Citrus Sinensis ID: 014747

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------42
Protein Sequence
MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHVSAFTL
Secondary Structure (PSIPRED)
cccccHHccHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHcccccHHHHHccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHcccccccEEEEEEEEEccccccccccccccHHHHHHHHHHcccEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEHHHcccccccccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHccccccccccccccccHccccHcccccHHHccccHcHHHHHHHHHHHHHcccHHHHHHHHHHcccccccHHHccHHHccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHHHHHccccEHHEEEccccccEEEEEEEEEEcccccccccccccHHHHHHHHHccccEEEEEEEEEcccc
Coil and Loop (DISEMBL)
MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSlvtetipchRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNrkktnqvtgwshasqnstlewpslkkqtltnydvtkalrlpsrelayqgsipqqlaytrpvDEQFRRmslnfprpnaetlsrhsllgpnglyghwqppksdklvkypnnidltpieipslrqpsessikiktdssnvepekssvqsistpndeieihrteepcsmisfetseapnsadvirqpspppvlTEVQDLIAAmspqvtetecqvgnslsdafdrseplqlhISTTMMDNFMKLAKSntdknletcGILAGSLKNRKFYITALiipkqestsdscqatnEEEIFevqdkrslfplgwihVSAFTL
Flexible Loop (DISEMBL)
mrssseginiaasaqrldvdnrIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNrkktnqvtgwshasqnstlewpslkkqtLTNYDVTKALRLPSRelayqgsipqqlaYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTpieipslrqpsessikiktdssnvepekssvqsistpndeieIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIipkqestsdscQATNEEEIFevqdkrslfplgWIHVSAFTL
Low Complexity Region (SEG)
MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQklylkkkllNALSELEELQPAVQQKINELNRKKTNQVTGWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHVSAFTL
Disordered region (IsUnstruct)
*************AQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSEL***********************************WPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYT***************************LGPNGLYGHWQ******LVKYPNNIDL*****************************************************************************************************************LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIP****************IFEVQDKRSLFPLGWIHVSAF**
Disordered Region (DISOPRED)
***********ASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRD***********LKKKLLNALSELEELQPAVQQ************************************************************************************************************************************************************************************************************************************PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHVSAFT*
Disordered Region (DISEMBL)
MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKK************NSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPS**************************NDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQ**********NEEEIFEVQDKRSLFPLGWIHVSAFTL
Disordered Region (DISPRO)
******GINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKK**********************************************************DEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHW*****************************************************************************************************************************SEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHVSAFTL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNAxxxxxxxxxxxxxxxxxxxxxKTNQVTGWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHVSAFTL
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	419	2.2.26 [Sep-21-2011]
Q8VYB5	507	AMSH-like ubiquitin thioe	yes	no	0.978	0.808	0.615	1e-139
Q5PNU3	507	AMSH-like ubiquitin thioe	no	no	0.957	0.790	0.442	9e-88
Q6NKP9	223	AMSH-like ubiquitin thioe	no	no	0.188	0.354	0.582	5e-23
Q96FJ0	436	AMSH-like protease OS=Hom	yes	no	0.749	0.720	0.241	3e-19
Q5R558	436	AMSH-like protease OS=Pon	yes	no	0.713	0.685	0.239	4e-19
Q9P371	435	AMSH-like protease sst2 O	yes	no	0.150	0.144	0.579	1e-18
Q54Q40	715	Probable ubiquitin thioes	yes	no	0.260	0.152	0.418	7e-18
Q6TH47	418	STAM-binding protein-like	yes	no	0.188	0.188	0.462	3e-16
O95630	424	STAM-binding protein OS=H	no	no	0.145	0.143	0.521	4e-16
Q76N33	436	AMSH-like protease OS=Mus	yes	no	0.181	0.174	0.467	1e-15

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

 Score =  495 bits (1274), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 255/414 (61%), Positives = 309/414 (74%), Gaps = 4/414 (0%)

Query: 1   MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSS 60
           M SS E I+IA SA+R+ VDNRI+L++Y+RIADNILKQA+IFR EKN+IDLYVMLLRFSS
Sbjct: 1   MGSSFETIDIATSARRIGVDNRISLKFYFRIADNILKQANIFRAEKNVIDLYVMLLRFSS 60

Query: 61  LVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWS 120
           L  ETIP HRDY  S KS K YL+ +LL+ L+ELE+L+P VQQ+I+EL  K   +    +
Sbjct: 61  LALETIPSHRDYRTSLKSNKEYLRMRLLDVLTELEKLKPVVQQRIDELYPKLKPRYNVQA 120

Query: 121 HASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLN 180
           H + N +L W S  K +  +YD  K    P     Y GS  QQ     P++E+FR+MS+N
Sbjct: 121 HPA-NGSLGWSSAVKPSFNSYDHAKVRNPPGHNSGYMGSRGQQFLNAAPLEERFRKMSVN 179

Query: 181 FPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIK 240
           F RPN ETLS+HS+LGP GL   WQPPK D  V+YP+NID +P+ IPS +Q  +S   I 
Sbjct: 180 F-RPNEETLSKHSILGPGGLSAQWQPPKYDTKVQYPSNIDFSPVVIPSFQQLVDSKPMI- 237

Query: 241 TDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTE 300
           T+ SN EPEK  V+     N++I+ + TEE  SMISFE  E+ N  ++IRQPSPPPVL E
Sbjct: 238 TNGSNDEPEKPIVEPSVASNEKIQKNYTEELSSMISFEEPESVNENNLIRQPSPPPVLAE 297

Query: 301 VQDLIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLET 359
           VQDL+ A+ P+V E EC + NSL D   RSE PL+LHI+T+MMD FM+LAKSNT KNLET
Sbjct: 298 VQDLVPALCPEVREPECMIENSLPDESLRSESPLELHIATSMMDTFMRLAKSNTKKNLET 357

Query: 360 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDK+SLFPLGWIH
Sbjct: 358 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKQSLFPLGWIH 411

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 =  324 bits (830), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 183/414 (44%), Positives = 257/414 (62%), Gaps = 13/414 (3%)

Query: 8   INIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP 67
           I++   A+ ++VDNRI LR YYRIADN+L+QA I+REEKN++DLY+MLLR+SSL++ETIP
Sbjct: 3   IDLNKVAREIEVDNRIPLRNYYRIADNLLRQASIYREEKNVVDLYIMLLRYSSLISETIP 62

Query: 68  CHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWSH----AS 123
            HRDY AS   ++L  +K+L   ++ELE L+P   Q +++LNR +       S     + 
Sbjct: 63  FHRDYQASLPQERLGSRKRLRAVINELESLKPEFNQLVDKLNRVEDESRQDGSDLPVVSY 122

Query: 124 QNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPR 183
            +  +EWP   K + +  D+ K L        Y  ++      T+ +D+QF+++S +F  
Sbjct: 123 SSDAVEWPPAHKASYSRPDINKPLPTSQPSWTYNNNLTSSSNRTQ-IDQQFQKLSFDFLP 181

Query: 184 PNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQ--PSESSIKIKT 241
           PN  TLSRHS LGPNGL      PKS+  V+YP+N D    +   L +  PS SS  +  
Sbjct: 182 PNQATLSRHSFLGPNGLKRQMVAPKSEIKVQYPSNTDWGSADNSGLIEAGPSSSSASLNG 241

Query: 242 DSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEV 301
           DS  V    S++ S+ + +D      +E   S    + +E P     ++QPSPPPVL +V
Sbjct: 242 DSQEV----STLNSVLSLDDGRWQRHSEAVNSQFISDATEDPFQFVGMKQPSPPPVLAQV 297

Query: 302 QDLIAAMSP-QVTETECQVGNSLSDAFDRSEPLQ-LHISTTMMDNFMKLAKSNTDKNLET 359
              +A + P +V +          +  + S   Q LH+   +MD+F++LA+SNT++NLET
Sbjct: 298 HQELAQICPSKVADPRPGPAIPSLEGKEGSNSYQHLHVPVRIMDDFLRLARSNTERNLET 357

Query: 360 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           CG+LAGSLKNR F+IT LIIPKQESTSDSCQ  NEEEIFEVQD+ SLFPLGWIH
Sbjct: 358 CGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIH 411

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

 Score =  109 bits (272), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 46/79 (58%), Positives = 64/79 (81%)

Query: 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE 394
           +HIS  ++++F +LA+ NT+K+LETCG LA  L+   FY+T LIIPKQESTS+SCQA NE
Sbjct: 49  VHISERLLEDFTELARENTEKDLETCGTLAAFLERGIFYVTTLIIPKQESTSNSCQAMNE 108

Query: 395 EEIFEVQDKRSLFPLGWIH 413
            E+F +Q++R L+P+GWIH
Sbjct: 109 VEVFSIQNERELYPVGWIH 127

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

 Score = 96.3 bits (238), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 99/410 (24%), Positives = 169/410 (41%), Gaps = 96/410 (23%)

Query: 4   SSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVT 63
           S  G NI  S         I  R Y+R    + + A ++ EE N+ + +V+  +F +L  
Sbjct: 34  SKLGCNITISED-------ITPRRYFRSGVEMERMASVYLEEGNLENAFVLYNKFITLFV 86

Query: 64  ETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWSHAS 123
           E +P HRDY                 A+ E ++    + +K+ E+   +T++        
Sbjct: 87  EKLPNHRDYQQC--------------AVPEKQD----IMKKLKEIAFPRTDE-------- 120

Query: 124 QNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPR 183
                    LK   L  Y+V     L S+   Y+  I ++L + R ++ + +R++     
Sbjct: 121 ---------LKNDLLKKYNVEYQEYLQSKN-KYKAEILKKLEHQRLIEAERKRIA----- 165

Query: 184 PNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDS 243
                                Q  +S++ + + + +    +    +R    S +  + D 
Sbjct: 166 -----------------QMRQQQLESEQFLFFEDQLKKQELARGQMRSQQTSGLSEQIDG 208

Query: 244 SNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQD 303
           S +     S  S    N  + +   ++P    S  T+ A +S  V R  +P   L+ VQ+
Sbjct: 209 SAL-----SCFSTHQNNSLLNVF-ADQPNK--SDATNYASHSPPVNRALTPAATLSAVQN 260

Query: 304 LIAAMSPQVTETECQVGNSLSDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGIL 363
           L+      V    C V                 +   +   F++LA+SNT + +ETCGIL
Sbjct: 261 LV------VEGLRCVV-----------------LPEDLCHKFLQLAESNTVRGIETCGIL 297

Query: 364 AGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
            G L + +F IT +I+PKQ +  D C   N EE+F VQD+  L  LGWIH
Sbjct: 298 CGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTLGWIH 347

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: -

>sp|Q5R558|STALP_PONAB AMSH-like protease OS=Pongo abelii GN=STAMBPL1 PE=2 SV=1

 Score = 96.3 bits (238), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 93/388 (23%), Positives = 163/388 (42%), Gaps = 89/388 (22%)

Query: 26  RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKK 85
           R Y+R    + + A ++ EE N+ + +V+  +F +L  E +P HRDY             
Sbjct: 49  RRYFRSGVEMERMASVYLEEGNLENAFVLYNKFITLFVEKLPNHRDYQQC---------- 98

Query: 86  KLLNALSELEELQPAVQQKINELNRKKTNQVTGWSHASQNSTLEWPSLKKQTLTNYDVTK 145
               A+ E ++    + +K+ E+   +T++                 LK   L  Y+V  
Sbjct: 99  ----AVPEKQD----IMKKLKEIAFPRTDE-----------------LKNDLLKKYNVEY 133

Query: 146 ALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQ 205
              L S+   Y+  I ++L + R ++ + +R++                          Q
Sbjct: 134 QEYLQSKN-QYKAEILKKLEHQRLIEAERKRIA----------------------QMRQQ 170

Query: 206 PPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVEPEKSSVQSISTPNDEIEI 265
             +S++ + + + +    +    +R    S +  + D S +     S  S    N  + +
Sbjct: 171 QLESEQFLFFEDQLKKQELARGQMRSQQTSGLSEQIDGSAL-----SCFSTHQNNSLLNV 225

Query: 266 HRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSD 325
              ++P    S  T+ A +S  V R  +P   L+ VQ+L+      V    C V      
Sbjct: 226 F-ADQPNK--SDATNYASHSPPVNRALTPAATLSAVQNLV------VEGLRCVV------ 270

Query: 326 AFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQEST 385
                      +   +   F++LA+SNT + +ETCGIL G L + +F IT +I+PKQ + 
Sbjct: 271 -----------LPKDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAG 319

Query: 386 SDSCQATNEEEIFEVQDKRSLFPLGWIH 413
            D C   N EE+F VQD+  L  LGWIH
Sbjct: 320 PDYCDVENVEELFNVQDQHDLLTLGWIH 347

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

Pongo abelii (taxid: 9601)

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 = 94.4 bits (233), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/69 (57%), Positives = 50/69 (72%)

Query: 345 FMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKR 404
           F+ + K NT KNLETCGIL G L+   F+IT L+IP QE+TSD+C  T+E  +FE QDK 
Sbjct: 273 FLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKH 332

Query: 405 SLFPLGWIH 413
           +L  LGWIH
Sbjct: 333 NLLTLGWIH 341

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

 Score = 92.0 bits (227), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 46/110 (41%), Positives = 67/110 (60%), Gaps = 1/110 (0%)

Query: 306 AAMSPQVTETECQVGNSLSDAFDRSEPL-QLHISTTMMDNFMKLAKSNTDKNLETCGILA 364
           A  +P +T T  +     S+A  +   L ++ +   +   FM+LA++NT +++ETCGIL+
Sbjct: 507 AVNTPSITPTTNKPNIDSSEASKKYSKLRKIIVHGEVFQEFMRLAENNTKRSIETCGILS 566

Query: 365 GSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV 414
           G+L N  F IT +IIPKQE T+D+C    E EIFE Q +  L  LGWIH 
Sbjct: 567 GTLSNDVFRITTIIIPKQEGTTDTCNTIEEHEIFEYQLENDLLTLGWIHT 616

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|Q6TH47|STBPA_DANRE STAM-binding protein-like A OS=Danio rerio GN=stambpa PE=2 SV=3

 Score = 86.7 bits (213), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 50/80 (62%)

Query: 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATN 393
           QL +   +   F+KLA++NT + +ETCGIL G L    F +T +I+PKQ    D C   N
Sbjct: 250 QLFVPAELCQRFLKLAETNTARAVETCGILCGKLMKNAFTVTHVIVPKQCGGPDYCDTEN 309

Query: 394 EEEIFEVQDKRSLFPLGWIH 413
           EEE+F +QD+  L  LGWIH
Sbjct: 310 EEELFLIQDQNDLITLGWIH 329

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.

Danio rerio (taxid: 7955)

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 = 86.3 bits (212), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 345 FMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKR 404
           F++LA +NT + +ETCGIL G L   +F IT ++IPKQ + SD C   NEEE+F +QD++
Sbjct: 267 FLQLASANTARGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQ 326

Query: 405 SLFPLGWIH 413
            L  LGWIH
Sbjct: 327 GLITLGWIH 335

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|Q76N33|STALP_MOUSE AMSH-like protease OS=Mus musculus GN=Stambpl1 PE=2 SV=1

 Score = 84.7 bits (208), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 49/77 (63%)

Query: 337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEE 396
           +S  +   F+ LA SNT + +ETCGIL G L + +F IT +++PKQ +  D C   N EE
Sbjct: 271 LSRDLCHKFLLLADSNTVRGIETCGILCGKLTHNEFTITHVVVPKQSAGPDYCDVENVEE 330

Query: 397 IFEVQDKRSLFPLGWIH 413
           +F VQD+  L  LGWIH
Sbjct: 331 LFNVQDQHGLLTLGWIH 347

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

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	419
255586071	514	amsh, putative [Ricinus communis] gi|223	0.985	0.803	0.710	1e-165
225455974	506	PREDICTED: AMSH-like ubiquitin thioleste	0.976	0.808	0.652	1e-153
224133090	497	predicted protein [Populus trichocarpa]	0.942	0.794	0.653	1e-147
356513064	509	PREDICTED: AMSH-like ubiquitin thioleste	0.978	0.805	0.632	1e-145
449439413	499	PREDICTED: AMSH-like ubiquitin thioester	0.959	0.805	0.628	1e-143
449516695	503	PREDICTED: AMSH-like ubiquitin thioester	0.959	0.799	0.622	1e-141
356531196	520	PREDICTED: AMSH-like ubiquitin thioleste	0.968	0.780	0.629	1e-140
357500307	513	STAM-binding protein [Medicago truncatul	0.988	0.807	0.607	1e-139
356520605	519	PREDICTED: AMSH-like ubiquitin thioleste	0.985	0.795	0.626	1e-138
297852504	507	mov34 family protein [Arabidopsis lyrata	0.978	0.808	0.620	1e-138

>gi|255586071|ref|XP_002533700.1| amsh, putative [Ricinus communis] gi|223526395|gb|EEF28683.1| amsh, putative [Ricinus communis]

 Score =  587 bits (1514), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 297/418 (71%), Positives = 339/418 (81%), Gaps = 5/418 (1%)

Query: 1   MRSSSE--GINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRF 58
           MRSSS    INIA SAQ++DVDNRI+LR+YYRIADNILKQADIFREEKNIIDLY+MLLRF
Sbjct: 1   MRSSSAPGRINIATSAQKIDVDNRISLRFYYRIADNILKQADIFREEKNIIDLYIMLLRF 60

Query: 59  SSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTG 118
           SSLV+ETIPCHRDY  S +S+K+YLK+KLLNA+ ELE+L+PAVQQKINELNRK T+QV G
Sbjct: 61  SSLVSETIPCHRDYRTSQQSKKIYLKQKLLNAVKELEQLKPAVQQKINELNRKHTHQVNG 120

Query: 119 WSHASQNSTLEWPSLKKQTLTNYD--VTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRR 176
           W   +QN +LEWP +KK+TLT YD   TKA+   +RE  Y GS  QQL+Y RPV EQFR+
Sbjct: 121 WGSVNQNDSLEWPPVKKKTLTGYDAGATKAVIPAAREFVYHGSRTQQLSYARPVGEQFRK 180

Query: 177 MSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESS 236
           MSLNFP+P  ETLSRHS+LGPNGL G WQPPKSDK V YP+NIDL+P+EIP      E+ 
Sbjct: 181 MSLNFPQPKEETLSRHSILGPNGLQGQWQPPKSDKGVWYPSNIDLSPVEIPRFDSSLENG 240

Query: 237 IKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPP 296
           + +K DSS+ E E  S QS+ T ND  +  R EE   MISFET+E P   D+IRQPSPP 
Sbjct: 241 LALKLDSSSSELETLSSQSVLTVNDNSQTSRVEELSPMISFETTETPVQTDLIRQPSPPA 300

Query: 297 VLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDK 355
           VL EVQDLI AMSPQ TE E ++  S  D   RSE PLQLHISTTMM+NFMKLAK+NTD+
Sbjct: 301 VLAEVQDLIPAMSPQATEAENKMDISSPDDIVRSESPLQLHISTTMMENFMKLAKANTDR 360

