~~s~i~~f~~~~~~~~  150 (187)
T cd08067          75 ESRGLSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNS-TPESQITCFWVMPPPEN  150 (187)
T ss_pred             HHcCCEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCC-CCCCcEEEEEEECCCCC
Confidence            3677899999999999999999999999999999865       899999999986443 44678999999998764

This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p

>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic

Probab=99.75  E-value=6.6e-19  Score=145.94  Aligned_cols=61  Identities=41%  Similarity=0.590  Sum_probs=55.3

Q ss_pred             cccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEee
Q 018828            3 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS   69 (350)
Q Consensus         3 ~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~   69 (350)
                      +..++++++||||||||++++|||..|++||..||++.+++|+||+||++.      +..++|||+.
T Consensus        59 ~~~~~g~~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~------~~~~~a~rl~  119 (119)
T cd08058          59 VQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR------NKDTGIFRLT  119 (119)
T ss_pred             HHhCCCCeEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC------CcccceEEeC
Confidence            457899999999999999999999999999999999999999999999762      4579999963

This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot

>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family

Probab=99.57  E-value=3.3e-15  Score=133.58  Aligned_cols=60  Identities=25%  Similarity=0.360  Sum_probs=54.4

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEee-CCCC
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS-DGKQ   73 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~-~~~~   73 (350)
                      .+++.+||||||||..+||||.+|+.||..||.+++++++|||||.        .+.++|||+. +.+.
T Consensus        72 ~~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~--------~~~l~afrl~~~~g~  132 (173)
T cd08066          72 QHDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK--------YNEFGIFRLTDPPGL  132 (173)
T ss_pred             hCCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC--------CcEEeEEEeecCCcc
Confidence            5789999999999999999999999999999999999999999972        4689999999 4443

AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al

>smart00232 JAB_MPN JAB/MPN domain

Probab=99.42  E-value=3.4e-13  Score=110.24  Aligned_cols=65  Identities=32%  Similarity=0.504  Sum_probs=57.9

Q ss_pred             cccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeC
Q 018828            3 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSD   70 (350)
Q Consensus         3 ~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~   70 (350)
                      ++..+++.+||||||||..+++||..|+.+|..||.....++.++++|..   +..|++.+.||++.+
T Consensus        70 ~~~~~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~---s~~g~~~~~af~~~~  134 (135)
T smart00232       70 KKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIK---SFQGRLSLRAFRLTP  134 (135)
T ss_pred             HhhCCCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCc---cccCcEEEEEEEecC
Confidence            45678899999999999999999999999999999999999999999864   334889999999865

Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.

>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h

Probab=99.35  E-value=3.2e-13  Score=127.10  Aligned_cols=111  Identities=12%  Similarity=0.088  Sum_probs=83.8

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccccCCc
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPI   80 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~~rp~   80 (350)
                      |+++++..+.+|||||||| +++|.+..++++|..||...+++|+||+||..   ++.|++.+.|||+.+......    
T Consensus        71 ~~r~v~~~e~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~---s~~g~l~lkAyrl~~~~~~~~----  142 (266)
T cd08065          71 LLREVNVDHNHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSK---TSQGSLSLKAYRLSEKFMELY----  142 (266)
T ss_pred             HHHHhCCCCcEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCc---ccccceeeEEEEEcHHHHHHh----
Confidence            3577888999999999999 99999999999999999988999999999864   245788999999987543111    


Q ss_pred             ccccCCCcchhcccccCCccccccccccccccCCccccccc
Q 018828           81 ALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGD  121 (350)
Q Consensus        81 ~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~  121 (350)
                      ..+..++..+++....++  +-|+.++|.++.+.+++.+|.
T Consensus       143 ~~~~~~~~~l~~~~~~~~--~if~eiPv~i~n~~l~~~~L~  181 (266)
T cd08065         143 KEGKFSTESLREANLTFS--NIFEEIPVVIRNSHLVNALLS  181 (266)
T ss_pred             hcCCcCHHHHHHhcCchh--cEEEEEEEEEEchHHHHHHHH
Confidence            112222222333322333  229999999999999999987

Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different

>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains

Probab=99.30  E-value=1.7e-12  Score=104.13  Aligned_cols=49  Identities=24%  Similarity=0.452  Sum_probs=45.2

Q ss_pred             ccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecccc
Q 018828            4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFS   52 (350)
Q Consensus         4 ~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~   52 (350)
                      ...+++.+||||||||..++|||..|+.+|..||...+.+|+||+|+-.
T Consensus        58 ~~~~~~~iVGwyhshp~~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~  106 (116)
T cd07767          58 KLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKP  106 (116)
T ss_pred             HhcCCCeEEEEEEcCCCCCCccCHHHHHHHHHHHHhCCCCEEEEEECCC
Confidence            4567899999999999999999999999999999988999999999854

MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J

>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors

Probab=99.25  E-value=2.7e-12  Score=104.58  Aligned_cols=39  Identities=38%  Similarity=0.809  Sum_probs=31.9

Q ss_pred             cccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCc
Q 018828            3 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT   41 (350)
Q Consensus         3 ~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~   41 (350)
                      +++...+.+||||||||.++||||..|+.||..||++.+
T Consensus        75 ~~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~  113 (114)
T PF01398_consen   75 KKVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNP  113 (114)
T ss_dssp             HHCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTT
T ss_pred             ccccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCC
Confidence            344455999999999999999999999999999999875

This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.

