Citrus Sinensis ID: 041233

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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
Protein Sequence
MSLHTISEWPCAGRVTAHAVTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcHHHHHHHHHHHHccccccEEEEEEEccEEEccEEEEEEEEEccccccccccccccHHHHHHHHHcccccEEEEEcccccccccccHHHHHHHHHHccccccEEEEEEcccccccccEEEEEcccccccccccccccccccccccccccccEEccccEEEEcccEEEEEccc
Secondary Structure Prediction (SSPRO)
cccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHHHHHccccHHHEEEcEccccEEEEEEEEEEcccccccccccccHHHHHHHHHccccEEEEEEcccccccEEEccccHccccHHHHHcHcEEEEEEcccccccccEEEEEcccccHHHHHHccccccccccccccccccccccccEEEccccEEEEEEcc
Coil and Loop (DISEMBL)
mslhtisewpcagrvtahavtlsspspvlfltakapqgalVTHVSvadsdkqsntepsvsnVLQDVHISAQLMEDFLELAKentdkdletcGVLGAFLENGTFYVTtliipkqdstssscqalnEEDVFAIQnerslfpmgwihthpsqscfmssvdlhthysyqMMVPEAFAIVlaptdssrsygifqltepsgmsvlkecqetgfhphkepadgspiyehcshvytnsnlrFEIFDLR
Flexible Loop (DISEMBL)
mslhtisewpcaGRVTAHAVTLSSPSPVLFLTAKAPQGALVTHVSVAdsdkqsntepsvSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR
Low Complexity Region (SEG)
MSLHTISEWPCAGRVTAHAVTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR
Disordered region (IsUnstruct)
*****ISEWPCAGRVTAHAVTLSSPSPVLFLTAKAPQGALVTHV*****************VLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPK********QALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLT***************************IYEHCSHVYTNSNLRFEIF***
Disordered Region (DISOPRED)
****T***********************************************************DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMS*************KEPADGSPIYEHCSHVYTNSNLRFEIFDLR
Disordered Region (DISEMBL)
MSLHTISEWPCAGRVTAHAVTLSSPSPVLFLTAKAPQGALVTHVS**************SNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR
Disordered Region (DISPRO)
********WPCAGRVTAHAVTLSSPS**********************************NVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSLHTISEWPCAGRVTAHAVTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR
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	240	2.2.26 [Sep-21-2011]
Q6NKP9	223	AMSH-like ubiquitin thioe	yes	no	0.833	0.896	0.735	6e-89
Q5PNU3	507	AMSH-like ubiquitin thioe	no	no	0.916	0.433	0.557	8e-73
Q8VYB5	507	AMSH-like ubiquitin thioe	no	no	0.733	0.347	0.613	1e-68
Q54Q40	715	Probable ubiquitin thioes	yes	no	0.675	0.226	0.432	1e-41
Q9P371	435	AMSH-like protease sst2 O	yes	no	0.720	0.397	0.435	7e-39
O95630	424	STAM-binding protein OS=H	yes	no	0.745	0.422	0.445	8e-37
Q63ZM7	416	STAM-binding protein-like	N/A	no	0.729	0.420	0.437	1e-35
Q8R424	424	STAM-binding protein OS=R	yes	no	0.712	0.403	0.426	1e-35
Q9CQ26	424	STAM-binding protein OS=M	yes	no	0.712	0.403	0.426	1e-35
Q96FJ0	436	AMSH-like protease OS=Hom	no	no	0.708	0.389	0.430	2e-35

>sp|Q6NKP9|AMSH2_ARATH AMSH-like ubiquitin thioesterase 2 OS=Arabidopsis thaliana GN=AMSH2 PE=2 SV=1

 Score =  327 bits (837), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 147/200 (73%), Positives = 176/200 (88%)

Query: 41  VTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLEN 100
           V+ V ++ +D  ++ E S + +L+DVHIS +L+EDF ELA+ENT+KDLETCG L AFLE 
Sbjct: 24  VSRVLISGTDNINHGESSEAKILRDVHISERLLEDFTELARENTEKDLETCGTLAAFLER 83

Query: 101 GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHT 160
           G FYVTTLIIPKQ+STS+SCQA+NE +VF+IQNER L+P+GWIHTHPSQ CFMSSVDLHT
Sbjct: 84  GIFYVTTLIIPKQESTSNSCQAMNEVEVFSIQNERELYPVGWIHTHPSQGCFMSSVDLHT 143

Query: 161 HYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIY 220
           HYSYQ+MVPEAFAIV+APTDSS+SYGIF+LT+P GM VL+ C ETGFHPHKEP DG+P+Y
Sbjct: 144 HYSYQVMVPEAFAIVVAPTDSSKSYGIFKLTDPGGMEVLRGCSETGFHPHKEPEDGNPVY 203

Query: 221 EHCSHVYTNSNLRFEIFDLR 240
           EHCS+VY NSNLRFEIFDLR
Sbjct: 204 EHCSNVYKNSNLRFEIFDLR 223

Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 4EC: .EC: 1EC: 9EC: .EC: -

>sp|Q5PNU3|AMSH3_ARATH AMSH-like ubiquitin thioesterase 3 OS=Arabidopsis thaliana GN=AMSH3 PE=1 SV=2

 Score =  273 bits (698), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 126/226 (55%), Positives = 168/226 (74%), Gaps = 6/226 (2%)

Query: 20  VTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSV-----SNVLQDVHISAQLME 74
           V +  PSP   L     + A +    VAD  +     PS+     SN  Q +H+  ++M+
Sbjct: 283 VGMKQPSPPPVLAQVHQELAQICPSKVADP-RPGPAIPSLEGKEGSNSYQHLHVPVRIMD 341

Query: 75  DFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNE 134
           DFL LA+ NT+++LETCGVL   L+N  F++TTLIIPKQ+STS SCQ LNEE++F +Q+ 
Sbjct: 342 DFLRLARSNTERNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDR 401

Query: 135 RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPS 194
            SLFP+GWIHTHP+Q+CFMSSVDLHTHYSYQ+M+PEA AIV+APTD S  +GIF L++PS
Sbjct: 402 LSLFPLGWIHTHPTQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDESTPHGIFHLSDPS 461

Query: 195 GMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           G+SV++ CQ+ GFHPH+E  DG+PIYEHCSHV+ N+ L++E+ DLR
Sbjct: 462 GVSVIRNCQQRGFHPHEESEDGNPIYEHCSHVFLNAKLKYEVLDLR 507

Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, but is not implicated in protein degradation by the 26S proteasome, deneddylation, or desumoylation. Required for intracellular trafficking (e.g. trafficking from the Golgi to the vacuole and the vacuolar trafficking of endocytosed cargo), endocytosis and vacuole biogenesis.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q8VYB5|AMSH1_ARATH AMSH-like ubiquitin thioesterase 1 OS=Arabidopsis thaliana GN=AMSH1 PE=2 SV=1

 Score =  259 bits (661), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 108/176 (61%), Positives = 141/176 (80%)

Query: 65  DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALN 124
           ++HI+  +M+ F+ LAK NT K+LETCG+L   L+N  FY+T LIIPKQ+STS SCQA N
Sbjct: 332 ELHIATSMMDTFMRLAKSNTKKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATN 391

Query: 125 EEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS 184
           EE++F +Q+++SLFP+GWIHTHP+QSCFMSS+D+HTHYSYQ+M+PEA AIV+AP DSSR+
Sbjct: 392 EEEIFEVQDKQSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPEAVAIVMAPQDSSRN 451

Query: 185 YGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           +GIF+LT P GM+V++ C   GFH H  P DG PIY  C  VY N NL+F++ DLR
Sbjct: 452 HGIFRLTTPGGMTVIRNCDRRGFHAHSSPEDGGPIYNTCKEVYMNPNLKFDVIDLR 507

Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q54Q40|D1039_DICDI Probable ubiquitin thioesterase DG1039 OS=Dictyostelium discoideum GN=DG1039 PE=3 SV=1

 Score =  170 bits (430), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 71/164 (43%), Positives = 113/164 (68%), Gaps = 2/164 (1%)

Query: 63  LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
           L+ + +  ++ ++F+ LA+ NT + +ETCG+L   L N  F +TT+IIPKQ+ T+ +C  
Sbjct: 534 LRKIIVHGEVFQEFMRLAENNTKRSIETCGILSGTLSNDVFRITTIIIPKQEGTTDTCNT 593

Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
           + E ++F  Q E  L  +GWIHTHP+Q CF+S+VD+HTH SYQ ++ EA A+V++P  ++
Sbjct: 594 IEEHEIFEYQLENDLLTLGWIHTHPTQDCFLSAVDVHTHCSYQYLLQEAIAVVISPM-AN 652

Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHV 226
            ++GIF+LT+P G+  +++C+   FHPH  P +G PIY    HV
Sbjct: 653 PNFGIFRLTDPPGLETVQKCKLKSFHPHP-PVNGIPIYTKVDHV 695

May be a zinc metalloprotease that specifically cleaves ubiquitin chains.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q9P371|SST2_SCHPO AMSH-like protease sst2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sst2 PE=1 SV=1

 Score =  160 bits (405), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 78/179 (43%), Positives = 117/179 (65%), Gaps = 6/179 (3%)

Query: 63  LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
           L+ +++   L + FL++ K NT K+LETCG+L   L    F++T L+IP Q++TS +C  
Sbjct: 260 LRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGT 319

Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
            +E  +F  Q++ +L  +GWIHTHP+Q+CFMSSVDLHTH SYQ+M+PEA AIV+AP  S 
Sbjct: 320 TDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAP--SK 377

Query: 183 RSYGIFQLTEPSGMSVLKECQETG-FHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
            + GIF+L +P G+  + +C++ G FHPH+       +     HV    N + ++ DLR
Sbjct: 378 NTSGIFRLLDPEGLQTIVKCRKPGLFHPHE--GKVYTMVAQPGHV-REINSKLQVVDLR 433

Zinc metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains (By similarity). Plays a role in the multivesicular body (MVB) sorting pathway. Required for ubiquitin-dependent sorting of proteins into the endosome and subsequent trafficking to the vacuole. May regulate MVB sorting through deubiquitination of ubiquitinated ESCRT proteins.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|O95630|STABP_HUMAN STAM-binding protein OS=Homo sapiens GN=STAMBP PE=1 SV=1

 Score =  153 bits (387), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 85/191 (44%), Positives = 122/191 (63%), Gaps = 12/191 (6%)

Query: 53  SNTE--PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLII 110
           SN+E  P++   L+ V +  +L   FL+LA  NT + +ETCG+L   L    F +T ++I
Sbjct: 243 SNSESIPTIDG-LRHVVVPGRLCPQFLQLASANTARGVETCGILCGKLMRNEFTITHVLI 301

Query: 111 PKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPE 170
           PKQ + S  C   NEE++F IQ+++ L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE
Sbjct: 302 PKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPE 361

Query: 171 AFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTN 229
           + AIV +P    +  G F+LT+  G+  +  C++ GFHPH K+P    P++  CSHV T 
Sbjct: 362 SVAIVCSP--KFQETGFFKLTD-HGLEEISSCRQKGFHPHSKDP----PLFCSCSHV-TV 413

Query: 230 SNLRFEIFDLR 240
            +    I DLR
Sbjct: 414 VDRAVTITDLR 424

Zinc metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains (By similarity). Functions at the endosome and is able to oppose the ubiquitin-dependent sorting of receptors to lysosomes. Plays a role in signal transduction for cell growth and MYC induction mediated by IL-2 and GM-CSF. Potentiates BMP (bone morphogenetic protein) signaling by antagonizing the inhibitory action of SMAD6 and SMAD7.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q63ZM7|STABP_XENLA STAM-binding protein-like OS=Xenopus laevis GN=stambp PE=2 SV=1

 Score =  150 bits (378), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 80/183 (43%), Positives = 114/183 (62%), Gaps = 8/183 (4%)

Query: 45  SVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFY 104
           S+  S   SN+    S+ L+ V I   +   FL+L++ NT + +ETCG+L   L    F 
Sbjct: 228 SLKPSSYGSNSSGVTSDGLRHVKIPRDVCCKFLQLSENNTQRGVETCGILCGKLLQNEFT 287

Query: 105 VTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSY 164
           VT +I+PKQ      C   +EE++F IQ+++ L  +GWIHTHP+Q+ F+SSVDLHTH SY
Sbjct: 288 VTHVIVPKQSGGPDYCNTESEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSY 347

Query: 165 QMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHC 223
           QMM+PE+ AIV +P    +  G F+LT+  GM  + EC++ GFHPH KEP    P++   
Sbjct: 348 QMMLPESIAIVCSP--KFQETGFFKLTD-YGMKEIGECRQKGFHPHCKEP----PLFSAG 400

Query: 224 SHV 226
            HV
Sbjct: 401 GHV 403

Zinc metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains (By similarity). Functions at the endosome and is able to oppose the ubiquitin-dependent sorting of receptors to lysosomes.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q8R424|STABP_RAT STAM-binding protein OS=Rattus norvegicus GN=Stambp PE=2 SV=1

 Score =  149 bits (377), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 76/178 (42%), Positives = 109/178 (61%), Gaps = 7/178 (3%)

Query: 63  LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
           L+ + +   L  +FL+LA  NT K +ETCGVL   L    F +T ++IP+Q+     C  
Sbjct: 254 LRHIVVPRNLCSEFLQLASANTAKGIETCGVLCGKLMRNEFTITHVLIPRQNGGPDYCHT 313

Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
            NEE++F +Q++  L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE+ AIV +P    
Sbjct: 314 ENEEEIFFMQDDLGLLTLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESIAIVCSP--KF 371

Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           +  G F+LT+  G+  +  C++ GFHPH       P++  CSHV     +   I DLR
Sbjct: 372 QETGFFKLTD-YGLQEISTCRQKGFHPH---GRDPPLFCDCSHVTVKDRI-VTITDLR 424

Zinc metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains (By similarity). Functions at the endosome and is able to oppose the ubiquitin-dependent sorting of receptors to lysosomes. Endosomal localization of AMSH is required for efficient EGFR degradation but not for its internalization. Plays a role in signal transduction for cell growth and MYC induction mediated by IL-2 and GM-CSF. Potentiates BMP (bone morphogenetic protein) signaling by antagonizing the inhibitory action of SMAD6 and SMAD7.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q9CQ26|STABP_MOUSE STAM-binding protein OS=Mus musculus GN=Stambp PE=2 SV=1

 Score =  149 bits (377), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 76/178 (42%), Positives = 109/178 (61%), Gaps = 7/178 (3%)

Query: 63  LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
           L+ + +   L  +FL+LA  NT K +ETCGVL   L    F +T ++IP+Q+     C  
Sbjct: 254 LRHIVVPRNLCSEFLQLASANTAKGIETCGVLCGKLMRNEFTITHVLIPRQNGGPDYCHT 313

Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
            NEE++F +Q++  L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE+ AIV +P    
Sbjct: 314 ENEEEIFFMQDDLGLLTLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESIAIVCSP--KF 371

Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           +  G F+LT+  G+  +  C++ GFHPH       P++  CSHV     +   I DLR
Sbjct: 372 QETGFFKLTD-YGLQEISTCRQKGFHPH---GRDPPLFCDCSHVTVKDRI-VTITDLR 424

Zinc metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains (By similarity). Functions at the endosome and is able to oppose the ubiquitin-dependent sorting of receptors to lysosomes. Endosomal localization of AMSH is required for efficient EGFR degradation but not for its internalization. Plays a role in signal transduction for cell growth and MYC induction mediated by IL-2 and GM-CSF. Potentiates BMP (bone morphogenetic protein) signaling by antagonizing the inhibitory action of SMAD6 and SMAD7.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

>sp|Q96FJ0|STALP_HUMAN AMSH-like protease OS=Homo sapiens GN=STAMBPL1 PE=1 SV=2

 Score =  149 bits (376), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 77/179 (43%), Positives = 113/179 (63%), Gaps = 9/179 (5%)

Query: 63  LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
           L+ V +   L   FL+LA+ NT + +ETCG+L   L +  F +T +I+PKQ +    C  
Sbjct: 266 LRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDM 325

Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
            N E++F +Q++  L  +GWIHTHP+Q+ F+SSVDLHTH SYQ+M+PEA AIV +P    
Sbjct: 326 ENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSP--KH 383

Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           +  GIF+LT  +GM  +  C++ GFHPH KEP     ++  C HV    +++  + DLR
Sbjct: 384 KDTGIFRLTN-AGMLEVSACKKKGFHPHTKEPR----LFSICKHVLV-KDIKIIVLDLR 436

Zinc metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains.

Homo sapiens (taxid: 9606)

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	240
224110952	221	predicted protein [Populus trichocarpa]	0.920	1.0	0.778	2e-99
255568810	265	amsh, putative [Ricinus communis] gi|223	0.945	0.856	0.735	9e-98
359473186	275	PREDICTED: AMSH-like ubiquitin thioleste	0.941	0.821	0.711	9e-95
356497755	291	PREDICTED: AMSH-like ubiquitin thioleste	0.912	0.752	0.699	1e-88
357485879	235	STAM-binding protein [Medicago truncatul	0.958	0.978	0.665	4e-88
297843878	223	hypothetical protein ARALYDRAFT_888336 [	0.833	0.896	0.745	5e-88
79340942	223	AMSH-like ubiquitin thiolesterase 2 [Ara	0.833	0.896	0.735	3e-87
145323832	222	AMSH-like ubiquitin thiolesterase 2 [Ara	0.829	0.896	0.73	4e-85
449464724	507	PREDICTED: AMSH-like ubiquitin thioester	0.895	0.424	0.592	2e-73
449501513	507	PREDICTED: AMSH-like ubiquitin thioester	0.895	0.424	0.592	2e-73

>gi|224110952|ref|XP_002315693.1| predicted protein [Populus trichocarpa] gi|222864733|gb|EEF01864.1| predicted protein [Populus trichocarpa]

 Score =  367 bits (942), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 172/221 (77%), Positives = 198/221 (89%)

Query: 20  VTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLEL 79
           VT +SP P+L    KAP+ A V+ + VADSD+ S  +PS S VLQDVHIS  LMEDFLEL
Sbjct: 1   VTQTSPCPILSCVEKAPKYAHVSLIPVADSDQSSCNQPSASGVLQDVHISPLLMEDFLEL 60

Query: 80  AKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFP 139
           A+ENT+KDLETCGVLGAFLE+GT+YVTTLIIPKQDSTSSSC+AL EE+ FAIQNERSLFP
Sbjct: 61  ARENTEKDLETCGVLGAFLEHGTYYVTTLIIPKQDSTSSSCEALKEEEFFAIQNERSLFP 120

Query: 140 MGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVL 199
           +GWIHTHPSQSCFMSS+DLHTH+SYQ MVPEAFAIV+APTD SRSYGIF+L++P GMSVL
Sbjct: 121 VGWIHTHPSQSCFMSSIDLHTHFSYQAMVPEAFAIVMAPTDQSRSYGIFRLSDPGGMSVL 180

Query: 200 KECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           KEC+E+GFHPH EPADGSPIYEHC++V+TN+NLRFEIFDLR
Sbjct: 181 KECEESGFHPHGEPADGSPIYEHCANVFTNTNLRFEIFDLR 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568810|ref|XP_002525376.1| amsh, putative [Ricinus communis] gi|223535339|gb|EEF37014.1| amsh, putative [Ricinus communis]

 Score =  362 bits (928), Expect = 9e-98,   Method: Compositional matrix adjust.
 Identities = 167/227 (73%), Positives = 196/227 (86%)

Query: 14  RVTAHAVTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSVSNVLQDVHISAQLM 73
           ++T H VT SSPSP+L    KAP+ A ++ +  A S+     +PS SN+LQD+HIS +LM
Sbjct: 39  QITVHTVTQSSPSPILSCVEKAPKHAHISPIPAAGSNTNPCNQPSSSNILQDIHISERLM 98

Query: 74  EDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQN 133
           EDFLELA+ENT+KDLETCGVL AFLE GT+YVTTLIIPKQ+STSSSC+A+ EE+ FAIQN
Sbjct: 99  EDFLELARENTEKDLETCGVLSAFLEMGTYYVTTLIIPKQNSTSSSCEAIKEEEFFAIQN 158

Query: 134 ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEP 193
           ERSL P+GWIHTHPSQSCFMSS+DLHT YSYQ+MVPEAFAIV+APTD+SRSYG+F+L++P
Sbjct: 159 ERSLHPVGWIHTHPSQSCFMSSIDLHTQYSYQVMVPEAFAIVMAPTDTSRSYGLFRLSDP 218

Query: 194 SGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
            GM VLKECQETGFHPH EPADG PIYEHCS+VY NSNLRFEIFDLR
Sbjct: 219 GGMGVLKECQETGFHPHGEPADGGPIYEHCSNVYANSNLRFEIFDLR 265

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473186|ref|XP_003631259.1| PREDICTED: AMSH-like ubiquitin thiolesterase 2-like [Vitis vinifera] gi|297739036|emb|CBI28525.3| unnamed protein product [Vitis vinifera]

 Score =  352 bits (902), Expect = 9e-95,   Method: Compositional matrix adjust.
 Identities = 163/229 (71%), Positives = 197/229 (86%), Gaps = 3/229 (1%)

Query: 15  VTAHAVTLSSPSPVLFLTAKAPQGALVTHVSVADSD---KQSNTEPSVSNVLQDVHISAQ 71
           +T HAVT +SPSP+++ T  A     ++H+ V+DS+    +S +E +VS  LQDVHISA+
Sbjct: 47  ITVHAVTKASPSPIIYCTENAHHDKHISHIEVSDSEPGHSKSCSETAVSKKLQDVHISAR 106

Query: 72  LMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAI 131
           LMEDFLELA++NT  DLETCG+LGAFL+ GTFYVTTLIIPKQ+STS+SCQA+ EE++FAI
Sbjct: 107 LMEDFLELARDNTKNDLETCGILGAFLKMGTFYVTTLIIPKQESTSNSCQAIKEEEIFAI 166

Query: 132 QNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLT 191
           QNE SLFP+GWIHTHPSQSCFMSS+DLHT YSYQ+MVPEAFAIV+APTD+SRSYGIF+L+
Sbjct: 167 QNEHSLFPVGWIHTHPSQSCFMSSIDLHTQYSYQVMVPEAFAIVMAPTDTSRSYGIFRLS 226

Query: 192 EPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           +P GMSVLK+C E GFH H EPADG PIYEHCS++Y NSNLRFEIFDLR
Sbjct: 227 DPVGMSVLKDCPEEGFHHHNEPADGGPIYEHCSNIYINSNLRFEIFDLR 275

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356497755|ref|XP_003517724.1| PREDICTED: AMSH-like ubiquitin thiolesterase 2-like [Glycine max]

 Score =  332 bits (850), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 156/223 (69%), Positives = 183/223 (82%), Gaps = 4/223 (1%)

Query: 18  HAVTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFL 77
             VT S PSP L      PQ A  +HV+  +S   S    S S+  +DVHIS +LMEDFL
Sbjct: 71  QKVTQSWPSPALCFVETVPQDAQSSHVTAFNSGDGS----SKSDNERDVHISMRLMEDFL 126

Query: 78  ELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSL 137
           +LAKENT+KDLETCG+LGA+LE GT Y+TTLIIPKQ+S S+SCQA NEE+VF I NERSL
Sbjct: 127 DLAKENTEKDLETCGILGAYLEKGTLYLTTLIIPKQESASNSCQATNEEEVFKILNERSL 186

Query: 138 FPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMS 197
           +P+GWIHTHPSQSCFMSSVDLHT YSYQ+M+PEAFAIVLAP D+SRS G+F+LT+P GM+
Sbjct: 187 YPVGWIHTHPSQSCFMSSVDLHTQYSYQVMIPEAFAIVLAPNDTSRSCGLFRLTKPEGMN 246