Query: 356 NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           NLETCG+LAGSLKNRKFY+TALIIPKQESTSDSCQ TNEEEIFEVQDKRSLFPLGWIH
Sbjct: 361 NLETCGVLAGSLKNRKFYVTALIIPKQESTSDSCQTTNEEEIFEVQDKRSLFPLGWIH 418

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225455974|ref|XP_002278560.1| PREDICTED: AMSH-like ubiquitin thiolesterase 1 [Vitis vinifera] gi|297734223|emb|CBI15470.3| unnamed protein product [Vitis vinifera]

 Score =  546 bits (1407), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 270/414 (65%), Positives = 332/414 (80%), Gaps = 5/414 (1%)

Query: 1   MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSS 60
           MR SS GINIAASAQ+LDVDNRI+LRYYYRIADNILKQADIFREEKNIIDLY+MLLRFSS
Sbjct: 1   MRPSSGGINIAASAQKLDVDNRISLRYYYRIADNILKQADIFREEKNIIDLYIMLLRFSS 60

Query: 61  LVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWS 120
           L +ETIPCHRDY AS +S+K YLKK LL AL ELEEL+PAV+QKI+ELN+K T QV  W 
Sbjct: 61  LTSETIPCHRDYKASLQSKKNYLKKNLLRALCELEELKPAVRQKIDELNQKHTYQVNRW- 119

Query: 121 HASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLN 180
               +S+LEWP ++KQTLT +++TK  R  +R+  YQGS  QQ +  +PV+EQFRR+S+ 
Sbjct: 120 --GADSSLEWPHVRKQTLTKHEMTKTPRPTARDFEYQGSKIQQFSRAKPVEEQFRRLSVG 177

Query: 181 FPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIK 240
             RP  ETLSRHS+LGPNGL+G WQPP  DK V+YP+N+DLTP++ PSL+   E  +   
Sbjct: 178 ILRPREETLSRHSILGPNGLHGQWQPPTIDKRVQYPSNLDLTPVQFPSLQHHVEDGLMNN 237

Query: 241 TDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTE 300
            ++S+ E E+SS++S+ T N++ +IH  EE  S+ISFET+E P++ ++IRQPSPPPVL +
Sbjct: 238 NEASSSEHEQSSLESVLTLNEDNQIHPAEELGSLISFETTETPHT-EIIRQPSPPPVLAD 296

Query: 301 VQDLIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLET 359
           VQDLI     QV+E   Q+    +D    SE PL++HIST +M++F+KLAKSNT +NLET
Sbjct: 297 VQDLIPETPTQVSEVNGQMETPSTDGLVCSEAPLEMHISTVLMESFLKLAKSNTVRNLET 356

Query: 360 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           CGILAGSLKNRKFY+TALIIPKQESTSDSCQ TNEEEIFEVQDK+SLFPLGWIH
Sbjct: 357 CGILAGSLKNRKFYVTALIIPKQESTSDSCQTTNEEEIFEVQDKQSLFPLGWIH 410

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133090|ref|XP_002321479.1| predicted protein [Populus trichocarpa] gi|222868475|gb|EEF05606.1| predicted protein [Populus trichocarpa]

 Score =  528 bits (1359), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 266/407 (65%), Positives = 318/407 (78%), Gaps = 12/407 (2%)

Query: 8   INIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP 67
           INI A  QRLDVDNR AL  Y+RIA+NILKQA+IFR EKNIIDLYVMLLRFSSLV+ETIP
Sbjct: 4   INIEARTQRLDVDNRFALNIYFRIANNILKQAEIFRAEKNIIDLYVMLLRFSSLVSETIP 63

Query: 68  CHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWSHASQNST 127
           CHR Y A  +S+K YL+KKLLNAL ELE+L+ AVQQ+INELNRK T+QV GW + SQN  
Sbjct: 64  CHRGYGAFPQSKKDYLRKKLLNALGELEQLKTAVQQRINELNRKHTHQVNGWGYNSQNDL 123

Query: 128 LEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAE 187
           LE P   K+ L              E  YQGS  +Q +Y RPV++QFRR+SLNF RPN E
Sbjct: 124 LEKPPYNKKILN-----------GNESLYQGSRTRQYSYVRPVEQQFRRVSLNFQRPNEE 172

Query: 188 TLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVE 247
           TLSRHS+LGPNGL   WQPP++++ VKYP+ IDLTP+EIP L++  ++ + +K++ S+ E
Sbjct: 173 TLSRHSILGPNGLNAKWQPPRTNEGVKYPSIIDLTPVEIPRLQESVKAELFVKSEHSSSE 232

Query: 248 PEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAA 307
           P +SS++SI +  D+ +  R EEPCS+ISFET E P    VIRQPSPPPVL EVQDLI A
Sbjct: 233 PGRSSLESILSVQDDNQKCRDEEPCSLISFETIETPVLPAVIRQPSPPPVLAEVQDLIPA 292

Query: 308 MSPQVTETECQVG-NSLSDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGS 366
             PQV+E E ++  +S +D      PLQLHISTT+M+NFMK+AKSNTDKNLETCG+LAGS
Sbjct: 293 TPPQVSEAENKMDISSPNDLICSEAPLQLHISTTLMENFMKMAKSNTDKNLETCGVLAGS 352

Query: 367 LKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           LKNRKFY+TALIIPKQESTSDSCQ TNEEEIFEVQDK+SLFPLGWIH
Sbjct: 353 LKNRKFYVTALIIPKQESTSDSCQTTNEEEIFEVQDKQSLFPLGWIH 399

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513064|ref|XP_003525234.1| PREDICTED: AMSH-like ubiquitin thiolesterase 1-like [Glycine max]

 Score =  520 bits (1340), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 260/411 (63%), Positives = 315/411 (76%), Gaps = 1/411 (0%)

Query: 4   SSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVT 63
           SSE INIAAS Q+LDVDNRIALR+YYRIADNILKQADIFR E NI+DLY+MLLRFSSLV+
Sbjct: 3   SSETINIAASTQKLDVDNRIALRFYYRIADNILKQADIFRAETNIVDLYIMLLRFSSLVS 62

Query: 64  ETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWSHAS 123
           ETIP HRDY +S + +K  L+KKLL++++ELE+L+P VQQKINE N ++  Q  GW    
Sbjct: 63  ETIPRHRDYRSSPQGKKEALRKKLLHSMNELEKLKPKVQQKINEFNSRRAYQPNGWEKCH 122

Query: 124 QNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPR 183
            N+ +++   KKQTLT+Y+  KA+   + E  YQGS  QQ +  RPV+E  RR+SL+  R
Sbjct: 123 SNNFMDFSPAKKQTLTSYNKKKAVIPTTGEFVYQGSRGQQFSSVRPVEENMRRLSLSLLR 182

Query: 184 PNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDS 243
           P  ETLSRHS+LGPNGL G W+PP SDK V+YP  IDL+P+EIPSL+QP       K D+
Sbjct: 183 PKEETLSRHSILGPNGLKGQWRPPASDKGVRYPTIIDLSPVEIPSLQQPLVDGSLTKKDN 242

Query: 244 SNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQD 303
           S  E  KS ++SI T +D+ +    +E  S+ISFE +E P   +V RQPSPPPVL EVQD
Sbjct: 243 SISEQHKSDLESILTQSDDCKAKHADEAPSLISFEATEIPAQIEVTRQPSPPPVLAEVQD 302

Query: 304 LIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLETCGI 362
           L+ AM P V E  C+    +SD+  R+E PLQLHIST+MM++FMKLAKSNTDKNLETCGI
Sbjct: 303 LVPAMLPHVIEEGCKTEIPMSDSIVRAESPLQLHISTSMMESFMKLAKSNTDKNLETCGI 362

Query: 363 LAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           LAG LKNRKFYIT LIIPKQE+TS SCQATNEEEIFEVQDK+SLFPLGWIH
Sbjct: 363 LAGLLKNRKFYITTLIIPKQEATSSSCQATNEEEIFEVQDKQSLFPLGWIH 413

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439413|ref|XP_004137480.1| PREDICTED: AMSH-like ubiquitin thioesterase 1-like [Cucumis sativus]

 Score =  513 bits (1321), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 260/414 (62%), Positives = 318/414 (76%), Gaps = 12/414 (2%)

Query: 1   MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSS 60
           MR SS+ INIAAS +R+ VDNR  LRYYYR+ADN+LKQADIFR EKNIIDLYVML+RFSS
Sbjct: 1   MRPSSDRINIAASTRRVVVDNRFPLRYYYRVADNVLKQADIFRAEKNIIDLYVMLMRFSS 60

Query: 61  LVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWS 120
           LVTETIP H +Y  + K QK + +KKLL+ALSELEEL+PAVQ+K++E+N K+  QV G  
Sbjct: 61  LVTETIPRHLEYGTTPKFQKNHFRKKLLDALSELEELKPAVQRKVDEINGKQKYQVNGRG 120

Query: 121 HASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLN 180
           +  QN +LEW S  KQ L N  + KA R P+RE+A QGS PQQ +Y+RP+         +
Sbjct: 121 NQQQNGSLEWHSGGKQYLPNNGMAKAGRSPAREIARQGSGPQQFSYSRPI---------H 171

Query: 181 FPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIK 240
            P P  ETLSRHS+LGPNGL G WQPP  DK V+YP  +D++P++IPSL+Q S   + I+
Sbjct: 172 IPLPKEETLSRHSILGPNGLRGQWQPPTIDKGVQYPRILDVSPVDIPSLQQ-SIDKLTIE 230

Query: 241 TDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTE 300
            D  N+E + S ++SI T N++ E + TE   S+ISFE  E P   +++RQPSPPPVL E
Sbjct: 231 KDLGNLEKKGSDIESICTQNNDHENNATETD-SLISFENVEMPAPIEIVRQPSPPPVLAE 289

Query: 301 VQDLIAAMSPQVTETECQVGNSLSDAFDRSEP-LQLHISTTMMDNFMKLAKSNTDKNLET 359
           VQDLI A+SPQV+E EC    SLSD F   EP +QLHISTTMM++FM+LAKSNT KNLET
Sbjct: 290 VQDLIPAVSPQVSEVECARDTSLSDGFVHPEPSMQLHISTTMMESFMRLAKSNTAKNLET 349

Query: 360 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           CG+LAGSLKNRKFYITALI+PKQEST ++CQATNEEEIF+VQDKRSLFPLGWIH
Sbjct: 350 CGVLAGSLKNRKFYITALIVPKQESTPNTCQATNEEEIFDVQDKRSLFPLGWIH 403

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449516695|ref|XP_004165382.1| PREDICTED: AMSH-like ubiquitin thioesterase 1-like [Cucumis sativus]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 260/418 (62%), Positives = 319/418 (76%), Gaps = 16/418 (3%)

Query: 1   MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSS 60
           MR SS+ INIAAS +R+ VDNR  LRYYYR+ADN+LKQADIFR EKNIIDLYVML+RFSS
Sbjct: 1   MRPSSDRINIAASTRRVVVDNRFPLRYYYRVADNVLKQADIFRAEKNIIDLYVMLMRFSS 60

Query: 61  LVTETIPCHRDYLASFKSQKLYLK----KKLLNALSELEELQPAVQQKINELNRKKTNQV 116
           LVTETIP H +Y  + K QK+ L+    +KLL+ALSELEEL+PAVQ+K++E+N K+  QV
Sbjct: 61  LVTETIPRHLEYGTTPKFQKIILESLFMQKLLDALSELEELKPAVQRKVDEINGKQKYQV 120

Query: 117 TGWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRR 176
            G  +  QN +LEW S  KQ L N  + KA R P+RE+A QGS PQQ +Y+RP+      
Sbjct: 121 NGRGNQQQNGSLEWHSGGKQYLPNNGMAKAGRSPAREIARQGSGPQQFSYSRPI------ 174

Query: 177 MSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESS 236
              + P P  ETLSRHS+LGPNGL G WQPP  DK V+YP  +D++P++IPSL+Q S   
Sbjct: 175 ---HIPLPKEETLSRHSILGPNGLRGQWQPPTIDKGVQYPRILDVSPVDIPSLQQ-SIDK 230

Query: 237 IKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPP 296
           + I+ D  N+E + S ++SI T N++ E + TE   S+ISFE  E P   +++RQPSPPP
Sbjct: 231 LTIEKDLGNLEKKGSDIESICTQNNDHENNATETD-SLISFENVEMPAPIEIVRQPSPPP 289

Query: 297 VLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSEP-LQLHISTTMMDNFMKLAKSNTDK 355
           VL EVQDLI A+SPQV+E EC    SLSD F   EP +QLHISTTMM++FM+LAKSNT K
Sbjct: 290 VLAEVQDLIPAVSPQVSEVECARDTSLSDGFVHPEPSMQLHISTTMMESFMRLAKSNTAK 349

Query: 356 NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           NLETCG+LAGSLKNRKFYITALI+PKQEST ++CQATNEEEIF+VQDKRSLFPLGWIH
Sbjct: 350 NLETCGVLAGSLKNRKFYITALIVPKQESTPNTCQATNEEEIFDVQDKRSLFPLGWIH 407

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531196|ref|XP_003534164.1| PREDICTED: AMSH-like ubiquitin thiolesterase 1-like [Glycine max]

 Score =  503 bits (1295), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 260/413 (62%), Positives = 312/413 (75%), Gaps = 7/413 (1%)

Query: 8   INIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP 67
           INIAASAQ++DVDNRI+LR+YYRIADNIL+QADIFR EKNIIDLYVMLLRFSSLV+ETIP
Sbjct: 12  INIAASAQKVDVDNRISLRFYYRIADNILRQADIFRAEKNIIDLYVMLLRFSSLVSETIP 71

Query: 68  CHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWSHASQNST 127
            HRDY +S + QK  LKKKLL +L+ELE L+P VQQKINELN K   Q  G      N++
Sbjct: 72  RHRDYRSSPQRQKESLKKKLLISLNELENLKPVVQQKINELNNKFAYQQNGQGKFISNNS 131

Query: 128 LEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAE 187
           L++  +KK T  +Y + KA+R  + E  YQGS  QQ +Y RPV+E  RR+SL  P P  E
Sbjct: 132 LDFSPVKKLTSASYGLIKAVRPTAGEFVYQGSRSQQFSYVRPVEEHVRRLSLTLPPPKEE 191

Query: 188 TLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVE 247
           TLSRHS+LGPNGL GHW+PP  DK +KYP+NIDL+P+E+PSL+Q  E     K D+S  E
Sbjct: 192 TLSRHSILGPNGLKGHWRPPIIDKGIKYPSNIDLSPVELPSLQQSMEDESLKKKDNSIAE 251

Query: 248 PEKSSVQSISTPNDEIEIH------RTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEV 301
             KS + SI T +++ ++         +EP S+ISFET+E     +VIRQPSPPPVL EV
Sbjct: 252 HHKSELASILTQSEDCQLQPHPQPEPDQEPPSLISFETTETSAQIEVIRQPSPPPVLAEV 311

Query: 302 QDLIAAMSPQVTETECQVG-NSLSDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETC 360
           QDL+ A+SP V E  C+    SL ++    +PLQLHIS  +M++FMKLAKSNT KNLETC
Sbjct: 312 QDLVPAVSPCVNEAGCKTEIPSLDNSVHAEDPLQLHISAALMESFMKLAKSNTKKNLETC 371

Query: 361 GILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           G+LAG LKNRKFYITALIIPKQESTSDSCQ TNEEEIFEVQDKRSLFPLGWIH
Sbjct: 372 GVLAGLLKNRKFYITALIIPKQESTSDSCQTTNEEEIFEVQDKRSLFPLGWIH 424

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357500307|ref|XP_003620442.1| STAM-binding protein [Medicago truncatula] gi|355495457|gb|AES76660.1| STAM-binding protein [Medicago truncatula]

 Score =  502 bits (1292), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 254/418 (60%), Positives = 314/418 (75%), Gaps = 4/418 (0%)

Query: 1   MRSSSEG---INIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLR 57
           MRSSS     INIA SAQ+LDVDNRI+LR+YYRIADNIL+QADIFR E+NIIDLYVMLLR
Sbjct: 1   MRSSSSTSGEINIAMSAQKLDVDNRISLRFYYRIADNILRQADIFRAERNIIDLYVMLLR 60

Query: 58  FSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVT 117
           FSSLV+ETIP HR+Y +S  ++K  LKK+LL +L+ELE+L+P VQQKINELN +  +Q  
Sbjct: 61  FSSLVSETIPRHREYRSSPSTKKQSLKKRLLISLNELEKLKPLVQQKINELNSRNAHQQN 120

Query: 118 GWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRM 177
           G  +   N+++++ S KKQTL      KA+R  ++E  YQGS  QQ  Y RPV+EQ RR+
Sbjct: 121 GRGNFHSNNSVDFSSAKKQTLPGNGQIKAVRETAKEFVYQGSSGQQFTYVRPVEEQVRRL 180

Query: 178 SLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSI 237
           SL  P P  ETLSRHS+ GPNGL G W+PP +   ++YP NIDL+P+E+PSL++P E + 
Sbjct: 181 SLTLPPPKQETLSRHSIFGPNGLNGQWRPPTTGTGIRYPTNIDLSPVELPSLQRPLEDAS 240

Query: 238 KIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPV 297
               D+S  E  K  + SI T +++ +  R +E  S+ISFE ++     ++IRQPSPPPV
Sbjct: 241 SSNKDNSIEELHKLDLNSIPTDSEDSQPQRAQESPSLISFEETDTSAQVELIRQPSPPPV 300

Query: 298 LTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKN 356
           L EV DL+ A+SP V E  C+     SD+  R+E PLQLHIST +M+NFMKLAKSNT KN
Sbjct: 301 LAEVHDLVPAVSPHVNEAGCKTEIPSSDSCVRAESPLQLHISTALMENFMKLAKSNTKKN 360

Query: 357 LETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV 414
           LETCG+LAG LKNRKFYITALIIPKQESTSDSCQ T+EEEIFEVQDKRSLFPLGWIH 
Sbjct: 361 LETCGVLAGLLKNRKFYITALIIPKQESTSDSCQTTHEEEIFEVQDKRSLFPLGWIHT 418

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356520605|ref|XP_003528952.1| PREDICTED: AMSH-like ubiquitin thiolesterase 1-like [Glycine max]

 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 265/423 (62%), Positives = 314/423 (74%), Gaps = 10/423 (2%)

Query: 1   MRSSSEG---INIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLR 57
           MRSSS     INIAASAQ++DVDNRI+LR+YYRIADNIL+QADIFR EKNIIDLYVMLLR
Sbjct: 1   MRSSSSDRNRINIAASAQKVDVDNRISLRFYYRIADNILRQADIFRAEKNIIDLYVMLLR 60

Query: 58  FSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVT 117
           FSSLV+ETIP HRDY +S   QK  LKKKLL +L+ELE L+P VQQKINELN K   Q  
Sbjct: 61  FSSLVSETIPRHRDYRSSPPRQKESLKKKLLISLNELENLKPVVQQKINELNSKLAYQQN 120

Query: 118 GWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRM 177
           G    S N++L++  +KKQT  +Y + KA+R  + E  YQGS  Q  +Y RPV+E  RR+
Sbjct: 121 GQGKFSSNNSLDFSPVKKQTSASYGLIKAVRPTAGEFVYQGSRSQPFSYVRPVEEHARRL 180