>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]

Probab=99.06  E-value=4.2e-11  Score=118.68  Aligned_cols=65  Identities=25%  Similarity=0.387  Sum_probs=56.3

Q ss_pred             ccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccc
Q 018828            4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHI   76 (350)
Q Consensus         4 ~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~   76 (350)
                      +..+.+-.+||.|.||+.+||+|.||++|+-+||.|.|.+|||||+|-..        ..|.||.++++.+..
T Consensus       320 Qdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~--------~tGiFrLt~~~Gm~~  384 (424)
T KOG2880|consen  320 QDQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSK--------TTGIFRLTDPGGMEV  384 (424)
T ss_pred             cccccceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccC--------CcceEEecCCcchHH
Confidence            34567889999999999999999999999999999999999999999531        256799998777644

>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding)

Probab=98.89  E-value=2.3e-09  Score=89.94  Aligned_cols=55  Identities=33%  Similarity=0.413  Sum_probs=44.9

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCC
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG   71 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~   71 (350)
                      .+++.+||||||||...|+||..|+.++..     .+.+.+|+++...      ...+.||+...+
T Consensus        67 ~~g~~~vG~~HSHP~~~~~PS~~D~~~~~~-----~~~~~lIv~~~~~------~~~~~~~~~~~~  121 (128)
T cd08070          67 ERGLEVVGIYHSHPDGPARPSETDLRLAWP-----PGVSYLIVSLAGG------APELRAWRLEGG  121 (128)
T ss_pred             HCCCeEEEEEeCCCCCCCCCCHHHHHhccC-----CCCeEEEEECCCC------CcEEEEEEEcCC
Confidence            356899999999999999999999997643     3799999997541      346999998764

This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.

>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]

Probab=98.86  E-value=3.2e-09  Score=89.82  Aligned_cols=41  Identities=32%  Similarity=0.455  Sum_probs=31.6

Q ss_pred             CCCceeeeeccCCCCCCCCChHHHHhHHHhhhh-CcCceEEEeccc
Q 018828            7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLL-DTGFIGLIFSCF   51 (350)
Q Consensus         7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~-~~pfVaLIvSP~   51 (350)
                      +++.|||||||||+..||||..|+.    +|.+ ..+|+.|+..|+
T Consensus        67 ~g~~vvg~yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~~~~  108 (134)
T COG1310          67 AGEVVVGWYHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPPG  108 (134)
T ss_pred             CCCEEEEEEcCCCCCCCCcCHHHHh----hccccCCCEEEEEcCCC
Confidence            4599999999999999999999999    3333 245666666553

>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic

Probab=98.71  E-value=2.8e-08  Score=86.33  Aligned_cols=71  Identities=14%  Similarity=0.284  Sum_probs=59.5

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhh-CcCceEEEeccccccccccCceEEEEEEeeCCCC
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLL-DTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ   73 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~-~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~   73 (350)
                      |.+++.+.+.+|||||+||...++++..|...|..|... .+++|.|++||...  ...|+..+.||++.+...
T Consensus        68 ~~~~v~~~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~--~~~~~l~i~ay~~~~~~~  139 (157)
T cd08057          68 LHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQ--SDSEKLEISTFTSAQREE  139 (157)
T ss_pred             HHHHhCCCCCEEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcc--cCCCcccEEEEEEecCCC
Confidence            457788999999999999999999999998888888765 78899999999541  345788999999997654

This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import

>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8

Probab=98.35  E-value=4.9e-07  Score=86.70  Aligned_cols=63  Identities=14%  Similarity=0.296  Sum_probs=52.3

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCC
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG   71 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~   71 (350)
                      |.+++++.+.+||||||||+.    +..|+..|..|+...++.|.|++||..    +.++.-+.||...+.
T Consensus        74 ~~kkv~~~e~vVGWY~tg~~~----~~~d~~ih~~~~~~~~~pv~l~vd~~~----~~~~lpi~aY~s~~~  136 (280)
T cd08062          74 MFKKVNAKEKIVGWYSTGPKL----RPNDLDINELFRRYCPNPVLVIIDVRP----KDLGLPTEAYIAVEE  136 (280)
T ss_pred             HHHHhCCCCCeEEEecCCCCC----CcchHHHHHHHHHhCCCCEEEEEecCC----CCCCCceEEEEEeee
Confidence            467889999999999999984    567889999999998889999999853    234567899988763

This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.

>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f

Probab=98.14  E-value=2.4e-06  Score=80.60  Aligned_cols=104  Identities=13%  Similarity=0.084  Sum_probs=67.5

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccccCCc
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPI   80 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~~rp~   80 (350)
                      |.++++..+.+|||||++|.+.  ++...|+.|..+|...+..|.|++||..    ..+++.+.||++.+......    
T Consensus        68 ~~kkv~~~~~vVGWY~tg~~~~--~~~~~Ih~~~~~~~~~~~pI~L~~D~~~----~~~~l~i~ay~~~~~~~~~~----  137 (265)
T cd08064          68 LHQKVNPKEVIVGWYATGSEIT--EHSALIHDYYSRECTSYNPIHLTVDTSL----DDGKMSIKAYVSSPLGVPGK----  137 (265)
T ss_pred             HHHHhCCCCcEEeeeeCCCCCC--ccHHHHHHHHHhhCCCCCCEEEEEeCCC----CCCCcceEEEEEEecccCCC----
Confidence            3578899999999999999433  3445555555544332377999999843    23468899999987432100    


Q ss_pred             ccccCCCcchhcccccCCccccccccccccccCCccccccccccccccccCCCcc
Q 018828           81 ALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRT  135 (350)
Q Consensus        81 ~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~t  135 (350)
                                       .....|=.+++....+..|+.-++    .+++..|..+
T Consensus       138 -----------------~~~~~F~~ip~~i~~~eaE~i~v~----~l~~~~~~~~  171 (265)
T cd08064         138 -----------------TLGSMFVPIPLELLYSEAERVALD----LLAKTLASPS  171 (265)
T ss_pred             -----------------CcceEEEEcceeeecCcHHHHHHH----HHHhhccCCc
Confidence                             001115556666777888888888    6676666554

Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap

>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8

Probab=98.14  E-value=3.6e-06  Score=80.51  Aligned_cols=60  Identities=22%  Similarity=0.242  Sum_probs=53.7

Q ss_pred             CCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCc-----CceEEEeccccccccccCceEEEEEEeeCCC
Q 018828            7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT-----GFIGLIFSCFSEDANKVGRIQVIAFQSSDGK   72 (350)
Q Consensus         7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~-----pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~   72 (350)
                      .++..+||.|.||.-.|++|.+||.||..||.+.+     .+|.++|++-      .|.+.++||++++.+
T Consensus       104 ~~Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~Sft------pGs~sl~ay~LT~~G  168 (252)
T cd08056         104 EDLEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFT------PGSCSLTAYKLTPEG  168 (252)
T ss_pred             CCCEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCC------CCceEEEEEecCHHH
Confidence            46889999999999999999999999999999886     7999999962      578899999999754

Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t

>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A

Probab=98.08  E-value=1.8e-06  Score=68.80  Aligned_cols=42  Identities=26%  Similarity=0.392  Sum_probs=31.8

Q ss_pred             cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828            5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC   50 (350)
Q Consensus         5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP   50 (350)
                      ..+++.+||+|||||...++||..|..+.....    +++.||++.
T Consensus        55 ~~~~~~~vg~~HSHP~~~a~pS~~D~~~~~~~~----~~~~iI~~~   96 (104)
T PF14464_consen   55 RERGLEIVGIWHSHPSGPAFPSSTDIRSMRDLA----PPSYIIVGN   96 (104)
T ss_dssp             HHHT-EEEEEEEEESSSSSS--HHHHHTHCCS-----SCEEEEEEE
T ss_pred             hcccceeeEEEEcCCCCCCCCCHHHHHhhhccC----CeEEEEEeC
Confidence            356789999999999999999999998654332    889999985

>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme

Probab=97.96  E-value=1.8e-05  Score=66.71  Aligned_cols=53  Identities=26%  Similarity=0.366  Sum_probs=40.4

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEec-cccccccccCceEEEEEEeeC
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFS-CFSEDANKVGRIQVIAFQSSD   70 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvS-P~~~d~~s~Gkv~i~AFR~~~   70 (350)
                      .+++.+||-|||||.-.++||..|+. ++    ..++.+.+|++ |+..       -.+.||+...
T Consensus        56 ~~g~~ivgi~HSHP~~~~~PS~~D~~-~~----~~~~~~~lIvs~~~~~-------~~~~a~~~~g  109 (117)
T cd08072          56 PLDMSIVGSVHSHPSGSPRPSDADLS-FF----SKTGLVHIIVGYPYDE-------DDWRAYDSDG  109 (117)
T ss_pred             cCCCeEEEEEEcCCCCCCCCCHHHHH-hh----hcCCCEEEEEECcCCC-------CCEEEEecCC
Confidence            45689999999999999999999976 22    23789999999 4531       1366776644

This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.

>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]

Probab=97.55  E-value=2.1e-05  Score=77.43  Aligned_cols=106  Identities=10%  Similarity=-0.149  Sum_probs=86.6

Q ss_pred             hHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccccCC--cccccCCC-cchhcccccCCcccccccccc
Q 018828           32 TQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKP--IALLPVNK-STVIDLESSLSSSESLSARSG  108 (350)
Q Consensus        32 TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~~rp--~~~~pl~k-~siid~~~~~g~~~~YYsl~i  108 (350)
                      -|+....-..+||+.|+||+... ...-...|.|++..+++.   +|+  ++.+|+++ ++++..++++| |  ||+++|
T Consensus       142 yq~~~~r~~a~~v~~i~S~~g~v-v~d~f~~In~~~~~~~~e---prqtts~~~~m~~~~s~q~~~~g~n-~--y~~~ei  214 (316)
T KOG1555|consen  142 YQALSSRAVAVVVDPIQSPYGKV-VPDAFSSINPQWISPGGE---PRQTTSNGGHMDMQESLQEDIHGLN-R--YYRIEI  214 (316)
T ss_pred             HhhhccCCcceeeecccCCCCCc-cCChhhhcCcccccCCCC---CccccccccccccchhHHhHhhccC-c--eEEEEe
Confidence            45556666789999999999743 222345799999999844   454  88999999 99999999999 4  999999


Q ss_pred             ccccCCccccccccccccccccCCCccccCCCccccccCCc
Q 018828          109 NVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANH  149 (350)
Q Consensus       109 ~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~N~  149 (350)
                      .|.+...|+.|+.    +++.+.|.+. ...+|....++|+
T Consensus       215 ~~~v~~~~~~~~~----nv~~~s~~~~-~~~~y~e~~k~~~  250 (316)
T KOG1555|consen  215 PLHVLPYEQLMLL----NVPLKSWKSL-QDVLYEEKLKAYL  250 (316)
T ss_pred             eEEechhhhhchh----ccchhhhhhc-chhhHHHHHHHhh
Confidence            9999999999999    9999999886 6666666677764

>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]

Probab=97.37  E-value=0.00018  Score=70.62  Aligned_cols=63  Identities=21%  Similarity=0.288  Sum_probs=55.1

Q ss_pred             cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCC
Q 018828            5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG   71 (350)
Q Consensus         5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~   71 (350)
                      ++-....||||-||- ++.+.|.-=|++|..||.+.+.-|++|.||..   ++.|...+.|||.+|.
T Consensus        94 vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~k---ssqG~L~lrAyrLTp~  156 (339)
T KOG1560|consen   94 VNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIK---SSQGTLSLRAYRLTPE  156 (339)
T ss_pred             cCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEecccc---ccCceEEeehhhcCHH
Confidence            444566899999995 88999999999999999999999999999964   5678999999999884

>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains

Probab=97.36  E-value=0.00019  Score=59.94  Aligned_cols=36  Identities=33%  Similarity=0.408  Sum_probs=31.0

Q ss_pred             ceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828           10 RVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC   50 (350)
Q Consensus        10 ~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP   50 (350)
                      .+||-|||||.-.+.||..|+. ++    ..++.+.||++.
T Consensus        60 ~ivgi~HSHP~~~a~PS~~D~~-~~----~~~~~~~iIvs~   95 (108)
T cd08073          60 EIVAVVHSHPDGSPAPSEADRA-QQ----EATGLPWIIVSW   95 (108)
T ss_pred             CEEEEEEcCCCCCCCCCHHHHH-Hh----hcCCCcEEEEEc
Confidence            7999999999999999999986 22    337889999995

This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.