Query: 198 VLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           +LK CQETGFHPHKEP +GSP+YEHCS+VY NSNLRFEIFDLR
Sbjct: 247 ILKNCQETGFHPHKEPDNGSPVYEHCSNVYKNSNLRFEIFDLR 289

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357485879|ref|XP_003613227.1| STAM-binding protein [Medicago truncatula] gi|355514562|gb|AES96185.1| STAM-binding protein [Medicago truncatula] gi|388510592|gb|AFK43362.1| unknown [Medicago truncatula]

 Score =  330 bits (845), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 155/233 (66%), Positives = 182/233 (78%), Gaps = 3/233 (1%)

Query: 11  CAGRVTAHAVTLSSPSPVLFLTAKAPQGALVTHVSV---ADSDKQSNTEPSVSNVLQDVH 67
           C      H VT SSPSP L       Q    +H++     D    S+ E S S  ++DVH
Sbjct: 3   CYKSFLDHKVTKSSPSPALCCVEPVTQDEQNSHITAFHSGDRSTNSDNESSSSKTVRDVH 62

Query: 68  ISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEED 127
           IS +LMEDFL+LAKENT+KDLETCG+LGAFLE GT Y+TTLIIPKQ+S S+SC A NEE+
Sbjct: 63  ISMRLMEDFLDLAKENTEKDLETCGILGAFLEKGTLYMTTLIIPKQESASNSCNATNEEE 122

Query: 128 VFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGI 187
           VF I NERSL+P+GWIHTHPSQSCFMSSVDLHT YSYQ M+PEAFAIVLAPTD+SRS G+
Sbjct: 123 VFTILNERSLYPVGWIHTHPSQSCFMSSVDLHTQYSYQAMIPEAFAIVLAPTDTSRSCGL 182

Query: 188 FQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           F+LTEP GM++L+ C E GFHPHKEP +G+P+YEHCS+VY NSNLRFEIFDLR
Sbjct: 183 FRLTEPDGMNILRNCPERGFHPHKEPDNGNPVYEHCSNVYRNSNLRFEIFDLR 235

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843878|ref|XP_002889820.1| hypothetical protein ARALYDRAFT_888336 [Arabidopsis lyrata subsp. lyrata] gi|297335662|gb|EFH66079.1| hypothetical protein ARALYDRAFT_888336 [Arabidopsis lyrata subsp. lyrata]

 Score =  329 bits (844), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 149/200 (74%), Positives = 176/200 (88%)

Query: 41  VTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLEN 100
           V+ V ++ +DK ++ E S   +L+DVHIS +L+EDF ELA+ENT+KDLETCG L AFLE 
Sbjct: 24  VSRVLISGTDKNNHGESSEPKILRDVHISERLLEDFTELARENTEKDLETCGTLAAFLER 83

Query: 101 GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHT 160
           G FYVTTLIIPKQ+STS+SCQA+NE +VF+IQNER L+P+GWIHTHPSQ CFMSSVDLHT
Sbjct: 84  GIFYVTTLIIPKQESTSNSCQAMNEVEVFSIQNERELYPVGWIHTHPSQGCFMSSVDLHT 143

Query: 161 HYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIY 220
           HYSYQ+MVPEAFAIV+APTDSS+SYGIF+LT+P GM VLK C ETGFHPHKEP DG+P+Y
Sbjct: 144 HYSYQVMVPEAFAIVVAPTDSSKSYGIFKLTDPGGMEVLKGCSETGFHPHKEPEDGNPVY 203

Query: 221 EHCSHVYTNSNLRFEIFDLR 240
           EHCS+VY NSNLRFEIFDLR
Sbjct: 204 EHCSNVYKNSNLRFEIFDLR 223

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79340942|ref|NP_172530.2| AMSH-like ubiquitin thiolesterase 2 [Arabidopsis thaliana] gi|75271673|sp|Q6NKP9.1|AMSH2_ARATH RecName: Full=AMSH-like ubiquitin thioesterase 2; AltName: Full=Deubiquitinating enzyme AMSH2 gi|46931320|gb|AAT06464.1| At1g10600 [Arabidopsis thaliana] gi|51969058|dbj|BAD43221.1| hypothetical protein [Arabidopsis thaliana] gi|332190485|gb|AEE28606.1| AMSH-like ubiquitin thiolesterase 2 [Arabidopsis thaliana]

 Score =  327 bits (837), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 147/200 (73%), Positives = 176/200 (88%)

Query: 41  VTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLEN 100
           V+ V ++ +D  ++ E S + +L+DVHIS +L+EDF ELA+ENT+KDLETCG L AFLE 
Sbjct: 24  VSRVLISGTDNINHGESSEAKILRDVHISERLLEDFTELARENTEKDLETCGTLAAFLER 83

Query: 101 GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHT 160
           G FYVTTLIIPKQ+STS+SCQA+NE +VF+IQNER L+P+GWIHTHPSQ CFMSSVDLHT
Sbjct: 84  GIFYVTTLIIPKQESTSNSCQAMNEVEVFSIQNERELYPVGWIHTHPSQGCFMSSVDLHT 143

Query: 161 HYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIY 220
           HYSYQ+MVPEAFAIV+APTDSS+SYGIF+LT+P GM VL+ C ETGFHPHKEP DG+P+Y
Sbjct: 144 HYSYQVMVPEAFAIVVAPTDSSKSYGIFKLTDPGGMEVLRGCSETGFHPHKEPEDGNPVY 203

Query: 221 EHCSHVYTNSNLRFEIFDLR 240
           EHCS+VY NSNLRFEIFDLR
Sbjct: 204 EHCSNVYKNSNLRFEIFDLR 223

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145323832|ref|NP_001077505.1| AMSH-like ubiquitin thiolesterase 2 [Arabidopsis thaliana] gi|332190487|gb|AEE28608.1| AMSH-like ubiquitin thiolesterase 2 [Arabidopsis thaliana]

 Score =  320 bits (819), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 146/200 (73%), Positives = 175/200 (87%), Gaps = 1/200 (0%)

Query: 41  VTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLEN 100
           V+ V ++ +D  ++ E S + +L+DVHIS +L+EDF ELA+ENT+KDLETCG L AFLE 
Sbjct: 24  VSRVLISGTDNINHGESSEAKILRDVHISERLLEDFTELARENTEKDLETCGTLAAFLER 83

Query: 101 GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHT 160
           G FYVTTLIIPKQ+STS+SCQA+NE +VF+IQNER L+P+GWIHTHPSQ CFMSSVDLHT
Sbjct: 84  GIFYVTTLIIPKQESTSNSCQAMNEVEVFSIQNERELYPVGWIHTHPSQGCFMSSVDLHT 143

Query: 161 HYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIY 220
           HYSYQ+MVPEAFAIV+APTDSS +YGIF+LT+P GM VL+ C ETGFHPHKEP DG+P+Y
Sbjct: 144 HYSYQVMVPEAFAIVVAPTDSS-NYGIFKLTDPGGMEVLRGCSETGFHPHKEPEDGNPVY 202

Query: 221 EHCSHVYTNSNLRFEIFDLR 240
           EHCS+VY NSNLRFEIFDLR
Sbjct: 203 EHCSNVYKNSNLRFEIFDLR 222

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464724|ref|XP_004150079.1| PREDICTED: AMSH-like ubiquitin thioesterase 3-like [Cucumis sativus]

 Score =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/226 (59%), Positives = 169/226 (74%), Gaps = 11/226 (4%)

Query: 20  VTLSSPSPVLFLTAKAPQG-ALVTHVSVADSD----KQSNTEPSVSNVLQDVHISAQLME 74
           V   SP PVL   AK  Q  A +    VAD      +QS  E   S   Q +HI  ++++
Sbjct: 288 VKQPSPPPVL---AKVQQEYATIPPSKVADPRPGVARQSQDE---SESFQRLHIPVKMLD 341

Query: 75  DFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNE 134
           DFL LA+ENT+K+LETCGVL   L+N  FY++TLIIPKQ+STS SCQ LNEE++F +Q+ 
Sbjct: 342 DFLRLARENTNKNLETCGVLAGSLKNRVFYISTLIIPKQESTSDSCQTLNEEEIFEVQDR 401

Query: 135 RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPS 194
            SLFP+GWIHTHPSQ+CFMSSVDLHTHYSYQ+M+PEA AIV+APTD+S  YGIF L++P 
Sbjct: 402 LSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAIAIVMAPTDTSSPYGIFHLSDPG 461

Query: 195 GMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           G+SV++ CQ+ GFHPH+EP DGSP+YEHCSHV  N N +F++ DLR
Sbjct: 462 GVSVIRNCQQRGFHPHEEPDDGSPLYEHCSHVMMNPNAKFDVMDLR 507

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449501513|ref|XP_004161388.1| PREDICTED: AMSH-like ubiquitin thioesterase 3-like [Cucumis sativus]

 Score =  281 bits (718), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/226 (59%), Positives = 169/226 (74%), Gaps = 11/226 (4%)

Query: 20  VTLSSPSPVLFLTAKAPQG-ALVTHVSVADSD----KQSNTEPSVSNVLQDVHISAQLME 74
           V   SP PVL   AK  Q  A +    VAD      +QS  E   S   Q +HI  ++++
Sbjct: 288 VKQPSPPPVL---AKVQQEYATIPPSKVADPRPGVARQSQDE---SESFQRLHIPVKMLD 341

Query: 75  DFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNE 134
           DFL LA+ENT+K+LETCGVL   L+N  FY++TLIIPKQ+STS SCQ LNEE++F +Q+ 
Sbjct: 342 DFLRLARENTNKNLETCGVLAGSLKNRIFYISTLIIPKQESTSDSCQTLNEEEIFEVQDR 401

Query: 135 RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPS 194
            SLFP+GWIHTHPSQ+CFMSSVDLHTHYSYQ+M+PEA AIV+APTD+S  YGIF L++P 
Sbjct: 402 LSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAIAIVMAPTDTSSPYGIFHLSDPG 461

Query: 195 GMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           G+SV++ CQ+ GFHPH+EP DGSP+YEHCSHV  N N +F++ DLR
Sbjct: 462 GVSVIRNCQQRGFHPHEEPDDGSPLYEHCSHVMMNPNAKFDVMDLR 507

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	240
TAIR|locus:2019903	223	AMSH2 "AT1G10600" [Arabidopsis	0.920	0.991	0.702	1.7e-84
TAIR|locus:504955440	507	AMSH3 "associated molecule wit	0.916	0.433	0.557	7.2e-68
TAIR|locus:2008184	507	AMSH1 "AT1G48790" [Arabidopsis	0.733	0.347	0.613	8.8e-63
DICTYBASE|DDB_G0284037	715	DDB_G0284037 "MPN/PAD-1 domain	0.783	0.262	0.391	4.8e-40
ASPGD|ASPL0000038640	544	AN3003 [Emericella nidulans (t	0.875	0.386	0.400	1.6e-38
POMBASE|SPAC19B12.10	435	sst2 "human AMSH/STAMBP protei	0.720	0.397	0.435	5.5e-38
UNIPROTKB|O95630	424	STAMBP "STAM-binding protein"	0.879	0.497	0.415	2.4e-37
UNIPROTKB|F1SLF9	424	STAMBP "Uncharacterized protei	0.745	0.422	0.439	2.4e-37
UNIPROTKB|Q17QR2	423	STAMBP "STAM binding protein"	0.75	0.425	0.433	6.3e-37
UNIPROTKB|E1BRS3	431	Gga.34764 "Uncharacterized pro	0.837	0.466	0.406	3.5e-36

TAIR|locus:2019903 AMSH2 "AT1G10600" [Arabidopsis thaliana (taxid:3702)]

 Score = 846 (302.9 bits), Expect = 1.7e-84, P = 1.7e-84
 Identities = 156/222 (70%), Positives = 187/222 (84%)

Query:    20 VTLSSPSPVLFLTAKAP-QGALVTHVSVADSDKQSNTEPSVSNVLQDVHISAQLMEDFLE 78
             VTLSSPSP L        + + V+ V ++ +D  ++ E S + +L+DVHIS +L+EDF E
Sbjct:     2 VTLSSPSPSLSCVENVTCKSSHVSRVLISGTDNINHGESSEAKILRDVHISERLLEDFTE 61

Query:    79 LAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLF 138
             LA+ENT+KDLETCG L AFLE G FYVTTLIIPKQ+STS+SCQA+NE +VF+IQNER L+
Sbjct:    62 LARENTEKDLETCGTLAAFLERGIFYVTTLIIPKQESTSNSCQAMNEVEVFSIQNERELY 121

Query:   139 PMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSV 198
             P+GWIHTHPSQ CFMSSVDLHTHYSYQ+MVPEAFAIV+APTDSS+SYGIF+LT+P GM V
Sbjct:   122 PVGWIHTHPSQGCFMSSVDLHTHYSYQVMVPEAFAIVVAPTDSSKSYGIFKLTDPGGMEV 181

Query:   199 LKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
             L+ C ETGFHPHKEP DG+P+YEHCS+VY NSNLRFEIFDLR
Sbjct:   182 LRGCSETGFHPHKEPEDGNPVYEHCSNVYKNSNLRFEIFDLR 223

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0005739 "mitochondrion" evidence=ISM

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

TAIR|locus:504955440 AMSH3 "associated molecule with the SH3 domain of STAM 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 689 (247.6 bits), Expect = 7.2e-68, P = 7.2e-68
 Identities = 126/226 (55%), Positives = 168/226 (74%)

Query:    20 VTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSV-----SNVLQDVHISAQLME 74
             V +  PSP   L     + A +    VAD  +     PS+     SN  Q +H+  ++M+
Sbjct:   283 VGMKQPSPPPVLAQVHQELAQICPSKVADP-RPGPAIPSLEGKEGSNSYQHLHVPVRIMD 341

Query:    75 DFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNE 134
             DFL LA+ NT+++LETCGVL   L+N  F++TTLIIPKQ+STS SCQ LNEE++F +Q+ 
Sbjct:   342 DFLRLARSNTERNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDR 401

Query:   135 RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPS 194
              SLFP+GWIHTHP+Q+CFMSSVDLHTHYSYQ+M+PEA AIV+APTD S  +GIF L++PS
Sbjct:   402 LSLFPLGWIHTHPTQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDESTPHGIFHLSDPS 461

Query:   195 GMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
             G+SV++ CQ+ GFHPH+E  DG+PIYEHCSHV+ N+ L++E+ DLR
Sbjct:   462 GVSVIRNCQQRGFHPHEESEDGNPIYEHCSHVFLNAKLKYEVLDLR 507

GO:0005634 "nucleus" evidence=ISM

GO:0000338 "protein deneddylation" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006897 "endocytosis" evidence=IMP

GO:0007033 "vacuole organization" evidence=IMP

GO:0016020 "membrane" evidence=IDA

GO:0016021 "integral to membrane" evidence=IDA

GO:0016926 "protein desumoylation" evidence=IDA

GO:0019941 "modification-dependent protein catabolic process" evidence=IDA

GO:0044090 "positive regulation of vacuole organization" evidence=IMP

GO:0046907 "intracellular transport" evidence=IMP

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

GO:0071108 "protein K48-linked deubiquitination" evidence=IDA

GO:0090316 "positive regulation of intracellular protein transport" evidence=IMP

TAIR|locus:2008184 AMSH1 "AT1G48790" [Arabidopsis thaliana (taxid:3702)]

 Score = 641 (230.7 bits), Expect = 8.8e-63, P = 8.8e-63
 Identities = 108/176 (61%), Positives = 141/176 (80%)

Query:    65 DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALN 124
             ++HI+  +M+ F+ LAK NT K+LETCG+L   L+N  FY+T LIIPKQ+STS SCQA N
Sbjct:   332 ELHIATSMMDTFMRLAKSNTKKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATN 391

Query:   125 EEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS 184
             EE++F +Q+++SLFP+GWIHTHP+QSCFMSS+D+HTHYSYQ+M+PEA AIV+AP DSSR+
Sbjct:   392 EEEIFEVQDKQSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPEAVAIVMAPQDSSRN 451

Query:   185 YGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
             +GIF+LT P GM+V++ C   GFH H  P DG PIY  C  VY N NL+F++ DLR
Sbjct:   452 HGIFRLTTPGGMTVIRNCDRRGFHAHSSPEDGGPIYNTCKEVYMNPNLKFDVIDLR 507

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

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

GO:0006623 "protein targeting to vacuole" evidence=RCA

GO:0016192 "vesicle-mediated transport" evidence=RCA

DICTYBASE|DDB_G0284037 DDB_G0284037 "MPN/PAD-1 domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 432 (157.1 bits), Expect = 4.8e-40, P = 4.8e-40
 Identities = 76/194 (39%), Positives = 124/194 (63%)

Query:    37 QGALVTHVSVADSDKQSNTEPSVSNV----LQDVHISAQLMEDFLELAKENTDKDLETCG 92
             Q   V   S+  +  + N + S ++     L+ + +  ++ ++F+ LA+ NT + +ETCG
Sbjct:   504 QSPAVNTPSITPTTNKPNIDSSEASKKYSKLRKIIVHGEVFQEFMRLAENNTKRSIETCG 563

Query:    93 VLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCF 152
             +L   L N  F +TT+IIPKQ+ T+ +C  + E ++F  Q E  L  +GWIHTHP+Q CF
Sbjct:   564 ILSGTLSNDVFRITTIIIPKQEGTTDTCNTIEEHEIFEYQLENDLLTLGWIHTHPTQDCF 623

Query:   153 MSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKE 212
             +S+VD+HTH SYQ ++ EA A+V++P  ++ ++GIF+LT+P G+  +++C+   FHPH  
Sbjct:   624 LSAVDVHTHCSYQYLLQEAIAVVISPM-ANPNFGIFRLTDPPGLETVQKCKLKSFHPHP- 681

Query:   213 PADGSPIYEHCSHV 226
             P +G PIY    HV
Sbjct:   682 PVNGIPIYTKVDHV 695

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0008237 "metallopeptidase activity" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

ASPGD|ASPL0000038640 AN3003 [Emericella nidulans (taxid:162425)]

 Score = 412 (150.1 bits), Expect = 1.6e-38, P = 1.6e-38
 Identities = 93/232 (40%), Positives = 130/232 (56%)

Query:    25 PSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPS---------VSN--VLQDVHISAQLM 73
             P P     A  P  A      V   DK+   +PS         + N   L+ V +  QL 
Sbjct:   315 PRPDKISQAVPPASAAAVPTKVPGDDKRKGLDPSSFTFKPSAYLENGTPLRTVFLPPQLR 374

Query:    74 EDFLELAKENTDKDLETCGVL-GAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQ 132
               FL LA  NT K+LETCG+L G  + N  F ++ L+IP+Q STS +C+ +NE  +F   
Sbjct:   375 SHFLSLAASNTRKNLETCGILCGTLISNALF-ISRLLIPEQISTSDTCETVNESAIFDYC 433

Query:   133 NERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTE 192
             +   L  +GWIHTHP+Q+CFMSS DLHTH  YQ+M+PE+ AIV AP+ +  ++G+F+LT+
Sbjct:   434 DSEDLMVLGWIHTHPTQTCFMSSRDLHTHCGYQVMLPESIAIVCAPSQTP-NWGVFRLTD 492

Query:   193 PSGMSVLKECQETG-FHPHKEPADGSPIYEHC---SHVYTNSNLRFEIFDLR 240
             P G+  +  C +TG FHPH E    + +Y       HV+  + L FE  D R
Sbjct:   493 PPGLKSVLSCTQTGLFHPHAE----TNLYTDALRPGHVFEANGLEFETVDQR 540

GO:0005768 "endosome" evidence=IEA

GO:0030133 "transport vesicle" evidence=IEA

GO:0032153 "cell division site" evidence=IEA

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

GO:0071585 "detoxification of cadmium ion" evidence=IEA

GO:0006897 "endocytosis" evidence=IEA

GO:0016579 "protein deubiquitination" evidence=IEA

GO:0043328 "protein targeting to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway" evidence=IEA

GO:0071276 "cellular response to cadmium ion" evidence=IEA

POMBASE|SPAC19B12.10 sst2 "human AMSH/STAMBP protein homolog, ubiquitin specific-protease" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 78/179 (43%), Positives = 117/179 (65%)

Query:    63 LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
             L+ +++   L + FL++ K NT K+LETCG+L   L    F++T L+IP Q++TS +C  
Sbjct:   260 LRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGT 319

Query:   123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
              +E  +F  Q++ +L  +GWIHTHP+Q+CFMSSVDLHTH SYQ+M+PEA AIV+AP  S 
Sbjct:   320 TDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAP--SK 377

Query:   183 RSYGIFQLTEPSGMSVLKECQETG-FHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
              + GIF+L +P G+  + +C++ G FHPH+       +     HV    N + ++ DLR
Sbjct:   378 NTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKV--YTMVAQPGHV-REINSKLQVVDLR 433

GO:0004221 "ubiquitin thiolesterase activity" evidence=ISS

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

GO:0005768 "endosome" evidence=IDA

GO:0006897 "endocytosis" evidence=IMP

GO:0008237 "metallopeptidase activity" evidence=IEA

GO:0016579 "protein deubiquitination" evidence=IDA

GO:0030133 "transport vesicle" evidence=IDA

GO:0032153 "cell division site" evidence=IDA

GO:0043328 "protein targeting to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway" evidence=IMP

GO:0045324 "late endosome to vacuole transport" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0071276 "cellular response to cadmium ion" evidence=IMP

GO:0071585 "detoxification of cadmium ion" evidence=IMP

UNIPROTKB|O95630 STAMBP "STAM-binding protein" [Homo sapiens (taxid:9606)]

 Score = 401 (146.2 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 93/224 (41%), Positives = 133/224 (59%)

Query:    20 VTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTE--PSVSNVLQDVHISAQLMEDFL 77
             +T+SS  P    T   P    V   S+      SN+E  P++   L+ V +  +L   FL
Sbjct:   211 LTVSSIQPSDCHTTVRPAKPPVVDRSLKPG-ALSNSESIPTIDG-LRHVVVPGRLCPQFL 268

Query:    78 ELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSL 137
             +LA  NT + +ETCG+L   L    F +T ++IPKQ + S  C   NEE++F IQ+++ L
Sbjct:   269 QLASANTARGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGL 328

Query:   138 FPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMS 197
               +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE+ AIV +P    +  G F+LT+  G+ 
Sbjct:   329 ITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSP--KFQETGFFKLTD-HGLE 385

Query:   198 VLKECQETGFHPH-KEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
              +  C++ GFHPH K+P    P++  CSHV T  +    I DLR
Sbjct:   386 EISSCRQKGFHPHSKDP----PLFCSCSHV-TVVDRAVTITDLR 424

GO:0006508 "proteolysis" evidence=IEA

GO:0008237 "metallopeptidase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0005769 "early endosome" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=TAS

GO:0007259 "JAK-STAT cascade" evidence=TAS

GO:0000281 "cytokinesis after mitosis" evidence=IMP

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

GO:0016579 "protein deubiquitination" evidence=IMP

GO:0032154 "cleavage furrow" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

UNIPROTKB|F1SLF9 STAMBP "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 401 (146.2 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 83/189 (43%), Positives = 120/189 (63%)

Query:    53 SNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPK 112
             S + P++   L+ V +  +L   FL+LA  NT + +ETCG+L   L    F +T ++IPK
Sbjct:   245 SGSTPTIDG-LRHVVVPEKLCPQFLQLASANTARGVETCGILCGKLMRNEFTITHVLIPK 303

Query:   113 QDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAF 172
             Q + S  C   NEE++F IQ+++ L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE+ 
Sbjct:   304 QSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESI 363