Query: 178 SLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSI 237
           SL  P P  ETLSRHS+LGPNGL G W+PP  DK +KYP+NIDL+P+E+PSL+   E   
Sbjct: 181 SLTLPPPKEETLSRHSILGPNGLKGQWRPPIIDKGIKYPSNIDLSPVELPSLQHSLEDES 240

Query: 238 KIKTDSSNVEPEKSSVQSISTPNDEI------EIHRTEEPCSMISFETSEAPNSADVIRQ 291
             K D+S  E  KS + SI T +++       +    +EP S+ISFET+E     +VIRQ
Sbjct: 241 LKKKDNSIAEHHKSELDSILTQSEDCQPHPQPQPQHDQEPPSLISFETTETSARIEVIRQ 300

Query: 292 PSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAK 350
           PSPPPVL EVQDL+ A+SP V E  C+     SD+    E P+QLHIST +M++FMKLAK
Sbjct: 301 PSPPPVLAEVQDLVPAVSPCVNEAGCKTEIPSSDSSVHVEAPMQLHISTALMESFMKLAK 360

Query: 351 SNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLG 410
           SNT KNLETCG+LAG LKNRKFYITALIIPKQESTSDSCQ TNEEEIFEVQDKRSLFPLG
Sbjct: 361 SNTKKNLETCGVLAGLLKNRKFYITALIIPKQESTSDSCQTTNEEEIFEVQDKRSLFPLG 420

Query: 411 WIH 413
           WIH
Sbjct: 421 WIH 423

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297852504|ref|XP_002894133.1| mov34 family protein [Arabidopsis lyrata subsp. lyrata] gi|297339975|gb|EFH70392.1| mov34 family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  497 bits (1279), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 257/414 (62%), Positives = 310/414 (74%), Gaps = 4/414 (0%)

Query: 1   MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSS 60
           M SSSE I+IA SA+R+ VDNRI+L++Y+RIADNILKQADIFR EKN+IDLYVMLLRFSS
Sbjct: 1   MGSSSEIIDIATSARRIGVDNRISLKFYFRIADNILKQADIFRAEKNVIDLYVMLLRFSS 60

Query: 61  LVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQVTGWS 120
           L  ETIP HRDY  S KS K YL+ +LL+ L+ELE+L+P VQ++I+EL  K   +    +
Sbjct: 61  LALETIPSHRDYRTSLKSNKEYLRMRLLDVLTELEKLKPVVQKRIDELYPKLKPRYNVQA 120

Query: 121 HASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLN 180
           H S N +L W S  K +L +YD  K    P     Y GS  QQ     P++E+FR+MS+N
Sbjct: 121 HPS-NGSLGWSSAVKPSLNSYDPAKVRNPPGHNFGYMGSRGQQFLNAAPLEERFRKMSVN 179

Query: 181 FPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIK 240
           F RPN ETLS+HS+LGP GL   WQPPK D  V+YP+NID +P+ IPS +Q  +S   I 
Sbjct: 180 F-RPNEETLSKHSILGPGGLSAQWQPPKYDTKVQYPSNIDFSPVVIPSFQQFVDSKPMI- 237

Query: 241 TDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTE 300
           T+ SN EPE+  V+     ++ I+ + TEE  SMISFE  E+ N  ++IRQPSPPPVL E
Sbjct: 238 TNGSNDEPERPIVEPSVASSENIQKNYTEELSSMISFEEPESVNDNNLIRQPSPPPVLAE 297

Query: 301 VQDLIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLET 359
           VQDL+ A+ P+V E EC + NSL D   RSE PL+LHI+TTMMD FM+LAKSNT KNLET
Sbjct: 298 VQDLVPALCPEVREPECIIENSLPDESLRSESPLELHIATTMMDTFMRLAKSNTKKNLET 357

Query: 360 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
           CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDK+SLFPLGWIH
Sbjct: 358 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKQSLFPLGWIH 411

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	419
TAIR|locus:2008184	507	AMSH1 "AT1G48790" [Arabidopsis	0.978	0.808	0.603	6.3e-124
TAIR|locus:504955440	507	AMSH3 "associated molecule wit	0.954	0.788	0.438	5.8e-82
POMBASE|SPAC19B12.10	435	sst2 "human AMSH/STAMBP protei	0.482	0.464	0.325	6.8e-26
DICTYBASE|DDB_G0284037	715	DDB_G0284037 "MPN/PAD-1 domain	0.257	0.151	0.422	8.5e-25
TAIR|locus:2019903	223	AMSH2 "AT1G10600" [Arabidopsis	0.286	0.538	0.430	5.4e-23
UNIPROTKB|F1SLF9	424	STAMBP "Uncharacterized protei	0.310	0.306	0.369	1.3e-20
UNIPROTKB|Q17QR2	423	STAMBP "STAM binding protein"	0.307	0.304	0.384	3.1e-20
MGI|MGI:1917777	424	Stambp "STAM binding protein"	0.539	0.533	0.284	4.4e-20
UNIPROTKB|O95630	424	STAMBP "STAM-binding protein"	0.245	0.242	0.401	8.5e-20
UNIPROTKB|E1BRS3	431	Gga.34764 "Uncharacterized pro	0.190	0.185	0.45	2e-19

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

 Score = 1218 (433.8 bits), Expect = 6.3e-124, P = 6.3e-124
 Identities = 250/414 (60%), Positives = 302/414 (72%)

Query:     1 MRSSSEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSS 60
             M SS E I+IA SA+R+ VDNRI+L++Y+RIADNILKQA+IFR EKN+IDLYVMLLRFSS
Sbjct:     1 MGSSFETIDIATSARRIGVDNRISLKFYFRIADNILKQANIFRAEKNVIDLYVMLLRFSS 60

Query:    61 LVTETIPCHRDYLASFKSQXXXXXXXXXNALSELEELQPAVQQKINELNRKKTNQVTGWS 120
             L  ETIP HRDY  S KS          + L+ELE+L+P VQQ+I+EL  K   +    +
Sbjct:    61 LALETIPSHRDYRTSLKSNKEYLRMRLLDVLTELEKLKPVVQQRIDELYPKLKPRYNVQA 120

Query:   121 HASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLN 180
             H + N +L W S  K +  +YD  K    P     Y GS  QQ     P++E+FR+MS+N
Sbjct:   121 HPA-NGSLGWSSAVKPSFNSYDHAKVRNPPGHNSGYMGSRGQQFLNAAPLEERFRKMSVN 179

Query:   181 FPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIK 240
             F RPN ETLS+HS+LGP GL   WQPPK D  V+YP+NID +P+ IPS +Q  +S   I 
Sbjct:   180 F-RPNEETLSKHSILGPGGLSAQWQPPKYDTKVQYPSNIDFSPVVIPSFQQLVDSKPMI- 237

Query:   241 TDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTE 300
             T+ SN EPEK  V+     N++I+ + TEE  SMISFE  E+ N  ++IRQPSPPPVL E
Sbjct:   238 TNGSNDEPEKPIVEPSVASNEKIQKNYTEELSSMISFEEPESVNENNLIRQPSPPPVLAE 297

Query:   301 VQDLIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLET 359
             VQDL+ A+ P+V E EC + NSL D   RSE PL+LHI+T+MMD FM+LAKSNT KNLET
Sbjct:   298 VQDLVPALCPEVREPECMIENSLPDESLRSESPLELHIATSMMDTFMRLAKSNTKKNLET 357

Query:   360 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
             CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDK+SLFPLGWIH
Sbjct:   358 CGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKQSLFPLGWIH 411

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

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

 Score = 822 (294.4 bits), Expect = 5.8e-82, P = 5.8e-82
 Identities = 182/415 (43%), Positives = 254/415 (61%)

Query:     8 INIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP 67
             I++   A+ ++VDNRI LR YYRIADN+L+QA I+REEKN++DLY+MLLR+SSL++ETIP
Sbjct:     3 IDLNKVAREIEVDNRIPLRNYYRIADNLLRQASIYREEKNVVDLYIMLLRYSSLISETIP 62

Query:    68 CHRDYLASFKSQXXXXXXXXXNALSELEELQPAVQQKINELNRKKTNQVTGWSH---ASQ 124
              HRDY AS   +           ++ELE L+P   Q +++LNR +       S     S 
Sbjct:    63 FHRDYQASLPQERLGSRKRLRAVINELESLKPEFNQLVDKLNRVEDESRQDGSDLPVVSY 122

Query:   125 NS-TLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPR 183
             +S  +EWP   K + +  D+ K L        Y  ++      T+ +D+QF+++S +F  
Sbjct:   123 SSDAVEWPPAHKASYSRPDINKPLPTSQPSWTYNNNLTSSSNRTQ-IDQQFQKLSFDFLP 181

Query:   184 PNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQ--PSESSIKIKT 241
             PN  TLSRHS LGPNGL      PKS+  V+YP+N D    +   L +  PS SS  +  
Sbjct:   182 PNQATLSRHSFLGPNGLKRQMVAPKSEIKVQYPSNTDWGSADNSGLIEAGPSSSSASLNG 241

Query:   242 DSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEV 301
             DS  V    S++ S+ + +D      +E   S    + +E P     ++QPSPPPVL +V
Sbjct:   242 DSQEV----STLNSVLSLDDGRWQRHSEAVNSQFISDATEDPFQFVGMKQPSPPPVLAQV 297

Query:   302 QDLIAAMSPQVTETECQVGNSLS--DAFDRSEPLQ-LHISTTMMDNFMKLAKSNTDKNLE 358
                +A + P     + + G ++   +  + S   Q LH+   +MD+F++LA+SNT++NLE
Sbjct:   298 HQELAQICPSKV-ADPRPGPAIPSLEGKEGSNSYQHLHVPVRIMDDFLRLARSNTERNLE 356

Query:   359 TCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
             TCG+LAGSLKNR F+IT LIIPKQESTSDSCQ  NEEEIFEVQD+ SLFPLGWIH
Sbjct:   357 TCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIH 411

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

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

 Score = 251 (93.4 bits), Expect = 6.8e-26, Sum P(2) = 6.8e-26
 Identities = 70/215 (32%), Positives = 104/215 (48%)

Query:   207 PKSDKLVKYPNNIDLTPIEIPSLR-QPSESSIKIKTDSSNVEPEKSSVQSISTPN-DEIE 264
             P  +K V Y +   L    +  L+  P  S+  +  DS  +    S +     P+ +   
Sbjct:   132 PSLEKPVSYVDEPILEQWALSDLQILPPSSTDLLSPDSQKLSKSSSDLPQFDYPSLNSSP 191

Query:   265 IHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETE----CQVG 320
                +  P S   FE +   +S  V    SP P L + +D+     P  T T        G
Sbjct:   192 TFNSNLPISSSRFEKTSLSDSKLV----SPEP-LDDNKDIQFIKKPIYTRTSEPRPKPAG 246

Query:   321 NSLSDAF-DRSEPLQ-LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALI 378
                  A+ +  +PL+ +++   +   F+ + K NT KNLETCGIL G L+   F+IT L+
Sbjct:   247 TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLV 306

Query:   379 IPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
             IP QE+TSD+C  T+E  +FE QDK +L  LGWIH
Sbjct:   307 IPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIH 341

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

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

 Score = 226 (84.6 bits), Expect = 8.5e-25, Sum P(3) = 8.5e-25
 Identities = 46/109 (42%), Positives = 67/109 (61%)

Query:   306 AAMSPQVTETECQVGNSLSDAFDRSEPLQ-LHISTTMMDNFMKLAKSNTDKNLETCGILA 364
             A  +P +T T  +     S+A  +   L+ + +   +   FM+LA++NT +++ETCGIL+
Sbjct:   507 AVNTPSITPTTNKPNIDSSEASKKYSKLRKIIVHGEVFQEFMRLAENNTKRSIETCGILS 566

Query:   365 GSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
             G+L N  F IT +IIPKQE T+D+C    E EIFE Q +  L  LGWIH
Sbjct:   567 GTLSNDVFRITTIIIPKQEGTTDTCNTIEEHEIFEYQLENDLLTLGWIH 615

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

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

 Score = 267 (99.0 bits), Expect = 5.4e-23, P = 5.4e-23
 Identities = 53/123 (43%), Positives = 81/123 (65%)

Query:   293 SPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSEPL--QLHISTTMMDNFMKLAK 350
             SP P L+ V++ +   S  V+       ++++        +   +HIS  ++++F +LA+
Sbjct:     6 SPSPSLSCVEN-VTCKSSHVSRVLISGTDNINHGESSEAKILRDVHISERLLEDFTELAR 64

Query:   351 SNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLG 410
              NT+K+LETCG LA  L+   FY+T LIIPKQESTS+SCQA NE E+F +Q++R L+P+G
Sbjct:    65 ENTEKDLETCGTLAAFLERGIFYVTTLIIPKQESTSNSCQAMNEVEVFSIQNERELYPVG 124

Query:   411 WIH 413
             WIH
Sbjct:   125 WIH 127

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

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

 Score = 212 (79.7 bits), Expect = 1.3e-20, Sum P(2) = 1.3e-20
 Identities = 51/138 (36%), Positives = 76/138 (55%)

Query:   281 EAPNSADVIRQPSPPPVLTEVQDL---IAAMSPQVTETECQVGN-SLSDAFDRSEPLQ-L 335
             E P S DV   P+ P + T+  D    +    P V +   + G  S S +    + L+ +
Sbjct:   201 EKP-SLDV--SPTAPVISTQPSDCNTTVRPAKPPVVDRSLKPGALSNSGSTPTIDGLRHV 257

Query:   336 HISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEE 395
              +   +   F++LA +NT + +ETCGIL G L   +F IT ++IPKQ + SD C   NEE
Sbjct:   258 VVPEKLCPQFLQLASANTARGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEE 317

Query:   396 EIFEVQDKRSLFPLGWIH 413
             E+F +QD++ L  LGWIH
Sbjct:   318 ELFLIQDQQGLITLGWIH 335

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 = 214 (80.4 bits), Expect = 3.1e-20, Sum P(2) = 3.1e-20
 Identities = 53/138 (38%), Positives = 77/138 (55%)

Query:   281 EAPNSADVIRQPSPPPVLTEVQDLIAAM---SPQVTETECQVG--NSLSDAFDRSEPLQL 335
             E P S DV   P+ P + T+  D  AA+    P V +   + G  N+L +A        +
Sbjct:   201 ETP-SLDVF--PTVPAIPTQPSDCNAAVRLAKPPVVDRSLKPGALNNL-EAPTIDGLRHV 256

Query:   336 HISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEE 395
              +   +   F++LA +NT + +ETCGIL G L   +F IT ++IPKQ + SD C   NEE
Sbjct:   257 VVPGKLCPQFLQLAGANTTRGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEE 316

Query:   396 EIFEVQDKRSLFPLGWIH 413
             E+F +QD++ L  LGWIH
Sbjct:   317 ELFLIQDQQGLITLGWIH 334

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

MGI|MGI:1917777 Stambp "STAM binding protein" [Mus musculus (taxid:10090)]

 Score = 206 (77.6 bits), Expect = 4.4e-20, Sum P(2) = 4.4e-20
 Identities = 68/239 (28%), Positives = 104/239 (43%)

Query:   184 PNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTP-IEIPSLRQPSESSIKIKTD 242
             P AE L    L      Y  ++  K  +  +   NI +   +E    R   +   +++ +
Sbjct:   101 PKAEELKTELLRRYTKEYEQYKERKKKEEEELARNIAIQQELEKEKQRVAQQKQKQLEQE 160

Query:   243 SSNVEPEKSSVQSISTPNDEI--EIHRTEE-PCSMISFETSEAPNSADVIRQPSPPPVLT 299
               +   E    Q +     +I  E  + +  PC  +     E P   DV   PS P   T
Sbjct:   161 QFHAFEEMIQRQELEKERLKIVQEFGKVDPGPCGPL-LPDLEKP-CVDVA--PSSPFSPT 216

Query:   300 EVQDLIAAM---SPQVTETECQVGN-SLSDAFDRSEPLQ-LHISTTMMDNFMKLAKSNTD 354
             +  D    M    P V +   + G  S+ +     E L+ + +   +   F++LA +NT 
Sbjct:   217 QTPDCNTGMRPAKPPVVDRSLKPGALSVIENVPTIEGLRHIVVPRNLCSEFLQLASANTA 276

Query:   355 KNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
             K +ETCG+L G L   +F IT ++IP+Q    D C   NEEEIF +QD   L  LGWIH
Sbjct:   277 KGIETCGVLCGKLMRNEFTITHVLIPRQNGGPDYCHTENEEEIFFMQDDLGLLTLGWIH 335

GO:0000281 "cytokinesis after mitosis" evidence=ISO

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005768 "endosome" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0007165 "signal transduction" evidence=TAS

GO:0008233 "peptidase activity" evidence=IEA

GO:0008237 "metallopeptidase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016579 "protein deubiquitination" evidence=ISO;IMP

GO:0016787 "hydrolase activity" evidence=IEA

GO:0032154 "cleavage furrow" evidence=ISO;IDA

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

GO:0046872 "metal ion binding" evidence=IEA

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

 Score = 202 (76.2 bits), Expect = 8.5e-20, Sum P(2) = 8.5e-20
 Identities = 43/107 (40%), Positives = 64/107 (59%)

Query:   310 PQVTETECQVGN-SLSDAFDRSEPLQLHISTT--MMDNFMKLAKSNTDKNLETCGILAGS 366
             P V +   + G  S S++    + L+ H+     +   F++LA +NT + +ETCGIL G 
Sbjct:   230 PPVVDRSLKPGALSNSESIPTIDGLR-HVVVPGRLCPQFLQLASANTARGVETCGILCGK 288

Query:   367 LKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
             L   +F IT ++IPKQ + SD C   NEEE+F +QD++ L  LGWIH
Sbjct:   289 LMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIH 335

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

 Score = 194 (73.4 bits), Expect = 2.0e-19, Sum P(2) = 2.0e-19
 Identities = 36/80 (45%), Positives = 50/80 (62%)

Query:   334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATN 393
             Q+ +   +   F++LA +NT + +ETCGIL G L   +F IT +I+PKQ    D C   N
Sbjct:   263 QVIVPRELCHKFLQLADANTARGVETCGILCGKLMRNEFTITHVIVPKQYGGPDYCNTEN 322

Query:   394 EEEIFEVQDKRSLFPLGWIH 413
             EEE+F +QD+  L  LGWIH
Sbjct:   323 EEELFLIQDQHGLVTLGWIH 342

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)
Q8VYB5	AMSH1_ARATH	3, ., 4, ., 1, 9, ., -	0.6159	0.9785	0.8086	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	LOW CONFIDENCE prediction!
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	419
cd08066	173	cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family	2e-44
cd08058	119	cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN)	2e-10
pfam01398	117	pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin pro	8e-08
cd07767	116	cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domain	1e-07
smart00232	135	smart00232, JAB_MPN, JAB/MPN domain	1e-04

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

 Score =  151 bits (385), Expect = 2e-44
 Identities = 48/80 (60%), Positives = 59/80 (73%)