>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6

Probab=96.95  E-value=0.0013  Score=63.01  Aligned_cols=67  Identities=12%  Similarity=0.134  Sum_probs=48.6

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCC
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGK   72 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~   72 (350)
                      |.+++...+.+||||++.|. ++.+  .|..-|..|....+.-|.|++||...  .+.++.-+.||++....
T Consensus        75 ~~kkV~~~~~vVGWY~tg~~-~~~~--~~~~Ih~~~~~~~~~pv~L~~D~~~~--~~~~~lpi~ay~s~~~~  141 (288)
T cd08063          75 QFKQVFKDLDFVGWYTTGPG-GPTE--SDLPIHKQILEINESPVLLLLDPEAN--ASGKDLPVTIYESVLEL  141 (288)
T ss_pred             HHHHhccCCceEEEEecCCC-CCCH--HHHHHHHHHHhhCCCcEEEEEccccc--cCCCCCceeEEEEEEec
Confidence            35678888999999999998 4444  45555555556667779999998541  13567789999987643

CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav

>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic

Probab=96.58  E-value=0.0035  Score=50.49  Aligned_cols=40  Identities=28%  Similarity=0.392  Sum_probs=31.3

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC   50 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP   50 (350)
                      ..+..+||-|||||.-.+.||..|+.....     ....-+|++.
T Consensus        53 ~~~~~~v~i~HsHP~g~~~PS~~D~~~~~~-----~~~~~iIv~~   92 (101)
T cd08059          53 EIGMKVVGLVHSHPSGSCRPSEADLSLFTR-----FGLYHVIVCY   92 (101)
T ss_pred             hCCCcEEEEEecCcCCCCCCCHHHHHHHHh-----cCCeEEEEEC
Confidence            345689999999999999999999983321     3667778763

This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.

>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain

Probab=96.22  E-value=0.0077  Score=58.40  Aligned_cols=62  Identities=23%  Similarity=0.322  Sum_probs=54.4

Q ss_pred             CCCCceeeeeccCCCC----CCCCChHHHHhHHHhhh------hCcCceEEEeccccccccccCceEEEEEEeeCCC
Q 018828            6 GRTTRVIGWYHSHPHI----TVLPSHVDVRTQAMYQL------LDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGK   72 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~----~~~PS~vDV~TQ~~yQ~------~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~   72 (350)
                      ..++..|||.++|+.-    .+++|..+|.+-+.+|.      ....||-+|++|-.     .|.+.+.|||+.+..
T Consensus        90 ~lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~-----~g~i~~~ayQvSdq~  161 (274)
T cd08061          90 ALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK-----DGQIHFEAYQVSDQA  161 (274)
T ss_pred             HcCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC-----CCceeeeeeeecHHH
Confidence            3568999999999987    89999999999999996      56899999999843     388999999998863

Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.

>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family

Probab=96.15  E-value=0.0074  Score=52.98  Aligned_cols=46  Identities=24%  Similarity=0.329  Sum_probs=35.5

Q ss_pred             ccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEec
Q 018828            4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFS   49 (350)
Q Consensus         4 ~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvS   49 (350)
                      +.+..+..||=+||||...+-||.+|..+-...=.-...++-||+.
T Consensus        68 ~s~g~~~ylGeWHtHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG  113 (131)
T TIGR02256        68 VSGGVDTYLGEWHTHPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG  113 (131)
T ss_pred             HhCCceEEEEecCcCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence            3455689999999999999999999998766543334556667766

This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.

>PLN03246 26S proteasome regulatory subunit; Provisional

Probab=95.58  E-value=0.018  Score=56.43  Aligned_cols=62  Identities=18%  Similarity=0.309  Sum_probs=46.6

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeC
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSD   70 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~   70 (350)
                      |.+++...+.+||||++-|..+    ..|+.-|..|....+.-|-|++|+.-    ..+++-+.||.+.+
T Consensus        79 ~~k~V~~~~~vVGWY~tg~~i~----~~d~~IH~~~~~~~~~Pv~L~vD~~~----~~~~lpi~aY~s~~  140 (303)
T PLN03246         79 MFKRINAKEHVVGWYSTGPKLR----ENDLDIHELFNDYVPNPVLVIIDVQP----KELGIPTKAYYAVE  140 (303)
T ss_pred             HHHHhCCCCcEEeeecCCCCCC----cchHHHHHHHHhhCCCCeEEEEecCC----CCCCCceEEEEEEE
Confidence            3567888999999999988854    35677778888877777778998632    23456788898765

>TIGR03735 PRTRC_A PRTRC system protein A

Probab=94.02  E-value=0.03  Score=52.23  Aligned_cols=43  Identities=16%  Similarity=0.137  Sum_probs=33.1

Q ss_pred             cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecccc
Q 018828            5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFS   52 (350)
Q Consensus         5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~   52 (350)
                      ..+++..|+-|||||..+++||..|..--     ..+--|+.|+...+
T Consensus       130 ~~~ge~lV~iyHSH~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~  172 (192)
T TIGR03735       130 LDDGEHLVVDLHSHGTGSAFFSETDDADD-----KGEVKISGVLGCLD  172 (192)
T ss_pred             HhCCCeEEEEEcCCCCCCCCCCcccchhh-----cCceEEEEEEEecC
Confidence            36788999999999999999999998722     12346677777554

A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.

>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]

Probab=93.41  E-value=0.062  Score=52.56  Aligned_cols=46  Identities=20%  Similarity=0.460  Sum_probs=33.2

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC   50 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP   50 (350)
                      |.+++...+.+|||||+=|..  .++.+||+.  ++-.+-+--|-+|+|.
T Consensus        82 mfkKvNakekivGWYhTGPkl--~~nDl~In~--l~k~y~pnpvLvIIdv  127 (309)
T KOG1556|consen   82 MFKKVNAKEKVVGWYHTGPKL--RENDLDINE--LLKRYVPNPVLVIIDV  127 (309)
T ss_pred             HHHHhcchhheeeeeccCCcc--ccchhhHHH--HHhhcCCCceEEEEec
Confidence            677889999999999998875  456666664  4445555566667774

>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p)

Probab=93.08  E-value=0.17  Score=46.38  Aligned_cols=40  Identities=15%  Similarity=0.252  Sum_probs=24.3

Q ss_pred             CCCceeeeeccCCCCC-CCCChHHHHhHHHhhh---hCcCceEEEec
Q 018828            7 RTTRVIGWYHSHPHIT-VLPSHVDVRTQAMYQL---LDTGFIGLIFS   49 (350)
Q Consensus         7 R~l~VVGWYHSHP~~~-~~PS~vDV~TQ~~yQ~---~~~pfVaLIvS   49 (350)
                      +++.+||+|||||.+. .-|+.+   +.+.-..   ..+..+.++++
T Consensus        68 ~gl~IvG~Yhsh~~~~d~~~~~~---a~kIadki~~~~~~a~ll~vd  111 (182)
T cd08060          68 SGLVIVGYYQANERLDDSSPSPV---AKKIADKIAENFSNACLLMVD  111 (182)
T ss_pred             CCCEEEEEEecCCcccCCCCcHH---HHHHHHHHHHhCCCCEEEEEe
Confidence            5789999999999985 233332   2222222   23456666666

This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.