Query:   173 AIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTNSN 231
             AIV +P    +  G F+LT+  G+  +  C++ GFHPH K+P    P++  CSHV T  +
Sbjct:   364 AIVCSP--KFQETGFFRLTD-HGLEEISSCRQKGFHPHSKDP----PLFCSCSHV-TVVD 415

Query:   232 LRFEIFDLR 240
                 I DLR
Sbjct:   416 RAVTIIDLR 424

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0032154 "cleavage furrow" evidence=IEA

GO:0016579 "protein deubiquitination" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0000281 "cytokinesis after mitosis" evidence=IEA

UNIPROTKB|Q17QR2 STAMBP "STAM binding protein" [Bos taurus (taxid:9913)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 82/189 (43%), Positives = 119/189 (62%)

Query:    53 SNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPK 112
             +N E    + L+ V +  +L   FL+LA  NT + +ETCG+L   L    F +T ++IPK
Sbjct:   243 NNLEAPTIDGLRHVVVPGKLCPQFLQLAGANTTRGVETCGILCGKLMRNEFTITHVLIPK 302

Query:   113 QDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAF 172
             Q + S  C   NEE++F IQ+++ L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE+ 
Sbjct:   303 QSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESI 362

Query:   173 AIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTNSN 231
             AIV +P    +  G F+LT+  G+  +  C++ GFHPH K+P    P++  CSHV T  +
Sbjct:   363 AIVCSP--KFQETGFFRLTD-HGLEEISSCRQKGFHPHSKDP----PLFCSCSHV-TVVD 414

Query:   232 LRFEIFDLR 240
                 + DLR
Sbjct:   415 RAVTVTDLR 423

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0032154 "cleavage furrow" evidence=IEA

GO:0016579 "protein deubiquitination" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0000281 "cytokinesis after mitosis" evidence=IEA

UNIPROTKB|E1BRS3 Gga.34764 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 87/214 (40%), Positives = 126/214 (58%)

Query:    14 RVTAHAVTLSSPSPVLFLTAKAPQGALVTHVSVADSDKQSNTEPSVSNVLQDVHISAQLM 73
             RV    +  +SPS V  +++K P    V   S+  S   S    +  + L+ V +  +L 
Sbjct:   217 RVPLSPIHPASPS-VGTVSSKPP----VVDRSLKPSALGSTEHTAGMDALRQVIVPRELC 271

Query:    74 EDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQN 133
               FL+LA  NT + +ETCG+L   L    F +T +I+PKQ      C   NEE++F IQ+
Sbjct:   272 HKFLQLADANTARGVETCGILCGKLMRNEFTITHVIVPKQYGGPDYCNTENEEELFLIQD 331

Query:   134 ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEP 193
             +  L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE+ AIV +P    +  G F+LTE 
Sbjct:   332 QHGLVTLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESIAIVCSP--KYQETGFFKLTE- 388

Query:   194 SGMSVLKECQETGFHPH-KEPADGSPIYEHCSHV 226
              G+  +  C++ GFHPH K+P    P++  C+HV
Sbjct:   389 HGLEEISSCRQKGFHPHSKDP----PLFTTCNHV 418

GO:0000281 "cytokinesis after mitosis" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0016579 "protein deubiquitination" evidence=IEA

GO:0032154 "cleavage furrow" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6NKP9	AMSH2_ARATH	3, ., 4, ., 1, 9, ., -	0.735	0.8333	0.8968	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.19	0.691
3rd Layer	3.4.17.n1	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	240
cd08066	173	cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family	1e-98
cd08058	119	cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN)	4e-25
cd07767	116	cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domain	1e-18
pfam01398	117	pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin pro	2e-17
smart00232	135	smart00232, JAB_MPN, JAB/MPN domain	4e-14
cd08069	268	cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: p	7e-06
cd08068	244	cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC3	0.004

>gnl|CDD|163697 cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family

 Score =  284 bits (729), Expect = 1e-98
 Identities = 92/178 (51%), Positives = 123/178 (69%), Gaps = 5/178 (2%)

Query: 63  LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
           L+ V + A LM+ FL+LA+ NT ++LETCG+L   L N  F++T LIIPKQ  TS SCQ 
Sbjct: 1   LRQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQT 60

Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
            NEE++F  Q++  L  +GWIHTHP+Q+CF+SSVDLHTH SYQ+M+PEA AIV AP    
Sbjct: 61  TNEEELFDFQDQHDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAP--KY 118

Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
             +GIF+LT+P G+  +  C++TGFHPH +     P+YE C HV     L+  + DLR
Sbjct: 119 NEFGIFRLTDPPGLDEILNCKKTGFHPHPKD---PPLYEDCGHVIWKDQLKVTVVDLR 173

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, all of which are components of ESCRT-III, suggested to be required for EGFR down-regulation. The function of AMSH-LP has not been elucidated; however, it exhibits two fundamentally distinct features from AMSH: first, there is a substitution in the critical amino acid residue in the SH3-binding motif (SBM) in the human AMSH-LP, but not in its mouse ortholog, and lacks STAM-binding ability; second, AMSH-LP lacks the ability to interact with CHMP proteins. It is therefore likely that AMSH and AMSH-LP play different roles on early endosomes. Length = 173

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

 Score = 95.3 bits (237), Expect = 4e-25
 Identities = 48/116 (41%), Positives = 73/116 (62%), Gaps = 2/116 (1%)

Query: 76  FLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNER 135
            L+ A+ NT   +E  G+L   L +  F    +I+PKQ +   SC   N E++F +Q  R
Sbjct: 6   MLQHAESNTG--IEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGR 63

Query: 136 SLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLT 191
            L  +GW H+HP+ + ++SSVD+HT  SYQ+M+PEA AIV++P   ++  GIF+LT
Sbjct: 64  PLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRNKDTGIFRLT 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|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains

 Score = 78.3 bits (193), Expect = 1e-18
 Identities = 30/104 (28%), Positives = 40/104 (38%), Gaps = 2/104 (1%)

Query: 76  FLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNER 135
           FL+ AK    K  E  G+L          V  +I    D             +   +   
Sbjct: 4   FLDAAKSINGK--EVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNA 61

Query: 136 SLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPT 179
            L  +GW HTHP  SCF+S  DL TH  +Q   PE   I++   
Sbjct: 62  GLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVK 105

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. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Length = 116

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

 Score = 74.7 bits (184), Expect = 2e-17
 Identities = 31/113 (27%), Positives = 48/113 (42%), Gaps = 8/113 (7%)

Query: 66  VHISAQLMEDFLELAKENTDKDLETCGVL-GAFLENGTFYVTTLIIPKQDSTSSSCQALN 124
           V I   ++   ++ A+       E  GVL G    +    VT      Q  T    +A+ 
Sbjct: 5   VVIHPLVLLKIVDHARRGGKSGEEVMGVLLGTLEGDRVIEVTNSFALPQSETEDDVEAVE 64

Query: 125 EEDVFA-------IQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPE 170
            +  +         +  R    +GW H+HP   C++SSVD+HT   YQ M+PE
Sbjct: 65  LDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMIPE 117

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 = 66.6 bits (163), Expect = 4e-14
 Identities = 33/112 (29%), Positives = 48/112 (42%), Gaps = 8/112 (7%)

Query: 89  ETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEE-----DVFAIQNERSLFPMGWI 143
           E CGVL          V  +     +    S Q  +E+     D    +  + L  +GW 
Sbjct: 23  EVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIVGWY 82

Query: 144 HTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS---SRSYGIFQLTE 192
           H+HP +S F S VD+ TH SYQ   P +  +++ P  S     S   F+LT 
Sbjct: 83  HSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 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|163700 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5

 Score = 45.7 bits (109), Expect = 7e-06
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 140 MGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS----YGIFQLTEPSG 195
           +GW H+HP   C++S +D++T    Q +     A+V+ P  S        G F+   P  
Sbjct: 90  VGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGY 149

Query: 196 M 196
            
Sbjct: 150 K 150

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

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 9/78 (11%)

Query: 99  ENGTFYVTTLIIP-----KQD----STSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQ 149
           E    +++ +II      ++D    S      A  E +    +  R +  +GW H+HP  
Sbjct: 42  EVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAERLTEETGRPMRVVGWYHSHPHI 101

Query: 150 SCFMSSVDLHTHYSYQMM 167
           + + S VD+ T   YQMM
Sbjct: 102 TVWPSHVDVRTQAMYQMM 119

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	240
KOG2880	424	consensus SMAD6 interacting protein AMSH, contains	100.0
cd08066	173	MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associ	100.0
cd08058	119	MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains w	99.96
cd08069	268	MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal	99.96
cd08068	244	MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subun	99.95
cd08067	187	MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deu	99.95
cd08056	252	MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains wit	99.94
KOG1554	347	consensus COP9 signalosome, subunit CSN5 [Posttran	99.91
cd07767	116	MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (al	99.9
smart00232	135	JAB_MPN JAB/MPN domain. Domain in Jun kinase activ	99.9
cd08065	266	MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains wi	99.89
cd08070	128	MPN_like Mpr1p, Pad1p N-terminal (MPN) domains wit	99.89
PF01398	114	JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; Inte	99.85
KOG1560	339	consensus Translation initiation factor 3, subunit	99.84
cd08072	117	MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1	99.81
cd08073	108	MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains	99.76
KOG1555	316	consensus 26S proteasome regulatory complex, subun	99.75
COG1310	134	Predicted metal-dependent protease of the PAD1/JAB	99.67
PF14464	104	Prok-JAB: Prokaryotic homologs of the JAB domain;	99.62
cd08057	157	MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domai	99.59
TIGR03735	192	PRTRC_A PRTRC system protein A. A novel genetic sy	99.44
cd08059	101	MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains	99.42
cd08064	265	MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains wi	99.41
cd08062	280	MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains w	99.39
cd08060	182	MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family	99.37
cd08061	274	MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein l	99.28
TIGR02256	131	ICE_VC0181 integrative and conjugative element pro	99.06
PLN03246	303	26S proteasome regulatory subunit; Provisional	98.97
KOG1795	2321	consensus U5 snRNP spliceosome subunit [RNA proces	98.94
cd08063	288	MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains wit	98.92
PF05021	306	NPL4: NPL4 family; InterPro: IPR007717 The HRD4 ge	98.6
COG5178	2365	PRP8 U5 snRNP spliceosome subunit [RNA processing	98.25
KOG1556	309	consensus 26S proteasome regulatory complex, subun	98.19
PF03665	196	UPF0172: Uncharacterised protein family (UPF0172);	97.82
KOG2834	510	consensus Nuclear pore complex, rNpl4 component (s	97.62
KOG2975	288	consensus Translation initiation factor 3, subunit	97.44
KOG3289	199	consensus Uncharacterized conserved protein encode	94.81
cd08071	113	MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466	94.54
PF14220	123	DUF4329: Domain of unknown function (DUF4329)	93.81
KOG3050	299	consensus COP9 signalosome, subunit CSN6 [Posttran	92.93
PF08084	125	PROCT: PROCT (NUC072) domain; InterPro: IPR012984	92.67
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	92.17
PF04002	123	RadC: RadC-like JAB domain; InterPro: IPR001405 Th	90.71
PRK00024	224	hypothetical protein; Reviewed	85.46
TIGR00608	218	radc DNA repair protein radc. This family is based	83.5

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

Probab=100.00  E-value=5.7e-57  Score=410.41  Aligned_cols=217  Identities=52%  Similarity=0.928  Sum_probs=193.1

Q ss_pred             eeeeccCCCcceeeeeccCC-CCcccccccCCCC---CCCCCCCCCCCceeEEEECHHHHHHHHHHHhccCCCCcceEEE
Q 041233           18 HAVTLSSPSPVLFLTAKAPQ-GALVTHVSVADSD---KQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGV   93 (240)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGl   93 (240)
                      +...-.||.|..+++..... .+.+++  +..++   ....+.+...+.++.|+||..+++.|++.|++|+.++.|+||+
T Consensus       204 ~l~~~~s~ep~~s~~~n~~~k~p~~~r--~l~p~a~~n~~~~~~~~~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGi  281 (424)
T KOG2880|consen  204 LLSVLSSPEPSDSCTTNVTIKSPSVDR--VLKPGATDNSNHGESSEGKILRDVHIPERLMEVFLQLAKSNTKKNLETCGI  281 (424)
T ss_pred             hhhhccCCCccccccccccccCCCCCc--ccccccccccccccccCCccceEEEecHHHHHHHHHHHhhcccccchHHHH
Confidence            35566778888887776542 233333  33332   3333444555569999999999999999999999999999999


Q ss_pred             eeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEE
Q 041233           94 LGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFA  173 (240)
Q Consensus        94 L~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~va  173 (240)
                      |+|++..+.++||++++|+|++++++|.+++++|+|.+|++++|..|||+||||+++||||++||||||+||.|+||++|
T Consensus       282 L~g~L~~n~f~IThliiPkQeatsd~C~t~neeelF~vQdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiA  361 (424)
T KOG2880|consen  282 LAGKLERNEFYITHLIIPKQEATSDSCNTMNEEELFEVQDQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIA  361 (424)
T ss_pred             hhhHhhcCcEEEEEEEeecccCCCccccccCHHHHheecccccceeeeeeecCCccchhheeccccccceeeeecchhee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCCceeEEEEeeCCCCcchhhcccCCCcccCCCCCCCCCcccccCceEecCCceeEEeeCC
Q 041233          174 IVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR  240 (240)
Q Consensus       174 IVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~fhph~~~~~~~~~y~~~~hv~~~~~~~~~~~dlr  240 (240)
                      |||+|+..  ..|+|||++|+||+++++|+++|||||+.  +|+|||++|+||||+.+.+++|+|||
T Consensus       362 IV~aPk~~--~tGiFrLt~~~Gm~~i~~C~~~GFHpH~~--~~~pl~~~~~~v~~~~~~k~~v~dLR  424 (424)
T KOG2880|consen  362 IVCAPKSK--TTGIFRLTDPGGMEVIRGCRKKGFHPHSE--KGPPLFEHCSHVYMHHNNKLCVIDLR  424 (424)
T ss_pred             EEeccccC--CcceEEecCCcchHHHhhcccCCCCCCCC--CCCCceeecceeEEcCCcceeeeeCC
Confidence            99999954  79999999999999999999999999997  68999999999999999999999998

>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family

Probab=100.00  E-value=4.5e-48  Score=327.71  Aligned_cols=173  Identities=53%  Similarity=1.009  Sum_probs=162.4

Q ss_pred             eeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEE
Q 041233           63 LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGW  142 (240)
Q Consensus        63 ~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGW  142 (240)
                      ++++.||++++++|++||+.++..|+|+||+|+|+..++.++|++++.++|.+++.++++.++++.++.++.+|+++|||
T Consensus         1 ~~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~~~e~~~~~~~~gle~vGw   80 (173)
T cd08066           1 LRQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTNEEELFDFQDQHDLITLGW   80 (173)
T ss_pred             CeEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCCHHHHHHHHHhCCCeeEEE
Confidence            36899999999999999999874579999999999877888999999999999999999989888888889999999999


Q ss_pred             EecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCCcccCCCCCCCCCcccc
Q 041233          143 IHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEH  222 (240)
Q Consensus       143 YHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~fhph~~~~~~~~~y~~  222 (240)
                      |||||+.+++||.+|++||++||.++|+++|||+||.  ...++||||++++|++|+++|+++|||||+++   .+||++
T Consensus        81 yHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~--~~~l~afrl~~~~g~~~~~~~~~~~~h~~~~~---~~~~~~  155 (173)
T cd08066          81 IHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK--YNEFGIFRLTDPPGLDEILNCKKTGFHPHPKD---PPLYED  155 (173)
T ss_pred             EeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC--CcEEeEEEeecCCcceecccCCcCccCCCCCC---CCccee
Confidence            9999999999999999999999999999999999985  46899999996699999999999999999986   699999


Q ss_pred             cCceEecCCceeEEeeCC
Q 041233          223 CSHVYTNSNLRFEIFDLR  240 (240)
Q Consensus       223 ~~hv~~~~~~~~~~~dlr  240 (240)
                      |+||+++++++|+|+|||
T Consensus       156 ~~~~~~~~~~~~~~~~~~  173 (173)
T cd08066         156 CGHVIWKDQLKVTVVDLR  173 (173)
T ss_pred             eeEEEEcCCCceEEEeCC
Confidence            999999999999999998

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

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

Probab=99.96  E-value=9.6e-29  Score=196.61  Aligned_cols=114  Identities=38%  Similarity=0.642  Sum_probs=93.6

Q ss_pred             HHHHHHHHHHhccCCCCcceEEEeeeeecC-----CEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEec
Q 041233           71 QLMEDFLELAKENTDKDLETCGVLGAFLEN-----GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHT  145 (240)
Q Consensus        71 ~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~-----~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHS  145 (240)
                      +++++|++||++++  |+|+||+|+|+.+.     ..++|+.+++.+....     ..+..+.+..+.++|+++||||||
T Consensus         1 ~~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~-----~~~~~~~~~~~~~~g~~~vG~YHS   73 (119)
T cd08058           1 DALLKMLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCT-----GENVEELFNVQTGRPLLVVGWYHS   73 (119)
T ss_pred             CHHHHHHHHhcCCC--CeEEEEEeeeEEecCccceeEEEEeecCCCCCCch-----hHHHHHHHHHHhCCCCeEEEEEec
Confidence            47899999999988  99999999998753     3467777776654221     111112333467899999999999


Q ss_pred             CCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEee
Q 041233          146 HPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLT  191 (240)
Q Consensus       146 HP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt  191 (240)
                      ||+++++||.+|+++|++||++.|++++||+||.++...+|||||+
T Consensus        74 HP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~~~~~~a~rl~  119 (119)
T cd08058          74 HPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRNKDTGIFRLT  119 (119)
T ss_pred             CCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCCCcccceEEeC
Confidence            9999999999999999999999999999999999876789999996

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

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

Probab=99.96  E-value=6.5e-28  Score=217.02  Aligned_cols=139  Identities=23%  Similarity=0.374  Sum_probs=118.9

Q ss_pred             CCCCCceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccCh--HHHHH--H-
Q 041233           57 PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNE--EDVFA--I-  131 (240)
Q Consensus        57 ~~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de--~e~~~--~-  131 (240)
                      ...+..++.|.|+..++.+|++||+++.  |.|+||+|+|+.++++++|+++|++|+.+++..++..++  +++.+  . 
T Consensus         3 ~~~~~~~~~V~Is~~allkil~Ha~~~~--p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~   80 (268)
T cd08069           3 KPDPDYFEKVYISSLALLKMLKHARAGG--PIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEML   80 (268)
T ss_pred             CCCCCcccEEEECHHHHHHHHHHHhccC--CceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHH
Confidence            3456788899999999999999999976  999999999998888999999999999888777666442  12333  2 


Q ss_pred             -hhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCC-C---ceeEEEEeeCCCCcch
Q 041233          132 -QNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS-S---RSYGIFQLTEPSGMSV  198 (240)
Q Consensus       132 -~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~-~---~~l~aFrLt~p~gm~~  198 (240)
                       +..+++.+||||||||.++||||.+|+++|..||.+.+++|+||++|..+ .   ..+||||+++ .++..
T Consensus        81 ~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~-~~~~~  151 (268)
T cd08069          81 KQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIP-PGYKP  151 (268)
T ss_pred             HHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEEC-ccccc
Confidence             24588999999999999999999999999999999999999999999876 3   3699999996 66653

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

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

Probab=99.95  E-value=1e-27  Score=212.69  Aligned_cols=127  Identities=24%  Similarity=0.347  Sum_probs=109.2

Q ss_pred             eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec-------CCEEEEEEEEecCCCCCCCceeccChHHHHHHh---h
Q 041233           64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE-------NGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQ---N  133 (240)
Q Consensus        64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~-------~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~---~  133 (240)
                      ..|.|+++++++|+.||+..+  |+|+||||+|+.+       ...+.|...+++++...+...+.+|++++++++   +
T Consensus         2 ~~V~Is~~~l~~il~HA~~~~--P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~   79 (244)
T cd08068           2 SKVHLSADVYLVCLTHALSTE--KEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAE   79 (244)
T ss_pred             cEEEECHHHHHHHHHHHHhCC--CcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHH
Confidence            579999999999999999988  9999999999874       234566566666666666677899999888763   4


Q ss_pred             h------CCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC-------ceeEEEEeeC
Q 041233          134 E------RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS-------RSYGIFQLTE  192 (240)
Q Consensus       134 ~------~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~-------~~l~aFrLt~  192 (240)
                      .      +|+.+||||||||+++++||.+|+++|.+||++.|+++|||+|+..+.       ..++|||+.+
T Consensus        80 ~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~  151 (244)
T cd08068          80 RLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQ  151 (244)
T ss_pred             HHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecC
Confidence            5      999999999999999999999999999999999999999999987752       4699999986

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

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

Probab=99.95  E-value=3.4e-27  Score=202.37  Aligned_cols=128  Identities=20%  Similarity=0.285  Sum_probs=109.4

Q ss_pred             ceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec--CCEEEEEEEEecCCCCCCCceeccChHH---HHHHhhhCC
Q 041233           62 VLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE--NGTFYVTTLIIPKQDSTSSSCQALNEED---VFAIQNERS  136 (240)
Q Consensus        62 ~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~--~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~~~~~g  136 (240)
                      ....|.|+..++.+|++||+..   ..|+||+|+|+.+  .+.++|+.++|+++..+++.++ +|+++   +++.++++|
T Consensus         3 ~pf~V~Is~~all~m~~Ha~~~---~~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e-~dp~~q~e~~~~l~~~g   78 (187)
T cd08067           3 QPFKVTVSSNALLLMDFHCHLT---TSEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCE-MDPVSETEIRESLESRG   78 (187)
T ss_pred             CCEEEEECHHHHHHHHHHhcCC---CcEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccc-cCHHHHHHHHHHHHHcC
Confidence            3467999999999999999985   3999999999964  4678999999999977766644 46654   444568899


Q ss_pred             CcceEEEecCCCCCCCCCHHHHHHHHhhhhcCC-------CEEEEEEccCCCC-----ceeEEEEeeCC
Q 041233          137 LFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVP-------EAFAIVLAPTDSS-----RSYGIFQLTEP  193 (240)
Q Consensus       137 l~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~p-------e~vaIVisP~~~~-----~~l~aFrLt~p  193 (240)
                      +++||||||||.++++||.+|++||++||.+++       ++|+|||||++..     ..+++|++.++
T Consensus        79 l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~  147 (187)
T cd08067          79 LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP  147 (187)
T ss_pred             CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence            999999999999999999999999999999987       6999999999853     24999999964

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

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

Probab=99.94  E-value=6.4e-26  Score=201.76  Aligned_cols=136  Identities=21%  Similarity=0.272  Sum_probs=124.9

Q ss_pred             eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecC---CEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcce
Q 041233           64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLEN---GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPM  140 (240)
Q Consensus        64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~---~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iV  140 (240)
                      ..++||++++++|+..|+.++    |+||+|+|+...   +..+|+++++|||.++.++|.+.+.  +.+++...||+.|
T Consensus        36 ~t~vlPknllkkFi~iaD~rt----Q~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~--~~~~~~l~~Le~L  109 (252)
T cd08056          36 YTYILPKNLLKKFISISDLRT----QIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQ--LPQHEYLEDLEPL  109 (252)
T ss_pred             CEEEeCHHHHHHHHHHhhhcc----eEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCcc--CccchhhCCCEee
Confidence            589999999999999999955    999999999743   6789999999999999999998764  5777888999999