Query: 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATN 393
           Q+ +   +MD F++LA+ NT +NLETCGIL G L N  F+IT LIIPKQ  TSDSCQ TN
Sbjct: 3   QVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTN 62

Query: 394 EEEIFEVQDKRSLFPLGWIH 413
           EEE+F+ QD+  L  LGWIH
Sbjct: 63  EEELFDFQDQHDLITLGWIH 82

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 = 58.0 bits (140), Expect = 2e-10
 Identities = 28/69 (40%), Positives = 40/69 (57%), Gaps = 2/69 (2%)

Query: 345 FMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKR 404
            ++ A+SNT   +E  G+L G L + +F    +I+PKQ +  DSC   N EE+F VQ  R
Sbjct: 6   MLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGR 63

Query: 405 SLFPLGWIH 413
            L  +GW H
Sbjct: 64  PLLVVGWYH 72

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

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

 Score = 50.1 bits (120), Expect = 8e-08
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSL-KNRKFYITALIIPKQESTSDSCQ 390
              + I   ++   +  A+       E  G+L G+L  +R   +T      Q  T D  +
Sbjct: 2   VRTVVIHPLVLLKIVDHARRGGKSGEEVMGVLLGTLEGDRVIEVTNSFALPQSETEDDVE 61

Query: 391 ATNEEEIFEV-------QDKRSLFPLGWIH 413
           A   +  +         +  R    +GW H
Sbjct: 62  AVELDHEYMEKMLEMLKKVNRDEEVVGWYH 91

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|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains

 Score = 49.4 bits (118), Expect = 1e-07
 Identities = 15/69 (21%), Positives = 24/69 (34%), Gaps = 2/69 (2%)

Query: 345 FMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKR 404
           F+  AKS   K  E  G+L GS   +   +  +I    +             +   +   
Sbjct: 4   FLDAAKSINGK--EVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNA 61

Query: 405 SLFPLGWIH 413
            L  +GW H
Sbjct: 62  GLRIVGWYH 70

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|214573 smart00232, JAB_MPN, JAB/MPN domain

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 9/86 (10%)

Query: 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATN 393
           ++ +   +  N +K A    D   E CG+L G     +  +  +     E   DS Q   
Sbjct: 1   EVKVHPLVPLNILKHAIR--DGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQE-Y 57

Query: 394 EEEIFEV------QDKRSLFPLGWIH 413
           +E+   +      +  + L  +GW H
Sbjct: 58  DEDYSHLMDEELKKVNKDLEIVGWYH 83

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	419
KOG2880	424	consensus SMAD6 interacting protein AMSH, contains	100.0
PF08969	115	USP8_dimer: USP8 dimerisation domain; InterPro: IP	99.9
cd08056	252	MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains wit	99.67
cd08066	173	MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associ	99.63
cd08067	187	MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deu	98.44
cd08058	119	MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains w	98.4
cd07767	116	MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (al	98.3
cd08069	268	MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal	98.16
PF01398	114	JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; Inte	98.09
smart00232	135	JAB_MPN JAB/MPN domain. Domain in Jun kinase activ	97.96
cd08061	274	MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein l	97.59
cd08068	244	MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subun	97.43
cd08070	128	MPN_like Mpr1p, Pad1p N-terminal (MPN) domains wit	97.35
PF04212	69	MIT: MIT (microtubule interacting and transport) d	97.09
cd02684	75	MIT_2 MIT: domain contained within Microtubule Int	97.05
cd02678	75	MIT_VPS4 MIT: domain contained within Microtubule	97.03
smart00745	77	MIT Microtubule Interacting and Trafficking molecu	97.0
cd02683	77	MIT_1 MIT: domain contained within Microtubule Int	96.88
cd02681	76	MIT_calpain7_1 MIT: domain contained within Microt	96.78
cd02656	75	MIT MIT: domain contained within Microtubule Inter	96.56
cd02677	75	MIT_SNX15 MIT: domain contained within Microtubule	96.49
PF14464	104	Prok-JAB: Prokaryotic homologs of the JAB domain;	96.36
cd02680	75	MIT_calpain7_2 MIT: domain contained within Microt	95.27
cd02682	75	MIT_AAA_Arch MIT: domain contained within Microtub	94.82
cd08065	266	MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains wi	94.47
COG1310	134	Predicted metal-dependent protease of the PAD1/JAB	94.15
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	91.2
TIGR02256	131	ICE_VC0181 integrative and conjugative element pro	90.79
cd08060	182	MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family	85.9
cd08072	117	MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1	84.84
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	84.4
PF05021	306	NPL4: NPL4 family; InterPro: IPR007717 The HRD4 ge	83.9
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	81.98
TIGR03735	192	PRTRC_A PRTRC system protein A. A novel genetic sy	81.29

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

Probab=100.00  E-value=1.3e-68  Score=527.53  Aligned_cols=327  Identities=34%  Similarity=0.502  Sum_probs=203.9

Q ss_pred             CCCchhhhhHHHhh---cccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccH
Q 014747            1 MRSSSEGINIAASA---QRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFK   77 (419)
Q Consensus         1 ~~~~~~~~eL~~~A---~~~e~n~~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~   77 (419)
                      |-+|....+.+..+   .+++||.+||+++|||+|++|+|||.||++|||+++|||||+||++||++|||+||||++.. 
T Consensus         1 ~~~S~~p~er~~~lsr~G~i~~n~~IplkryfRsg~ei~rmA~VY~~EgN~enafvLy~ry~tLfiEkipkHrDy~s~k-   79 (424)
T KOG2880|consen    1 MDGSLEPEERVRALSRLGAIEVNKNIPLKRYFRSGTEILRMANVYLEEGNVENAFVLYLRYITLFIEKIPKHRDYRSVK-   79 (424)
T ss_pred             CCCCcChHHHHHHHHhcCceeecCCCCHHHhhhhhHHHHHHHHHHHhcCCcchhhhHHHHHHHHHHHhcccCcchhhhc-
Confidence            44666666665544   45899999999999999999999999999999999999999999999999999999999554 


Q ss_pred             HHHHHHHHHHHHH-HHHHHhhcHHHHHHHHHHHHhhhhhcccccccCCCCCccccccccccccchh-hhhhcccchhhhh
Q 014747           78 SQKLYLKKKLLNA-LSELEELQPAVQQKINELNRKKTNQVTGWSHASQNSTLEWPSLKKQTLTNYD-VTKALRLPSRELA  155 (419)
Q Consensus        78 ~~k~~l~k~l~~v-l~~lE~LK~~I~~~Y~e~~~~~~~~~~~~~~~~~~s~~~~~~~~dp~l~~~~-~~~av~laq~e~~  155 (419)
                      .++..++++|+.+ ++.+++||++|.++|+.++..+...++...                    .+ .+.+  .-|++.+
T Consensus        80 ~ek~d~~~klk~~~~p~~deL~~~ll~rY~~eyn~y~~~K~k~~--------------------~E~~k~l--e~~~~~E  137 (424)
T KOG2880|consen   80 PEKEDIRKKLKEEAFPRIDELKAKLLKRYNVEYNEYDHSKKKNL--------------------AERFKKL--EVQREEE  137 (424)
T ss_pred             hhHHHHHHHHHHHhhhhHHHHHHHHHHHHhhHHHHHHHHHhhhH--------------------HHHHHHh--hcchhhH
Confidence            6777777777665 899999999999999988775433111000                    00 0000  0122222


Q ss_pred             hcCCchhhhhccchHHHHHhhhccCCCCCcchhhccccccCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCcc
Q 014747          156 YQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSES  235 (419)
Q Consensus       156 ~~~~r~~~~~rr~~~~~~~r~~~~~~~~~~ee~l~r~~~~~~~g~~~~~~~~~~~~~~~y~~~~d~~~~~l~~~~~~~~~  235 (419)
                      .+++|.++..+++....+|                                               ...+.+++.|....
T Consensus       138 ~e~kr~aq~k~Q~l~~~~f-----------------------------------------------~~~~~~~~~q~~~s  170 (424)
T KOG2880|consen  138 TERKRSAQTKQQQLESSQF-----------------------------------------------SPLEPPSFKQLLDS  170 (424)
T ss_pred             HHHHHHHHHhhhcCCcccC-----------------------------------------------CccCchHHHhhhcc
Confidence            2223323332222222222                                               22222222222111


Q ss_pred             cccccCCCCCCCCCcCcccccCCCCCccccCCCCCCCCCCCccCCCCCCCccccCCCCCCCccchhhhhhhccCCCcccc
Q 014747          236 SIKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTET  315 (419)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~s~l~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~p~PPpv~~~~~~~~~~~~p~~~~~  315 (419)
                      +.....+. .+-+..+...+.++....+...-+....+.++|++...-..+..+   .+|++++...+       .+.+ 
T Consensus       171 ~~m~s~~~-~gl~e~~~~~~~~p~~~~~~~~~s~~l~~~~s~ep~~s~~~n~~~---k~p~~~r~l~p-------~a~~-  238 (424)
T KOG2880|consen  171 GPMPSNQS-NGLPEQPIGEPLVPSNESRSLNYSELLSVLSSPEPSDSCTTNVTI---KSPSVDRVLKP-------GATD-  238 (424)
T ss_pred             cCCCcCCC-CCCcCCCcCCCCcccccccccCCchhhhhccCCCccccccccccc---cCCCCCccccc-------cccc-
Confidence            11110000 000001111111110000000001011122222222211122212   23333322211       1100 


Q ss_pred             ccccCCCCCCCCCCCC-CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccCh
Q 014747          316 ECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE  394 (419)
Q Consensus       316 ~p~~~~~~~~~~~~~~-l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~e  394 (419)
                           .........+. +|+|+||.+||+.||+||.+||.||+||||||||+|++|.|+|||||||||++|||+|.|+||
T Consensus       239 -----n~~~~~~~~~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~ne  313 (424)
T KOG2880|consen  239 -----NSNHGESSEGKILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNE  313 (424)
T ss_pred             -----ccccccccCCccceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCH
Confidence                 00001111122 899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCCceeeeeeee
Q 014747          395 EEIFEVQDKRSLFPLGWIHV  414 (419)
Q Consensus       395 e~~f~~~~~~~l~~lgwiHT  414 (419)
                      ||||++||+++|+|||||||
T Consensus       314 eelF~vQdq~~L~tlGWIHT  333 (424)
T KOG2880|consen  314 EELFEVQDQHELLTLGWIHT  333 (424)
T ss_pred             HHHheecccccceeeeeeec
Confidence            99999999999999999999

>PF08969 USP8_dimer: USP8 dimerisation domain; InterPro: IPR015063 This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8)

Probab=99.90  E-value=9.8e-24  Score=182.17  Aligned_cols=103  Identities=35%  Similarity=0.534  Sum_probs=87.1

Q ss_pred             hhhhhHHHhhccc-ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHH-H
Q 014747            5 SEGINIAASAQRL-DVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKL-Y   82 (419)
Q Consensus         5 ~~~~eL~~~A~~~-e~n~~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~-~   82 (419)
                      ....+|.++|..+ +||+++|+++|+|+|.+|+++|.+|+++||+|+|||+|+||++|| ++||+||||+........ .
T Consensus        10 ~s~~~L~~~a~~~~~~~~~~~l~~y~rsa~~l~~~A~~~~~egd~E~AYvl~~R~~~L~-~ki~~Hpdy~~~~~~~~~~~   88 (115)
T PF08969_consen   10 SSLEELNKLADVFPEFDKNIPLKRYLRSANKLLREAEEYRQEGDEEQAYVLYMRYLTLV-EKIPKHPDYKKDKNSYKKLL   88 (115)
T ss_dssp             CCHHHHHHCCCT-GGGSTTS-HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH-CCHCCSCCCCCTHHCCHHHH
T ss_pred             hhHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH-HHhhcCccccccchHHHHHH
Confidence            3457899999998 999999999999999999999999999999999999999999999 999999999976654444 2


Q ss_pred             HHHHHHHH-HHHHHhhcHHHHHHHHHH
Q 014747           83 LKKKLLNA-LSELEELQPAVQQKINEL  108 (419)
Q Consensus        83 l~k~l~~v-l~~lE~LK~~I~~~Y~e~  108 (419)
                      ..+++..+ |+++|.||++|+++|+++
T Consensus        89 ~~~~~~~~il~~lE~Lk~~L~~rY~~e  115 (115)
T PF08969_consen   89 GKKKLNEVILEELEKLKPSLKERYEEE  115 (115)
T ss_dssp             HHHHHHHCHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            23555444 899999999999999874

It has no known function. ; PDB: 2XZE_B 2A9U_A.

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

Probab=99.67  E-value=4.2e-17  Score=158.44  Aligned_cols=76  Identities=20%  Similarity=0.350  Sum_probs=72.9

Q ss_pred             eEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccC---CeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceee
Q 014747          333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPL  409 (419)
Q Consensus       333 ~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~---~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~l  409 (419)
                      .+++||.+|+.+|+.+|..||    ++||+|+|+...   |.+.|++++||.|.||.|+|++.++.  +++++.+||.+|
T Consensus        36 ~t~vlPknllkkFi~iaD~rt----Q~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~--~~~~~l~~Le~L  109 (252)
T cd08056          36 YTYILPKNLLKKFISISDLRT----QIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQL--PQHEYLEDLEPL  109 (252)
T ss_pred             CEEEeCHHHHHHHHHHhhhcc----eEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccC--ccchhhCCCEee
Confidence            479999999999999999999    899999999987   89999999999999999999999874  999999999999


Q ss_pred             eeeee
Q 014747          410 GWIHV  414 (419)
Q Consensus       410 gwiHT  414 (419)
                      |||||
T Consensus       110 GWIHT  114 (252)
T cd08056         110 GWIHT  114 (252)
T ss_pred             EEEEc
Confidence            99999

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

>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family

Probab=99.63  E-value=6e-16  Score=143.20  Aligned_cols=83  Identities=58%  Similarity=0.997  Sum_probs=80.8

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeee
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW  411 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgw  411 (419)
                      +|.|+||.+++++|+.+|..||.+++|+||+|+|+...+.+.|+++++|.|.+++++|...+++++|.+++.+||-+|||
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            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eee
Q 014747          412 IHV  414 (419)
Q Consensus       412 iHT  414 (419)
                      |||
T Consensus        81 yHS   83 (173)
T cd08066          81 IHT   83 (173)
T ss_pred             Eec
Confidence            999

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

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

Probab=98.44  E-value=4e-07  Score=85.62  Aligned_cols=78  Identities=23%  Similarity=0.327  Sum_probs=67.0

Q ss_pred             EeeeCHHHHHHHHHHHhhhcccccchhhhhccccc--CCeeEEEEEeeccCCCCCCCccc--cChHHHHHHhhcCCceee
Q 014747          334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK--NRKFYITALIIPKQESTSDSCQA--TNEEEIFEVQDKRSLFPL  409 (419)
Q Consensus       334 ~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~--~~~~~it~liiP~q~~t~d~C~~--~~ee~~f~~~~~~~l~~l  409 (419)
                      .|.|.....=+-+..|...+   .|.||+|+|+..  .+.+.|+..+...+..+++.|++  ..+.+++++.++.|+.++
T Consensus         6 ~V~Is~~all~m~~Ha~~~~---~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~gl~vV   82 (187)
T cd08067           6 KVTVSSNALLLMDFHCHLTT---SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRGLSVV   82 (187)
T ss_pred             EEEECHHHHHHHHHHhcCCC---cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcCCEEE
Confidence            47788777777777888755   999999999975  46899999998899999999986  457788999999999999


Q ss_pred             eeeee
Q 014747          410 GWIHV  414 (419)
Q Consensus       410 gwiHT  414 (419)
                      ||+|+
T Consensus        83 GwYHS   87 (187)
T cd08067          83 GWYHS   87 (187)
T ss_pred             EEEec
Confidence            99998

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

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

Probab=98.40  E-value=3.3e-07  Score=79.41  Aligned_cols=72  Identities=39%  Similarity=0.703  Sum_probs=61.8

Q ss_pred             HHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747          341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV  414 (419)
Q Consensus       341 l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT  414 (419)
                      .+.+++..|..++  ..|+||+|+|+...+.+.+.++-|+.+...++++...++.+.+....+.|+..+||.|+
T Consensus         2 ~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~~~~~~~~~~~~~~g~~~vG~YHS   73 (119)
T cd08058           2 ALLKMLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGRPLLVVGWYHS   73 (119)
T ss_pred             HHHHHHHHhcCCC--CeEEEEEeeeEEecCccceeEEEEeecCCCCCCchhHHHHHHHHHHhCCCCeEEEEEec
Confidence            4678888999866  78999999999988777777788888888888887766667788889999999999998

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

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

Probab=98.30  E-value=7.9e-07  Score=75.14  Aligned_cols=70  Identities=20%  Similarity=0.190  Sum_probs=57.9

Q ss_pred             HHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747          343 DNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV  414 (419)
Q Consensus       343 ~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT  414 (419)
                      ..|+..|..++  ..|.||+|.|+...+.+.|++++...+..+.+.|.......+...+...|+-.+||+||
T Consensus         2 k~il~~a~~~~--~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhs   71 (116)
T cd07767           2 KMFLDAAKSIN--GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHT   71 (116)
T ss_pred             HhHHHHHhcCC--CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEc
Confidence            46888898874  56899999999999999999998888888777765543335677888899999999999

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

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

Probab=98.16  E-value=6e-06  Score=81.63  Aligned_cols=81  Identities=20%  Similarity=0.332  Sum_probs=69.2

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccCh--HHHHH--Hh--hcCC
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE--EEIFE--VQ--DKRS  405 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~e--e~~f~--~~--~~~~  405 (419)
                      +..|.|+...+.+++..|..  ....|.||+|+|+...+.+.||+.+...+.++++.|+...|  +.+++  ..  ...+
T Consensus         9 ~~~V~Is~~allkil~Ha~~--~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~~   86 (268)
T cd08069           9 FEKVYISSLALLKMLKHARA--GGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRP   86 (268)
T ss_pred             ccEEEECHHHHHHHHHHHhc--cCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCCC
Confidence            67899999999999999988  56789999999999899999999998889999999998764  33444  22  3488


Q ss_pred             ceeeeeeee
Q 014747          406 LFPLGWIHV  414 (419)
Q Consensus       406 l~~lgwiHT  414 (419)
                      +.++||.||
T Consensus        87 ~~vVGWYHS   95 (268)
T cd08069          87 ENVVGWYHS   95 (268)
T ss_pred             ceeEeeecc
Confidence            999999999

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

>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=98.09  E-value=5.3e-06  Score=70.77  Aligned_cols=81  Identities=21%  Similarity=0.371  Sum_probs=70.0

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCC-eeEEEEEeeccCCCCCCCccccChHH---HHHHhhc--CC
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-KFYITALIIPKQESTSDSCQATNEEE---IFEVQDK--RS  405 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~-~~~it~liiP~q~~t~d~C~~~~ee~---~f~~~~~--~~  405 (419)
                      ..+|.|.+..+-+++..|..++..  |.||+|.|+...+ .+.||..+.-.+.++.+.|....++.   .++...+  .+
T Consensus         3 ~~~V~i~p~vll~i~~h~~r~~~~--~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (114)
T PF01398_consen    3 VQTVQIHPLVLLKIIDHATRSSPN--EVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPN   80 (114)
T ss_dssp             CEEEEEEHHHHHHHHHHHHHHHCT--EEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTT
T ss_pred             cEEEEECHHHHHHHHHHHhcCCCC--EEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccccc
Confidence            478999999999999999887777  9999999999999 99999999999999999999987763   3444332  56


Q ss_pred             ceeeeeeee
Q 014747          406 LFPLGWIHV  414 (419)
Q Consensus       406 l~~lgwiHT  414 (419)
                      +..+||.||
T Consensus        81 ~~iVGWY~s   89 (114)
T PF01398_consen   81 LEIVGWYHS   89 (114)
T ss_dssp             SEEEEEEEE
T ss_pred             ceEEEEEEc
Confidence            999999999

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.