>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport

Probab=88.81  E-value=1  Score=44.70  Aligned_cols=60  Identities=20%  Similarity=0.282  Sum_probs=51.9

Q ss_pred             CCceeeeeccCCC---------------CCCCCChHHHHhHHHhhhh-------------CcCceEEEeccccccccccC
Q 018828            8 TTRVIGWYHSHPH---------------ITVLPSHVDVRTQAMYQLL-------------DTGFIGLIFSCFSEDANKVG   59 (350)
Q Consensus         8 ~l~VVGWYHSHP~---------------~~~~PS~vDV~TQ~~yQ~~-------------~~pfVaLIvSP~~~d~~s~G   59 (350)
                      ++..|||.=+|+.               -..++|..+|.+=+.+|..             ...||-+|+++     ...|
T Consensus        57 GL~rVG~IfTdl~~~~~~~g~v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg-----~~~g  131 (306)
T PF05021_consen   57 GLERVGWIFTDLTDDGSGDGTVKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSG-----DEEG  131 (306)
T ss_pred             CCEEEEEEEecCcccccCCCceeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeC-----CCCC
Confidence            6899999999998               7889999999999999974             35799999997     2468


Q ss_pred             ceEEEEEEeeCCC
Q 018828           60 RIQVIAFQSSDGK   72 (350)
Q Consensus        60 kv~i~AFR~~~~~   72 (350)
                      ++.+.|||+.+..
T Consensus       132 ~i~~~ayQvS~q~  144 (306)
T PF05021_consen  132 EIHFEAYQVSNQC  144 (306)
T ss_pred             ceeeEEeeehHHH
Confidence            9999999998754

Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	350
4b4t_V	306	Near-Atomic Resolution Structural Model Of The Yeas		1e-04
4f7o_A	257	Crystal Structure Of Csn5 Length = 257		8e-04

>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 306

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 5   TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVI 64
           TGR   V+GWYHSHP      S VDV TQ  ++ L++  + ++           G++ + 
Sbjct: 98  TGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVK---GKVVID 154
Query: 65  AFQSSD 70
           AF+  D
Sbjct: 155 AFRLID 160

>pdb|4F7O|A Chain A, Crystal Structure Of Csn5 Length = 257

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 22/43 (51%)
Query: 5   TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLI 47
            GR    IGWYHSHP      S +DV TQ + Q     F+ ++
Sbjct: 127 VGRLENAIGWYHSHPGYGCWLSGIDVSTQXLNQQFQEPFVAVV 169

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	350
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	3e-11
2znr_A	178	AMSH-like protease; metal binding protein, alterna	4e-09
2kcq_A	153	MOV34/MPN/PAD-1 family; NESG, structure, structura	6e-07
2kks_A	146	Uncharacterized protein; NESG, structural genomics	1e-05

>3rzv_A STAM-binding protein; ubiquitin hydrolase, endosome-associated deubiquitinat enzyme, hydrolase; 1.67A {Homo sapiens} PDB: 3rzu_A Length = 211

 Score = 61.2 bits (148), Expect = 3e-11
 Identities = 13/52 (25%), Positives = 25/52 (48%)

Query: 3   VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSED 54
           +   +    +GW H+HP  T   S VD+ T   YQ++    + ++ S   ++
Sbjct: 109 IQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQE 160

>2znr_A AMSH-like protease; metal binding protein, alternative splicing, hydrolase, metal-binding, metalloprotease, UBL conjugation pathway, zinc; 1.20A {Homo sapiens} PDB: 2znv_A Length = 178

 Score = 54.3 bits (130), Expect = 4e-09
 Identities = 17/54 (31%), Positives = 24/54 (44%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSED 54
             V        +GW H+HP  T   S VD+ T   YQL+    I ++ S   +D
Sbjct: 74  FNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKD 127

>2kcq_A MOV34/MPN/PAD-1 family; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Salinibacter ruber dsm 13855} Length = 153

 Score = 47.8 bits (113), Expect = 6e-07
 Identities = 16/84 (19%), Positives = 26/84 (30%), Gaps = 10/84 (11%)

Query: 1   MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR 60
                 +   V+G YHSHP     PS  D+      +    GF  +I S        +  
Sbjct: 68  DAAAQEQGLDVVGVYHSHPDHPARPSATDLE-----EATFPGFTYVIVSVRDGAPEALT- 121

Query: 61  IQVIAFQSSDGKQNHISKPIALLP 84
               A+  +  +     + I    
Sbjct: 122 ----AWALAPDRSEFHREDIVRPD 141

>2kks_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; NMR {Desulfitobacterium hafniense} Length = 146

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 14/70 (20%), Positives = 19/70 (27%), Gaps = 10/70 (14%)

Query: 4   LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQV 63
           +      ++G +HSHP     PS  D R        D     LI S              
Sbjct: 69  MRKNGWVMLGNFHSHPATPARPSAEDKRLAF-----DPSLSYLIISLAEPQKPVCK---- 119

Query: 64  IAFQSSDGKQ 73
            +F       
Sbjct: 120 -SFLIKKDGV 128

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	350
4b4t_V	306	26S proteasome regulatory subunit RPN11; hydrolase	99.97
2znr_A	178	AMSH-like protease; metal binding protein, alterna	99.69
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	99.63
2kcq_A	153	MOV34/MPN/PAD-1 family; NESG, structure, structura	99.43
2kks_A	146	Uncharacterized protein; NESG, structural genomics	99.28
2o95_A	187	26S proteasome non-ATPase regulatory subunit 7; PS	99.2
1oi0_A	124	AF2198, hypothetical protein AF2198; proteasome, d	98.98
4e0q_A	141	COP9 signalosome complex subunit 6; MPN (MPR1P and	98.78
2og4_A	254	PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN	98.67
2p8r_A	273	PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t	98.49
4b4t_U	338	RPN8, 26S proteasome regulatory subunit RPN8; hydr	97.41
3sbg_A	565	PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain,	96.92