Q ss_pred             EEEecCCCCCCCCCHHHHHHHHhhhhcCC-----CEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCC
Q 041233          141 GWIHTHPSQSCFMSSVDLHTHYSYQMMVP-----EAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETG  206 (240)
Q Consensus       141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~p-----e~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~  206 (240)
                      ||+||||..++|||+.|+++|++||.+.|     ++|+++||++.++.+++||+||+ +|++|++++++..
T Consensus       110 GWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~SftpGs~sl~ay~LT~-~G~~wg~~n~d~~  179 (252)
T cd08056         110 GWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFTPGSCSLTAYKLTP-EGYEWGKQNKDLG  179 (252)
T ss_pred             EEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCCCCceEEEEEecCH-HHHHHHHhCcccc
Confidence            99999999999999999999999999998     89999999998888999999995 8999999999754

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

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

Probab=99.91  E-value=5.1e-24  Score=190.31  Aligned_cols=135  Identities=24%  Similarity=0.390  Sum_probs=117.4

Q ss_pred             CCCCceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHh-----
Q 041233           58 SVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQ-----  132 (240)
Q Consensus        58 ~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~-----  132 (240)
                      ..+..++.|.|+.-+++||+.||+++.  ++|++|+|.|+.+++++.|..+|..|.++|+.++++..++.-+.++     
T Consensus        47 ~Dp~~fk~vkISalAllKm~~hA~~Gg--nlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~  124 (347)
T KOG1554|consen   47 TDPHYFKHVKISALALLKMVMHARSGG--NLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEA  124 (347)
T ss_pred             CCCchhhhhhhHHHHHHHHHHHHhcCC--CeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHH
Confidence            455577889999999999999999987  9999999999999999999999999999999998876654333221     


Q ss_pred             h--hCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCc----eeEEEEeeCCCC
Q 041233          133 N--ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSR----SYGIFQLTEPSG  195 (240)
Q Consensus       133 ~--~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~----~l~aFrLt~p~g  195 (240)
                      .  .+-+.+||||||||+.+||+|.+|+.||.--|....+++|||++|.++-.    .+||||.-+ +|
T Consensus       125 k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp-~g  192 (347)
T KOG1554|consen  125 KNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYP-KG  192 (347)
T ss_pred             HHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeeccc-CC
Confidence            2  35588999999999999999999999999999999999999999998732    499999994 77

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

Probab=99.90  E-value=4.3e-23  Score=160.86  Aligned_cols=106  Identities=27%  Similarity=0.328  Sum_probs=88.1

Q ss_pred             HHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCC
Q 041233           74 EDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFM  153 (240)
Q Consensus        74 ~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fp  153 (240)
                      ++|++||+.++  +.|+||+|+|+.+++.++|++++++++..+...............+...|+++||||||||..+++|
T Consensus         2 k~il~~a~~~~--~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhshp~~~~~~   79 (116)
T cd07767           2 KMFLDAAKSIN--GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCFL   79 (116)
T ss_pred             HhHHHHHhcCC--CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEcCCCCCCcc
Confidence            68999999987  9999999999998888899999999986654332211101122235678999999999999999999


Q ss_pred             CHHHHHHHHhhhhcCCCEEEEEEccCCC
Q 041233          154 SSVDLHTHYSYQMMVPEAFAIVLAPTDS  181 (240)
Q Consensus       154 Ss~Dl~tq~syQ~~~pe~vaIVisP~~~  181 (240)
                      |..|+.+|..||.+.+++++||+++...
T Consensus        80 s~~dv~~~~~~q~~~~~~v~li~~~~~~  107 (116)
T cd07767          80 SPNDLATHELFQRYFPEKVMIIVDVKPK  107 (116)
T ss_pred             CHHHHHHHHHHHHhCCCCEEEEEECCCc
Confidence            9999999999999999999999999886

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

>smart00232 JAB_MPN JAB/MPN domain

Probab=99.90  E-value=2.4e-22  Score=160.05  Aligned_cols=125  Identities=26%  Similarity=0.360  Sum_probs=105.0

Q ss_pred             EEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCce--eccChHHHHHH---hhhCCCcce
Q 041233           66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSC--QALNEEDVFAI---QNERSLFPM  140 (240)
Q Consensus        66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~--~~~de~e~~~~---~~~~gl~iV  140 (240)
                      |.|...++++|++||.++.  +.|+||+|+|+..++.+.|+++++.|+...++.+  +..++.+....   +...++++|
T Consensus         2 v~i~~~v~~~i~~h~~~~~--p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   79 (135)
T smart00232        2 VKVHPLVPLNILKHAIRDG--PEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIV   79 (135)
T ss_pred             EEEcHHHHHHHHHHHhcCC--CcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceEE
Confidence            6889999999999999987  9999999999998888999999999887665553  33333322221   346889999


Q ss_pred             EEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC---ceeEEEEeeC
Q 041233          141 GWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS---RSYGIFQLTE  192 (240)
Q Consensus       141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~---~~l~aFrLt~  192 (240)
                      |||||||..+++||..|+.+|..||..++.++.+++++..+.   ..++||++++
T Consensus        80 Gwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~  134 (135)
T smart00232       80 GWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP  134 (135)
T ss_pred             EEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence            999999999999999999999999999999999999988764   2599999974

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=99.89  E-value=1.7e-22  Score=181.65  Aligned_cols=139  Identities=21%  Similarity=0.301  Sum_probs=113.0

Q ss_pred             EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCce-eccCh-H---HHHHHhhhCCC--
Q 041233           65 DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSC-QALNE-E---DVFAIQNERSL--  137 (240)
Q Consensus        65 ~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~-~~~de-~---e~~~~~~~~gl--  137 (240)
                      .|.|+..++.+|++||.++.  |.|+||+|+|...+++++||++|+.|+..+++.. +..++ .   ++++..++.|.  
T Consensus         2 ~V~I~~~vllkIv~H~~~~~--p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e   79 (266)
T cd08065           2 SVQIDGLVVLKIIKHCKEEL--PELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDH   79 (266)
T ss_pred             EEEEeHHHHHHHHHHHhcCC--CcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCC
Confidence            58999999999999999988  9999999999998899999999999987664431 11222 2   23333455555  


Q ss_pred             cceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCC---CCceeEEEEeeCCCCcchhhcccCCCcccC
Q 041233          138 FPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTD---SSRSYGIFQLTEPSGMSVLKECQETGFHPH  210 (240)
Q Consensus       138 ~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~---~~~~l~aFrLt~p~gm~~~~~c~~~~fhph  210 (240)
                      .+|||||||| .++|.|..+++++++||...+++|+||+||..   +...+||||+++ .||...   ++..|.+.
T Consensus        80 ~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~-~~~~~~---~~~~~~~~  150 (266)
T cd08065          80 NHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSE-KFMELY---KEGKFSTE  150 (266)
T ss_pred             cEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcH-HHHHHh---hcCCcCHH
Confidence            9999999999 89999999999999999988999999999984   235799999995 898774   44556653

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

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

Probab=99.89  E-value=3.9e-22  Score=160.35  Aligned_cols=115  Identities=22%  Similarity=0.256  Sum_probs=99.7

Q ss_pred             HHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCC-ceeccChHHHHHH---hhhCCCcceEEEecC
Q 041233           71 QLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSS-SCQALNEEDVFAI---QNERSLFPMGWIHTH  146 (240)
Q Consensus        71 ~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~-~~~~~de~e~~~~---~~~~gl~iVGWYHSH  146 (240)
                      .++++|++||+.+.  |.|+||+|+|+.+.....|+.+++++|...+. ..+.+|++++.++   .++.|+.+|||||||
T Consensus         2 ~~~~~il~ha~~~~--P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~g~~~vG~~HSH   79 (128)
T cd08070           2 ELLEAILAHAEAEY--PEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVVGIYHSH   79 (128)
T ss_pred             HHHHHHHHHHHhCC--CCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHCCCeEEEEEeCC
Confidence            57899999999988  99999999999876666788999999987776 7888999887776   356899999999999


Q ss_pred             CCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeC
Q 041233          147 PSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTE  192 (240)
Q Consensus       147 P~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~  192 (240)
                      |+.+++||.+|+.++     ..++.+++|++...+...+++|++.+
T Consensus        80 P~~~~~PS~~D~~~~-----~~~~~~~lIv~~~~~~~~~~~~~~~~  120 (128)
T cd08070          80 PDGPARPSETDLRLA-----WPPGVSYLIVSLAGGAPELRAWRLEG  120 (128)
T ss_pred             CCCCCCCCHHHHHhc-----cCCCCeEEEEECCCCCcEEEEEEEcC
Confidence            999999999999864     34578999999887656899999985

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.

>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=99.85  E-value=4.6e-21  Score=150.49  Aligned_cols=107  Identities=25%  Similarity=0.429  Sum_probs=86.8

Q ss_pred             ceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCC-EEEEEEEEecCCCCCCCceeccChHHH---HHHhh--hC
Q 041233           62 VLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENG-TFYVTTLIIPKQDSTSSSCQALNEEDV---FAIQN--ER  135 (240)
Q Consensus        62 ~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~-~~~Vt~l~~ppq~~ts~~~~~~de~e~---~~~~~--~~  135 (240)
                      ..+.|.|...++.+|++||.+..  +.|+||+|+|..+++ .++|+++|+.|...+...+...+....   ++..+  ..
T Consensus         2 s~~~V~i~p~vll~i~~h~~r~~--~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (114)
T PF01398_consen    2 SVQTVQIHPLVLLKIIDHATRSS--PNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNP   79 (114)
T ss_dssp             SCEEEEEEHHHHHHHHHHHHHHH--CTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCST
T ss_pred             CcEEEEECHHHHHHHHHHHhcCC--CCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhccccc
Confidence            35789999999999999999976  779999999999888 999999999998877776665554322   22222  14


Q ss_pred             CCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCC
Q 041233          136 SLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPE  170 (240)
Q Consensus       136 gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe  170 (240)
                      .+.+||||||||..++|||..|+++|..||.+.|+
T Consensus        80 ~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~  114 (114)
T PF01398_consen   80 NLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN  114 (114)
T ss_dssp             TSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred             cceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence            59999999999999999999999999999998874

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.

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

Probab=99.84  E-value=6.8e-21  Score=169.95  Aligned_cols=148  Identities=19%  Similarity=0.364  Sum_probs=117.6

Q ss_pred             CCCceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCC-C-Ccee--ccChH-HHHHH--
Q 041233           59 VSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDST-S-SSCQ--ALNEE-DVFAI--  131 (240)
Q Consensus        59 ~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~t-s-~~~~--~~de~-e~~~~--  131 (240)
                      .+.+.+.|.|+..++.+|++||+++.-+..=+.|+|+|.+.+++++||++||.|+... + +...  ..+++ +.++.  
T Consensus         8 ~~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~m   87 (339)
T KOG1560|consen    8 ESPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAM   87 (339)
T ss_pred             CCCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHH
Confidence            4456789999999999999999998722233579999999899999999999887432 1 1111  12222 12222  


Q ss_pred             h-----hhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCce---eEEEEeeCCCCcchhhccc
Q 041233          132 Q-----NERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS---YGIFQLTEPSGMSVLKECQ  203 (240)
Q Consensus       132 ~-----~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~---l~aFrLt~p~gm~~~~~c~  203 (240)
                      +     ...+...||||.||- .++|+|..-+++||.||.+.|++|++|+||.+++++   +|||||| |+.|++   |+
T Consensus        88 lrrlr~vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLT-p~am~~---~k  162 (339)
T KOG1560|consen   88 LRRLRYVNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLT-PEAMAA---HK  162 (339)
T ss_pred             HHHhhhcCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcC-HHHHHH---Hh
Confidence            1     135788999999995 789999888999999999999999999999998764   9999999 588887   99


Q ss_pred             CCCcccCC
Q 041233          204 ETGFHPHK  211 (240)
Q Consensus       204 ~~~fhph~  211 (240)
                      +++|.|+.
T Consensus       163 ekdwtpea  170 (339)
T KOG1560|consen  163 EKDWTPEA  170 (339)
T ss_pred             cCCCCHHH
Confidence            99999984

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

Probab=99.81  E-value=3.6e-19  Score=142.00  Aligned_cols=109  Identities=20%  Similarity=0.215  Sum_probs=88.7

Q ss_pred             ECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCC
Q 041233           68 ISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHP  147 (240)
Q Consensus        68 I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP  147 (240)
                      |++++++.|++||++.+  |+|+||+|+|+.+    .|+.++++++...++..+..+.     .+.+.|++++|.|||||
T Consensus         1 i~~~~~~~i~~ha~~~~--P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~~~f~~-----~~~~~g~~ivgi~HSHP   69 (117)
T cd08072           1 ISRDLLDSILEAAKSSH--PNEFAALLRGKDG----VITELLILPGTESGEVSAVFPL-----LMLPLDMSIVGSVHSHP   69 (117)
T ss_pred             CCHHHHHHHHHHHhhcC--CceEEEEEEeecc----EEEEEEECCCCCCCCcceeech-----HHhcCCCeEEEEEEcCC
Confidence            57899999999999988  9999999999775    6889999887655443332222     24578999999999999


Q ss_pred             CCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeC
Q 041233          148 SQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTE  192 (240)
Q Consensus       148 ~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~  192 (240)
                      +.++.||..|++.     +..|+.+++|+|+......++||++..
T Consensus        70 ~~~~~PS~~D~~~-----~~~~~~~~lIvs~~~~~~~~~a~~~~g  109 (117)
T cd08072          70 SGSPRPSDADLSF-----FSKTGLVHIIVGYPYDEDDWRAYDSDG  109 (117)
T ss_pred             CCCCCCCHHHHHh-----hhcCCCEEEEEECcCCCCCEEEEecCC
Confidence            9999999999874     346899999999755446799999874

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.

>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=99.76  E-value=6.5e-18  Score=133.12  Aligned_cols=102  Identities=19%  Similarity=0.172  Sum_probs=83.9

Q ss_pred             HHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCC-ceeccChHHHHHHhhhCCCcceEEEecCCCCC
Q 041233           72 LMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSS-SCQALNEEDVFAIQNERSLFPMGWIHTHPSQS  150 (240)
Q Consensus        72 ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~-~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~  150 (240)
                      +++.|++||+..+  |.|+||||+|+.     .++.+++.+|...+. ..|.+|+++++++++ .+ ++||.|||||+.+
T Consensus         2 i~~~i~~ha~~~~--P~E~CGll~g~~-----~~~~~~p~~N~~~~p~~~F~idp~e~~~a~~-~~-~ivgi~HSHP~~~   72 (108)
T cd08073           2 LEDAILAHAKAEY--PREACGLVVRKG-----RKLRYIPCRNIAADPEEHFEISPEDYAAAED-EG-EIVAVVHSHPDGS   72 (108)
T ss_pred             HHHHHHHHHhHCC--CCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHHHhc-CC-CEEEEEEcCCCCC
Confidence            6789999999988  999999999966     256678888876554 678999999998774 33 8999999999999


Q ss_pred             CCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEE
Q 041233          151 CFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQ  189 (240)
Q Consensus       151 ~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFr  189 (240)
                      +.||..|+..     +..++..+||+|...+  .+++|+
T Consensus        73 a~PS~~D~~~-----~~~~~~~~iIvs~~~~--~~~~~~  104 (108)
T cd08073          73 PAPSEADRAQ-----QEATGLPWIIVSWPEG--DLRVFR  104 (108)
T ss_pred             CCCCHHHHHH-----hhcCCCcEEEEEcCCC--CEEEEe
Confidence            9999999963     3568899999997644  466765

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.

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

Probab=99.75  E-value=1e-18  Score=159.23  Aligned_cols=139  Identities=27%  Similarity=0.390  Sum_probs=112.6

Q ss_pred             CCCCCCCCCCceeEEEECHHHHHHHHHHHhccCCCCcc-eEEEe-ee---ee-cCCEEEEEEEEecCCCCCCCc--eecc
Q 041233           52 QSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLE-TCGVL-GA---FL-ENGTFYVTTLIIPKQDSTSSS--CQAL  123 (240)
Q Consensus        52 ~~~~~~~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~E-vcGlL-~G---~~-~~~~~~Vt~l~~ppq~~ts~~--~~~~  123 (240)
                      .-.++.+..+..++++|...++.+|++|++...  +.| +.|++ +|   .+ +..++.|.+++..++.++.-+  .+..
T Consensus        19 ~~~~d~~~~~~~e~v~i~slall~m~rh~r~~~--p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~   96 (316)
T KOG1555|consen   19 ELLGDEPHSDEKETVYISSLALLKMLRHDRAGS--PEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAV   96 (316)
T ss_pred             cccCccccccCcceeeeehhhhhhcccccccCC--chhhccceeecccccceeeecceeeeeeeccccccceecccchhc
Confidence            344567777888999999999999999999977  999 89999 88   32 456778888999999998887  4555


Q ss_pred             ChHHHHHH-------hhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCc---eeEEEEeeCC
Q 041233          124 NEEDVFAI-------QNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSR---SYGIFQLTEP  193 (240)
Q Consensus       124 de~e~~~~-------~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~---~l~aFrLt~p  193 (240)
                      |+  .++.       +..+.+.+||||||||.++|+||..|+.||.+||+..+.+++.+++|..+..   -..+|++.++
T Consensus        97 d~--V~q~q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~  174 (316)
T KOG1555|consen   97 DP--VFQTQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINP  174 (316)
T ss_pred             cH--HHHHHHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCc
Confidence            55  3333       3446688999999999999999999999999999998888888877766532   3778888875


Q ss_pred             C
Q 041233          194 S  194 (240)
Q Consensus       194 ~  194 (240)
                      .
T Consensus       175 ~  175 (316)
T KOG1555|consen  175 Q  175 (316)
T ss_pred             c
Confidence            3

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

Probab=99.67  E-value=6.9e-16  Score=125.02  Aligned_cols=113  Identities=20%  Similarity=0.317  Sum_probs=79.1

Q ss_pred             EEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCce-eccChHH--HHHHhhhCCCcceEE
Q 041233           66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSC-QALNEED--VFAIQNERSLFPMGW  142 (240)
Q Consensus        66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~-~~~de~e--~~~~~~~~gl~iVGW  142 (240)
                      +.|+++++..|+.||+.++  |.|+||+|+|...+     ...+..++...+... +..+++.  .+..++..|+.+|||
T Consensus         2 ~~i~~~~l~~il~~a~~~~--p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~g~~vvg~   74 (134)
T COG1310           2 LVIPKEVLGAILEHARREH--PREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEYSLFYLAAEDAGEVVVGW   74 (134)
T ss_pred             ceecHHHHHHHHHHHHhcC--ChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHHHHHHHHHhhCCCEEEEE
Confidence            5689999999999999988  99999999998754     344455554444332 3344332  333467788999999


Q ss_pred             EecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeC
Q 041233          143 IHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTE  192 (240)
Q Consensus       143 YHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~  192 (240)
                      |||||+.+++||..|++    .|...+-.+.||+.+...   ...|+..+
T Consensus        75 yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~~~~~---~~~~~~~~  117 (134)
T COG1310          75 YHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPPGR---VHKGRAVD  117 (134)
T ss_pred             EcCCCCCCCCcCHHHHh----hccccCCCEEEEEcCCCc---eeEEeeec
Confidence            99999999999999998    334444444555554433   44444443

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

Probab=99.62  E-value=1.9e-15  Score=116.18  Aligned_cols=98  Identities=24%  Similarity=0.351  Sum_probs=70.2

Q ss_pred             HHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHH----HhhhCCCcceEEEec
Q 041233           70 AQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFA----IQNERSLFPMGWIHT  145 (240)
Q Consensus        70 ~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~----~~~~~gl~iVGWYHS  145 (240)
                      ++++++|++|++.+.  |.|+||+|+|......+.++....            .++.+.++    .+.+.++.+||+|||
T Consensus         2 ~~~~~~i~~~~~~~~--p~E~~G~L~g~~~~~~~~~~~~~~------------~~p~~~~~~~~~~~~~~~~~~vg~~HS   67 (104)
T PF14464_consen    2 EEVLEQIIAHARAAY--PNEACGLLLGRRDDQRFIVVPNVN------------PDPRDSFRRERFEARERGLEIVGIWHS   67 (104)
T ss_dssp             -HHHHHHHHHHHHHT--TS-EEEEEEEEEECCEEEEEEEEE--------------HHCHHHHHH-HHHHHT-EEEEEEEE
T ss_pred             HHHHHHHHHHHhhCC--CCeEEEEEEEEecCCEEEEEeCCC------------CCcHHHHHHHhhhhhcccceeeEEEEc
Confidence            578999999999988  999999999998666666666553            23333333    356789999999999


Q ss_pred             CCCCCCCCCHHHHHHHHhhhhcCC-CEEEEEEccCCCCceeEEEEe
Q 041233          146 HPSQSCFMSSVDLHTHYSYQMMVP-EAFAIVLAPTDSSRSYGIFQL  190 (240)
Q Consensus       146 HP~~~~fpSs~Dl~tq~syQ~~~p-e~vaIVisP~~~~~~l~aFrL  190 (240)
                      ||+..++||.+|+.+..     .. ..++||++. .+  +. +|||
T Consensus        68 HP~~~a~pS~~D~~~~~-----~~~~~~~iI~~~-~~--~~-~W~~  104 (104)
T PF14464_consen   68 HPSGPAFPSSTDIRSMR-----DLAPPSYIIVGN-PE--DR-AWRL  104 (104)
T ss_dssp             ESSSSSS--HHHHHTHC-----CS-SCEEEEEEE-CE--SC-CEEE
T ss_pred             CCCCCCCCCHHHHHhhh-----ccCCeEEEEEeC-CC--CC-eEEC
Confidence            99999999999998642     22 778999987 21  23 7765

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

Probab=99.59  E-value=5.3e-14  Score=116.92  Aligned_cols=126  Identities=14%  Similarity=0.190  Sum_probs=93.6

Q ss_pred             EEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHH---HHHHh--hhCCCcce
Q 041233           66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEED---VFAIQ--NERSLFPM  140 (240)
Q Consensus        66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~~--~~~gl~iV  140 (240)
                      |.|.+.++.+|++|+.+....+.+++|+|+|...++.++|+++|+.|...+++. ...|.+.   +++..  -..++.+|
T Consensus         1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~-~~~d~~y~~~m~~~~~~v~~~~~vV   79 (157)
T cd08057           1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEES-IFIDTEYLEKRYNLHKKVYPQEKIV   79 (157)
T ss_pred             CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcc-hhhhHHHHHHHHHHHHHhCCCCCEE
Confidence            467888999999999875434788999999999999999999999998765544 2333321   22211  23678999


Q ss_pred             EEEecCCCCCCCCCHHHHHHHHhhhhc-CCCEEEEEEccCC----CCceeEEEEeeC
Q 041233          141 GWIHTHPSQSCFMSSVDLHTHYSYQMM-VPEAFAIVLAPTD----SSRSYGIFQLTE  192 (240)
Q Consensus       141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~-~pe~vaIVisP~~----~~~~l~aFrLt~  192 (240)
                      ||||+++...+.++..|...|..|... .+..++++++|..    +...++||++..
T Consensus        80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~  136 (157)
T cd08057          80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQ  136 (157)
T ss_pred             EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEec
Confidence            999999987766777775555544443 6778999999965    234699999995

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

>TIGR03735 PRTRC_A PRTRC system protein A

Probab=99.44  E-value=1.2e-12  Score=112.68  Aligned_cols=114  Identities=21%  Similarity=0.180  Sum_probs=87.6

Q ss_pred             EECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecC
Q 041233           67 HISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTH  146 (240)
Q Consensus        67 ~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSH  146 (240)
                      .|+++++++|+.||+++.  |+|+||+|+|..+++   +..++++.|...+...+.+++.     +..+|+.+|+.||||
T Consensus        74 ~Ip~~l~~~ii~hAr~~~--P~EacG~Iag~~~~~---~~r~~p~~N~~~Sp~~~~~d~~-----~~~~ge~lV~iyHSH  143 (192)
T TIGR03735        74 PIPASLLEEFAEAARAAL--PNEVAAWIVWNSETG---SLRLAALESIEASPGHIDYRRP-----RLDDGEHLVVDLHSH  143 (192)
T ss_pred             CCCHHHHHHHHHHHHhcC--CcceEEEEEEcCCCC---EEEEEeccccccCCceEEEcch-----HHhCCCeEEEEEcCC
Confidence            799999999999999988  999999999964333   4467888888888888888875     348899999999999


Q ss_pred             CCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeCCCCc
Q 041233          147 PSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGM  196 (240)
Q Consensus       147 P~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~p~gm  196 (240)
                      |..++|||.+|+.--     ...--++.|+.-.+....--+|||-- .|+
T Consensus       144 ~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~~~~p~~~~Rl~~-~G~  187 (192)
T TIGR03735       144 GTGSAFFSETDDADD-----KGEVKISGVLGCLDQGTPQAVFRLCL-LGV  187 (192)
T ss_pred             CCCCCCCCcccchhh-----cCceEEEEEEEecCCCCceEEEEEEe-cce
Confidence            999999999998631     11124566666555433345778873 454

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.