>smart00232 JAB_MPN JAB/MPN domain

Probab=97.96  E-value=2.3e-05  Score=67.67  Aligned_cols=77  Identities=22%  Similarity=0.373  Sum_probs=59.5

Q ss_pred             eeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHH------hhcCCcee
Q 014747          335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV------QDKRSLFP  408 (419)
Q Consensus       335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~------~~~~~l~~  408 (419)
                      |.|...++.+.++.|..+  ...|.||+|.|+...+.+.|++.+...+....+++... +.+.++.      +...++-.
T Consensus         2 v~i~~~v~~~i~~h~~~~--~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~   78 (135)
T smart00232        2 VKVHPLVPLNILKHAIRD--GPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEY-DEDYSHLMDEELKKVNKDLEI   78 (135)
T ss_pred             EEEcHHHHHHHHHHHhcC--CCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhh-hhhHHHHHHHHHHhhCCCceE
Confidence            678888999999999876  67899999999998889999987775666677776322 3233322      23689999


Q ss_pred             eeeeee
Q 014747          409 LGWIHV  414 (419)
Q Consensus       409 lgwiHT  414 (419)
                      +||+||
T Consensus        79 vGwyhs   84 (135)
T smart00232       79 VGWYHS   84 (135)
T ss_pred             EEEEEc
Confidence            999999

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

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

Probab=97.59  E-value=0.00011  Score=72.98  Aligned_cols=78  Identities=21%  Similarity=0.335  Sum_probs=66.4

Q ss_pred             eeeCHHHHHHHHHHHhhhcccccchhhhhcccccCC-------eeEEEEEeeccCCCCCCCccccCh---HHHHHHhhcC
Q 014747          335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-------KFYITALIIPKQESTSDSCQATNE---EEIFEVQDKR  404 (419)
Q Consensus       335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~-------~~~it~liiP~q~~t~d~C~~~~e---e~~f~~~~~~  404 (419)
                      -+--..++..|+.++-.+|  +...||+|-|+....       .-.|....-|.|.|++|.++...+   +.+..++..-
T Consensus        14 ef~~~~~~~~f~~~~w~~~--~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA~~l   91 (274)
T cd08061          14 EFDNPSIVEFFLYVFWRKT--GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIAAAL   91 (274)
T ss_pred             EEecHHHHHHHHHHHHHhh--cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHHHHc
Confidence            4566789999999855544  689999999998754       799999999999999999998653   6677888889


Q ss_pred             Cceeeeeeee
Q 014747          405 SLFPLGWIHV  414 (419)
Q Consensus       405 ~l~~lgwiHT  414 (419)
                      ||..+|||+|
T Consensus        92 GL~~VG~IfT  101 (274)
T cd08061          92 GLERVGWIFT  101 (274)
T ss_pred             CCeEEEEEEe
Confidence            9999999999

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.

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

Probab=97.43  E-value=0.00034  Score=68.58  Aligned_cols=80  Identities=21%  Similarity=0.363  Sum_probs=57.7

Q ss_pred             eEeeeCHHHHHHHHHHHhhhcccccchhhhhccccc-------CCeeEEEEEeec-cCCCCCCCccccChHHHH--HHhh
Q 014747          333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-------NRKFYITALIIP-KQESTSDSCQATNEEEIF--EVQD  402 (419)
Q Consensus       333 ~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~-------~~~~~it~liiP-~q~~t~d~C~~~~ee~~f--~~~~  402 (419)
                      ..|.|+.+.+.+-+..|.  +.--.|.||+|+|+..       .....|+..+.+ .....+|.|++.-|+.+-  ...+
T Consensus         2 ~~V~Is~~~l~~il~HA~--~~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~   79 (244)
T cd08068           2 SKVHLSADVYLVCLTHAL--STEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAE   79 (244)
T ss_pred             cEEEECHHHHHHHHHHHH--hCCCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHH
Confidence            468999999999887765  4567899999999985       334455565554 445677878776665432  2233


Q ss_pred             c------CCceeeeeeee
Q 014747          403 K------RSLFPLGWIHV  414 (419)
Q Consensus       403 ~------~~l~~lgwiHT  414 (419)
                      .      +++.++||.|+
T Consensus        80 ~~~~~~~rgl~vVGwYHS   97 (244)
T cd08068          80 RLTEETGRPMRVVGWYHS   97 (244)
T ss_pred             HHHhhccCCceEEEEEec
Confidence            4      99999999998

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

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

Probab=97.35  E-value=0.00042  Score=60.69  Aligned_cols=73  Identities=19%  Similarity=0.269  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCC-CccccChHHHHHHh---hcCCceeeeeeee
Q 014747          340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSD-SCQATNEEEIFEVQ---DKRSLFPLGWIHV  414 (419)
Q Consensus       340 ~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d-~C~~~~ee~~f~~~---~~~~l~~lgwiHT  414 (419)
                      +++.++|..|..  .-..|.||+|.|+-......|+.++-.....++. .+...+-++++...   .+.++-.+||.||
T Consensus         2 ~~~~~il~ha~~--~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~g~~~vG~~HS   78 (128)
T cd08070           2 ELLEAILAHAEA--EYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVVGIYHS   78 (128)
T ss_pred             HHHHHHHHHHHh--CCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHCCCeEEEEEeC
Confidence            467788888877  5589999999999888777787655333333333 45556666555444   4689999999999

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.

>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking

Probab=97.09  E-value=0.0035  Score=49.20  Aligned_cols=69  Identities=16%  Similarity=0.174  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 014747           28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV  101 (419)
Q Consensus        28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I  101 (419)
                      |+..|..++++|-.+.+.|+++.|+-+|..-+.+++.-+..-+     ....+..++.++..-+.++|.||..|
T Consensus         1 y~~~A~~~~~~Av~~D~~g~~~~A~~~Y~~ai~~l~~~~~~~~-----~~~~~~~l~~k~~~yl~RAE~lk~~L   69 (69)
T PF04212_consen    1 YLDKAIELIKKAVEADEAGNYEEALELYKEAIEYLMQALKSES-----NPERRQALRQKMKEYLERAEKLKEYL   69 (69)
T ss_dssp             -HHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHST-----THHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            7889999999999999999999999999999999987766542     33566778899999999999999865

; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....

>cd02684 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules

Probab=97.05  E-value=0.0047  Score=50.02  Aligned_cols=71  Identities=15%  Similarity=0.110  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHH
Q 014747           29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK  104 (419)
Q Consensus        29 lRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~  104 (419)
                      +..|..++++|--.-..|+++.||-+|..-+++|+..+..-+     .+..+..++.++...+.++|.||..|+..
T Consensus         3 l~~Ai~lv~~Av~~D~~g~y~eA~~lY~~ale~~~~~~k~e~-----~~~~k~~lr~k~~eyl~RAE~LK~~l~~~   73 (75)
T cd02684           3 LEKAIALVVQAVKKDQRGDAAAALSLYCSALQYFVPALHYET-----DAQRKEALRQKVLQYVSRAEELKALIASD   73 (75)
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhhCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            346889999998899999999999999999999987774422     34567789999999999999999988753

This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear.

>cd02678 MIT_VPS4 MIT: domain contained within Microtubule Interacting and Trafficking molecules

Probab=97.03  E-value=0.0043  Score=49.86  Aligned_cols=71  Identities=13%  Similarity=0.127  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747           28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ  103 (419)
Q Consensus        28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~  103 (419)
                      |+..|..++++|--.-..|+++.|+-+|..-+++++..+..-|+     ...+..++.++..-+.++|.||..|++
T Consensus         2 ~~~~A~~l~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~~k~e~~-----~~~k~~~~~k~~eyl~RaE~LK~~l~~   72 (75)
T cd02678           2 FLQKAIELVKKAIEEDNAGNYEEALRLYQHALEYFMHALKYEKN-----PKSKESIRAKCTEYLDRAEKLKEYLAK   72 (75)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            67889999999999999999999999999999999877766443     356778889999999999999998853

This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.

>smart00745 MIT Microtubule Interacting and Trafficking molecule domain

Probab=97.00  E-value=0.0065  Score=48.51  Aligned_cols=73  Identities=16%  Similarity=0.165  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747           26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ  103 (419)
Q Consensus        26 r~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~  103 (419)
                      +.|+..|.+++.+|--+.+.|+++.|+-+|..-+.+++..+..-|     .+..+..+..++..-+.++|.||..|..
T Consensus         2 ~~~~~~A~~li~~Av~~d~~g~~~eAl~~Y~~a~e~l~~~~~~~~-----~~~~~~~~~~k~~eyl~raE~lk~~~~~   74 (77)
T smart00745        2 RDYLSKAKELISKALKADEAGDYEEALELYKKAIEYLLEGIKVES-----DSKRREAVKAKAAEYLDRAEEIKKSLLE   74 (77)
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            357889999999999999999999999999999999988776533     3456778889999999999999998864

>cd02683 MIT_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules

Probab=96.88  E-value=0.0066  Score=49.41  Aligned_cols=69  Identities=19%  Similarity=0.244  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747           30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ  103 (419)
Q Consensus        30 Rsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~  103 (419)
                      ..|..+++.|--+-+.|+++.|+.+|..-+++|+..|..-||-     ..+..++.++..-+.++|.||..|++
T Consensus         4 ~~a~~l~~~Ave~D~~g~y~eAl~~Y~~aie~l~~~lk~e~d~-----~~k~~~r~ki~eY~~RAE~Lk~~l~~   72 (77)
T cd02683           4 LAAKEVLKRAVELDQEGRFQEALVCYQEGIDLLMQVLKGTKDE-----AKKKNLRQKISEYMDRAEAIKKRLDQ   72 (77)
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhhCCCH-----HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5688999999999999999999999999999998777664433     45778889999999999999999864

This sub-family of MIT domains is found in proteins with unknown function, co-occuring with an as yet undescribed domain. The molecular function of the MIT domain is unclear.

>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules

Probab=96.78  E-value=0.008  Score=49.00  Aligned_cols=71  Identities=15%  Similarity=0.002  Sum_probs=58.3

Q ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747           29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ  103 (419)
Q Consensus        29 lRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~  103 (419)
                      -+.|..+++.|--+-+.|+++.|+.+|..-+++++..+-.+    ..+...+..++.++..-+.++|.||..|..
T Consensus         3 e~~Ai~~a~~Ave~D~~g~y~eA~~~Y~~aie~l~~~~~~~----~~n~~~k~~ir~K~~eYl~RAE~Lk~~l~~   73 (76)
T cd02681           3 ERDAVQFARLAVQRDQEGRYSEAVFYYKEAAQLLIYAEMAG----TLNDSHLKTIQEKSNEYLDRAQALHQLVQG   73 (76)
T ss_pred             HHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHhc----CCChHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            47899999999999999999999999999999998754332    113344566788999999999999998854

This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.

>cd02656 MIT MIT: domain contained within Microtubule Interacting and Trafficking molecules

Probab=96.56  E-value=0.022  Score=45.43  Aligned_cols=70  Identities=17%  Similarity=0.179  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747           29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ  103 (419)
Q Consensus        29 lRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~  103 (419)
                      +..|..+++.|--+-..|+++.|+-+|..-+.+++..+..-+     ....+..++.++..-+.++|.||..|..
T Consensus         3 ~~~a~~l~~~Av~~D~~g~~~~Al~~Y~~a~e~l~~~~~~~~-----~~~~k~~l~~k~~~yl~RaE~Lk~~l~~   72 (75)
T cd02656           3 LQQAKELIKQAVKEDEDGNYEEALELYKEALDYLLQALKAEK-----EPKLRKLLRKKVKEYLDRAEFLKELLKK   72 (75)
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            567889999999999999999999999999999987774433     2466778889999999999999998854

The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear.

>cd02677 MIT_SNX15 MIT: domain contained within Microtubule Interacting and Trafficking molecules

Probab=96.49  E-value=0.023  Score=46.11  Aligned_cols=68  Identities=16%  Similarity=0.154  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHH
Q 014747           28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPA  100 (419)
Q Consensus        28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~  100 (419)
                      |+..|..++++|--.-.+|+++.||-+|..-+++++..++.-+     ....|..++.++.+-+.++|+|+..
T Consensus         2 ~l~~A~~l~~~Ave~d~~~~y~eA~~~Y~~~i~~~~~~~k~e~-----~~~~k~~ir~K~~eYl~RAE~i~~~   69 (75)
T cd02677           2 YLEQAAELIRLALEKEEEGDYEAAFEFYRAGVDLLLKGVQGDS-----SPERREAVKRKIAEYLKRAEEILRL   69 (75)
T ss_pred             hHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6778999999999999999999999999999999988877643     3466788999999999999999864

This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.

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

Probab=96.36  E-value=0.0054  Score=51.00  Aligned_cols=62  Identities=19%  Similarity=0.412  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHH----HhhcCCceeeeeeee
Q 014747          339 TTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFE----VQDKRSLFPLGWIHV  414 (419)
Q Consensus       339 ~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~----~~~~~~l~~lgwiHT  414 (419)
                      .++.++++..+..+  ...|+||+|.|.-....+.|+..+-            ....+.|.    ...+.++-.+|+.||
T Consensus         2 ~~~~~~i~~~~~~~--~p~E~~G~L~g~~~~~~~~~~~~~~------------~~p~~~~~~~~~~~~~~~~~~vg~~HS   67 (104)
T PF14464_consen    2 EEVLEQIIAHARAA--YPNEACGLLLGRRDDQRFIVVPNVN------------PDPRDSFRRERFEARERGLEIVGIWHS   67 (104)
T ss_dssp             -HHHHHHHHHHHHH--TTS-EEEEEEEEEECCEEEEEEEEE--------------HHCHHHHHH-HHHHHT-EEEEEEEE
T ss_pred             HHHHHHHHHHHhhC--CCCeEEEEEEEEecCCEEEEEeCCC------------CCcHHHHHHHhhhhhcccceeeEEEEc
Confidence            45778888888777  6789999999999777887777654            22222222    567899999999999

>cd02680 MIT_calpain7_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules

Probab=95.27  E-value=0.12  Score=42.11  Aligned_cols=64  Identities=20%  Similarity=0.123  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHH----HHHHHHHhhcHHHH
Q 014747           30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLL----NALSELEELQPAVQ  102 (419)
Q Consensus        30 Rsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~----~vl~~lE~LK~~I~  102 (419)
                      .-|..++++|----..||++.||-+|+-.+++|+.      + +  ...-+..++.++.    ..+.++|+||..|.
T Consensus         4 ~kai~Lv~~A~~eD~~gny~eA~~lY~~ale~~~~------e-k--n~~~k~~i~~K~~~~a~~yl~RAE~Lk~~l~   71 (75)
T cd02680           4 ERAHFLVTQAFDEDEKGNAEEAIELYTEAVELCIN------T-S--NETMDQALQTKLKQLARQALDRAEALKESMS   71 (75)
T ss_pred             HHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHHH------h-c--ChhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45788999998888889999999999999999975      2 2  3344566777775    88999999998875

This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.

>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules

Probab=94.82  E-value=0.18  Score=41.13  Aligned_cols=68  Identities=13%  Similarity=0.061  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 014747           29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV  101 (419)
Q Consensus        29 lRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I  101 (419)
                      -++|..+++.|--+.++|+++.|.++|..-+++++.-+..-||-.     .+..++.+|.+-+.++|.||..+
T Consensus         3 ~~~A~~~a~~AVe~D~~gr~~eAi~~Y~~aIe~L~q~~~~~pD~~-----~k~~yr~ki~eY~~Rae~Lk~~v   70 (75)
T cd02682           3 EEMARKYAINAVKAEKEGNAEDAITNYKKAIEVLSQIVKNYPDSP-----TRLIYEQMINEYKRRIEVLEKQN   70 (75)
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHhCCChH-----HHHHHHHHHHHHHHHHHHHHHHc
Confidence            467889999999999999999999999999999998888777664     35567788999999999999876

This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.

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

Probab=94.47  E-value=0.068  Score=52.87  Aligned_cols=80  Identities=15%  Similarity=0.177  Sum_probs=56.6

Q ss_pred             EeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCcc--c---cChHHHHHHhhcCCc--
Q 014747          334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQ--A---TNEEEIFEVQDKRSL--  406 (419)
Q Consensus       334 ~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~--~---~~ee~~f~~~~~~~l--  406 (419)
                      .|.|..-..-+-+..+..+-  ..|.||.|.|...++.+-||..+--....+.+.+.  .   .--.++++...+.|+  
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            47777777777777777655  78999999999999999999864433344434321  1   112455666667777  


Q ss_pred             eeeeeeeec
Q 014747          407 FPLGWIHVS  415 (419)
Q Consensus       407 ~~lgwiHT~  415 (419)
                      .++||-||.
T Consensus        80 ~iVGWY~S~   88 (266)
T cd08065          80 NHVGWYQST   88 (266)
T ss_pred             cEEEeEeec
Confidence            899999994

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

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

Probab=94.15  E-value=0.072  Score=46.99  Aligned_cols=75  Identities=20%  Similarity=0.440  Sum_probs=46.3

Q ss_pred             eeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHH-HHHhhcCCceeeeeee
Q 014747          335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEI-FEVQDKRSLFPLGWIH  413 (419)
Q Consensus       335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~-f~~~~~~~l~~lgwiH  413 (419)
                      +.|+.+++..-|..|.....  .|.||+|+|+-....++  -+..+..+. .+.-....+-.+ .......|+.++||.|
T Consensus         2 ~~i~~~~l~~il~~a~~~~p--~E~~g~l~~~~~~~~~~--~~~n~~~~~-~~~~~~~~~~~~~~~~~~~~g~~vvg~yH   76 (134)
T COG1310           2 LVIPKEVLGAILEHARREHP--REVCGLLAGTREGERYF--PLKNVSVEP-VEYFEIDPEYSLFYLAAEDAGEVVVGWYH   76 (134)
T ss_pred             ceecHHHHHHHHHHHHhcCC--hheEEEEEeecccceee--ccccccCCc-ceeEeeCHHHHHHHHHHhhCCCEEEEEEc
Confidence            56888899988888887755  99999999997662222  112222222 222222233333 2333345699999999


Q ss_pred             e
Q 014747          414 V  414 (419)
Q Consensus       414 T  414 (419)
                      |
T Consensus        77 S   77 (134)
T COG1310          77 S   77 (134)
T ss_pred             C
Confidence            8

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=91.20  E-value=0.85  Score=46.81  Aligned_cols=73  Identities=18%  Similarity=0.156  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHH
Q 014747           28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK  104 (419)
Q Consensus        28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~  104 (419)
                      .+.-|.+++++|----..+|++.||-+|+-.++-|+..|..    .....+-|..++.++-+-|.++|+||.-|++.
T Consensus         6 ~l~kaI~lv~kA~~eD~a~nY~eA~~lY~~aleYF~~~lKY----E~~~~kaKd~IraK~~EYLdRAEkLK~yL~~~   78 (439)
T KOG0739|consen    6 FLQKAIDLVKKAIDEDNAKNYEEALRLYQNALEYFLHALKY----EANNKKAKDSIRAKFTEYLDRAEKLKAYLKEK   78 (439)
T ss_pred             HHHHHHHHHHHHhhhcchhchHHHHHHHHHHHHHHHHHHHh----hhcChhHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            67788999999998888999999999999999999877653    32233567788899999999999999977744

>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family

Probab=90.79  E-value=0.41  Score=42.96  Aligned_cols=65  Identities=22%  Similarity=0.172  Sum_probs=43.1

Q ss_pred             hhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccc----cC-hHHHHHHhhc--CCceeeeeeee
Q 014747          350 KSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQA----TN-EEEIFEVQDK--RSLFPLGWIHV  414 (419)
Q Consensus       350 ~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~----~~-ee~~f~~~~~--~~l~~lgwiHT  414 (419)
                      ..+....-||||||.|.-..+.++|+.+..|.-......|.-    .. .+.|=++..+  ..+..||==||
T Consensus        10 ~Q~~~~~~EtGGiLiG~~~~~~~ii~~~t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWHt   81 (131)
T TIGR02256        10 RQWHDLSTETGGVLIGERRGAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHT   81 (131)
T ss_pred             HhCcCCCCccceEEEEEEcCCcEEEEEEEcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecCc
Confidence            344455669999999999888999999888764333222222    11 3444445444  34889998898

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.