>4b4t_V 26S proteasome regulatory subunit RPN11; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.97  E-value=5.5e-33  Score=263.71  Aligned_cols=139  Identities=21%  Similarity=0.224  Sum_probs=95.3

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccc---c
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHI---S   77 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~---~   77 (350)
                      |+++++|++++||||||||+|+||||++||+||..||.+.++|||||+||+++   ..|++.++|||++++.....   +
T Consensus        94 ~~~~v~~~~~vVGWYhShP~~~~~~S~~Di~tq~~yQ~~~~~~V~lV~Dp~~t---~~G~~~i~Afr~~~~~~~~~~~~~  170 (306)
T 4b4t_V           94 MLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQS---VKGKVVIDAFRLIDTGALINNLEP  170 (306)
T ss_dssp             HHHHHSCCCCCSEEEEECCSSSCCCCHHHHHHHHHHHHHCSSCEEEEECSSSS---SSCSSCEEEEECCHHHHHHCCCCC
T ss_pred             HHHHhCCCcceeeEEecCCCCCCcCCHHHHHHHHHHHhcCCCcEEEEECCCcC---CCCceeeeEEEecCccccccccCc
Confidence            46788999999999999999999999999999999999999999999999863   35899999999998654321   1


Q ss_pred             --CCcccccCCCcchhcccccCCccccccccccccccCCccccccccccccccccCCCccccCCCccccccCC
Q 018828           78 --KPIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDAN  148 (350)
Q Consensus        78 --rp~~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~N  148 (350)
                        ...+.+++.++.+.++.++++.+  ||+|+|+|+++.+|+++|+    .||+|+|.++|++.+|..+.+.|
T Consensus       171 ~~~~s~~~~~~~~~~~~~~~~~~~~--yy~l~i~~~ks~le~~~L~----~L~~~~w~~~l~~~~~~~~~~~~  237 (306)
T 4b4t_V          171 RQTTSNTGLLNKANIQALIHGLNRH--YYSLNIDYHKTAKETKMLM----NLHKEQWQSGLKMYDYEEKEESN  237 (306)
T ss_dssp             SCC------------------------CEEECSCCCCCSSCTHHHH----HHHHC----------CHHHHHHH
T ss_pred             ccccccccccCchhhhhhhccccce--EEEeeeEEEeCcHHHHHHH----HHHhcccccccccCcHHHHHHHH
Confidence              23567788888888888777766  9999999999999999999    99999999999999998887766

>2znr_A AMSH-like protease; metal binding protein, alternative splicing, hydrolase, metal-binding, metalloprotease, UBL conjugation pathway, zinc; 1.20A {Homo sapiens} PDB: 2znv_A

Probab=99.69  E-value=1.3e-17  Score=147.52  Aligned_cols=61  Identities=26%  Similarity=0.418  Sum_probs=55.0

Q ss_pred             cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCC
Q 018828            5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ   73 (350)
Q Consensus         5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~   73 (350)
                      .++++.+||||||||+++||||.+|++||..||++++++|+|||||...        .++|||+++++.
T Consensus        78 ~~~~l~~vGwyHSHP~~~~~pS~~Dv~tq~~yq~~~~~~v~iIvsp~~~--------~~~afrl~~~g~  138 (178)
T 2znr_A           78 DQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHK--------DTGIFRLTNAGM  138 (178)
T ss_dssp             HHHTCEEEEEEEECSSSCSCCCHHHHHHHHHHHHHCTTCEEEEEEGGGT--------EEEEEEECHHHH
T ss_pred             HhCCCEEEEEEeCCCCCCCCCCHHHHHHHHHHHhhcCCEEEEEEcCCCC--------cceEEEEECCcE
Confidence            3578999999999999999999999999999999999999999999751        279999997654

>3rzv_A STAM-binding protein; ubiquitin hydrolase, endosome-associated deubiquitinat enzyme, hydrolase; 1.67A {Homo sapiens} PDB: 3rzu_A

Probab=99.63  E-value=1.7e-16  Score=145.14  Aligned_cols=60  Identities=25%  Similarity=0.373  Sum_probs=54.5

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCC
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ   73 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~   73 (350)
                      .+++.+||||||||+++||||.+||.||..||.+.+++|+|||||..        ..++|||+++.+.
T Consensus       112 ~~~l~~vGWyHSHP~~~~~pS~~Dl~tq~~~q~~~~~~I~IVvsP~~--------~~lgaFrLtp~G~  171 (211)
T 3rzv_A          112 QQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKF--------QETGFFKLTDHGL  171 (211)
T ss_dssp             HHTCEEEEEEEECTTSCSCCCHHHHHHHHHHHHHCTTCEEEEEETTT--------TEEEEEEECHHHH
T ss_pred             hCCCEEEEEEeCCCCCCCCCCHHHHHHHHHHHhcCCCeEEEEEcCCC--------CeeeEEEeccchh
Confidence            36899999999999999999999999999999999999999999964        1599999997654

>2kcq_A MOV34/MPN/PAD-1 family; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Salinibacter ruber dsm 13855}

Probab=99.43  E-value=1.1e-13  Score=118.08  Aligned_cols=67  Identities=25%  Similarity=0.342  Sum_probs=50.4

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCc-eEEEEEEeeCCCCccccCCcccc
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGR-IQVIAFQSSDGKQNHISKPIALL   83 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gk-v~i~AFR~~~~~~~~~~rp~~~~   83 (350)
                      .+++.+||||||||+++||||.+|+.++     ..+++++|||++.+      |+ ..+.|||+.+.+..-.+.++.+.
T Consensus        73 ~~g~~ivG~yHSHP~~~~~PS~~D~~~~-----~~~~~~~lIvs~~~------~~~~~~~af~~~~~~g~~~e~~i~v~  140 (153)
T 2kcq_A           73 EQGLDVVGVYHSHPDHPARPSATDLEEA-----TFPGFTYVIVSVRD------GAPEALTAWALAPDRSEFHREDIVRP  140 (153)
T ss_dssp             HHTCEEEEEEEECSSSSSSCCHHHHHTC-----CCTTSEEEEEEEET------TEEEEEEEEEECTTCSCEEEECCBCC
T ss_pred             HCCCeEEEEEeCCCCCCCCCCHHHHHhh-----hcCCCeEEEEECCC------CCccEEEEEEEeCCCCcEEEEEEEEe
Confidence            3568999999999999999999998754     35899999999864      34 47999999654433223344443