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

Probab=99.42  E-value=1.3e-12  Score=100.72  Aligned_cols=101  Identities=24%  Similarity=0.292  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCC
Q 041233           71 QLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQS  150 (240)
Q Consensus        71 ~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~  150 (240)
                      ++++.|+.+++..+  |.|+||+|+|..++   .+.++.+.++..     +..++.+ ++.+.+.+...||.|||||+..
T Consensus         1 ~~~~~i~~~~~~~~--p~E~~gll~~~~~~---~~~~~~~~~~~~-----~~~~~~~-~~~a~~~~~~~v~i~HsHP~g~   69 (101)
T cd08059           1 DLLKTILVHAKDAH--PDEFCGFLSGSKDN---VMDELIFLPFVS-----GSVSAVI-DLAALEIGMKVVGLVHSHPSGS   69 (101)
T ss_pred             CHHHHHHHHHHhcC--ChhhheeeecCCCC---eEEEEEeCCCcC-----CccChHH-HHHHhhCCCcEEEEEecCcCCC
Confidence            36788999999987  99999999997654   566666665532     2233433 5667788999999999999999


Q ss_pred             CCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEE
Q 041233          151 CFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIF  188 (240)
Q Consensus       151 ~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aF  188 (240)
                      +.||..|+...     ..+...+||++... ...++||
T Consensus        70 ~~PS~~D~~~~-----~~~~~~~iIv~~~~-~~~~~~~  101 (101)
T cd08059          70 CRPSEADLSLF-----TRFGLYHVIVCYPY-ENSWKCY  101 (101)
T ss_pred             CCCCHHHHHHH-----HhcCCeEEEEECCC-cccEEEC
Confidence            99999999743     23467788887654 3456665

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.

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

Probab=99.41  E-value=5.9e-12  Score=113.21  Aligned_cols=127  Identities=13%  Similarity=0.208  Sum_probs=94.3

Q ss_pred             EEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChH---HHHHHhh--hCCCcce
Q 041233           66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEE---DVFAIQN--ERSLFPM  140 (240)
Q Consensus        66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~---e~~~~~~--~~gl~iV  140 (240)
                      |.|.+-++.+|++|+.+....+..++|.|+|...++.++|+++|+.|...+++.. ..|.+   ++++...  ..+..+|
T Consensus         1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~-~~d~~y~~~m~~~~kkv~~~~~vV   79 (265)
T cd08064           1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQV-AVDMEYHRTMYELHQKVNPKEVIV   79 (265)
T ss_pred             CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeE-EEcHHHHHHHHHHHHHhCCCCcEE
Confidence            4677889999999987744447889999999998899999999999886655543 33432   2222222  4678999


Q ss_pred             EEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC--ceeEEEEeeCCCCc
Q 041233          141 GWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS--RSYGIFQLTEPSGM  196 (240)
Q Consensus       141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~--~~l~aFrLt~p~gm  196 (240)
                      |||||+|.  .-.+...++.++++|...+..|.++++|..++  ..++||++.+ .|+
T Consensus        80 GWY~tg~~--~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~-~~~  134 (265)
T cd08064          80 GWYATGSE--ITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSP-LGV  134 (265)
T ss_pred             eeeeCCCC--CCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEe-ccc
Confidence            99999983  22346668888888766557799999997654  4699999995 563

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

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

Probab=99.39  E-value=9.4e-12  Score=113.02  Aligned_cols=127  Identities=13%  Similarity=0.191  Sum_probs=95.6

Q ss_pred             EEEECHHHHHHHHHHHhccCC-CCcceEEEeeeeecCCEEEEEEEEecCCCCCCCce--eccChH---HHHHHh--hhCC
Q 041233           65 DVHISAQLMEDFLELAKENTD-KDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSC--QALNEE---DVFAIQ--NERS  136 (240)
Q Consensus        65 ~V~I~~~ll~k~l~hA~~~~~-~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~--~~~de~---e~~~~~--~~~g  136 (240)
                      .|.|.+.++.+|+.|+.+... .+.+++|.|+|...++.++|+++|+.|...+++..  ...|.+   ++++..  -..+
T Consensus         2 ~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~~   81 (280)
T cd08062           2 KVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNAK   81 (280)
T ss_pred             eEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCCC
Confidence            588999999999999876431 26789999999998899999999999886554432  233432   122221  2367


Q ss_pred             CcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC--ceeEEEEeeCCCCc
Q 041233          137 LFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS--RSYGIFQLTEPSGM  196 (240)
Q Consensus       137 l~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~--~~l~aFrLt~p~gm  196 (240)
                      +.+||||||+|.    ++..|+..|..|+...+..|+++++|..+.  ..+++|.-.+ ++.
T Consensus        82 e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~~-~~~  138 (280)
T cd08062          82 EKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVE-EVH  138 (280)
T ss_pred             CCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEee-ecc
Confidence            899999999986    566788888888888888899999998743  3589998874 554

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.

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

Probab=99.37  E-value=8e-12  Score=107.01  Aligned_cols=107  Identities=14%  Similarity=0.097  Sum_probs=82.0

Q ss_pred             ECHHHHHHHHHHHhccCCCCcceEEEeeeeec-CCEEEEEEEEecCCCCCCCceeccChHH---HHHH---hhhCCCcce
Q 041233           68 ISAQLMEDFLELAKENTDKDLETCGVLGAFLE-NGTFYVTTLIIPKQDSTSSSCQALNEED---VFAI---QNERSLFPM  140 (240)
Q Consensus        68 I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~-~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~---~~~~gl~iV  140 (240)
                      |+..++.+|+.||....  +.|+||+|+|+.. ++...|+.++|..+.     ++.++|.+   +.++   .+.+|+.+|
T Consensus         1 is~~ay~ki~~HA~k~p--~~evcGlLlG~~~~~~~~~V~d~vPl~h~-----~~~l~P~~Eval~~ve~~~~~~gl~Iv   73 (182)
T cd08060           1 LSTLAYVKMLLHAAKYP--HCAVNGLLLGKKSSGGSVEITDAVPLFHS-----CLALAPMLEVALALVDAYCKSSGLVIV   73 (182)
T ss_pred             CCHHHHHHHHHHHHHcC--CchheEEEEeeecCCCCEEEEEEEEcCCC-----ccccCHHHHHHHHHHHHHHHHCCCEEE
Confidence            57789999999999966  8899999999986 667899999998773     46677753   5544   467899999


Q ss_pred             EEEecCCCCC-CCCCHHHHHHHHhhhhcCCCEEEEEEccCCC
Q 041233          141 GWIHTHPSQS-CFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS  181 (240)
Q Consensus       141 GWYHSHP~~~-~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~  181 (240)
                      |+|||||... ..|+..=..-.-.-+...+.++.++++-..-
T Consensus        74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l  115 (182)
T cd08060          74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKL  115 (182)
T ss_pred             EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccc
Confidence            9999999753 3466555444444556778899888886554

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.

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

Probab=99.28  E-value=5.3e-11  Score=107.83  Aligned_cols=133  Identities=20%  Similarity=0.347  Sum_probs=104.8

Q ss_pred             EEEC-HHHHHHHHHHHhccCCCCcceEEEeeeeecCC-------EEEEEEEEecCCCCCCCceeccCh---HHHHHHhhh
Q 041233           66 VHIS-AQLMEDFLELAKENTDKDLETCGVLGAFLENG-------TFYVTTLIIPKQDSTSSSCQALNE---EDVFAIQNE  134 (240)
Q Consensus        66 V~I~-~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~-------~~~Vt~l~~ppq~~ts~~~~~~de---~e~~~~~~~  134 (240)
                      |.+. ..+++.|+......+  ..+.||+|+|+.+..       ...|..++.|||.++.+.+.....   +.+-+.+..
T Consensus        13 vef~~~~~~~~f~~~~w~~~--~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA~~   90 (274)
T cd08061          13 VEFDNPSIVEFFLYVFWRKT--GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIAAA   90 (274)
T ss_pred             EEEecHHHHHHHHHHHHHhh--cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHHHH
Confidence            3443 346666666566666  788999999998543       579999999999999888776542   234445778


Q ss_pred             CCCcceEEEecCCCC----CCCCCHHHHHHHHhhhh------cCCCEEEEEEccCCC-CceeEEEEeeCCCCcchhhc
Q 041233          135 RSLFPMGWIHTHPSQ----SCFMSSVDLHTHYSYQM------MVPEAFAIVLAPTDS-SRSYGIFQLTEPSGMSVLKE  201 (240)
Q Consensus       135 ~gl~iVGWYHSHP~~----~~fpSs~Dl~tq~syQ~------~~pe~vaIVisP~~~-~~~l~aFrLt~p~gm~~~~~  201 (240)
                      .||+.|||+.||+..    +.|||+.++.+.+.||.      ....++.+|+++..+ ...+.||++++ .+|+.+++
T Consensus        91 lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~g~i~~~ayQvSd-q~~~lv~~  167 (274)
T cd08061          91 LGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKDGQIHFEAYQVSD-QAMALVRD  167 (274)
T ss_pred             cCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCCCceeeeeeeecH-HHHHHHHc
Confidence            999999999999977    78999999999999996      456888999999754 35799999998 58887663

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=99.06  E-value=3e-09  Score=86.75  Aligned_cols=105  Identities=15%  Similarity=0.063  Sum_probs=66.8

Q ss_pred             HHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCC-CCCCCceeccCh---HHHHH-Hhhh--CCCcceEEEe
Q 041233           72 LMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQ-DSTSSSCQALNE---EDVFA-IQNE--RSLFPMGWIH  144 (240)
Q Consensus        72 ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq-~~ts~~~~~~de---~e~~~-~~~~--~gl~iVGWYH  144 (240)
                      ++..|.++.+.. ..+.|+||+|+|...++.+.|+.+..|.. ...+...+.-+.   ++.++ +.++  ..+..||-+|
T Consensus         2 v~~~~~~~~Q~~-~~~~EtGGiLiG~~~~~~~ii~~~t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWH   80 (131)
T TIGR02256         2 VVAMLKSYRQWH-DLSTETGGVLIGERRGAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWH   80 (131)
T ss_pred             HHHHHHHHHhCc-CCCCccceEEEEEEcCCcEEEEEEEcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecC
Confidence            445556666554 36889999999998777888888775432 322233333221   22222 2222  3388999999


Q ss_pred             cCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEc
Q 041233          145 THPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLA  177 (240)
Q Consensus       145 SHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVis  177 (240)
                      |||...+.||.+|+.+....-......+.||+.
T Consensus        81 tHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG  113 (131)
T TIGR02256        81 THPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG  113 (131)
T ss_pred             cCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence            999999999999998866543322234455554

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=98.97  E-value=1.4e-08  Score=93.32  Aligned_cols=131  Identities=15%  Similarity=0.205  Sum_probs=91.9

Q ss_pred             CceeEEEECHHHHHHHHHHHhccCCC-CcceEEEeeeeecCCEEEEEEEEecCCCCCCCc--eeccChH---HHHHHhh-
Q 041233           61 NVLQDVHISAQLMEDFLELAKENTDK-DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSS--CQALNEE---DVFAIQN-  133 (240)
Q Consensus        61 ~~~~~V~I~~~ll~k~l~hA~~~~~~-p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~--~~~~de~---e~~~~~~-  133 (240)
                      .+...|.|...++.+|+.|+.+.... ..-+.|.|+|...++.++|+++|+.|....++.  ....|.+   ++++... 
T Consensus         3 ~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~k~   82 (303)
T PLN03246          3 RGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMFKR   82 (303)
T ss_pred             CCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHHHH
Confidence            35577999999999999999886411 233899999999889999999999886433322  1223321   2222222 


Q ss_pred             -hCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC--ceeEEEEeeCCCCc
Q 041233          134 -ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS--RSYGIFQLTEPSGM  196 (240)
Q Consensus       134 -~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~--~~l~aFrLt~p~gm  196 (240)
                       ..+..+||||+|-|.    ++..|+.-|..|....+..+.+++++..+.  ..++||.... .|.
T Consensus        83 V~~~~~vVGWY~tg~~----i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~~-~~~  143 (303)
T PLN03246         83 INAKEHVVGWYSTGPK----LRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAVE-EVK  143 (303)
T ss_pred             hCCCCcEEeeecCCCC----CCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEEE-ecc
Confidence             367899999999765    455666666667777788888999876532  4589998763 444

>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]

Probab=98.94  E-value=1.5e-09  Score=112.17  Aligned_cols=150  Identities=20%  Similarity=0.239  Sum_probs=120.2

Q ss_pred             eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeee--cC-CEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcce
Q 041233           64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFL--EN-GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPM  140 (240)
Q Consensus        64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~--~~-~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iV  140 (240)
                      -...+|.+++++|+..++.    ...+.|++.|..  ++ ..-+|.++.-+||-++-..+....  .+.....-.+++.+
T Consensus      2095 ~tyilPkNllkkFi~isD~----r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~--~lP~~~~l~d~e~L 2168 (2321)
T KOG1795|consen 2095 YTYILPKNLLKKFITISDL----RTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPS--FLPIHGVLEDLEPL 2168 (2321)
T ss_pred             ceeeccHHHHhhheeecch----hhhhheeeeccCCCCCCccceEEEEEeccccccccccccCc--cCCcchhccCCccc
Confidence            4578999999999999988    569999999975  33 345899999999976543333211  12233456799999


Q ss_pred             EEEecCCCCCCCCCHHHHHHHHhhhhcC-CCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCCcccCCCCCCCCCc
Q 041233          141 GWIHTHPSQSCFMSSVDLHTHYSYQMMV-PEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPI  219 (240)
Q Consensus       141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~-pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~fhph~~~~~~~~~  219 (240)
                      ||+||.|+.-.++|+.|+.+|...-... ..+|.|.|+.+.++.++.||.|++ +|.+|+..+++.|=.|+..   .+.-
T Consensus      2169 gw~hTq~~el~~lsp~dV~th~ki~~~~k~k~i~~t~~~tpgs~sl~ay~lt~-~G~eWg~~n~d~g~~~~gy---~pt~ 2244 (2321)
T KOG1795|consen 2169 GWIHTQPNELPQLSPQDVTTHAKILVDNKEKCIIITCSFTPGSCSLTAYKLTP-SGYEWGEVNKDKGNNPKGY---LPTH 2244 (2321)
T ss_pred             chhhcCccccccCCHHHhhhhhhhhhcCccceEEEEeeccCCcceeeeeccCc-cccccchhcccccCCcccc---CccH
Confidence            9999999999999999999998665544 478999999999999999999995 9999999999998888875   3566


Q ss_pred             cccc
Q 041233          220 YEHC  223 (240)
Q Consensus       220 y~~~  223 (240)
                      |++|
T Consensus      2245 ~e~~ 2248 (2321)
T KOG1795|consen 2245 YEKV 2248 (2321)
T ss_pred             HHHH
Confidence            7777

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

Probab=98.92  E-value=1.7e-08  Score=91.95  Aligned_cols=129  Identities=13%  Similarity=0.150  Sum_probs=87.6

Q ss_pred             EEEECHHHHHHHHHHHhccCCC----CcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHH---HHHHh--hhC
Q 041233           65 DVHISAQLMEDFLELAKENTDK----DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEED---VFAIQ--NER  135 (240)
Q Consensus        65 ~V~I~~~ll~k~l~hA~~~~~~----p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~~--~~~  135 (240)
                      .|.|.+.++.+|+.|+.+...+    +.-++|.|+|..+++.++|+++|+.|...+++.....|.+.   +++..  -..
T Consensus         2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV~~   81 (288)
T cd08063           2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQVFK   81 (288)
T ss_pred             eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHhcc
Confidence            4677888889999998874321    45689999999988899999999988755442222344321   22211  235


Q ss_pred             CCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCC--C--ceeEEEEeeCCCCcc
Q 041233          136 SLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS--S--RSYGIFQLTEPSGMS  197 (240)
Q Consensus       136 gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~--~--~~l~aFrLt~p~gm~  197 (240)
                      ++.+||||+|.+. +.+.+...++.+  |....+..|+++++|...  .  ..++||+-.. .|..
T Consensus        82 ~~~vVGWY~tg~~-~~~~~~~~Ih~~--~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~-~~~~  143 (288)
T cd08063          82 DLDFVGWYTTGPG-GPTESDLPIHKQ--ILEINESPVLLLLDPEANASGKDLPVTIYESVL-ELVD  143 (288)
T ss_pred             CCceEEEEecCCC-CCCHHHHHHHHH--HHhhCCCcEEEEEccccccCCCCCceeEEEEEE-eccC
Confidence            7899999999876 344444445544  445556679999999773  2  3599998774 4543

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

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

Probab=98.60  E-value=4.4e-07  Score=83.62  Aligned_cols=110  Identities=22%  Similarity=0.331  Sum_probs=87.3

Q ss_pred             EEEeeeeecC-C------EEEEEEEEecCCCCCCCceeccCh---HHHHHHhhhCCCcceEEEecCCC------------
Q 041233           91 CGVLGAFLEN-G------TFYVTTLIIPKQDSTSSSCQALNE---EDVFAIQNERSLFPMGWIHTHPS------------  148 (240)
Q Consensus        91 cGlL~G~~~~-~------~~~Vt~l~~ppq~~ts~~~~~~de---~e~~~~~~~~gl~iVGWYHSHP~------------  148 (240)
                      +|+|+|+.+. .      ...|..++.|||.++.+.....+.   +.+=+.+..-||+.|||+=||+.            
T Consensus         2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lGL~rVG~IfTdl~~~~~~~g~v~~~   81 (306)
T PF05021_consen    2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALGLERVGWIFTDLTDDGSGDGTVKCK   81 (306)
T ss_pred             eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCCCEEEEEEEecCcccccCCCceeec
Confidence            7999999753 2      478999999999998887665432   22333467789999999999997            


Q ss_pred             ---CCCCCCHHHHHHHHhhhhcCC-------------CEEEEEEccCCCC-ceeEEEEeeCCCCcchhhc
Q 041233          149 ---QSCFMSSVDLHTHYSYQMMVP-------------EAFAIVLAPTDSS-RSYGIFQLTEPSGMSVLKE  201 (240)
Q Consensus       149 ---~~~fpSs~Dl~tq~syQ~~~p-------------e~vaIVisP~~~~-~~l~aFrLt~p~gm~~~~~  201 (240)
                         .+.|+|+..+...+.+|...|             .+|.+|+++..+. ..+.||+.++ .+|+.+++
T Consensus        82 r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~~g~i~~~ayQvS~-q~~~Lv~~  150 (306)
T PF05021_consen   82 RHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDEEGEIHFEAYQVSN-QCVALVRA  150 (306)
T ss_pred             cccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCCCCceeeEEeeehH-HHHHHHHC
Confidence               789999999999999999653             5789999986553 4699999997 68887653

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 [].

>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]

Probab=98.25  E-value=2.2e-06  Score=88.92  Aligned_cols=138  Identities=18%  Similarity=0.288  Sum_probs=101.7

Q ss_pred             eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec--C-CEEEEEEEEecCCCCCCCceecc--ChHHHHHHhhhCCCc
Q 041233           64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE--N-GTFYVTTLIIPKQDSTSSSCQAL--NEEDVFAIQNERSLF  138 (240)
Q Consensus        64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~--~-~~~~Vt~l~~ppq~~ts~~~~~~--de~e~~~~~~~~gl~  138 (240)
                      .+..||.+++++|++..+.    ...+.|++.|+..  + ..-+|.++...||.+.-..+...  -+.++   -...||+
T Consensus      2134 ~~y~lP~NLl~kF~~isD~----~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~dl---p~~e~le 2206 (2365)
T COG5178        2134 QMYRLPLNLLEKFMRISDP----HVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPHDL---PGDEDLE 2206 (2365)
T ss_pred             ccccccHHHHHhhheeccc----ceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCCCC---CCcccce
Confidence            4578999999999999988    6699999999763  2 23478888888887643322221  11111   1236899


Q ss_pred             ceEEEecCCCCCCCCCHHHHHHHHhhhhcCC--CEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCC------CcccC
Q 041233          139 PMGWIHTHPSQSCFMSSVDLHTHYSYQMMVP--EAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQET------GFHPH  210 (240)
Q Consensus       139 iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~p--e~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~------~fhph  210 (240)
                      +|||+|+..+.-.|++..++.+|..- ...|  ++|.|.++-..++.+++||.++. +|.+|...+++-      ||||-
T Consensus      2207 ~lGwihtq~~el~~l~~~~v~th~k~-~~d~~~d~v~ltv~~~pgsiSl~ay~v~k-eG~~Wg~~n~di~~~~a~g~ep~ 2284 (2365)
T COG5178        2207 ILGWIHTQDDELPYLEVAGVLTHRKK-IVDPEWDAVTLTVSYLPGSISLRAYVVKK-EGCNWGSKNMDINSDEAIGVEPV 2284 (2365)
T ss_pred             eeEEEecCCcccchhhhhhhhhhhhc-ccCccccceeeeeeeccceeeeeeeeehh-ccccccccccccccccccccccc
Confidence            99999999988899999999988633 3444  56777777677777899999997 899998766532      66654

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

Probab=98.19  E-value=2.6e-05  Score=69.69  Aligned_cols=125  Identities=15%  Similarity=0.215  Sum_probs=85.3

Q ss_pred             CceeEEEECHHHHHHHHHHHhccCC-CCcceEEEeeeeecCCEEEEEEEEecCCCCCC--CceeccCh---HHHHHHhh-
Q 041233           61 NVLQDVHISAQLMEDFLELAKENTD-KDLETCGVLGAFLENGTFYVTTLIIPKQDSTS--SSCQALNE---EDVFAIQN-  133 (240)
Q Consensus        61 ~~~~~V~I~~~ll~k~l~hA~~~~~-~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts--~~~~~~de---~e~~~~~~-  133 (240)
                      .....|.+-+.+++..+.|-..-.+ ..--+.|+|+|....+++.|++.|..|-+...  .++-..|.   +.+|.... 
T Consensus         6 ~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfkK   85 (309)
T KOG1556|consen    6 LTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFKK   85 (309)
T ss_pred             cccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHHH
Confidence            3456788888899999999776442 23457899999998889999999998875432  23333342   22444333 


Q ss_pred             -hCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCce--eEEEE
Q 041233          134 -ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS--YGIFQ  189 (240)
Q Consensus       134 -~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~--l~aFr  189 (240)
                       .....+||||||-|.    +-..||.-...+-...|..+-+|++.+....+  ..||-
T Consensus        86 vNakekivGWYhTGPk----l~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~  140 (309)
T KOG1556|consen   86 VNAKEKVVGWYHTGPK----LRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYI  140 (309)
T ss_pred             hcchhheeeeeccCCc----cccchhhHHHHHhhcCCCceEEEEecccccCCCCchhee
Confidence             356789999999764    55556655555566788899999998776433  44443