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

Probab=85.90  E-value=2.4  Score=39.94  Aligned_cols=70  Identities=20%  Similarity=0.198  Sum_probs=49.2

Q ss_pred             CHHHHHHHHHHHhhhcccccchhhhhccccc-CCeeEEEEEeeccCCCCCCCccccChH------HHHHHhhcCCceeee
Q 014747          338 STTMMDNFMKLAKSNTDKNLETCGILAGSLK-NRKFYITALIIPKQESTSDSCQATNEE------EIFEVQDKRSLFPLG  410 (419)
Q Consensus       338 p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~-~~~~~it~liiP~q~~t~d~C~~~~ee------~~f~~~~~~~l~~lg  410 (419)
                      +.....+.+..|..  ---.|-||+|.|+.. .+...|+. +||-..    +|....-.      .+-.++.++||-.+|
T Consensus         2 s~~ay~ki~~HA~k--~p~~evcGlLlG~~~~~~~~~V~d-~vPl~h----~~~~l~P~~Eval~~ve~~~~~~gl~IvG   74 (182)
T cd08060           2 STLAYVKMLLHAAK--YPHCAVNGLLLGKKSSGGSVEITD-AVPLFH----SCLALAPMLEVALALVDAYCKSSGLVIVG   74 (182)
T ss_pred             CHHHHHHHHHHHHH--cCCchheEEEEeeecCCCCEEEEE-EEEcCC----CccccCHHHHHHHHHHHHHHHHCCCEEEE
Confidence            34455566666766  335699999999987 66788887 488554    34444322      345677889999999


Q ss_pred             eeee
Q 014747          411 WIHV  414 (419)
Q Consensus       411 wiHT  414 (419)
                      +-|.
T Consensus        75 ~Yhs   78 (182)
T cd08060          75 YYQA   78 (182)
T ss_pred             EEec
Confidence            9996

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.

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

Probab=84.84  E-value=2.3  Score=36.97  Aligned_cols=66  Identities=27%  Similarity=0.346  Sum_probs=41.4

Q ss_pred             eCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEee-ccCCCCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747          337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALII-PKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV  414 (419)
Q Consensus       337 ~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~lii-P~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT  414 (419)
                      |+.++.+..++.|..  .--.|.||+|+|+-.    .|+.++. |.... ++...   ...+  .....++-.+|=.|+
T Consensus         1 i~~~~~~~i~~ha~~--~~P~E~CGlL~G~~~----~v~~~~~~~n~~~-~~~~~---~f~~--~~~~~g~~ivgi~HS   67 (117)
T cd08072           1 ISRDLLDSILEAAKS--SHPNEFAALLRGKDG----VITELLILPGTES-GEVSA---VFPL--LMLPLDMSIVGSVHS   67 (117)
T ss_pred             CCHHHHHHHHHHHhh--cCCceEEEEEEeecc----EEEEEEECCCCCC-CCcce---eech--HHhcCCCeEEEEEEc
Confidence            467788877777754  445799999999764    5666554 42222 11111   1111  245688999999998

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.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=84.40  E-value=2.7  Score=28.19  Aligned_cols=41  Identities=15%  Similarity=0.161  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccC-CCcC
Q 014747           31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP-CHRD   71 (419)
Q Consensus        31 sa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLp-kHPd   71 (419)
                      +|..+...|.+|...|+++.|--++-+-..+.-..+. .|||
T Consensus         1 ta~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~G~~Hpd   42 (42)
T PF13374_consen    1 TASALNNLANAYRAQGRYEEALELLEEALEIRERLLGPDHPD   42 (42)
T ss_dssp             -HHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH----------
T ss_pred             CHHHHHHHHHHHHhhhhcchhhHHHHHHHHHHHHHhcccccC
Confidence            3567788899999999999999999999999855543 4775

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

Probab=83.90  E-value=1.5  Score=44.71  Aligned_cols=55  Identities=29%  Similarity=0.457  Sum_probs=45.2

Q ss_pred             hhhhcccccC-C------eeEEEEEeeccCCCCCCCccc---cChHHHHHHhhcCCceeeeeeee
Q 014747          360 CGILAGSLKN-R------KFYITALIIPKQESTSDSCQA---TNEEEIFEVQDKRSLFPLGWIHV  414 (419)
Q Consensus       360 Cgil~g~l~~-~------~~~it~liiP~q~~t~d~C~~---~~ee~~f~~~~~~~l~~lgwiHT  414 (419)
                      ||+|=|+-.. .      .-.|-...-|.|+|+.|+-+-   .+|+.+=.++..-||.-+|||-|
T Consensus         2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lGL~rVG~IfT   66 (306)
T PF05021_consen    2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALGLERVGWIFT   66 (306)
T ss_pred             eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCCCEEEEEEEe
Confidence            6788887653 3      577778888999999998765   46777888888999999999998

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 [].

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=81.98  E-value=15  Score=42.03  Aligned_cols=28  Identities=11%  Similarity=0.056  Sum_probs=15.1

Q ss_pred             HHHHHHHHHhhccCCCcCcccccHHHHH
Q 014747           54 MLLRFSSLVTETIPCHRDYLASFKSQKL   81 (419)
Q Consensus        54 ly~Ry~~LvvekLpkHPdyk~~~~~~k~   81 (419)
                      -|++-++=|+..|--|+.+....-++|.
T Consensus       423 qYykLIEecISqIvlHr~~~DPdf~yr~  450 (1102)
T KOG1924|consen  423 QYYKLIEECISQIVLHRTGMDPDFKYRF  450 (1102)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCcchhh
Confidence            3566666666666666666533333333

>TIGR03735 PRTRC_A PRTRC system protein A

Probab=81.29  E-value=2.9  Score=39.98  Aligned_cols=73  Identities=10%  Similarity=0.069  Sum_probs=49.6

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeee
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW  411 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgw  411 (419)
                      ++.=.||.+|.++|+..|...  --.|+||+++|.-..+.+.+  .-+......++.-.....      .+++|+..++=
T Consensus        70 ~~~g~Ip~~l~~~ii~hAr~~--~P~EacG~Iag~~~~~~~r~--~p~~N~~~Sp~~~~~d~~------~~~~ge~lV~i  139 (192)
T TIGR03735        70 FLCGPIPASLLEEFAEAARAA--LPNEVAAWIVWNSETGSLRL--AALESIEASPGHIDYRRP------RLDDGEHLVVD  139 (192)
T ss_pred             EecCCCCHHHHHHHHHHHHhc--CCcceEEEEEEcCCCCEEEE--EeccccccCCceEEEcch------HHhCCCeEEEE
Confidence            455689999999999998875  46899999999855556533  222333444444444222      22777888888


Q ss_pred             eee
Q 014747          412 IHV  414 (419)
Q Consensus       412 iHT  414 (419)
                      +|.
T Consensus       140 yHS  142 (192)
T TIGR03735       140 LHS  142 (192)
T ss_pred             EcC
Confidence            886

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	419
3rzu_A	187	The Crystal Structure Of The Catalytic Domain Of Am		3e-17
2znr_A	178	Crystal Structure Of The Dub Domain Of Human Amsh-L		7e-17
3rzv_A	211	The Crystal Structure Of A E280a Mutant Of The Cata		1e-16
2znv_A	178	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		3e-16
2xze_A	146	Structural Basis For Amsh-Escrt-Iii Chmp3 Interacti		6e-04

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

Iteration: 1
 Score = 86.3 bits (212), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)
Query: 345 FMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKR 404
           F++LA +NT + +ETCGIL G L   +F IT ++IPKQ + SD C   NEEE+F +QD++
Sbjct: 30  FLQLASANTARGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQ 89
Query: 405 SLFPLGWIH 413
            L  LGWIH
Sbjct: 90  GLITLGWIH 98

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

Iteration: 1
 Score = 85.1 bits (209), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 49/73 (67%)
Query: 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV 400
           +   F++LA+SNT + +ETCGIL G L + +F IT +I+PKQ +  D C   N EE+F V
Sbjct: 17  LCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNV 76
Query: 401 QDKRSLFPLGWIH 413
           QD+  L  LGWIH
Sbjct: 77  QDQHDLLTLGWIH 89

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

Iteration: 1
 Score = 84.3 bits (207), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV 400
           +   F++LA +NT + + TCGIL G L   +F IT ++IPKQ + SD C   NEEE+F +
Sbjct: 50  LCPQFLQLASANTARGVATCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLI 109
Query: 401 QDKRSLFPLGWIH 413
           QD++ L  LGWIH
Sbjct: 110 QDQQGLITLGWIH 122

>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 = 82.8 bits (203), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 48/73 (65%)
Query: 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV 400
           +   F++LA+SNT + + TCGIL G L + +F IT +I+PKQ +  D C   N EE+F V
Sbjct: 17  LCHKFLQLAESNTVRGIATCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNV 76
Query: 401 QDKRSLFPLGWIH 413
           QD+  L  LGWIH
Sbjct: 77  QDQHDLLTLGWIH 89

>pdb|2XZE|A Chain A, Structural Basis For Amsh-Escrt-Iii Chmp3 Interaction Length = 146

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 17 LDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDY 72
          ++V+  I  R Y+R    I++ A I+ EE NI   +++  ++ +L  E +P HRDY
Sbjct: 25 VEVNEDIPPRRYFRSGVEIIRMASIYSEEGNIEHAFILYNKYITLFIEKLPKHRDY 80

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	419
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	5e-28
2znr_A	178	AMSH-like protease; metal binding protein, alterna	2e-24
2xze_A	146	STAM-binding protein; hydrolase-protein transport	6e-22
2og4_A	254	PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN	4e-13
3sbg_A	565	PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain,	8e-11
2a9u_A	144	Ubiquitin carboxyl-terminal hydrolase 8; coil-COIL	9e-09
2p8r_A	273	PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

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

 Score =  108 bits (272), Expect = 5e-28
 Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 13/132 (9%)

Query: 282 APNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSEPLQLHISTTM 341
             +      +P+ PPV+          S +             D         + +   +
Sbjct: 4   GSSDCHTTVRPAKPPVVDR--------SLKPGALSNSESIPTIDGLR-----HVVVPGRL 50

Query: 342 MDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQ 401
              F++LA +NT + + TCGIL G L   +F IT ++IPKQ + SD C   NEEE+F +Q
Sbjct: 51  CPQFLQLASANTARGVATCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQ 110

Query: 402 DKRSLFPLGWIH 413
           D++ L  LGWIH
Sbjct: 111 DQQGLITLGWIH 122

>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 = 98.6 bits (245), Expect = 2e-24
 Identities = 38/85 (44%), Positives = 54/85 (63%), Gaps = 1/85 (1%)

Query: 330 SEPLQ-LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS 388
            E L+ + +   +   F++LA+SNT + +ETCGIL G L + +F IT +I+PKQ +  D 
Sbjct: 5   MEGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDY 64

Query: 389 CQATNEEEIFEVQDKRSLFPLGWIH 413
           C   N EE+F VQD+  L  LGWIH
Sbjct: 65  CDMENVEELFNVQDQHDLLTLGWIH 89

>2xze_A STAM-binding protein; hydrolase-protein transport complex; 1.75A {Homo sapiens} Length = 146

 Score = 90.6 bits (224), Expect = 6e-22
 Identities = 27/104 (25%), Positives = 52/104 (50%), Gaps = 1/104 (0%)

Query: 9   NIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC 68
            ++     ++V+  I  R Y+R    I++ A I+ EE NI   +++  ++ +L  E +P 
Sbjct: 17  ALSQLGSAVEVNEDIPPRRYFRSGVEIIRMASIYSEEGNIEHAFILYNKYITLFIEKLPK 76

Query: 69  HRDY-LASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRK 111
           HRDY  A    +K  +KK    A  + EEL+  + ++  +   +
Sbjct: 77  HRDYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYTE 120

>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 = 68.1 bits (166), Expect = 4e-13
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFY---ITALIIPKQESTSDSCQ 390
              +   ++  F++++        +    + G           I  +++  Q     S Q
Sbjct: 39  VYVLPKNLLKKFIEISDVKI----QVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQ 94

Query: 391 ATNEEEIFEVQDKRSLFPLGWIH 413
            +N  +I ++ D   L  LGWIH
Sbjct: 95  ISNIPDIGDLPDTEGLELLGWIH 117

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

 Score = 62.9 bits (152), Expect = 8e-11
 Identities = 30/196 (15%), Positives = 65/196 (33%), Gaps = 10/196 (5%)

Query: 224 IEIPSLRQPSESSIKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAP 283
           + I +L Q     I +  +      ++  +  +     E + +  E   +    +T    
Sbjct: 237 VNISALTQTEIKDIILGQNIKAPSVKRQKMAELEAARSEKQ-NDEEAAGASTVMKTKTIN 295

Query: 284 NSADVIRQPSPPPVLTEVQDL---IAAMSPQVTETECQVGNSLSDAFDRSEPLQLHISTT 340
              + I   +     ++           +   T    ++ N    A D  E   +++   
Sbjct: 296 AQGEEIVVVASADYESQTFSSKNEWRKSAIANTLLYLRLKNIYVSADDFVEEQNVYV--- 352

Query: 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFY---ITALIIPKQESTSDSCQATNEEEI 397
           +  N +K     +D  ++    + G           I  +++  Q     S Q +N  +I
Sbjct: 353 LPKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDI 412

Query: 398 FEVQDKRSLFPLGWIH 413
            ++ D   L  LGWIH
Sbjct: 413 GDLPDTEGLELLGWIH 428

>2a9u_A Ubiquitin carboxyl-terminal hydrolase 8; coil-COIL, protease, SH3-binding, thiol protease, UBL conjugation pathway, structural genomics; 2.10A {Homo sapiens} SCOP: a.118.23.1 Length = 144

 Score = 53.2 bits (127), Expect = 9e-09
 Identities = 17/98 (17%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 19  VDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDY-LASFK 77
              +I+ + Y   A  I K A+  R +++    YV+ +++ ++    I    D+      
Sbjct: 29  KPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVY-NLIKKRPDFKQQQDY 87

Query: 78  SQKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQ 115
              +     +  A+ E E L  +++ +  E   +K  +
Sbjct: 88  FHSILGPGNIKKAVEEAERLSESLKLRYEEAEVRKKLE 125

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

 Score = 53.8 bits (129), Expect = 3e-08
 Identities = 14/93 (15%), Positives = 30/93 (32%), Gaps = 10/93 (10%)

Query: 324 SDAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFY---ITALIIP 380
           SD    +      +   ++  F+ ++    D   +  G + G           I  +++ 
Sbjct: 31  SDDVKDTGY-TYILPKNILKKFITIS----DLRTQIAGFMYGVSPPDNPQVKEIRCIVLV 85

Query: 381 KQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413
            Q  +        +    E+       PLGW+H
Sbjct: 86  PQTGSHQQVNLPTQLPDHELLR--DFEPLGWMH 116

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.8 bits (97), Expect = 4e-04
 Identities = 56/370 (15%), Positives = 98/370 (26%), Gaps = 97/370 (26%)

Query: 131 PSLKKQTLTNYDVTKALRLPSRE----------LAYQGSIPQQLA-------Y------- 166
             + K  L+  ++   +                L+ Q  + Q+         Y       
Sbjct: 39  QDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPI 98

Query: 167 ----------TRPVDEQFRRM--------SLNFPRPNAETLSRHSL--LGPNG---LYG- 202
                     TR   EQ  R+          N  R       R +L  L P     + G 
Sbjct: 99  KTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV 158

Query: 203 -----HW---QPPKSDKLV-KYPNNID-LTPIEIPSLRQPSESSIKIKTDSSNVEPEKSS 252
                 W       S K+  K    I  L    + +   P      ++     ++P  +S
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLN---LKNCNSPETVLEMLQKLLYQIDPNWTS 215

Query: 253 VQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQD--LIAAMSP 310
               S  N ++ IH  +     +  ++    N   V+           VQ+     A + 
Sbjct: 216 RSDHS-SNIKLRIHSIQAELRRL-LKSKPYENCLLVLL---------NVQNAKAWNAFNL 264

Query: 311 Q----VTETECQVGNSLS-------------DAFDRSEPLQLHISTTMMDNFMKLAKSNT 353
                +T    QV + LS                   E   L +          L +   
Sbjct: 265 SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ-DLPREVL 323

Query: 354 DKNLETCGILAGSLKNR----KFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPL 409
             N     I+A S+++       +              S       E  ++ D+ S+FP 
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPP 383