>2kks_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; NMR {Desulfitobacterium hafniense}

Probab=99.28  E-value=1.8e-12  Score=109.74  Aligned_cols=57  Identities=25%  Similarity=0.244  Sum_probs=46.5

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCC
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGK   72 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~   72 (350)
                      .+++.+||||||||+++||||.+|+.+|.     .+++++||+++..     .+...+.|||..++.
T Consensus        71 ~~g~~ivG~~HSHP~~~~~PS~~D~~~~~-----~~~~~~lIvs~~~-----~~~~~~~af~~~~~~  127 (146)
T 2kks_A           71 KNGWVMLGNFHSHPATPARPSAEDKRLAF-----DPSLSYLIISLAE-----PQKPVCKSFLIKKDG  127 (146)
T ss_dssp             HHTCEEEEEEEEESSSCSSCCHHHHTTCC-----SSSCEEEEEECSC-----SSSCEEEEEEECSSC
T ss_pred             HCCCEEEEEEeCCCcCCCCCCHHHHHhhh-----cCCCeEEEEEccC-----CCceEEEEEEEeCCe
Confidence            46789999999999999999999999642     4789999999854     124579999995543

>2o95_A 26S proteasome non-ATPase regulatory subunit 7; PSMD7, MOV34, JAB1/MPN, metal-free dimer, UN function; HET: SO4 12P ETE PG4 PGE; 1.95A {Homo sapiens} PDB: 2o96_A

Probab=99.20  E-value=8.3e-12  Score=109.22  Aligned_cols=62  Identities=16%  Similarity=0.306  Sum_probs=53.3

Q ss_pred             ccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCC
Q 018828            2 TVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG   71 (350)
Q Consensus         2 ~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~   71 (350)
                      .+++++++++||||||||++    |..|+.+|..||.+.+++|+||+||...    .+++.+.||++.+.
T Consensus        83 ~~~v~~~~~iVGWY~s~~~~----s~~d~~i~~~~~~~~~~~v~Livd~~~~----~~~l~i~ay~~~~~  144 (187)
T 2o95_A           83 FKKVNARERIVGWYHTGPKL----HKNDIAINELMKRYCPNSVLVIIDVKPK----DLGLPTEAYISVEE  144 (187)
T ss_dssp             HHTTSSSCEEEEEEECCSSC----CTTHHHHHHHHTTTCTTCEEEEECCCTT----C-CCSEEEEEEEEE
T ss_pred             HHHhCCCCCEEEEEcCCCcC----CcccHHHHHHHHhcCCCCEEEEECCCCC----CCCcCeEEEEEech
Confidence            46788999999999999987    7899999999999999999999999642    23478999999864

>1oi0_A AF2198, hypothetical protein AF2198; proteasome, deubiquitination, archaea, hydrolase; 1.5A {Archaeoglobus fulgidus} SCOP: c.97.3.1 PDB: 1r5x_A

Probab=98.98  E-value=3.6e-10  Score=93.32  Aligned_cols=51  Identities=22%  Similarity=0.237  Sum_probs=40.3

Q ss_pred             CCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEe
Q 018828            7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQS   68 (350)
Q Consensus         7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~   68 (350)
                      +++.+||||||||+.+||||.+|+.++.     .++.+.||+++...      .-.+.||+.
T Consensus        61 ~~~~ivG~~HSHP~~~~~PS~~D~~~~~-----~~~~~~lIvs~~~~------~~~~~~f~~  111 (124)
T 1oi0_A           61 IGMKVFGTVHSHPSPSCRPSEEDLSLFT-----RFGKYHIIVCYPYD------ENSWKCYNR  111 (124)
T ss_dssp             CCCEEEEEEEEESSSCCSCCHHHHHHHH-----HSCSEEEEEETTCC------TTCEEEEET
T ss_pred             CCCEEEEEEEECcCCCCccCHHHHHhhh-----cCCCEEEEEEccCC------CceEEEEec
Confidence            6789999999999999999999999754     27899999996431      123666665

>4e0q_A COP9 signalosome complex subunit 6; MPN (MPR1P and PAD1P N-terminal) domain, unknown function; 2.50A {Drosophila melanogaster}

Probab=98.78  E-value=3.8e-10  Score=96.63  Aligned_cols=61  Identities=21%  Similarity=0.309  Sum_probs=44.5

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEe
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQS   68 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~   68 (350)
                      |.+++++.+++||||||||.    |+..|+..|..|+...+..|+||+||-.   ...|++-+.||++
T Consensus        78 ~~k~v~~~e~iVGWY~s~~~----~~~~d~~i~~~~~~~~~~pV~L~~Dp~~---~~~g~Lp~~ay~s  138 (141)
T 4e0q_A           78 QYKQVFSDLDFIGWYTTGDN----PTADDIKIQRQIAAINECPIMLQLNPLS---RSVDHLPLKLFES  138 (141)
T ss_dssp             HHHHHSTTCEEEEEEEEEC-----------CHHHHHHHTTCCCEEEEESCSC---CCCTTHHHHHHCC
T ss_pred             HHHHhCCCccEEEEEeCCCC----CCcchHHHHHHHHHHCCCCEEEEECCCc---cCCCeEEEEEEEE
Confidence            45788999999999999995    8889999999999999999999999853   2345666666654

>2og4_A PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN domain, protein-PR interaction, PRP8P, pseudoenzyme, spliceosome activation; 2.00A {Saccharomyces cerevisiae}

Probab=98.67  E-value=1.9e-08  Score=94.68  Aligned_cols=62  Identities=15%  Similarity=0.243  Sum_probs=54.7