>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function

Probab=97.82  E-value=0.00033  Score=60.79  Aligned_cols=112  Identities=13%  Similarity=0.075  Sum_probs=75.0

Q ss_pred             EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCC--EEEEEEEEecCCCCCCCceeccChHHHHH---HhhhCCCcc
Q 041233           65 DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENG--TFYVTTLIIPKQDSTSSSCQALNEEDVFA---IQNERSLFP  139 (240)
Q Consensus        65 ~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~--~~~Vt~l~~ppq~~ts~~~~~~de~e~~~---~~~~~gl~i  139 (240)
                      .+.|+..++.||+-||-.-.  -.-++|+|+|+..++  .+.|+.++|.-=....-  ..+-|-.+.+   +....|+.+
T Consensus         3 ~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L--~PmlEvAL~qvd~~~~~~gl~I   78 (196)
T PF03665_consen    3 SVEISSRAYAKMILHAAKYP--HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSL--SPMLEVALAQVDAYAKSNGLVI   78 (196)
T ss_pred             eEEEcHHHHHHHHHHhccCC--CCceeeEEEeccCCCCceEEEeeceeccccccCc--chHHHHHHHHHHHHHhhCCCEE
Confidence            58899999999999998853  466899999997543  39999999863211111  1111111222   245789999


Q ss_pred             eEEEecCCC-CCCCCCHHHHHHHHhhhhcCCCEEEEEEccCC
Q 041233          140 MGWIHTHPS-QSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTD  180 (240)
Q Consensus       140 VGWYHSHP~-~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~  180 (240)
                      ||+||..-. ...-|+..-..-.-.-....+.++.|+++-++
T Consensus        79 vGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~k  120 (196)
T PF03665_consen   79 VGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKK  120 (196)
T ss_pred             EEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcc
Confidence            999998653 23446666444444444568899999998654

>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]

Probab=97.62  E-value=0.00042  Score=66.61  Aligned_cols=128  Identities=21%  Similarity=0.343  Sum_probs=97.0

Q ss_pred             CHHHHHHHHHHHhccCCCCcceEEEeeeeec-CCEE------EEEEEEecCCCCCCCceeccChH--HHHH-HhhhCCCc
Q 041233           69 SAQLMEDFLELAKENTDKDLETCGVLGAFLE-NGTF------YVTTLIIPKQDSTSSSCQALNEE--DVFA-IQNERSLF  138 (240)
Q Consensus        69 ~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~-~~~~------~Vt~l~~ppq~~ts~~~~~~de~--e~~~-~~~~~gl~  138 (240)
                      ..++++.|++.-+..   .....|+|+|... ++.+      +|..++.|||.++.+.....+..  ...+ .+..-||+
T Consensus       181 ~~~~v~~Fl~~wr~s---g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lGLr  257 (510)
T KOG2834|consen  181 NAELVNHFLNEWRAS---GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLGLR  257 (510)
T ss_pred             chHHHHHHHHHHHHh---hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcCce
Confidence            457999999998885   6888999999974 3444      88999999999998877665322  2233 35788999


Q ss_pred             ceEEEecCC---------------CCCCCCCHHHHHHHHhhhhcCCC-------------EEEEEEccCCC-CceeEEEE
Q 041233          139 PMGWIHTHP---------------SQSCFMSSVDLHTHYSYQMMVPE-------------AFAIVLAPTDS-SRSYGIFQ  189 (240)
Q Consensus       139 iVGWYHSHP---------------~~~~fpSs~Dl~tq~syQ~~~pe-------------~vaIVisP~~~-~~~l~aFr  189 (240)
                      -||||-|--               ..+.|+|+.+..+.+.+|.+.|.             +|.+|++-..+ ...+-.|+
T Consensus       258 RVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~~~s~~~~fgSkfVT~visg~~~~~V~f~~YQ  337 (510)
T KOG2834|consen  258 RVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNICEWSRDGHFGSKFVTLVISGDLDGEVHFEGYQ  337 (510)
T ss_pred             eeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchheeeccccccceeEEEEEecCCCcceeeeeee
Confidence            999997643               24689999999999999987763             56677765444 34699999


Q ss_pred             eeCCCCcchhh
Q 041233          190 LTEPSGMSVLK  200 (240)
Q Consensus       190 Lt~p~gm~~~~  200 (240)
                      .++ .+|..+.
T Consensus       338 VSn-qc~alv~  347 (510)
T KOG2834|consen  338 VSN-QCMALVE  347 (510)
T ss_pred             hhH-HHHHHhh
Confidence            998 6887533

>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]

Probab=97.44  E-value=0.0011  Score=59.74  Aligned_cols=130  Identities=12%  Similarity=0.203  Sum_probs=84.0

Q ss_pred             eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccC--hHHHHHHhhh--CCCcc
Q 041233           64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALN--EEDVFAIQNE--RSLFP  139 (240)
Q Consensus        64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~d--e~e~~~~~~~--~gl~i  139 (240)
                      ..|.|-.-++-.++.+.....++..-++|-|+|..+++.++||++|..|-...++.++.-.  ..++++.-.+  -+..+
T Consensus        21 ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm~y~~~M~~l~~k~npnE~v  100 (288)
T KOG2975|consen   21 LTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDMEYAKNMYELHKKVNPNELV  100 (288)
T ss_pred             ceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeHHHHHHHHHHhcccCCCcee
Confidence            4566666666677777666554556689999999999999999999877554445433211  1234443333  46789


Q ss_pred             eEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCC--CceeEEEEeeCCCCcch
Q 041233          140 MGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS--SRSYGIFQLTEPSGMSV  198 (240)
Q Consensus       140 VGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~--~~~l~aFrLt~p~gm~~  198 (240)
                      ||||=|-++-+.+  +.=+|.-  |-.-.++.+-+.++-.-.  .-.+|||--+. -|+..
T Consensus       101 vGWyaTg~dvt~~--sslihdy--Yare~~~pvhLtVDT~~~n~rm~ikaYvss~-~Gvpg  156 (288)
T KOG2975|consen  101 VGWYATGHDVTEH--SSLIHDY--YAREAPNPVHLTVDTSLQNGRMSIKAYVSSL-MGVPG  156 (288)
T ss_pred             EEEEecCCCcccc--hhHHHHH--hhccCCCCeEEEEeccccCCccceeEEEEec-cCCCC
Confidence            9999887765553  3334443  444567777777775433  23599998774 56543

>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]

Probab=94.81  E-value=0.5  Score=40.74  Aligned_cols=124  Identities=17%  Similarity=0.145  Sum_probs=76.9

Q ss_pred             EEEECHHHHHHHHHHHhccCCCCcc-eEEEeeeee--cCCEEEEEEEEecCCCCCCCceeccChHHHH--HH---hhhCC
Q 041233           65 DVHISAQLMEDFLELAKENTDKDLE-TCGVLGAFL--ENGTFYVTTLIIPKQDSTSSSCQALNEEDVF--AI---QNERS  136 (240)
Q Consensus        65 ~V~I~~~ll~k~l~hA~~~~~~p~E-vcGlL~G~~--~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~--~~---~~~~g  136 (240)
                      .+.|+..++-+|+-||..-   |.- +-|+|+|..  +++.++|+.++|.--+..    ....+.|+.  .+   ....|
T Consensus         3 ~veis~~aY~kmiLH~aky---ph~aVnGLLla~~~~kg~~v~itdcVPLfH~~l----aLaPmlEvAl~lId~~~~~~G   75 (199)
T KOG3289|consen    3 EVEISALAYVKMILHAAKY---PHAAVNGLLLAPATGKGECVEITDCVPLFHSHL----ALAPMLEVALNLIDVWGAQAG   75 (199)
T ss_pred             ceeehhhHHHHHHHHhccC---cccceeeEEEeccCCCCCeEEEEecchhhcccc----ccccHHHHHHHHHHHHHHhcC
Confidence            4789999999999999874   444 579999965  457899999998633221    111122221  11   34789


Q ss_pred             CcceEEEecCCCC-CCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCc-----eeEEEEeeCCCCcch
Q 041233          137 LFPMGWIHTHPSQ-SCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSR-----SYGIFQLTEPSGMSV  198 (240)
Q Consensus       137 l~iVGWYHSHP~~-~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~-----~l~aFrLt~p~gm~~  198 (240)
                      +.++|.||+--.. ...|...-....-.-+...|.+..|+.+-+.-..     .+-.|-  + .|..|
T Consensus        76 lviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e--~-~g~rW  140 (199)
T KOG3289|consen   76 LVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLE--D-QGLRW  140 (199)
T ss_pred             eEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEee--c-cCcce
Confidence            9999999985431 1223333333333345567888888887654321     244443  3 57777

>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family

Probab=94.54  E-value=0.53  Score=37.19  Aligned_cols=72  Identities=21%  Similarity=0.157  Sum_probs=49.9

Q ss_pred             CcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCCCHHHHHHHHh
Q 041233           87 DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYS  163 (240)
Q Consensus        87 p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~s  163 (240)
                      +.|...+|+=...++.+....+..    ++-+ ....++.++++.+...+..-+..-|.||+..+.||..|++.-..
T Consensus        15 ~~E~~~vl~Ld~~~~li~~~~l~~----G~~~-~~~v~~R~i~~~aL~~~A~~vil~HNHPsG~~~PS~~D~~~T~~   86 (113)
T cd08071          15 DQEEFVVLLLDTKNRLIAVETISV----GTLN-SSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTKR   86 (113)
T ss_pred             CceEEEEEEecCCCCEEEEEEEee----cCCc-ceecCHHHHHHHHHHHhhheEEEEeeCCCCCCCCCHHHHHHHHH
Confidence            678777665333333333333332    2222 24557889998888888899999999999999999999876543

Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains 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. However, to date, the name RadC has been misleading and no function has been determined.

>PF14220 DUF4329: Domain of unknown function (DUF4329)

Probab=93.81  E-value=0.52  Score=38.16  Aligned_cols=65  Identities=22%  Similarity=0.360  Sum_probs=41.3

Q ss_pred             CCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCC-----CCCCCCHHHHHH
Q 041233           86 KDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPS-----QSCFMSSVDLHT  160 (240)
Q Consensus        86 ~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~-----~~~fpSs~Dl~t  160 (240)
                      ++.|.||++ ++..++.+.-+.    |..+..+.|.....      ....+...|+-||||..     ..-.||..|+..
T Consensus        19 ~nrEy~G~I-~~~~~G~y~~t~----p~~G~~~~~~~~~~------~~p~g~~~vA~yHTHG~~~~~y~~evfS~~D~~~   87 (123)
T PF14220_consen   19 ENREYCGYI-GKDEDGKYFATE----PRRGENASCYPSNP------PCPNGSTIVASYHTHGAYSDGYDNEVFSPQDIRG   87 (123)
T ss_pred             CCcEEEEEE-EEcCCCcEEeec----CccCCCCCcCCCCc------ccccccceeeEeecccccCCCccccCCCHHHhhh
Confidence            588999976 455555544332    23334444443332      12358899999999985     345699999875


Q ss_pred             H
Q 041233          161 H  161 (240)
Q Consensus       161 q  161 (240)
                      -
T Consensus        88 ~   88 (123)
T PF14220_consen   88 D   88 (123)
T ss_pred             h
Confidence            3

>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=92.93  E-value=0.4  Score=43.32  Aligned_cols=90  Identities=16%  Similarity=0.258  Sum_probs=56.3

Q ss_pred             Cc-ceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhh-----hCCCcceEEEecCCCCCCCCCHHHHHH
Q 041233           87 DL-ETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQN-----ERSLFPMGWIHTHPSQSCFMSSVDLHT  160 (240)
Q Consensus        87 p~-EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~-----~~gl~iVGWYHSHP~~~~fpSs~Dl~t  160 (240)
                      |. .+-|-|+|+..++.++|.+.|...-....+. ..+|-+-+.+-++     =.++.++|||-+-  ..  +...|++.
T Consensus        35 p~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~-~~~dke~l~kk~eqykqVFpdl~vlGwYttG--~d--~t~sd~~i  109 (299)
T KOG3050|consen   35 PVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDT-ETIDKEYLEKKEEQYKQVFPDLYVLGWYTTG--SD--PTPSDIHI  109 (299)
T ss_pred             cHHHhhhhheecccCceEEEeeeeEEEecchhhh-hhccHHHHHHHHHHHHHhcccceEEEEeecC--CC--CChhhhHH
Confidence            66 7889999999999999999987754433222 1334322222221     2689999999763  23  46677777


Q ss_pred             HHhhhhcCCCEEEEEEccCCC
Q 041233          161 HYSYQMMVPEAFAIVLAPTDS  181 (240)
Q Consensus       161 q~syQ~~~pe~vaIVisP~~~  181 (240)
                      |...-....--+++-..|...
T Consensus       110 ~k~l~~i~esplflkLNp~t~  130 (299)
T KOG3050|consen  110 HKQLMDINESPLFLKLNPATN  130 (299)
T ss_pred             HHHHHhhhcCceEEEecchhc
Confidence            664444444456666666443

>PF08084 PROCT: PROCT (NUC072) domain; InterPro: IPR012984 The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family []

Probab=92.67  E-value=0.092  Score=42.67  Aligned_cols=33  Identities=21%  Similarity=0.258  Sum_probs=28.3

Q ss_pred             EEEEEEccCCCCceeEEEEeeCCCCcchhhcccC
Q 041233          171 AFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQE  204 (240)
Q Consensus       171 ~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~  204 (240)
                      .|.|.|+.+.++.++.||+||+ +|.+|++++++
T Consensus         1 ~i~it~sftpGSvsL~Ay~LT~-~G~eWg~~nkD   33 (125)
T PF08084_consen    1 TITITCSFTPGSVSLSAYKLTP-EGYEWGRQNKD   33 (125)
T ss_dssp             -EEEEEEEETTEEEEEEEEE-H-HHHHHHHCTTT
T ss_pred             CEEEEEeccCCceEEEEEecCH-HHHHHHhhccc
Confidence            3788999999988999999995 99999999887

; PDB: 2P87_A 2P8R_A 3SBG_A 2OG4_A.

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=92.17  E-value=0.35  Score=46.55  Aligned_cols=128  Identities=20%  Similarity=0.289  Sum_probs=91.3

Q ss_pred             CHHHHHHHHHHHhccCCCCcceEEEeeeeecC--C-----EEEEEEEEecCCCCCCCceec--cChHHHHHH-hhhCCCc
Q 041233           69 SAQLMEDFLELAKENTDKDLETCGVLGAFLEN--G-----TFYVTTLIIPKQDSTSSSCQA--LNEEDVFAI-QNERSLF  138 (240)
Q Consensus        69 ~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~--~-----~~~Vt~l~~ppq~~ts~~~~~--~de~e~~~~-~~~~gl~  138 (240)
                      .+.+++.|++.=+..   +.+..|+|.|....  +     .-.|..++.|||....+-...  -..+.+.+. +..-||+
T Consensus       240 ~~~iv~~Fi~~WR~s---G~QRfGy~yG~y~~y~n~PLGiKaVveaIyEPpQ~de~DG~t~ee~~de~l~d~~a~~~GL~  316 (571)
T COG5100         240 GKHIVENFIRNWRES---GRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASGTGLE  316 (571)
T ss_pred             CchHHHHHHHHHHHh---hhhhheeeeeehhhccCCcchhHHHhhhhcCCccccCCCceEeeeecccccccccccccCce
Confidence            457899999887774   67889999998632  1     126677888999877665332  111123322 3567899


Q ss_pred             ceEEEecCC---------------CCCCCCCHHHHHHHHhhhhcCC-------------CEEEEEEccCCC-CceeEEEE
Q 041233          139 PMGWIHTHP---------------SQSCFMSSVDLHTHYSYQMMVP-------------EAFAIVLAPTDS-SRSYGIFQ  189 (240)
Q Consensus       139 iVGWYHSHP---------------~~~~fpSs~Dl~tq~syQ~~~p-------------e~vaIVisP~~~-~~~l~aFr  189 (240)
                      .+|.+-|--               .-+-|+|+..+...+.+|.+.|             .++.+|++-..+ +.++..|+
T Consensus       317 riG~IfTDl~d~gs~~GsV~ckrh~dsyFLSSLEv~~~A~~Qt~hpn~~k~sr~g~FgSkfvT~Visgnl~GeI~~~sYQ  396 (571)
T COG5100         317 RIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSYQ  396 (571)
T ss_pred             eeeeeeeehhhccCCCCceeeeccccceehhhhhhHHHhhhhhcCCCcccccccccccceeEEEEEecccCceeeeeEEe
Confidence            999987643               2357899999999999999876             457788876554 46799999


Q ss_pred             eeCCCCcchhh
Q 041233          190 LTEPSGMSVLK  200 (240)
Q Consensus       190 Lt~p~gm~~~~  200 (240)
                      .++ .+|+.++
T Consensus       397 VSn-~~~ALv~  406 (571)
T COG5100         397 VSN-QCMALVK  406 (571)
T ss_pred             ehh-hhhHHhh
Confidence            997 7887654

>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []

Probab=90.71  E-value=2.3  Score=33.86  Aligned_cols=74  Identities=19%  Similarity=0.116  Sum_probs=41.5

Q ss_pred             CcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhh
Q 041233           87 DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQ  165 (240)
Q Consensus        87 p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ  165 (240)
                      +.|...+|+=...++.+....+.    .++.+. -..+++++++.+-..+-.-|-..|-||+..+.||..|+..-...+
T Consensus        20 ~~E~~~~l~Ld~~~~li~~~~v~----~G~~~~-~~v~~R~I~~~al~~~A~~vIl~HNHPsG~~~PS~~D~~~T~~L~   93 (123)
T PF04002_consen   20 DQEQFRVLYLDSKNRLIGDEVVS----EGTIDS-APVDPREIFRRALRLNASSVILAHNHPSGDPEPSDADIALTRRLK   93 (123)
T ss_dssp             TS-EEEEEEE-TTSBEEEEEEEE----ESTT-G-GGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHHHHH
T ss_pred             CCeEEEEEEECCCCcEEEEEEec----ccCCCc-ccccHHHHHHHHHhhCCceEEEEEEcCCCCCCCCHhHHHHHHHHH
Confidence            55776655432233334444443    233333 345788999988777777788889999999999999986544333

However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.

>PRK00024 hypothetical protein; Reviewed

Probab=85.46  E-value=9.5  Score=33.68  Aligned_cols=89  Identities=18%  Similarity=0.100  Sum_probs=55.4

Q ss_pred             CHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCC
Q 041233           69 SAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPS  148 (240)
Q Consensus        69 ~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~  148 (240)
                      +.+.+.++++..-...  +.|...+|+=...++.+....++    .++-+. ...++.++|+.+-..+-.-|=.-|=||+
T Consensus       105 ~~~~~~~~l~~~l~~~--~~E~f~vl~Ld~~~~li~~~~i~----~Gt~~~-~~v~pRei~~~Al~~~A~~iIl~HNHPS  177 (224)
T PRK00024        105 SPEDVADYLMAELRDE--EQEHFVVLFLDTKNRVIADEELF----IGTLNS-SIVHPREIVKRALKLNAAALILAHNHPS  177 (224)
T ss_pred             CHHHHHHHHHHHccCC--CceEEEEEEECCCCCEeeEEEee----eecCCe-EEEcHHHHHHHHHHhhccceEEEecCCC
Confidence            3334445554433333  67877776533333333433332    233233 4567899999877777777777899999


Q ss_pred             CCCCCCHHHHHHHHhh
Q 041233          149 QSCFMSSVDLHTHYSY  164 (240)
Q Consensus       149 ~~~fpSs~Dl~tq~sy  164 (240)
                      ..+.||..|+..-...
T Consensus       178 G~~~PS~~D~~~T~~l  193 (224)
T PRK00024        178 GDPEPSQADILITKRL  193 (224)
T ss_pred             CCCCCCHHHHHHHHHH
Confidence            9999999998764433

>TIGR00608 radc DNA repair protein radc

Probab=83.50  E-value=17  Score=32.10  Aligned_cols=88  Identities=18%  Similarity=0.094  Sum_probs=54.3

Q ss_pred             CHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCC
Q 041233           69 SAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPS  148 (240)
Q Consensus        69 ~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~  148 (240)
                      +.+.+.+++...-...  +.|...+|+=...++.+....++    .++-+. -..++.++|+.+-..+-.-|=.-|=||+
T Consensus        99 s~~~v~~~l~~~l~~~--~~E~f~vl~Ld~~n~li~~~~i~----~Gt~~~-~~v~pReI~~~Al~~~A~~vIlaHNHPS  171 (218)
T TIGR00608        99 SPEAAAEFLHTDLAHE--TREHFMVLFLDRKNRLIAKEVVF----IGTVNH-VPVHPREIFKEALKLSASALILAHNHPS  171 (218)
T ss_pred             CHHHHHHHHHHHhcCC--CceEEEEEEECCCCcEEEEEEee----cCCCCe-EEEcHHHHHHHHHHhhCCeEEEEeecCC
Confidence            3444445555444433  67777666422223333333332    233333 4567899998877766666667799999


Q ss_pred             CCCCCCHHHHHHHHh
Q 041233          149 QSCFMSSVDLHTHYS  163 (240)
Q Consensus       149 ~~~fpSs~Dl~tq~s  163 (240)
                      ..+.||..|+..-..
T Consensus       172 G~~~PS~~Di~~T~~  186 (218)
T TIGR00608       172 GEPSPSQEDILITER  186 (218)
T ss_pred             CCCCCCHHHHHHHHH
Confidence            999999999875433

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	240
3rzu_A	187	The Crystal Structure Of The Catalytic Domain Of Am		6e-38
3rzv_A	211	The Crystal Structure Of A E280a Mutant Of The Cata		2e-37
2znr_A	178	Crystal Structure Of The Dub Domain Of Human Amsh-L		1e-36
2znv_A	178	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		5e-36
4b4t_V	306	Near-Atomic Resolution Structural Model Of The Yeas		1e-08

>pdb|3RZU|A Chain A, The Crystal Structure Of The Catalytic Domain Of Amsh Length = 187

Iteration: 1
 Score =  154 bits (388), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 85/191 (44%), Positives = 122/191 (63%), Gaps = 12/191 (6%)
Query: 53  SNTE--PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLII 110
           SN+E  P++   L+ V +  +L   FL+LA  NT + +ETCG+L   L    F +T ++I
Sbjct: 6   SNSESIPTIDG-LRHVVVPGRLCPQFLQLASANTARGVETCGILCGKLMRNEFTITHVLI 64
Query: 111 PKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPE 170
           PKQ + S  C   NEE++F IQ+++ L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE
Sbjct: 65  PKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPE 124
Query: 171 AFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTN 229
           + AIV +P    +  G F+LT+  G+  +  C++ GFHPH K+P    P++  CSHV T 
Sbjct: 125 SVAIVCSP--KFQETGFFKLTD-HGLEEISSCRQKGFHPHSKDP----PLFCSCSHV-TV 176
Query: 230 SNLRFEIFDLR 240
            +    I DLR
Sbjct: 177 VDRAVTITDLR 187

>pdb|3RZV|A Chain A, The Crystal Structure Of A E280a Mutant Of The Catalytic Domain Of Amsh Length = 211