Query: 410 GWIHVSAFTL 419
              H+    L
Sbjct: 384 S-AHIPTILL 392

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	419
2xze_A	146	STAM-binding protein; hydrolase-protein transport	99.95
2a9u_A	144	Ubiquitin carboxyl-terminal hydrolase 8; coil-COIL	99.9
2og4_A	254	PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN	99.84
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	99.81
2p8r_A	273	PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t	99.77
2znr_A	178	AMSH-like protease; metal binding protein, alterna	99.69
3sbg_A	565	PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain,	99.61
2kks_A	146	Uncharacterized protein; NESG, structural genomics	98.6
2kcq_A	153	MOV34/MPN/PAD-1 family; NESG, structure, structura	98.46
1oi0_A	124	AF2198, hypothetical protein AF2198; proteasome, d	97.5
4b4t_V	306	26S proteasome regulatory subunit RPN11; hydrolase	97.39
2cpt_A	117	SKD1 protein, vacuolar sorting protein 4B; MIT, he	97.08
4a5x_A	86	MITD1, MIT domain-containing protein 1; protein tr	97.0
1wfd_A	93	Hypothetical protein 1500032H18; MIT domain, struc	96.98
2v6x_A	85	Vacuolar protein sorting-associated protein 4; pro	96.84
2w2u_A	83	Hypothetical P60 katanin; hydrolase transport comp	96.62
2v6y_A	83	AAA family ATPase, P60 katanin; MIT, VPS4, archaea	96.37
2ymb_A	257	MITD1, MIT domain-containing protein 1; protein tr	95.24
2o95_A	187	26S proteasome non-ATPase regulatory subunit 7; PS	92.08
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	87.92

>2xze_A STAM-binding protein; hydrolase-protein transport complex; 1.75A {Homo sapiens}

Probab=99.95  E-value=7.5e-28  Score=215.48  Aligned_cols=110  Identities=24%  Similarity=0.400  Sum_probs=98.9

Q ss_pred             hhhhhHHHhhcccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHH
Q 014747            5 SEGINIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLK   84 (419)
Q Consensus         5 ~~~~eL~~~A~~~e~n~~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~   84 (419)
                      ....+|+++|.+++||++|||++|||+|++|+++|.+|+++||+++|||+|+||++||+++||+||||+.....++..++
T Consensus        13 ~~i~~L~~~A~~~~v~~~i~l~~ylrta~~llr~A~~y~~egd~e~AYily~R~~~L~~e~IpkHpdy~~~~~~~~~~~l   92 (146)
T 2xze_A           13 DRVRALSQLGSAVEVNEDIPPRRYFRSGVEIIRMASIYSEEGNIEHAFILYNKYITLFIEKLPKHRDYKSAVIPEKKDTV   92 (146)
T ss_dssp             HHHHHHHHHHTCCCCCTTSCHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTGGGSTTTTTCCCTTHHHHH
T ss_pred             cCHHHHHHHHhhccCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHcccCccchhhhhHHHHHHH
Confidence            45678999999999999999999999999999999999999999999999999999999999999999986655566666


Q ss_pred             HHHHHH-HHHHHhhcHHHHHHHHHHHHhhhh
Q 014747           85 KKLLNA-LSELEELQPAVQQKINELNRKKTN  114 (419)
Q Consensus        85 k~l~~v-l~~lE~LK~~I~~~Y~e~~~~~~~  114 (419)
                      ++++.+ +++||.||+.|+++|+++++.+..
T Consensus        93 ~~l~~~~~~~lE~LK~~L~~rY~~e~~~~~~  123 (146)
T 2xze_A           93 KKLKEIAFPKAEELKAELLKRYTKEYTEYNE  123 (146)
T ss_dssp             HHHHHTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777776 999999999999999976664433

>2a9u_A Ubiquitin carboxyl-terminal hydrolase 8; coil-COIL, protease, SH3-binding, thiol protease, UBL conjugation pathway, structural genomics; 2.10A {Homo sapiens} SCOP: a.118.23.1

Probab=99.90  E-value=7.9e-24  Score=188.95  Aligned_cols=104  Identities=18%  Similarity=0.231  Sum_probs=90.6

Q ss_pred             hhHHHhhcccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHH-HHHH
Q 014747            8 INIAASAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLY-LKKK   86 (419)
Q Consensus         8 ~eL~~~A~~~e~n~~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~-l~k~   86 (419)
                      .+|.+.+  ..+|.+||+++|||+|++|+++|.+|+++||+|+|||+||||++|| ++||+||||+......+.. .+++
T Consensus        20 e~L~k~~--~~~d~~ipl~~y~rsa~~L~r~A~~y~~EGd~E~AYilymRy~~L~-~kIpkHpdyk~~~~~~k~~l~k~~   96 (144)
T 2a9u_A           20 KDLNKKT--EVKPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVY-NLIKKRPDFKQQQDYFHSILGPGN   96 (144)
T ss_dssp             HHHHGGG--CCCGGGSCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-HHHTTSHHHHHTHHHHHHHHCHHH
T ss_pred             HHHHHhc--ccccccCcHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-HHHhcCcchhhhhHHHHHHHHHhH
Confidence            3555544  7788899999999999999999999999999999999999999999 7999999999766544555 3678


Q ss_pred             HHHHHHHHHhhcHHHHHHHHH-HHHhhhh
Q 014747           87 LLNALSELEELQPAVQQKINE-LNRKKTN  114 (419)
Q Consensus        87 l~~vl~~lE~LK~~I~~~Y~e-~~~~~~~  114 (419)
                      ++.||+++|.||+.|+++|++ +++.+.+
T Consensus        97 ~~~vl~~lE~LK~~L~~rYe~~e~~~~l~  125 (144)
T 2a9u_A           97 IKKAVEEAERLSESLKLRYEEAEVRKKLE  125 (144)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999 7775544

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

Probab=99.84  E-value=2.4e-22  Score=193.11  Aligned_cols=79  Identities=19%  Similarity=0.341  Sum_probs=76.1

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccC---CeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCcee
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFP  408 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~---~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~  408 (419)
                      .++++||.+|+.+|+.+|..||    +|||||||++..   +++.|+|+|||+|.||+|+|++.||+++|+|||.+||.+
T Consensus        37 ~~t~vlPknLlkkFi~IAD~~T----q~cG~LyG~~~~d~~~v~eI~~ivippQ~gt~~s~~~~~~~p~~~~~~l~dLe~  112 (254)
T 2og4_A           37 QNVYVLPKNLLKKFIEISDVKI----QVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLEL  112 (254)
T ss_dssp             SCEEEEEHHHHHHHHHTSCSSS----CCEEEEEEEECSSCTTEEEEEEEECCCEEEETTEEEECCCCCCTTSTTCTTCEE
T ss_pred             CcEEEcCHHHHHHHHHHhhccc----eEEEEEEccCCCCCCCeEEEEEEEECCccCCCceEECCCcCccccchhhcCCEe
Confidence            6889999999999999999999    699999999964   589999999999999999999999999999999999999


Q ss_pred             eeeeee
Q 014747          409 LGWIHV  414 (419)
Q Consensus       409 lgwiHT  414 (419)
                      ||||||
T Consensus       113 LGWIHT  118 (254)
T 2og4_A          113 LGWIHT  118 (254)
T ss_dssp             EEEEEE
T ss_pred             cceEee
Confidence            999999

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

Probab=99.81  E-value=6.7e-21  Score=179.75  Aligned_cols=83  Identities=42%  Similarity=0.790  Sum_probs=82.0

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeee
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW  411 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgw  411 (419)
                      ++.|+||.+|+.+||.+|..||.+++|+||+|+|+...+.+.|+++++|.|.+|+++|++.+++++|+|++.+||..|||
T Consensus        41 lr~v~Ipk~ll~kfL~~A~~~tp~~~EvcGlL~Gk~~~~~~~I~~v~~ppq~gt~~~v~~~~~~e~~~~~~~~~l~~vGW  120 (211)
T 3rzv_A           41 LRHVVVPGRLCPQFLQLASANTARGVATCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGW  120 (211)
T ss_dssp             BCCEEEETTHHHHHHHHHHHHHHTTCCCEEEEEEEEETTEEEEEEEEECCEEECSSCEEECCHHHHHHHHHHHTCEEEEE
T ss_pred             cEEEEECHHHHHHHHHHHHhCCCCCceEEEEEEeEcCCCCEEEEEEEeCCccCCCCceeccChHHHHHHHhhCCCEEEEE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eee
Q 014747          412 IHV  414 (419)
Q Consensus       412 iHT  414 (419)
                      |||
T Consensus       121 yHS  123 (211)
T 3rzv_A          121 IHT  123 (211)
T ss_dssp             EEE
T ss_pred             EeC
Confidence            999

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

Probab=99.77  E-value=4.6e-20  Score=178.93  Aligned_cols=77  Identities=17%  Similarity=0.371  Sum_probs=73.6

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccC---CeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCcee
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFP  408 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~---~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~  408 (419)
                      .+.++||.+|+.+|+.||..||    +|||||||++..   +++.|+|+|||+|.||+|+|++.||+..++|+  +||.+
T Consensus        38 ~~t~vlPknllkkFi~IADlrT----q~~G~LyG~s~~d~~~vkeI~~ivipPQ~gt~~sv~~~~~~p~~~~l--~dLe~  111 (273)
T 2p8r_A           38 GYTYILPKNILKKFITISDLRT----QIAGFMYGVSPPDNPQVKEIRCIVLVPQTGSHQQVNLPTQLPDHELL--RDFEP  111 (273)
T ss_dssp             SCEEEEEHHHHHHHHHTSCSSS----CCEEEEEEECCTTCTTEEEEEEEECCSBEECSSCEECCSSCCCCTTT--TTSEE
T ss_pred             ccEEEecHHHHHHHHHHhhccc----eEEEEEeccCCCCCCCeEEEEEEEECCccCCCceEECCCcCcchhhh--ccccc
Confidence            5789999999999999999999    799999999963   58999999999999999999999999999998  99999


Q ss_pred             eeeeee
Q 014747          409 LGWIHV  414 (419)
Q Consensus       409 lgwiHT  414 (419)
                      ||||||
T Consensus       112 LGWIHT  117 (273)
T 2p8r_A          112 LGWMHT  117 (273)
T ss_dssp             EEEEEE
T ss_pred             cceEee
Confidence            999999

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

Probab=99.69  E-value=9.6e-18  Score=154.29  Aligned_cols=83  Identities=43%  Similarity=0.795  Sum_probs=81.6

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeee
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW  411 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgw  411 (419)
                      ++.|+||.+++.+|+.+|..||.+++|+||+|+|+...+.+.|++++++.|.+++++|++.+++++|++++++||.+|||
T Consensus         8 ~~~v~i~~~~l~k~l~hA~~~~~~~~EvcGlL~G~~~~~~~~V~~v~~~pq~~t~~~~~~~~~~e~~~~~~~~~l~~vGw   87 (178)
T 2znr_A            8 LRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTLGW   87 (178)
T ss_dssp             CCCEEEETTHHHHHHHHHHHHHTTTCCCEEEEEEEEETTEEEEEEEEECCEEEETTEEEECCHHHHHHHHHHHTCEEEEE
T ss_pred             cEEEEECHHHHHHHHHHHHhCCCCCceEEEEEeeEecCCCeEEEEEEeCCcCCCCCeeccCCHHHHHHHHHhCCCEEEEE
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eee
Q 014747          412 IHV  414 (419)
Q Consensus       412 iHT  414 (419)
                      |||
T Consensus        88 yHS   90 (178)
T 2znr_A           88 IHT   90 (178)
T ss_dssp             EEE
T ss_pred             EeC
Confidence            999

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

Probab=99.61  E-value=7.9e-17  Score=166.49  Aligned_cols=77  Identities=17%  Similarity=0.298  Sum_probs=69.1

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhccccc---CCeeEEEEEeeccCCCCCCCcccc--ChHHHHHHhhcCCc
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK---NRKFYITALIIPKQESTSDSCQAT--NEEEIFEVQDKRSL  406 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~---~~~~~it~liiP~q~~t~d~C~~~--~ee~~f~~~~~~~l  406 (419)
                      -+.++||.+|+.+|+.+|..||    ++||+|||+..   .|++.|+|++||+|.||+|+|++.  .++++  ||..+||
T Consensus       348 ~~tyVlPkNLLkKFI~IADlrT----QicGyLyG~sp~dn~nVkEI~cIVipPQ~Gt~~sv~lp~lp~he~--~~~l~dL  421 (565)
T 3sbg_A          348 QNVYVLPKNLLKKFIEISDVKI----QVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGD--LPDTEGL  421 (565)
T ss_dssp             SCEEEEEHHHHHHHHHHSCSSS----CCEEEEEEEEETTEEEEEEEEEEECCCEEECSSCEEECCCCCCTT--STTCTTC
T ss_pred             CcEEEccHHHHHHHHHHhhccc----eeEEEEecCCCCCCCCeEEEEEEEECCccCCCceEECCCCCcccc--ccccccC
Confidence            3679999999999999999999    79999999998   378999999999999999999998  45544  4447999


Q ss_pred             eeeeeeee
Q 014747          407 FPLGWIHV  414 (419)
Q Consensus       407 ~~lgwiHT  414 (419)
                      .+||||||
T Consensus       422 e~LGWIHT  429 (565)
T 3sbg_A          422 ELLGWIHT  429 (565)
T ss_dssp             EEEEEEEE
T ss_pred             Eecceeee
Confidence            99999999

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

Probab=98.60  E-value=6.5e-08  Score=85.35  Aligned_cols=77  Identities=16%  Similarity=0.307  Sum_probs=63.3

Q ss_pred             eeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeec-cCCCCCCCccccChHHHHHHh---hcCCceeee
Q 014747          335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIP-KQESTSDSCQATNEEEIFEVQ---DKRSLFPLG  410 (419)
Q Consensus       335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP-~q~~t~d~C~~~~ee~~f~~~---~~~~l~~lg  410 (419)
                      |.||.+++.+++..|..+  ...|+||+|+|+...+.+.|+.++.. ....+++ ....+.++++..+   +++|+-.+|
T Consensus         2 l~i~~~~l~~i~~ha~~~--~p~E~cGlL~G~~~~~~~~v~~~~p~~n~~~~~~-~f~~dp~~~~~~~~~~~~~g~~ivG   78 (146)
T 2kks_A            2 ITLTKKQMEEMLAHARQA--LPNEACGLLGGRRDGDDRWVERVYPLNNLDQSPE-HFSMDPREQLTAVKDMRKNGWVMLG   78 (146)
T ss_dssp             EEEEHHHHHHHHHHHHHH--TTSCEEEEEEEEEETTEEEEEEEECCCCCSCCSS-SCCCCHHHHHHHHHHHHHHTCEEEE
T ss_pred             EEECHHHHHHHHHHHHhc--CCcceEEEEEEEEcCCCcEEEEEEECCCcCCCCc-eEEECHHHHHHHHHHHHHCCCEEEE
Confidence            679999999999999986  47899999999999888999987654 3445555 4567777887776   678999999


Q ss_pred             eeee
Q 014747          411 WIHV  414 (419)
Q Consensus       411 wiHT  414 (419)
                      |+||
T Consensus        79 ~~HS   82 (146)
T 2kks_A           79 NFHS   82 (146)
T ss_dssp             EEEE
T ss_pred             EEeC
Confidence            9999

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

Probab=98.46  E-value=1.7e-07  Score=83.28  Aligned_cols=77  Identities=14%  Similarity=0.228  Sum_probs=63.0

Q ss_pred             eeeCHHHHHHHHHHHhhhcccccchhhhhccccc-CCeeEEEEEeeccCC---CCCCCccccChHHHHHHhh---cCCce
Q 014747          335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-NRKFYITALIIPKQE---STSDSCQATNEEEIFEVQD---KRSLF  407 (419)
Q Consensus       335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~-~~~~~it~liiP~q~---~t~d~C~~~~ee~~f~~~~---~~~l~  407 (419)
                      |.|+.+++.+++..|..  ....|+||+|+|+.. .+.+.|+.+ +|-+.   +++.+|...+.++++..++   +.++.
T Consensus         1 l~i~~~~l~~i~~ha~~--~~p~E~cGlL~G~~~~~~~~~v~~~-~p~~n~~~~~~~~~f~~dp~~~~~~~~~~~~~g~~   77 (153)
T 2kcq_A            1 MKTTPDILDQIRVHGAD--AYPEEGCGFLLGTVTDDGDNRVAAL-HRATNRRSEQRTRRYELTADDYRAADAAAQEQGLD   77 (153)
T ss_dssp             CBCCHHHHHHHHHHHHH--HTTSCCCEEEEEEECTTSCEEEEEE-EESSCCCCCCCSCCSSCCCCSHHHHHHHHHHHTCE
T ss_pred             CEeCHHHHHHHHHHHHh--cCCcceEEEEEEeeccCCCeEEEEE-EECCCCCCCCCCcEEEECHHHHHHHHHHHHHCCCe
Confidence            46899999999999997  456899999999998 788999874 56554   4666777777777777764   57999


Q ss_pred             eeeeeee
Q 014747          408 PLGWIHV  414 (419)
Q Consensus       408 ~lgwiHT  414 (419)
                      .+||+||
T Consensus        78 ivG~yHS   84 (153)
T 2kcq_A           78 VVGVYHS   84 (153)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEeC
Confidence            9999998

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

Probab=97.50  E-value=9.2e-05  Score=63.32  Aligned_cols=66  Identities=24%  Similarity=0.303  Sum_probs=45.6

Q ss_pred             eeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEe-eccCCCCCCCccccChHHHHH-HhhcCCceeeeee
Q 014747          335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALI-IPKQESTSDSCQATNEEEIFE-VQDKRSLFPLGWI  412 (419)
Q Consensus       335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~li-iP~q~~t~d~C~~~~ee~~f~-~~~~~~l~~lgwi  412 (419)
                      |.|+.++.++++..|..  .-..|.||+|+|+..    .|++++ +| ..+++       ....|. ..+.+++-.+||.
T Consensus         4 v~i~~~~l~~i~~ha~~--~~P~E~cGlL~g~~~----~v~~~~~~p-~~~~~-------~~~~f~~~~~~~~~~ivG~~   69 (124)
T 1oi0_A            4 MKISRGLLKTILEAAKS--AHPDEFIALLSGSKD----VMDELIFLP-FVSGS-------VSAVIHLDMLPIGMKVFGTV   69 (124)
T ss_dssp             CEECHHHHHHHHHHHHH--HTTSCCEEEEEESTT----EECEEEECC-CCC--------------------CCCEEEEEE
T ss_pred             EEEcHHHHHHHHHHHHh--cCCCeeEEEEecccC----EEEEEEECC-CCCCC-------cCceeeeeeccCCCEEEEEE
Confidence            78999999999999997  455699999999974    677766 67 44432       112231 3566899999999


Q ss_pred             ee
Q 014747          413 HV  414 (419)
Q Consensus       413 HT  414 (419)
                      |+
T Consensus        70 HS   71 (124)
T 1oi0_A           70 HS   71 (124)
T ss_dssp             EE
T ss_pred             EE
Confidence            98

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

Probab=97.39  E-value=0.00019  Score=70.82  Aligned_cols=82  Identities=18%  Similarity=0.311  Sum_probs=65.8