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhh-hCcCceEEEeccccccccccCceEEEEEEeeCCCC
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQL-LDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ   73 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~-~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~   73 (350)
                      ..++..+||.|.||.-+|++|.+||.||..||. +++.+|+|+|+|.      .|.+.++||++++.+.
T Consensus       107 l~dLe~LGWIHTqptq~~fLSs~Dl~tH~~~~~~~~~eaIaIvcsft------pgs~sl~af~LT~~G~  169 (254)
T 2og4_A          107 TEGLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFST------PGSVSLSAYNLTDEGY  169 (254)
T ss_dssp             CTTCEEEEEEEEESSCCSSCCHHHHHHHHHHHTTTCTTCEEEEEEEE------TTEEEEEEEEECHHHH
T ss_pred             hcCCEecceEeeCCCCCcccCHHHHHHHHHHHHhcCCCeEEEEEecC------CCCceeEEEEcChhhh
Confidence            367899999999999999999999999999998 6789999999973      3667899999987553

>2p8r_A PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, translation; 2.10A {Caenorhabditis elegans} PDB: 2p87_A

Probab=98.49  E-value=1.2e-07  Score=90.07  Aligned_cols=60  Identities=23%  Similarity=0.308  Sum_probs=52.6

Q ss_pred             CCCceeeeeccCCCCCCCCChHHHHhHHHhhhh----C-cCceEEEeccccccccccCceEEEEEEeeCCC
Q 018828            7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLL----D-TGFIGLIFSCFSEDANKVGRIQVIAFQSSDGK   72 (350)
Q Consensus         7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~----~-~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~   72 (350)
                      .++..+||.|.||.-+|++|.+||.||..||.+    + +.+|+|+|+|.      .|.+.++||++++.+
T Consensus       107 ~dLe~LGWIHTqp~e~~~LSs~Dl~tH~~~~~~~~~~~~~e~I~Ivcsft------pgs~sl~af~LT~~G  171 (273)
T 2p8r_A          107 RDFEPLGWMHTQPNELPQLSPQDVTTHAKLLTDNISWDGEKTVMITCSFT------PGSVSLTAYKLTPSG  171 (273)
T ss_dssp             TTSEEEEEEEEESSCCSSCCHHHHHHHHHHHHHCTTCCTTTCEEEEEEEE------TTEEEEEEEEECHHH
T ss_pred             ccccccceEeeCCCCCCCcCHHHHHHHHHHHhcccccCCCceEEEEEecC------CCCceeEEEEcChHH
Confidence            678999999999999999999999999999974    3 48999999973      367789999998754

>4b4t_U RPN8, 26S proteasome regulatory subunit RPN8; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.41  E-value=9.9e-05  Score=70.79  Aligned_cols=62  Identities=19%  Similarity=0.352  Sum_probs=47.0

Q ss_pred             CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCc-CceEEEeccccccccccCceEEEEEEeeC
Q 018828            1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT-GFIGLIFSCFSEDANKVGRIQVIAFQSSD   70 (350)
Q Consensus         1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~-pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~   70 (350)
                      |.+++...+.+|||||++|.    |+..|+..|..|+...+ .-|-+++++.    ...+++-+.||.+.+
T Consensus        79 ~~kkV~~~e~iVGWY~tg~~----~~~~d~~Ih~~~~~~~~~~pi~l~~d~~----~~~~~lpi~aY~s~~  141 (338)
T 4b4t_U           79 MCKKINAKEKLIGWYHSGPK----LRASDLKINELFKKYTQNNPLLLIVDVK----QQGVGLPTDAYVAIE  141 (338)
T ss_dssp             HHHHHCCSCEEEEEEECCSS----CCSTHHHHHHHHGGGCCSCCCEEEECSC----CCSSSCSEEEEEEEE
T ss_pred             HHhhcCccCCEEEEEecCCC----CCccHHHHHHHHHhccCCCcEEEEecCC----CCCCCcceEEEEeeh
Confidence            35678889999999999885    67789999999998764 4455666653    234567799998765

>3sbg_A PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain, JAB1/MPN domain; 3.28A {Saccharomyces cerevisiae}

Probab=96.92  E-value=0.00058  Score=70.09  Aligned_cols=61  Identities=15%  Similarity=0.259  Sum_probs=49.0

Q ss_pred             CCCceeeeeccCCCCCCCCChHHHHhHHHhhhhC-cCceEEEeccccccccccCceEEEEEEeeCCCC
Q 018828            7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLD-TGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ   73 (350)
Q Consensus         7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~-~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~   73 (350)
                      .++..+||.|.||.-.|++|.+||.||...-.-. ..+|-|.|+      ...|.+.+.||.+++.++
T Consensus       419 ~dLe~LGWIHTqp~et~fLSs~Dl~THakl~~~n~~~~I~itvs------ftPGS~SLsAy~LT~eGy  480 (565)
T 3sbg_A          419 EGLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIF------STPGSVSLSAYNLTDEGY  480 (565)
T ss_dssp             TTCEEEEEEEEESSCCSSCCHHHHHHHHHHHSSSCTTCEEEEEE------EETTEEEEEEEEECHHHH
T ss_pred             ccCEecceeeecCCcccccCHHHHHHHHHHHHhCCCCeEEEEEE------ecCCceEEEEEecCHhHH
Confidence            6789999999999999999999999998773222 256666665      235889999999998664

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	350
d1oi0a_	121	Hypothetical protein AF2198 {Archaeon Archaeoglobu	98.56

>d1oi0a_ c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: JAB1/MPN domain
family: JAB1/MPN domain
domain: Hypothetical protein AF2198
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.56  E-value=2.4e-08  Score=81.44  Aligned_cols=40  Identities=28%  Similarity=0.308  Sum_probs=34.0

Q ss_pred             CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828            6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC   50 (350)
Q Consensus         6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP   50 (350)
                      .+++.+||||||||..+|+||..|+.+...     .+.+.+|+++
T Consensus        60 ~~~~~ivgi~HSHP~~~a~PS~~D~~~~~~-----~g~~~~Ivs~   99 (121)
T d1oi0a_          60 PIGMKVFGTVHSHPSPSCRPSEEDLSLFTR-----FGKYHIIVCY   99 (121)
T ss_dssp             -CCCEEEEEEEEESSSCCSCCHHHHHHHHH-----SCSEEEEEET
T ss_pred             hcCCeEEEEEEecCCCCCCcCHHHHHhhhc-----cCCEEEEEeC
Confidence            457899999999999999999999987653     5788899885