Iteration: 1
 Score =  152 bits (384), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 84/191 (43%), Positives = 121/191 (63%), Gaps = 12/191 (6%)
Query: 53  SNTE--PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLII 110
           SN+E  P++   L+ V +  +L   FL+LA  NT + + TCG+L   L    F +T ++I
Sbjct: 30  SNSESIPTIDG-LRHVVVPGRLCPQFLQLASANTARGVATCGILCGKLMRNEFTITHVLI 88
Query: 111 PKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPE 170
           PKQ + S  C   NEE++F IQ+++ L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE
Sbjct: 89  PKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPE 148
Query: 171 AFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTN 229
           + AIV +P    +  G F+LT+  G+  +  C++ GFHPH K+P    P++  CSHV T 
Sbjct: 149 SVAIVCSP--KFQETGFFKLTD-HGLEEISSCRQKGFHPHSKDP----PLFCSCSHV-TV 200
Query: 230 SNLRFEIFDLR 240
            +    I DLR
Sbjct: 201 VDRAVTITDLR 211

>pdb|2ZNR|A Chain A, Crystal Structure Of The Dub Domain Of Human Amsh-Lp Length = 178

Iteration: 1
 Score =  149 bits (377), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 77/179 (43%), Positives = 113/179 (63%), Gaps = 9/179 (5%)
Query: 63  LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
           L+ V +   L   FL+LA+ NT + +ETCG+L   L +  F +T +I+PKQ +    C  
Sbjct: 8   LRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDM 67
Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
            N E++F +Q++  L  +GWIHTHP+Q+ F+SSVDLHTH SYQ+M+PEA AIV +P    
Sbjct: 68  ENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSP--KH 125
Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           +  GIF+LT  +GM  +  C++ GFHPH KEP     ++  C HV    +++  + DLR
Sbjct: 126 KDTGIFRLTN-AGMLEVSACKKKGFHPHTKEPR----LFSICKHVLVK-DIKIIVLDLR 178

>pdb|2ZNV|A Chain A, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 178

Iteration: 1
 Score =  147 bits (371), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 76/179 (42%), Positives = 112/179 (62%), Gaps = 9/179 (5%)
Query: 63  LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
           L+ V +   L   FL+LA+ NT + + TCG+L   L +  F +T +I+PKQ +    C  
Sbjct: 8   LRCVVLPEDLCHKFLQLAESNTVRGIATCGILCGKLTHNEFTITHVIVPKQSAGPDYCDM 67
Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
            N E++F +Q++  L  +GWIHTHP+Q+ F+SSVDLHTH SYQ+M+PEA AIV +P    
Sbjct: 68  ENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSP--KH 125
Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
           +  GIF+LT  +GM  +  C++ GFHPH KEP     ++  C HV    +++  + DLR
Sbjct: 126 KDTGIFRLTN-AGMLEVSACKKKGFHPHTKEPR----LFSICKHVLVK-DIKIIVLDLR 178

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 10/105 (9%)
Query: 88  LETCGV-LGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAI-------QNERSLFP 139
           +E  G+ LG F+++ T  V  +    Q  T  S +A+  +DVF         Q  R    
Sbjct: 47  MEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAV--DDVFQAKMMDMLKQTGRDQMV 104
Query: 140 MGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS 184
           +GW H+HP   C++SSVD++T  S++ +   A A+V+ P  S + 
Sbjct: 105 VGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKG 149

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	240
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	4e-65
2znr_A	178	AMSH-like protease; metal binding protein, alterna	6e-60
2og4_A	254	PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN	1e-26
2p8r_A	273	PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t	1e-23
3sbg_A	565	PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain,	2e-23
2kks_A	146	Uncharacterized protein; NESG, structural genomics	1e-07
2kcq_A	153	MOV34/MPN/PAD-1 family; NESG, structure, structura	7e-05

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

 Score =  200 bits (509), Expect = 4e-65
 Identities = 77/192 (40%), Positives = 114/192 (59%), Gaps = 7/192 (3%)

Query: 49  SDKQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTL 108
               ++      + L+ V +  +L   FL+LA  NT + + TCG+L   L    F +T +
Sbjct: 27  GALSNSESIPTIDGLRHVVVPGRLCPQFLQLASANTARGVATCGILCGKLMRNEFTITHV 86

Query: 109 IIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMV 168
           +IPKQ + S  C   NEE++F IQ+++ L  +GWIHTHP+Q+ F+SSVDLHTH SYQMM+
Sbjct: 87  LIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMML 146

Query: 169 PEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYT 228
           PE+ AIV +P    +  G F+LT+  G+  +  C++ GFHPH   +   P++  CSHV  
Sbjct: 147 PESVAIVCSPK--FQETGFFKLTDH-GLEEISSCRQKGFHPH---SKDPPLFCSCSHVT- 199

Query: 229 NSNLRFEIFDLR 240
             +    I DLR
Sbjct: 200 VVDRAVTITDLR 211

>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 =  186 bits (472), Expect = 6e-60
 Identities = 75/184 (40%), Positives = 111/184 (60%), Gaps = 7/184 (3%)

Query: 57  PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDST 116
           P     L+ V +   L   FL+LA+ NT + +ETCG+L   L +  F +T +I+PKQ + 
Sbjct: 2   PGHMEGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAG 61

Query: 117 SSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVL 176
              C   N E++F +Q++  L  +GWIHTHP+Q+ F+SSVDLHTH SYQ+M+PEA AIV 
Sbjct: 62  PDYCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVC 121

Query: 177 APTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEI 236
           +P    +  GIF+LT   GM  +  C++ GFHPH +      ++  C HV    +++  +
Sbjct: 122 SPK--HKDTGIFRLTNA-GMLEVSACKKKGFHPHTKE---PRLFSICKHVL-VKDIKIIV 174

Query: 237 FDLR 240
            DLR
Sbjct: 175 LDLR 178

>2og4_A PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN domain, protein-PR interaction, PRP8P, pseudoenzyme, spliceosome activation; 2.00A {Saccharomyces cerevisiae} Length = 254

 Score =  102 bits (256), Expect = 1e-26
 Identities = 29/165 (17%), Positives = 60/165 (36%), Gaps = 7/165 (4%)

Query: 68  ISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFY-VTTLIIPKQDSTSSSCQALNEE 126
           +   L++ F+E++           G+     ++     + T+++  Q     S Q  N  
Sbjct: 42  LPKNLLKKFIEISDVKIQVAAFIYGMSAK--DHPKVKEIKTVVLVPQLGHVGSVQISNIP 99

Query: 127 DVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAF-AIVLAPTDSSRSY 185
           D+  + +   L  +GWIHT   +  FM++ ++ TH             I +  T  S S 
Sbjct: 100 DIGDLPDTEGLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSL 159

Query: 186 GIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNS 230
             + LT   G    +E ++      +          H   + ++ 
Sbjct: 160 SAYNLT-DEGYQWGEENKDIMNVLSEGFEP--TFSTHAQLLLSDR 201

>2p8r_A PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, translation; 2.10A {Caenorhabditis elegans} PDB: 2p87_A Length = 273

 Score = 95.0 bits (236), Expect = 1e-23
 Identities = 28/151 (18%), Positives = 58/151 (38%), Gaps = 15/151 (9%)

Query: 68  ISAQLMEDFLELAKENTDKDLETCGVL-GAFL-ENGTFY-VTTLIIPKQDSTSSSCQALN 124
           +   +++ F+ ++   T    +  G + G    +N     +  +++  Q  +        
Sbjct: 43  LPKNILKKFITISDLRT----QIAGFMYGVSPPDNPQVKEIRCIVLVPQTGSHQQVNLPT 98

Query: 125 EEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYS-----YQMMVPEAFAIVLAPT 179
           +     +  +    P+GW+HT P++   +S  D+ TH             +   I  + T
Sbjct: 99  QLPDHELLRD--FEPLGWMHTQPNELPQLSPQDVTTHAKLLTDNISWDGEKTVMITCSFT 156

Query: 180 DSSRSYGIFQLTEPSGMSVLKECQETGFHPH 210
             S S   ++LT PSG    K   + G +P 
Sbjct: 157 PGSVSLTAYKLT-PSGYEWGKANTDKGNNPK 186

>3sbg_A PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain, JAB1/MPN domain; 3.28A {Saccharomyces cerevisiae} Length = 565

 Score = 97.1 bits (241), Expect = 2e-23
 Identities = 29/168 (17%), Positives = 58/168 (34%), Gaps = 5/168 (2%)

Query: 68  ISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEED 127
           +   L++ F+E++           G+           + T+++  Q     S Q  N  D
Sbjct: 353 LPKNLLKKFIEISDVKIQVAAFIYGMSAK-DHPKVKEIKTVVLVPQLGHVGSVQISNIPD 411

Query: 128 VFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAF-AIVLAPTDSSRSYG 186
           +  + +   L  +GWIHT   +  FM++ ++ TH             I +  T  S S  
Sbjct: 412 IGDLPDTEGLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLS 471

Query: 187 IFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRF 234
            + LT   G    +E ++      +          H   + ++     
Sbjct: 472 AYNLT-DEGYQWGEENKDIMNVLSEGFEP--TFSTHAQLLLSDRITGN 516

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

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 20/131 (15%), Positives = 44/131 (33%), Gaps = 11/131 (8%)

Query: 66  VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNE 125
           + ++ + ME+ L  A++      E CG+LG   +    +V  +        S    +++ 
Sbjct: 2   ITLTKKQMEEMLAHARQ--ALPNEACGLLGGRRDGDDRWVERVYPLNNLDQSPEHFSMDP 59

Query: 126 EDVFAIQNE---RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEA-FAIVLAPTDS 181
            +      +        +G  H+HP+     S+ D           P   + I+      
Sbjct: 60  REQLTAVKDMRKNGWVMLGNFHSHPATPARPSAEDKR-----LAFDPSLSYLIISLAEPQ 114

Query: 182 SRSYGIFQLTE 192
                 F + +
Sbjct: 115 KPVCKSFLIKK 125

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

 Score = 40.8 bits (95), Expect = 7e-05
 Identities = 22/133 (16%), Positives = 41/133 (30%), Gaps = 12/133 (9%)

Query: 66  VHISAQLMEDFLELAKENTDKDLETCGVL-GAFLENGTFYVTTLIIPKQDSTSSSCQ--A 122
           +  +  +++       +      E CG L G   ++G   V  L       +    +   
Sbjct: 1   MKTTPDILDQIRVHGAD--AYPEEGCGFLLGTVTDDGDNRVAALHRATNRRSEQRTRRYE 58

Query: 123 LNEEDVFAIQNE---RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPT 179
           L  +D  A       + L  +G  H+HP      S+ DL             + IV    
Sbjct: 59  LTADDYRAADAAAQEQGLDVVGVYHSHPDHPARPSATDL----EEATFPGFTYVIVSVRD 114

Query: 180 DSSRSYGIFQLTE 192
            +  +   + L  
Sbjct: 115 GAPEALTAWALAP 127

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	240
2znr_A	178	AMSH-like protease; metal binding protein, alterna	100.0
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	100.0
2og4_A	254	PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN	99.97
2p8r_A	273	PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t	99.96
4b4t_V	306	26S proteasome regulatory subunit RPN11; hydrolase	99.96
2kks_A	146	Uncharacterized protein; NESG, structural genomics	99.93
2kcq_A	153	MOV34/MPN/PAD-1 family; NESG, structure, structura	99.93
3sbg_A	565	PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain,	99.84
1oi0_A	124	AF2198, hypothetical protein AF2198; proteasome, d	99.81
2o95_A	187	26S proteasome non-ATPase regulatory subunit 7; PS	99.81
4e0q_A	141	COP9 signalosome complex subunit 6; MPN (MPR1P and	99.66
4b4t_U	338	RPN8, 26S proteasome regulatory subunit RPN8; hydr	99.07
2qlc_A	126	DNA repair protein RADC homolog; MCSG, structural	94.5

>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=100.00  E-value=4.5e-51  Score=346.05  Aligned_cols=173  Identities=43%  Similarity=0.802  Sum_probs=162.9

Q ss_pred             CceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcce
Q 041233           61 NVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPM  140 (240)
Q Consensus        61 ~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iV  140 (240)
                      .++++|.|+++++++|++||+.++.++.|+||+|+|+..++.++|++++++||.++++++++.++++++++++++|+++|
T Consensus         6 ~~~~~v~i~~~~l~k~l~hA~~~~~~~~EvcGlL~G~~~~~~~~V~~v~~~pq~~t~~~~~~~~~~e~~~~~~~~~l~~v   85 (178)
T 2znr_A            6 EGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTL   85 (178)
T ss_dssp             CSCCCEEEETTHHHHHHHHHHHHHTTTCCCEEEEEEEEETTEEEEEEEEECCEEEETTEEEECCHHHHHHHHHHHTCEEE
T ss_pred             CCcEEEEECHHHHHHHHHHHHhCCCCCceEEEEEeeEecCCCeEEEEEEeCCcCCCCCeeccCCHHHHHHHHHhCCCEEE
Confidence            45788999999999999999998744589999999999888999999999999999999999999999999999999999


Q ss_pred             EEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCCcccCCCCCCCCCcc
Q 041233          141 GWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIY  220 (240)
Q Consensus       141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~fhph~~~~~~~~~y  220 (240)
                      |||||||+++++||.+|+++|++||+++|++++||+||+.+  .++||||+ ++|++++++|+++|||||++   +++||
T Consensus        86 GwyHSHP~~~~~pS~~Dv~tq~~yq~~~~~~v~iIvsp~~~--~~~afrl~-~~g~~~~~~~~~~~f~p~~~---~~~~~  159 (178)
T 2znr_A           86 GWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHK--DTGIFRLT-NAGMLEVSACKKKGFHPHTK---EPRLF  159 (178)
T ss_dssp             EEEEECSSSCSCCCHHHHHHHHHHHHHCTTCEEEEEEGGGT--EEEEEEEC-HHHHHHHHHCCCCSSCCCCC---SSCSE
T ss_pred             EEEeCCCCCCCCCCHHHHHHHHHHHhhcCCEEEEEEcCCCC--cceEEEEE-CCcEeeecccCCCCcccCCC---CCCce
Confidence            99999999999999999999999999999999999999985  49999999 59999999999999999984   57999


Q ss_pred             cccCceEecCCceeEEeeCC
Q 041233          221 EHCSHVYTNSNLRFEIFDLR  240 (240)
Q Consensus       221 ~~~~hv~~~~~~~~~~~dlr  240 (240)
                      ++|+||++++++ |+|+|||
T Consensus       160 ~~~~~~~~~~~~-~~~~~~r  178 (178)
T 2znr_A          160 SICKHVLVKDIK-IIVLDLR  178 (178)
T ss_dssp             EECSSEEEECCC-CEEEECC
T ss_pred             EEeceEEEeCCe-eEEEecC
Confidence            999999999999 9999999

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

Probab=100.00  E-value=2.6e-50  Score=349.49  Aligned_cols=178  Identities=43%  Similarity=0.787  Sum_probs=166.1

Q ss_pred             CCCCCCceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhC
Q 041233           56 EPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNER  135 (240)
Q Consensus        56 ~~~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~  135 (240)
                      ......+++.|.||++++++|++||+.++.+++|+||+|+|+..++.++|+++++++|.++++++++.++++++++++.+
T Consensus        34 ~~~~~~~lr~v~Ipk~ll~kfL~~A~~~tp~~~EvcGlL~Gk~~~~~~~I~~v~~ppq~gt~~~v~~~~~~e~~~~~~~~  113 (211)
T 3rzv_A           34 SIPTIDGLRHVVVPGRLCPQFLQLASANTARGVATCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQ  113 (211)
T ss_dssp             CCCCBTTBCCEEEETTHHHHHHHHHHHHHHTTCCCEEEEEEEEETTEEEEEEEEECCEEECSSCEEECCHHHHHHHHHHH
T ss_pred             ccccccccEEEEECHHHHHHHHHHHHhCCCCCceEEEEEEeEcCCCCEEEEEEEeCCccCCCCceeccChHHHHHHHhhC
Confidence            44445678999999999999999999987446899999999998889999999999999999999999999999999999


Q ss_pred             CCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCCcccCCCCCC
Q 041233          136 SLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPAD  215 (240)
Q Consensus       136 gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~fhph~~~~~  215 (240)
                      ++++||||||||++++|||+.|+++|++||.++|++|+|||||...  +++||||+ |+||+|+++|+++|||||+.   
T Consensus       114 ~l~~vGWyHSHP~~~~~pS~~Dl~tq~~~q~~~~~~I~IVvsP~~~--~lgaFrLt-p~G~~~~~~c~~~~fhph~~---  187 (211)
T 3rzv_A          114 GLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQ--ETGFFKLT-DHGLEEISSCRQKGFHPHSK---  187 (211)
T ss_dssp             TCEEEEEEEECTTSCSCCCHHHHHHHHHHHHHCTTCEEEEEETTTT--EEEEEEEC-HHHHHHHHHCCCCSSCCCCC---
T ss_pred             CCEEEEEEeCCCCCCCCCCHHHHHHHHHHHhcCCCeEEEEEcCCCC--eeeEEEec-cchhhhhhccccCCcccCCC---
Confidence            9999999999999999999999999999999999999999999965  79999999 59999999999999999996   


Q ss_pred             CCCcccccCceEecCCceeEEeeCC
Q 041233          216 GSPIYEHCSHVYTNSNLRFEIFDLR  240 (240)
Q Consensus       216 ~~~~y~~~~hv~~~~~~~~~~~dlr  240 (240)
                      +++||++|+||++++++ |+|+|||
T Consensus       188 ~~~~~~~~~hv~~~~~~-~~~~dlr  211 (211)
T 3rzv_A          188 DPPLFCSCSHVTVVDRA-VTITDLR  211 (211)
T ss_dssp             SSCSEEECSSEEEECCC-CEEEECC
T ss_pred             CCCceEEeeeEEEcCCE-eEEEeCC
Confidence            47999999999998887 9999999

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

Probab=99.97  E-value=3.1e-31  Score=234.02  Aligned_cols=139  Identities=19%  Similarity=0.270  Sum_probs=127.0

Q ss_pred             ceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec---CCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCc
Q 041233           62 VLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE---NGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLF  138 (240)
Q Consensus        62 ~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~---~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~  138 (240)
                      ..+.+.||++++++|+.+|+.++    |+||+|+|+..   ++..+|++++++||.++.++|.+.++...+++++..+|+
T Consensus        36 ~~~t~vlPknLlkkFi~IAD~~T----q~cG~LyG~~~~d~~~v~eI~~ivippQ~gt~~s~~~~~~~p~~~~~~l~dLe  111 (254)
T 2og4_A           36 EQNVYVLPKNLLKKFIEISDVKI----QVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLE  111 (254)
T ss_dssp             TSCEEEEEHHHHHHHHHTSCSSS----CCEEEEEEEECSSCTTEEEEEEEECCCEEEETTEEEECCCCCCTTSTTCTTCE
T ss_pred             CCcEEEcCHHHHHHHHHHhhccc----eEEEEEEccCCCCCCCeEEEEEEEECCccCCCceEECCCcCccccchhhcCCE
Confidence            44789999999999999999965    89999999983   357899999999999999999998877777777789999


Q ss_pred             ceEEEecCCCCCCCCCHHHHHHHHhhhhcC-CCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCC
Q 041233          139 PMGWIHTHPSQSCFMSSVDLHTHYSYQMMV-PEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQET  205 (240)
Q Consensus       139 iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~-pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~  205 (240)
                      ++||+||||++++|||+.||+||++||.++ +++|+|||+|+.++.+++|||||+ +|++|++++++.
T Consensus       112 ~LGWIHTqptq~~fLSs~Dl~tH~~~~~~~~~eaIaIvcsftpgs~sl~af~LT~-~G~~Wg~~n~d~  178 (254)
T 2og4_A          112 LLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLTD-EGYQWGEENKDI  178 (254)
T ss_dssp             EEEEEEEESSCCSSCCHHHHHHHHHHHTTTCTTCEEEEEEEETTEEEEEEEEECH-HHHHHHHTCCSC
T ss_pred             ecceEeeCCCCCcccCHHHHHHHHHHHHhcCCCeEEEEEecCCCCceeEEEEcCh-hhhhhhhhcccc
Confidence            999999999999999999999999999954 999999999998888899999995 899999998764

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

Probab=99.96  E-value=5.8e-30  Score=227.96  Aligned_cols=142  Identities=18%  Similarity=0.278  Sum_probs=124.6

Q ss_pred             ceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec---CCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCc
Q 041233           62 VLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE---NGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLF  138 (240)
Q Consensus        62 ~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~---~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~  138 (240)
                      ..+.+.||++++++|+..|+.++    |+||+|+|+..   .+..+|++++++||.++.++|.+.++....++.  .+|+
T Consensus        37 ~~~t~vlPknllkkFi~IADlrT----q~~G~LyG~s~~d~~~vkeI~~ivipPQ~gt~~sv~~~~~~p~~~~l--~dLe  110 (273)
T 2p8r_A           37 TGYTYILPKNILKKFITISDLRT----QIAGFMYGVSPPDNPQVKEIRCIVLVPQTGSHQQVNLPTQLPDHELL--RDFE  110 (273)
T ss_dssp             SSCEEEEEHHHHHHHHHTSCSSS----CCEEEEEEECCTTCTTEEEEEEEECCSBEECSSCEECCSSCCCCTTT--TTSE
T ss_pred             CccEEEecHHHHHHHHHHhhccc----eEEEEEeccCCCCCCCeEEEEEEEECCccCCCceEECCCcCcchhhh--cccc
Confidence            34789999999999999999965    99999999983   367899999999999999999988753333333  8999


Q ss_pred             ceEEEecCCCCCCCCCHHHHHHHHhhhhc---C--CCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccC-----CCcc
Q 041233          139 PMGWIHTHPSQSCFMSSVDLHTHYSYQMM---V--PEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQE-----TGFH  208 (240)
Q Consensus       139 iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~---~--pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~-----~~fh  208 (240)
                      ++||+||||++++|||+.||+||++||.+   +  +++|+|+|+|+.++.+++|||||+ +|++|++++++     .|||
T Consensus       111 ~LGWIHTqp~e~~~LSs~Dl~tH~~~~~~~~~~~~~e~I~Ivcsftpgs~sl~af~LT~-~G~~Wg~~n~d~~~~~~Gf~  189 (273)
T 2p8r_A          111 PLGWMHTQPNELPQLSPQDVTTHAKLLTDNISWDGEKTVMITCSFTPGSVSLTAYKLTP-SGYEWGKANTDKGNNPKGYM  189 (273)
T ss_dssp             EEEEEEEESSCCSSCCHHHHHHHHHHHHHCTTCCTTTCEEEEEEEETTEEEEEEEEECH-HHHHHHHHCCCCSSCCTTCC
T ss_pred             ccceEeeCCCCCCCcCHHHHHHHHHHHhcccccCCCceEEEEEecCCCCceeEEEEcCh-HHhhhhhhccccccCCCCCC
Confidence            99999999999999999999999999985   4  499999999998888899999996 89999998875     4788


Q ss_pred             cC
Q 041233          209 PH  210 (240)
Q Consensus       209 ph  210 (240)
                      |+
T Consensus       190 p~  191 (273)
T 2p8r_A          190 PT  191 (273)
T ss_dssp             GG
T ss_pred             cc
Confidence            76

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

Probab=99.96  E-value=5.3e-29  Score=226.44  Aligned_cols=141  Identities=23%  Similarity=0.417  Sum_probs=119.8

Q ss_pred             CCCCCCCceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeee-cCCEEEEEEEEecCCCCCCCceeccChHHHHHH--
Q 041233           55 TEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFL-ENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAI--  131 (240)
Q Consensus        55 ~~~~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~-~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~--  131 (240)
                      .+....+....|+|+..++.+|++||+++.  +.|+||+|+|.. ++++++|+++|+.|+.++++++++.+++...++  
T Consensus        16 ~~~~~~~~~~~V~is~lallkm~~Ha~~~~--~~eV~GlLlG~~~~~~~v~Vt~~f~~P~~~~~~~v~~~d~~y~~~m~~   93 (306)
T 4b4t_V           16 ADTGRDDTKETVYISSIALLKMLKHGRAGV--PMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMD   93 (306)
T ss_dssp             -CCCCCSSCCEEEECHHHHHHHHHHTCSCS--SSCCEEEEEEEEETTTEEEEEEEECCCCEESSSCEECCCHHHHHHHHH
T ss_pred             CCCCCCCCCCEEEEeHHHHHHHHHHhcCCC--CceEEEEEeeEEcCCeEEEEEEEEeCCcCCCCCchhcCCHHHHHHHHH
Confidence            344555677999999999999999999977  999999999986 566899999999999999999888887533332  