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCC-eeEEEEEeeccCCCCCCCccccChHHHHHHhh-----cCC
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-KFYITALIIPKQESTSDSCQATNEEEIFEVQD-----KRS  405 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~-~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~-----~~~  405 (419)
                      ...|.|..--.=+.+..|..+  ...|.||+|.|+..++ .+.||+.+-..++++.+.|+..+++-..++.+     ..+
T Consensus        24 ~~~V~is~lallkm~~Ha~~~--~~~eV~GlLlG~~~~~~~v~Vt~~f~~P~~~~~~~v~~~d~~y~~~m~~~~~~v~~~  101 (306)
T 4b4t_V           24 KETVYISSIALLKMLKHGRAG--VPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQTGRD  101 (306)
T ss_dssp             CCEEEECHHHHHHHHHHTCSC--SSSCCEEEEEEEEETTTEEEEEEEECCCCEESSSCEECCCHHHHHHHHHHHHHHSCC
T ss_pred             CCEEEEeHHHHHHHHHHhcCC--CCceEEEEEeeEEcCCeEEEEEEEEeCCcCCCCCchhcCCHHHHHHHHHHHHHhCCC
Confidence            467999988888888888754  4579999999997755 79999998878999999999988763333332     377


Q ss_pred             ceeeeeeeec
Q 014747          406 LFPLGWIHVS  415 (419)
Q Consensus       406 l~~lgwiHT~  415 (419)
                      +.++||.||.
T Consensus       102 ~~vVGWYhSh  111 (306)
T 4b4t_V          102 QMVVGWYHSH  111 (306)
T ss_dssp             CCCSEEEEEC
T ss_pred             cceeeEEecC
Confidence            8999999993

>2cpt_A SKD1 protein, vacuolar sorting protein 4B; MIT, helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.7.14.1

Probab=97.08  E-value=0.0026  Score=54.53  Aligned_cols=76  Identities=11%  Similarity=0.048  Sum_probs=63.1

Q ss_pred             CCHH-HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 014747           23 IALR-YYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV  101 (419)
Q Consensus        23 iplr-~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I  101 (419)
                      ++-. .++.-|..++++|--+-..|+++.||.+|...+++|+..|..-+    .....+..++.++..-+.++|.||..|
T Consensus         8 m~~~~~~l~kAi~lv~~Ave~D~ag~y~eAl~lY~~Aie~l~~alk~e~----~~~~~k~~lr~K~~eYl~RAE~LK~~l   83 (117)
T 2cpt_A            8 MSSTSPNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEA----QGDKAKQSIRAKCTEYLDRAEKLKEYL   83 (117)
T ss_dssp             SCCCCHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTSC----CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHhcc----CCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334 58889999999999999999999999999999999987765321    133557788999999999999999977


Q ss_pred             H
Q 014747          102 Q  102 (419)
Q Consensus       102 ~  102 (419)
                      .
T Consensus        84 ~   84 (117)
T 2cpt_A           84 K   84 (117)
T ss_dssp             H
T ss_pred             h
Confidence            5

>4a5x_A MITD1, MIT domain-containing protein 1; protein transport, ESCRT, cytokinesis, midbody; HET: P15; 1.91A {Homo sapiens}

Probab=97.00  E-value=0.0036  Score=50.81  Aligned_cols=69  Identities=16%  Similarity=0.193  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747           30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ  103 (419)
Q Consensus        30 Rsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~  103 (419)
                      -.|..++++|--+...|+++.|+.+|..-+++++..+..-+     .+..|..++.++..-+.++|.||..|++
T Consensus        14 ~~A~~lv~~Ave~D~~g~y~eAl~lY~~Aie~ll~alk~e~-----d~~~k~~lr~K~~eYl~RAE~LK~~l~~   82 (86)
T 4a5x_A           14 TAAATVLKRAVELDSESRYPQALVCYQEGIDLLLQVLKGTK-----DNTKRCNLREKISKYMDRAENIKKYLDQ   82 (86)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46889999999999999999999999999999988875533     2345778889999999999999998864

>1wfd_A Hypothetical protein 1500032H18; MIT domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.7.14.1

Probab=96.98  E-value=0.0048  Score=50.63  Aligned_cols=72  Identities=15%  Similarity=0.147  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHH
Q 014747           28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK  104 (419)
Q Consensus        28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~  104 (419)
                      ++..|..++++|--+...||++.||.+|..-+++++..|..-+     ....+..++.++..-+.++|.||..|...
T Consensus        11 ~l~~Ai~lv~~Ave~D~~g~y~eAl~~Y~~Aie~l~~alk~e~-----~~~~k~~l~~K~~eYl~RAE~LK~~l~~~   82 (93)
T 1wfd_A           11 DSTAAVAVLKRAVELDAESRYQQALVCYQEGIDMLLQVLKGTK-----ESSKRCVLRTKISGYMDRAENIKKYLDQE   82 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4567889999999999999999999999999999988775433     33567788899999999999999998754

>2v6x_A Vacuolar protein sorting-associated protein 4; protein transport, vacuole, endosome, transport, ESCRT-III, VPS2, VPS4, SKD1, VPS4B, VPS4A; 1.98A {Saccharomyces cerevisiae}

Probab=96.84  E-value=0.0061  Score=48.87  Aligned_cols=76  Identities=9%  Similarity=0.114  Sum_probs=63.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747           24 ALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ  103 (419)
Q Consensus        24 plr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~  103 (419)
                      |-..++..|..++++|--.-..||++.|+.+|..-+++++..+..=+     .+..+..++.++..-+.++|.||..|++
T Consensus         5 ~~~~~l~~A~~l~~~Av~~D~~g~y~eAl~~Y~~aie~l~~a~k~e~-----~~~~k~~l~~k~~eYl~RAE~Lk~~l~~   79 (85)
T 2v6x_A            5 STGDFLTKGIELVQKAIDLDTATQYEEAYTAYYNGLDYLMLALKYEK-----NPKSKDLIRAKFTEYLNRAEQLKKHLES   79 (85)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            33447889999999999999999999999999999999987763222     3456778999999999999999998864


Q ss_pred             H
Q 014747          104 K  104 (419)
Q Consensus       104 ~  104 (419)
                      .
T Consensus        80 ~   80 (85)
T 2v6x_A           80 E   80 (85)
T ss_dssp             H
T ss_pred             c
Confidence            3

>2w2u_A Hypothetical P60 katanin; hydrolase transport complex, nucleotide-binding, ESCRT, AAA-ATPase, cytokinesis, ATP-binding; 2.20A {Sulfolobus acidocaldarius}

Probab=96.62  E-value=0.0039  Score=50.30  Aligned_cols=72  Identities=14%  Similarity=0.041  Sum_probs=60.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHH
Q 014747           24 ALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPA  100 (419)
Q Consensus        24 plr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~  100 (419)
                      |-..++..|..++++|-.+-+.|+++.||.+|..-+++++..|..=||-     ..+..++.++.+-+.++|.||..
T Consensus        11 ~~~~~~~~Ai~lv~~Ave~D~~g~y~eAl~lY~~aie~l~~alk~e~d~-----~~k~~ir~K~~eY~~RAE~LK~~   82 (83)
T 2w2u_A           11 AQVMLEEMARKYAINAVKADKEGNAEEAITNYKKAIEVLAQLVSLYRDG-----STAAIYEQMINEYKRRIEVLKEL   82 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSTTS-----STHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CchHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHCCCH-----HHHHHHHHHHHHHHHHHHHHHhh
Confidence            4556999999999999999999999999999999999998776543332     34667889999999999999964

>2v6y_A AAA family ATPase, P60 katanin; MIT, VPS4, archaea, AAA-ATPase, ATP-binding, microtubule INT and trafficking domain, nucleotide-binding; HET: SRT; 2.40A {Sulfolobus solfataricus} PDB: 2v6y_B*

Probab=96.37  E-value=0.0056  Score=49.18  Aligned_cols=69  Identities=9%  Similarity=0.021  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 014747           28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV  101 (419)
Q Consensus        28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I  101 (419)
                      ++..|..++++|--+-+.||++.||.+|..-+++++..|..-||-     ..+..++.++..-+.++|.||..|
T Consensus         7 ~~~~Ai~lv~~Ave~D~~g~y~eAl~lY~~aie~l~~~lk~e~d~-----~~k~~ir~K~~eY~~RAE~Lk~~l   75 (83)
T 2v6y_A            7 LEDMARKYAILAVKADKEGKVEDAITYYKKAIEVLSQIIVLYPES-----VARTAYEQMINEYKKRISYLEKVL   75 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHCTTC-----TTHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHCCCH-----HHHHHHHHHHHHHHHHHHHHHHHc
Confidence            788999999999999999999999999999999998776433332     346678899999999999999866

>2ymb_A MITD1, MIT domain-containing protein 1; protein transport, membrane, PLD; 3.40A {Homo sapiens}

Probab=95.24  E-value=0.0032  Score=60.89  Aligned_cols=73  Identities=15%  Similarity=0.162  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHHH
Q 014747           28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKI  105 (419)
Q Consensus        28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~Y  105 (419)
                      ++.+|.+++++|--+.+.|+++.||.+|..-+++++..+..-+     .+..|..++.++..-+.++|+||..|+++-
T Consensus        19 ~~~~Ai~lv~~AVe~D~~g~y~eAl~lY~eaIe~Ll~alk~e~-----d~~~k~~lr~Ki~eYl~RAE~LK~~L~k~k   91 (257)
T 2ymb_A           19 QSTAAATVLKRAVELDSESRYPQALVCYQEGIDLLLQVLKGTK-----DNTKRCNLREKISKYMDRAENIKKYLDQEK   91 (257)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            7889999999999999999999999999999999988876433     234577888999999999999999998754

>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=92.08  E-value=0.29  Score=44.08  Aligned_cols=83  Identities=8%  Similarity=0.162  Sum_probs=54.0

Q ss_pred             CeEeeeCHHHHHHHHHHHhhhcc--cccchhhhhcccccCCeeEEEEEeeccCCCCCCCc--cccChHHH---HHHhh--
Q 014747          332 PLQLHISTTMMDNFMKLAKSNTD--KNLETCGILAGSLKNRKFYITALIIPKQESTSDSC--QATNEEEI---FEVQD--  402 (419)
Q Consensus       332 l~~v~~p~~l~~~fl~~a~~Nt~--~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C--~~~~ee~~---f~~~~--  402 (419)
                      ...|.|.+-..-+-+..|.....  ...|-||+|.|+..++.+.|++.+-=...++.+.+  ...+.+-+   ++...  
T Consensus         7 ~~~V~i~plvllkI~~H~~r~~~~~~~~~V~G~LLG~~~~~~v~V~~~f~lp~~~~~~~~~~~~~d~ey~~~m~~~~~~v   86 (187)
T 2o95_A            7 VQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFLDHDYLENMYGMFKKV   86 (187)
T ss_dssp             CSEEEECHHHHHHHHHHHHHHHHTTCCSCCEEEEEEEESSSEEEEEEEEEECEEECSSCTTSEEECHHHHHHHHHHHHTT
T ss_pred             CCEEEEchHHHHHHHHHHhhhcccCCCcEEEEEEEEEEcCCEEEEEEEEEeCCcccCCCcchhhcCHHHHHHHHHHHHHh
Confidence            45688888877777777655432  46799999999999999999886543333333322  12332311   21111  


Q ss_pred             cCCceeeeeeee
Q 014747          403 KRSLFPLGWIHV  414 (419)
Q Consensus       403 ~~~l~~lgwiHT  414 (419)
                      ..++..+||-||
T Consensus        87 ~~~~~iVGWY~s   98 (187)
T 2o95_A           87 NARERIVGWYHT   98 (187)
T ss_dssp             SSSCEEEEEEEC
T ss_pred             CCCCCEEEEEcC
Confidence            358999999998

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=87.92  E-value=0.099  Score=53.26  Aligned_cols=75  Identities=13%  Similarity=0.069  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHH
Q 014747           26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK  104 (419)
Q Consensus        26 r~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~  104 (419)
                      ..|+..|.+++++|--+-+.||++.||.+|...+.+++..|..    .......+..++.++..-+.++|.||..|+++
T Consensus         5 ~~~~~~A~~~~~~Av~~D~~g~~~eA~~~Y~~a~~~l~~~~k~----e~~~~~~k~~ir~k~~ey~~Rae~Lk~~l~k~   79 (444)
T 2zan_A            5 NTNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKY----EAQGDKAKQSIRAKCTEYLDRAEKLKEYLKKK   79 (444)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHh----hccChHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            3478899999999999999999999999999999999877632    11122335678888999999999999998654

---

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	419
d2a9ua1	134	a.118.23.1 (A:6-139) Ubiquitin carboxyl-terminal h	1e-18

>d2a9ua1 a.118.23.1 (A:6-139) Ubiquitin carboxyl-terminal hydrolase 8, USH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 134

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: USP8 N-terminal domain-like
family: USP8 N-terminal domain-like
domain: Ubiquitin carboxyl-terminal hydrolase 8, USH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 79.5 bits (196), Expect = 1e-18
 Identities = 17/97 (17%), Positives = 40/97 (41%), Gaps = 2/97 (2%)

Query: 20  DNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDY-LASFKS 78
             +I+ + Y   A  I K A+  R +++    YV+ +++ ++    I    D+       
Sbjct: 23  PEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVY-NLIKKRPDFKQQQDYF 81

Query: 79  QKLYLKKKLLNALSELEELQPAVQQKINELNRKKTNQ 115
             +     +  A+ E E L  +++ +  E   +K  +
Sbjct: 82  HSILGPGNIKKAVEEAERLSESLKLRYEEAEVRKKLE 118

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	419
d2a9ua1	134	Ubiquitin carboxyl-terminal hydrolase 8, USH8 {Hum	99.92
d1wfda_	93	Hypothetical protein 1500032H18Rik {Mouse (Mus mus	97.32
d1oi0a_	121	Hypothetical protein AF2198 {Archaeon Archaeoglobu	97.09
d1wr0a1	77	Vacuolar sorting protein 4b (VPS4B, SKD1 protein)	96.63

>d2a9ua1 a.118.23.1 (A:6-139) Ubiquitin carboxyl-terminal hydrolase 8, USH8 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: USP8 N-terminal domain-like
family: USP8 N-terminal domain-like
domain: Ubiquitin carboxyl-terminal hydrolase 8, USH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1.5e-25  Score=195.87  Aligned_cols=105  Identities=18%  Similarity=0.286  Sum_probs=92.9

Q ss_pred             hhHHHhhcccccCC-CCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHH-HH
Q 014747            8 INIAASAQRLDVDN-RIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYL-KK   85 (419)
Q Consensus         8 ~eL~~~A~~~e~n~-~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l-~k   85 (419)
                      ..|.+.+..++||+ +||+++|+|+|++|+++|.+|+++||+|+|||+||||++|| ++||+||||+......+..+ .+
T Consensus        10 ~sl~dL~k~~e~~~~~i~~k~y~rsa~~l~~~A~~y~~egd~E~AYily~Ry~~L~-eki~kHpdyk~~~~~~~~~l~~~   88 (134)
T d2a9ua1          10 SSLKDLNKKTEVKPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVY-NLIKKRPDFKQQQDYFHSILGPG   88 (134)
T ss_dssp             SSHHHHHGGGCCCGGGSCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-HHHTTSHHHHHTHHHHHHHHCHH
T ss_pred             hhHHHHHHhhccCcccCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-HHHHcCcccccchhHHHHHHhhh
Confidence            46889999999986 69999999999999999999999999999999999999998 99999999986554444433 47


Q ss_pred             HHHHHHHHHHhhcHHHHHHHHHHHHhhh
Q 014747           86 KLLNALSELEELQPAVQQKINELNRKKT  113 (419)
Q Consensus        86 ~l~~vl~~lE~LK~~I~~~Y~e~~~~~~  113 (419)
                      .++.+|+++|.||+.|+++|++++...+
T Consensus        89 ~~~~~l~~~E~Lk~~L~~rYe~~~~~~~  116 (134)
T d2a9ua1          89 NIKKAVEEAERLSESLKLRYEEAEVRKK  116 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999999999876443

>d1wfda_ a.7.14.1 (A:) Hypothetical protein 1500032H18Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Spectrin repeat-like
superfamily: MIT domain
family: MIT domain
domain: Hypothetical protein 1500032H18Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.32  E-value=0.00052  Score=54.49  Aligned_cols=72  Identities=15%  Similarity=0.147  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHH
Q 014747           28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK  104 (419)
Q Consensus        28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~  104 (419)
                      .+-.|..++++|--+.+.||++.|+.+|...+++++..+..-+     ....+..++.++..-+.++|.||..|...
T Consensus        11 ~~~~A~~l~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~~~~e~-----~~~~k~~l~~k~~eYl~RAE~LK~~l~~~   82 (93)
T d1wfda_          11 DSTAAVAVLKRAVELDAESRYQQALVCYQEGIDMLLQVLKGTK-----ESSKRCVLRTKISGYMDRAENIKKYLDQE   82 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhhccC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4668999999999999999999999999999999988775332     34567788899999999999999988643

>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=97.09  E-value=0.00026  Score=58.72  Aligned_cols=68  Identities=22%  Similarity=0.244  Sum_probs=45.1

Q ss_pred             EeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHH-HhhcCCceeeeee
Q 014747          334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFE-VQDKRSLFPLGWI  412 (419)
Q Consensus       334 ~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~-~~~~~~l~~lgwi  412 (419)
                      .|.|+.+++...++.|..+..+  |.||+|+|+-  +  .|+.+++......+.       ...|. .++..++-.+||.
T Consensus         3 ~l~I~~~~l~~i~~hA~~~~P~--E~cGlL~G~~--~--~i~~~~~~~n~~~~~-------~~~~~~~~~~~~~~ivgi~   69 (121)
T d1oi0a_           3 SMKISRGLLKTILEAAKSAHPD--EFIALLSGSK--D--VMDELIFLPFVSGSV-------SAVIHLDMLPIGMKVFGTV   69 (121)
T ss_dssp             SCEECHHHHHHHHHHHHHHTTS--CCEEEEEEST--T--EECEEEECCCCC--------------------CCCEEEEEE
T ss_pred             eEEECHHHHHHHHHHHHhcCCc--eeEEEEEecC--C--cEEEEEEcCCCCCCc-------ccccccchhhcCCeEEEEE
Confidence            3789999999999999988766  9999999963  2  566655544333222       22232 2567899999999


Q ss_pred             ee
Q 014747          413 HV  414 (419)
Q Consensus       413 HT  414 (419)
                      |+
T Consensus        70 HS   71 (121)
T d1oi0a_          70 HS   71 (121)
T ss_dssp             EE
T ss_pred             Ee
Confidence            98

>d1wr0a1 a.7.14.1 (A:5-81) Vacuolar sorting protein 4b (VPS4B, SKD1 protein) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Spectrin repeat-like
superfamily: MIT domain
family: MIT domain
domain: Vacuolar sorting protein 4b (VPS4B, SKD1 protein)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.63  E-value=0.0008  Score=51.44  Aligned_cols=71  Identities=11%  Similarity=0.038  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 014747           27 YYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV  101 (419)
Q Consensus        27 ~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I  101 (419)
                      .-+..|..++++|--+-+.||++.|+.+|...+++++.-|..-+    .....|..++.++..-+.++|.||..|
T Consensus         6 ~~l~~A~~l~~~Av~~D~~~~y~~A~~~Y~~a~~~l~~~l~~e~----~~~~~k~~l~~k~~~Yl~RAE~LK~~l   76 (77)
T d1wr0a1           6 PNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEA----QGDKAKQSIRAKCTEYLDRAEKLKEYL   76 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSC----CTGGGGHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhccC----CCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34678999999999999999999999999999999977665322    123446778899999999999999654