Q ss_pred             -h--hhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCc---eeEEEEeeCCCCcch
Q 041233          132 -Q--NERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSR---SYGIFQLTEPSGMSV  198 (240)
Q Consensus       132 -~--~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~---~l~aFrLt~p~gm~~  198 (240)
                       .  ..+++.+||||||||.++||||..|++||+.||.+.+++|+||+||..+..   .++|||+++ .|+..
T Consensus        94 ~~~~v~~~~~vVGWYhShP~~~~~~S~~Di~tq~~yQ~~~~~~V~lV~Dp~~t~~G~~~i~Afr~~~-~~~~~  165 (306)
T 4b4t_V           94 MLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLID-TGALI  165 (306)
T ss_dssp             HHHHHSCCCCCSEEEEECCSSSCCCCHHHHHHHHHHHHHCSSCEEEEECSSSSSSCSSCEEEEECCH-HHHHH
T ss_pred             HHHHhCCCcceeeEEecCCCCCCcCCHHHHHHHHHHHhcCCCcEEEEECCCcCCCCceeeeEEEecC-ccccc
Confidence             2  247799999999999999999999999999999999999999999987644   599999996 55443

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

Probab=99.93  E-value=2.6e-25  Score=181.54  Aligned_cols=121  Identities=16%  Similarity=0.274  Sum_probs=106.6

Q ss_pred             EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHh---hhCCCcceE
Q 041233           65 DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQ---NERSLFPMG  141 (240)
Q Consensus        65 ~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~---~~~gl~iVG  141 (240)
                      +|.|++.++++|++||+.+.  |.|+||+|+|+.+.+...|+.+++.+|...+...+..|++++++++   +.+|+.+||
T Consensus         1 ml~i~~~~l~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~v~~~~p~~n~~~~~~~f~~dp~~~~~~~~~~~~~g~~ivG   78 (146)
T 2kks_A            1 MITLTKKQMEEMLAHARQAL--PNEACGLLGGRRDGDDRWVERVYPLNNLDQSPEHFSMDPREQLTAVKDMRKNGWVMLG   78 (146)
T ss_dssp             CEEEEHHHHHHHHHHHHHHT--TSCEEEEEEEEEETTEEEEEEEECCCCCSCCSSSCCCCHHHHHHHHHHHHHHTCEEEE
T ss_pred             CEEECHHHHHHHHHHHHhcC--CcceEEEEEEEEcCCCcEEEEEEECCCcCCCCceEEECHHHHHHHHHHHHHCCCEEEE
Confidence            37899999999999999987  9999999999988778899999999988777677889998888774   678999999


Q ss_pred             EEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCC-CceeEEEEeeC
Q 041233          142 WIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS-SRSYGIFQLTE  192 (240)
Q Consensus       142 WYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~-~~~l~aFrLt~  192 (240)
                      ||||||+.+++||.+|+.++     ..++.++||+++..+ ...+++|++.+
T Consensus        79 ~~HSHP~~~~~PS~~D~~~~-----~~~~~~~lIvs~~~~~~~~~~af~~~~  125 (146)
T 2kks_A           79 NFHSHPATPARPSAEDKRLA-----FDPSLSYLIISLAEPQKPVCKSFLIKK  125 (146)
T ss_dssp             EEEEESSSCSSCCHHHHTTC-----CSSSCEEEEEECSCSSSCEEEEEEECS
T ss_pred             EEeCCCcCCCCCCHHHHHhh-----hcCCCeEEEEEccCCCceEEEEEEEeC
Confidence            99999999999999999852     468999999999873 35799999964

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

Probab=99.93  E-value=1.4e-25  Score=184.39  Aligned_cols=120  Identities=18%  Similarity=0.281  Sum_probs=103.7

Q ss_pred             EEECHHHHHHHHHHHhccCCCCcceEEEeeeeec-CCEEEEEEEEecCCC--CCCCceeccChHHHHHHh---hhCCCcc
Q 041233           66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLE-NGTFYVTTLIIPKQD--STSSSCQALNEEDVFAIQ---NERSLFP  139 (240)
Q Consensus        66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~-~~~~~Vt~l~~ppq~--~ts~~~~~~de~e~~~~~---~~~gl~i  139 (240)
                      +.|+++++++|++||+.++  |.|+||+|+|+.+ ++.+.|+.+++.+|.  .++..++.++++++++++   +++|+.+
T Consensus         1 l~i~~~~l~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~v~~~~p~~n~~~~~~~~~f~~dp~~~~~~~~~~~~~g~~i   78 (153)
T 2kcq_A            1 MKTTPDILDQIRVHGADAY--PEEGCGFLLGTVTDDGDNRVAALHRATNRRSEQRTRRYELTADDYRAADAAAQEQGLDV   78 (153)
T ss_dssp             CBCCHHHHHHHHHHHHHHT--TSCCCEEEEEEECTTSCEEEEEEEESSCCCCCCCSCCSSCCCCSHHHHHHHHHHHTCEE
T ss_pred             CEeCHHHHHHHHHHHHhcC--CcceEEEEEEeeccCCCeEEEEEEECCCCCCCCCCcEEEECHHHHHHHHHHHHHCCCeE
Confidence            3589999999999999987  9999999999987 678899999999987  566677888888887774   4689999


Q ss_pred             eEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC-ceeEEEEeeC
Q 041233          140 MGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS-RSYGIFQLTE  192 (240)
Q Consensus       140 VGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~-~~l~aFrLt~  192 (240)
                      ||||||||+.+++||.+|+.+     +..+++++||+++..+. ..+++|++++
T Consensus        79 vG~yHSHP~~~~~PS~~D~~~-----~~~~~~~~lIvs~~~~~~~~~~af~~~~  127 (153)
T 2kcq_A           79 VGVYHSHPDHPARPSATDLEE-----ATFPGFTYVIVSVRDGAPEALTAWALAP  127 (153)
T ss_dssp             EEEEEECSSSSSSCCHHHHHT-----CCCTTSEEEEEEEETTEEEEEEEEEECT
T ss_pred             EEEEeCCCCCCCCCCHHHHHh-----hhcCCCeEEEEECCCCCccEEEEEEEeC
Confidence            999999999999999999974     24689999999986654 4699999964

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

Probab=99.84  E-value=3.1e-21  Score=183.17  Aligned_cols=139  Identities=18%  Similarity=0.255  Sum_probs=118.4

Q ss_pred             CceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec-C--CEEEEEEEEecCCCCCCCceecc--ChHHHHHHhhhC
Q 041233           61 NVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE-N--GTFYVTTLIIPKQDSTSSSCQAL--NEEDVFAIQNER  135 (240)
Q Consensus        61 ~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~-~--~~~~Vt~l~~ppq~~ts~~~~~~--de~e~~~~~~~~  135 (240)
                      .....+.+|++++.+|+..|+.++    |+||+|+|+.. +  +..+|++++.|||.++.++|.+.  .+.++|.  ...
T Consensus       346 e~~~tyVlPkNLLkKFI~IADlrT----QicGyLyG~sp~dn~nVkEI~cIVipPQ~Gt~~sv~lp~lp~he~~~--~l~  419 (565)
T 3sbg_A          346 EEQNVYVLPKNLLKKFIEISDVKI----QVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLP--DTE  419 (565)
T ss_dssp             TTSCEEEEEHHHHHHHHHHSCSSS----CCEEEEEEEEETTEEEEEEEEEEECCCEEECSSCEEECCCCCCTTST--TCT
T ss_pred             CCCcEEEccHHHHHHHHHHhhccc----eeEEEEecCCCCCCCCeEEEEEEEECCccCCCceEECCCCCcccccc--ccc
Confidence            335789999999999999999965    99999999974 2  56899999999999999999875  1111111  358


Q ss_pred             CCcceEEEecCCCCCCCCCHHHHHHHHhhhhcC-CCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCC
Q 041233          136 SLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMV-PEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETG  206 (240)
Q Consensus       136 gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~-pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~  206 (240)
                      +|+++||+||||++.+|||+.|+++|+++.... ...|.|+|+.+.++.++.||+|++ +|.+|++++++.+
T Consensus       420 dLe~LGWIHTqp~et~fLSs~Dl~THakl~~~n~~~~I~itvsftPGS~SLsAy~LT~-eGyeWG~~N~d~~  490 (565)
T 3sbg_A          420 GLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLTD-EGYQWGEENKDIM  490 (565)
T ss_dssp             TCEEEEEEEEESSCCSSCCHHHHHHHHHHHSSSCTTCEEEEEEEETTEEEEEEEEECH-HHHHHHHTTTTCC
T ss_pred             cCEecceeeecCCcccccCHHHHHHHHHHHHhCCCCeEEEEEEecCCceEEEEEecCH-hHHHHHhhccccc
Confidence            999999999999999999999999999886543 478999999999989999999995 9999999998764

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

Probab=99.81  E-value=4.9e-20  Score=146.36  Aligned_cols=109  Identities=25%  Similarity=0.244  Sum_probs=82.9

Q ss_pred             EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHH-HhhhCCCcceEEE
Q 041233           65 DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFA-IQNERSLFPMGWI  143 (240)
Q Consensus        65 ~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~-~~~~~gl~iVGWY  143 (240)
                      +|.|++.++++|++||+..+  |+|+||+|+|+..    .|+.+++.++.+++.+       ..|+ .+..+|+.+||||
T Consensus         3 ~v~i~~~~l~~i~~ha~~~~--P~E~cGlL~g~~~----~v~~~~~~p~~~~~~~-------~~f~~~~~~~~~~ivG~~   69 (124)
T 1oi0_A            3 SMKISRGLLKTILEAAKSAH--PDEFIALLSGSKD----VMDELIFLPFVSGSVS-------AVIHLDMLPIGMKVFGTV   69 (124)
T ss_dssp             SCEECHHHHHHHHHHHHHHT--TSCCEEEEEESTT----EECEEEECCCCC--------------------CCCEEEEEE
T ss_pred             EEEEcHHHHHHHHHHHHhcC--CCeeEEEEecccC----EEEEEEECCCCCCCcC-------ceeeeeeccCCCEEEEEE
Confidence            47899999999999999988  9999999999874    7888998875443221       1121 2456899999999


Q ss_pred             ecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEee
Q 041233          144 HTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLT  191 (240)
Q Consensus       144 HSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt  191 (240)
                      ||||+.+++||.+|+.++.     .++.++||+++..+...+++|+..
T Consensus        70 HSHP~~~~~PS~~D~~~~~-----~~~~~~lIvs~~~~~~~~~~f~~~  112 (124)
T 1oi0_A           70 HSHPSPSCRPSEEDLSLFT-----RFGKYHIIVCYPYDENSWKCYNRK  112 (124)
T ss_dssp             EEESSSCCSCCHHHHHHHH-----HSCSEEEEEETTCCTTCEEEEETT
T ss_pred             EECcCCCCccCHHHHHhhh-----cCCCEEEEEEccCCCceEEEEecC
Confidence            9999999999999998642     578899999987654457777653

>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=99.81  E-value=4.4e-19  Score=149.77  Aligned_cols=131  Identities=13%  Similarity=0.142  Sum_probs=102.3

Q ss_pred             CceeEEEECHHHHHHHHHHHhccC--CCCcceEEEeeeeecCCEEEEEEEEecCCCCCCC--ceeccChHHHHHH---hh
Q 041233           61 NVLQDVHISAQLMEDFLELAKENT--DKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSS--SCQALNEEDVFAI---QN  133 (240)
Q Consensus        61 ~~~~~V~I~~~ll~k~l~hA~~~~--~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~--~~~~~de~e~~~~---~~  133 (240)
                      .+...|.|...++.+|+.||.+..  ..+.|+||+|+|+..++.++|+++|+.|+..++.  .....|++.+.+.   ..
T Consensus         5 ~~~~~V~i~plvllkI~~H~~r~~~~~~~~~V~G~LLG~~~~~~v~V~~~f~lp~~~~~~~~~~~~~d~ey~~~m~~~~~   84 (187)
T 2o95_A            5 LAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFLDHDYLENMYGMFK   84 (187)
T ss_dssp             CSCSEEEECHHHHHHHHHHHHHHHHTTCCSCCEEEEEEEESSSEEEEEEEEEECEEECSSCTTSEEECHHHHHHHHHHHH
T ss_pred             CCCCEEEEchHHHHHHHHHHhhhcccCCCcEEEEEEEEEEcCCEEEEEEEEEeCCcccCCCcchhhcCHHHHHHHHHHHH
Confidence            345789999999999999987640  1289999999999988899999999999865443  2445665422221   12


Q ss_pred             --hCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC--ceeEEEEeeCCCCc
Q 041233          134 --ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS--RSYGIFQLTEPSGM  196 (240)
Q Consensus       134 --~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~--~~l~aFrLt~p~gm  196 (240)
                        ..++.+||||||||..    |..|+..|..||...|.+++||+||..+.  ..++||++.+ .+.
T Consensus        85 ~v~~~~~iVGWY~s~~~~----s~~d~~i~~~~~~~~~~~v~Livd~~~~~~~l~i~ay~~~~-~~~  146 (187)
T 2o95_A           85 KVNARERIVGWYHTGPKL----HKNDIAINELMKRYCPNSVLVIIDVKPKDLGLPTEAYISVE-EVH  146 (187)
T ss_dssp             TTSSSCEEEEEEECCSSC----CTTHHHHHHHHTTTCTTCEEEEECCCTTC-CCSEEEEEEEE-ECC
T ss_pred             HhCCCCCEEEEEcCCCcC----CcccHHHHHHHHhcCCCCEEEEECCCCCCCCcCeEEEEEec-hhc
Confidence              3689999999999974    77888888889999999999999997753  4699999984 444

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

Probab=99.66  E-value=2.5e-16  Score=128.39  Aligned_cols=116  Identities=12%  Similarity=0.081  Sum_probs=85.5

Q ss_pred             ceeEEEECHHHHHHHHHHHhccC---CCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHH---HHHHh--h
Q 041233           62 VLQDVHISAQLMEDFLELAKENT---DKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEED---VFAIQ--N  133 (240)
Q Consensus        62 ~~~~V~I~~~ll~k~l~hA~~~~---~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~~--~  133 (240)
                      +...|.|...++.+|++|+.+..   ..+.+++|+|+|..+++.++|+++|+.|...+++.. ..|.+-   +++..  -
T Consensus         4 ~~~~V~ihplvll~I~dH~~R~~~~~g~~~~V~G~LLG~~~~~~veV~nsF~~p~~~~~~~~-~~d~~y~~~m~~~~k~v   82 (141)
T 4e0q_A            4 MSVTISLHPLVIMNISEHWTRFRAQHGEPRQVYGALIGKQKGRNIEIMNSFELKTDVIGDET-VINKDYYNKKEQQYKQV   82 (141)
T ss_dssp             -CEEEEECHHHHHHHHHHHHCC------CCEEEEEEEEEEETTEEEEEEEEECCEEEETTEE-EECHHHHHHHHHHHHHH
T ss_pred             CcEEEEEecHHHHHHHHHHhhhcccCCCCcEEEEEEEEEEeCCEEEEEEEEEecccCCCCce-eecHHHHHHHHHHHHHh
Confidence            44789999999999999996631   136899999999998899999999999987655543 445421   22221  2


Q ss_pred             hCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC
Q 041233          134 ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS  182 (240)
Q Consensus       134 ~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~  182 (240)
                      ..++.+||||||||    .++..|+..|..|+...+..|+|+++|..+.
T Consensus        83 ~~~e~iVGWY~s~~----~~~~~d~~i~~~~~~~~~~pV~L~~Dp~~~~  127 (141)
T 4e0q_A           83 FSDLDFIGWYTTGD----NPTADDIKIQRQIAAINECPIMLQLNPLSRS  127 (141)
T ss_dssp             STTCEEEEEEEEEC-----------CHHHHHHHTTCCCEEEEESCSCCC
T ss_pred             CCCccEEEEEeCCC----CCCcchHHHHHHHHHHCCCCEEEEECCCccC
Confidence            36799999999997    3889999999999999999999999998764

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

Probab=99.07  E-value=2.8e-09  Score=97.71  Aligned_cols=126  Identities=14%  Similarity=0.223  Sum_probs=89.5

Q ss_pred             eeEEEECHHHHHHHHHHHhc-cCCCCcceEEEeeeeecCCEEEEEEEEecCCCCC--CCceeccChH---HHHHHhh--h
Q 041233           63 LQDVHISAQLMEDFLELAKE-NTDKDLETCGVLGAFLENGTFYVTTLIIPKQDST--SSSCQALNEE---DVFAIQN--E  134 (240)
Q Consensus        63 ~~~V~I~~~ll~k~l~hA~~-~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~t--s~~~~~~de~---e~~~~~~--~  134 (240)
                      ...|.|-+.++.+|+.|+.+ ....+..+.|.|+|..+++.++|+++|+.|-..+  .......|.+   .+++...  .
T Consensus         5 ~~~V~vhPlVll~I~dH~~R~~~~~~~rViG~LLG~~~~~~veV~nsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~kkV~   84 (338)
T 4b4t_U            5 HEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWFLDHNYIENMNEMCKKIN   84 (338)
T ss_dssp             CSEEEECHHHHHHHHHHHHHHTTTCCSCCEEEEEEEECSSEEEEEEEEECCEEECSSSTTCEEECHHHHHHHHHHHHHHC
T ss_pred             CCEEEEecHHHHHHHHHHHHhhcCCCCeEEEEEEeEEcCCEEEEEEEEEeccccCCCCCccccccHHHHHHHHHHHhhcC
Confidence            46799999999999999765 2223567999999999999999999999885332  2233344532   2222211  3


Q ss_pred             CCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcC-CCEEEEEEccCCCC--ceeEEEEeeC
Q 041233          135 RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMV-PEAFAIVLAPTDSS--RSYGIFQLTE  192 (240)
Q Consensus       135 ~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~-pe~vaIVisP~~~~--~~l~aFrLt~  192 (240)
                      ..+.+||||||+|.    ++..|+..|..|+... +..+.+++++....  ..++||....
T Consensus        85 ~~e~iVGWY~tg~~----~~~~d~~Ih~~~~~~~~~~pi~l~~d~~~~~~~lpi~aY~s~~  141 (338)
T 4b4t_U           85 AKEKLIGWYHSGPK----LRASDLKINELFKKYTQNNPLLLIVDVKQQGVGLPTDAYVAIE  141 (338)
T ss_dssp             CSCEEEEEEECCSS----CCSTHHHHHHHHGGGCCSCCCEEEECSCCCSSSCSEEEEEEEE
T ss_pred             ccCCEEEEEecCCC----CCccHHHHHHHHHhccCCCcEEEEecCCCCCCCcceEEEEeeh
Confidence            67899999999864    6677877777777765 45677788776553  2499998663

>2qlc_A DNA repair protein RADC homolog; MCSG, structural genomics, PSI-2, structure initiative; HET: DNA; 2.30A {Chlorobium tepidum tls}

Probab=94.50  E-value=0.31  Score=38.30  Aligned_cols=74  Identities=20%  Similarity=0.183  Sum_probs=50.1

Q ss_pred             CcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhh
Q 041233           87 DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQ  165 (240)
Q Consensus        87 p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ  165 (240)
                      +.|...+|+=...++.+....++.    ++-+. ...++.|+|+.+...+-.-+...|-||+..+.||..|+..-...+
T Consensus        23 ~~E~f~vl~Ld~~n~li~~~~l~~----Gt~~~-~~v~pRei~~~Al~~~A~~vIl~HNHPSG~~~PS~~D~~~T~~l~   96 (126)
T 2qlc_A           23 TKEHLFVLFLSTKNQILRHETITI----GTLTA-SLIHPREIFKAAIRESAHSIILVHNHPSGDVQPSNADKQVTSILK   96 (126)
T ss_dssp             TSCEEEEEEECTTCBEEEEEEEEE----SSCCG-GGCCHHHHHHHHHHTTCSEEEEEEECSSSCCSCCHHHHHHHHHHH
T ss_pred             CCeEEEEEEEcCCCCEEEEEEecC----CCCCc-EeecHHHHHHHHHHcCCcEEEEEecCCCCCCCCCHHHHHHHHHHH
Confidence            678765554222233344444442    22222 355789999988888889999999999999999999987544333

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	240
d1oi0a_	121	c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeo	4e-08

>d1oi0a_ c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 121

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]

 Score = 48.1 bits (114), Expect = 4e-08
 Identities = 29/123 (23%), Positives = 41/123 (33%), Gaps = 17/123 (13%)

Query: 66  VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNE 125
           + IS  L++  LE AK       E   +L          +  LI     S S S     +
Sbjct: 4   MKISRGLLKTILEAAKSAHPD--EFIALLSGS----KDVMDELIFLPFVSGSVSAVIHLD 57

Query: 126 EDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSY 185
                      +   G +H+HPS SC  S  DL           +   IV  P D   S+
Sbjct: 58  ------MLPIGMKVFGTVHSHPSPSCRPSEEDLSLFT----RFGKYHIIVCYPYD-ENSW 106

Query: 186 GIF 188
             +
Sbjct: 107 KCY 109

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	240
d1oi0a_	121	Hypothetical protein AF2198 {Archaeon Archaeoglobu	99.83

>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=99.83  E-value=9.4e-21  Score=148.94  Aligned_cols=109  Identities=25%  Similarity=0.235  Sum_probs=83.4

Q ss_pred             EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEe
Q 041233           65 DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIH  144 (240)
Q Consensus        65 ~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYH  144 (240)
                      .|.|+++++++|++||++++  |+|+||+|+|+.+    .|+.+++.+|...+..  +..+    ..+.+.|++++||||
T Consensus         3 ~l~I~~~~l~~i~~hA~~~~--P~E~cGlL~G~~~----~i~~~~~~~n~~~~~~--~~~~----~~~~~~~~~ivgi~H   70 (121)
T d1oi0a_           3 SMKISRGLLKTILEAAKSAH--PDEFIALLSGSKD----VMDELIFLPFVSGSVS--AVIH----LDMLPIGMKVFGTVH   70 (121)
T ss_dssp             SCEECHHHHHHHHHHHHHHT--TSCCEEEEEESTT----EECEEEECCCCC-------------------CCCEEEEEEE
T ss_pred             eEEECHHHHHHHHHHHHhcC--CceeEEEEEecCC----cEEEEEEcCCCCCCcc--cccc----cchhhcCCeEEEEEE
Confidence            47899999999999999998  9999999999753    5778888888754332  1111    114578999999999


Q ss_pred             cCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEe
Q 041233          145 THPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQL  190 (240)
Q Consensus       145 SHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrL  190 (240)
                      |||+.+++||..|++++.     .++.+++|+++-.+...+++|+.
T Consensus        71 SHP~~~a~PS~~D~~~~~-----~~g~~~~Ivs~p~~~~~~~~~~~  111 (121)
T d1oi0a_          71 SHPSPSCRPSEEDLSLFT-----RFGKYHIIVCYPYDENSWKCYNR  111 (121)
T ss_dssp             EESSSCCSCCHHHHHHHH-----HSCSEEEEEETTCCTTCEEEEET
T ss_pred             ecCCCCCCcCHHHHHhhh-----ccCCEEEEEeCCCCCCCEEEEeC
Confidence            999999999999998753     46788899987666567999974