Citrus Sinensis ID: 015628

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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---
Protein Sequence
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED
Secondary Structure (PSIPRED)
cEEEEEcccccEEEEEEcccccHHHHHHHHHHHccccccccccEEEEEEcccccccccHHHcccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEEEEccHHHHHHHHHHHHHHcccccccHHHcEEEEccEEEcccccHHHcccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccHHHHHHHHHccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHHHcHHHHHHHHHHHHcccHHHHHHHHHcHHHHHHHHcccccccccccccccccccccEEEEcHHHHHHHHHHHHccccHHHEEEEEEEccccHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
MKVFVKTlkgthfeievkpedkvsdVKKNIetvqgsdvypasQQMLIHqgkvlkdvttleenkvaENSFVVVMLTKskvsssgastvsaapanqaqttssapptstqptttsqtpaptvappqsvpesapppaapapapapapapapapapvsssvsdvYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYsgipeqtavppvarasaggqagnppaqtqaqqpaapaptsgpnanpldlfpqglpnmgsnagagtLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLinepveggegnvLGQLAsampqavtvtpEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED
Flexible Loop (DISEMBL)
mkvfvktlkgthfeievkpedkvsdvkKNIETvqgsdvypasqQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSssgastvsaapanqaqttssapptstqpTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED
Low Complexity Region (SEG)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLtkskvsssgastvsaAPANqaqttssapptstqptttsqtpaptvappqsvpesapppaapapapapapapapapapvsssvsDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARasaggqagnppaqtqaqqpaapaptsgpNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED
Disordered region (IsUnstruct)
****VKTLKGTHFEI**********************VYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT******************************************************************************************NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI**************************************************************LDFLR***QFQALRTMVQANPQILQPML*******PHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLA******VT*******AIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH******
Disordered Region (DISOPRED)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV************************************************************************************************************************************************************************************************************************************************************************************************EAIERLEAMGFDRALVLEVFFACNKNEELAANYL**H******
Disordered Region (DISEMBL)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS*******************************************************************************SDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVA***************************GPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED
Disordered Region (DISPRO)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS******************************************************************************************VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTA*******************************************************GTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP****************PQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHM*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED
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	403	2.2.26 [Sep-21-2011]
Q84L31	419	Putative DNA repair prote	yes	no	0.957	0.921	0.697	1e-159
Q84L30	378	Putative DNA repair prote	no	no	0.935	0.997	0.704	1e-147
Q40742	392	Probable DNA repair prote	yes	no	0.952	0.979	0.626	1e-131
Q84L33	371	Putative DNA repair prote	no	no	0.908	0.986	0.578	1e-118
Q84L32	368	Putative DNA repair prote	no	no	0.908	0.994	0.530	1e-112
P54727	409	UV excision repair protei	yes	no	0.920	0.907	0.389	4e-63
P54728	416	UV excision repair protei	yes	no	0.905	0.877	0.369	4e-62
Q4KMA2	415	UV excision repair protei	yes	no	0.923	0.896	0.371	6e-62
Q29RK4	408	UV excision repair protei	yes	no	0.905	0.894	0.366	2e-59
P54725	363	UV excision repair protei	no	no	0.853	0.947	0.375	8e-54

>sp|Q84L31|RD23C_ARATH Putative DNA repair protein RAD23-3 OS=Arabidopsis thaliana GN=RAD23-3 PE=2 SV=2

 Score =  562 bits (1449), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 304/436 (69%), Positives = 343/436 (78%), Gaps = 50/436 (11%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+FVKTLKGTHFEIEVKPED V DVKKNIE+VQG+DVYPA++QMLIHQGKVLKD TT+E
Sbjct: 1   MKIFVKTLKGTHFEIEVKPEDSVVDVKKNIESVQGADVYPAAKQMLIHQGKVLKDETTIE 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAP--- 117
           ENKVAENSF+V+M+ KSK +S+ AS+ SA   +QA+   S PP+++QP+ + QTPA    
Sbjct: 61  ENKVAENSFIVIMMNKSKPASAAASSASAG-TSQAK---SIPPSTSQPSISPQTPASVSA 116

Query: 118 -------------------------TVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPV 152
                                    TV  P  +PE       P PA   +  PAP  APV
Sbjct: 117 PVAPAPTRPPPPAPTPTPAPVAATETVTTP--IPE-------PVPATISSSTPAPDSAPV 167

Query: 153 SSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY 212
            S   DVYGQAASNL AGSNLE+T+QQILDMGGG+WDRETV+ ALRAA+NNPERAVEYLY
Sbjct: 168 GSQ-GDVYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLY 226

Query: 213 SGIPEQTAVPPVARA-SAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGS 271
           +GIPEQ  VPPVAR  ++ GQ  NPPAQTQ  QPAA AP SGPNANPLDLFPQGLPN+G 
Sbjct: 227 TGIPEQAEVPPVARPPASAGQPANPPAQTQ--QPAA-APASGPNANPLDLFPQGLPNVGG 283

Query: 272 NAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLIN 331
           N GAGTLDFLRNSQQFQALR MVQANPQ+LQPMLQELGKQNP+LMRLIQ+HQ DFLRLIN
Sbjct: 284 NPGAGTLDFLRNSQQFQALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLIN 343

Query: 332 EPVEGG--EGNVLGQLASAM--PQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNE 387
           EPVEGG   GN+LGQ+A+ M  PQA+ VT EEREAIERLEAMGF+RALVLEVFFACNKNE
Sbjct: 344 EPVEGGGESGNLLGQMAAGMPQPQAIQVTHEEREAIERLEAMGFERALVLEVFFACNKNE 403

Query: 388 ELAANYLLDHMHEFED 403
           ELAANYLLDHMHEFE+
Sbjct: 404 ELAANYLLDHMHEFEE 419

May be involved in nucleotide excision repair.
Arabidopsis thaliana (taxid: 3702)

>sp|Q84L30|RD23D_ARATH Putative DNA repair protein RAD23-4 OS=Arabidopsis thaliana GN=RAD23-4 PE=2 SV=2

 Score =  521 bits (1343), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 284/403 (70%), Positives = 315/403 (78%), Gaps = 26/403 (6%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+FVKTL G++FEIEVKP DKVSDVK  IETV+G++ YPA++QMLIHQGKVLKD TTLE
Sbjct: 1   MKIFVKTLSGSNFEIEVKPADKVSDVKTAIETVKGAE-YPAAKQMLIHQGKVLKDETTLE 59

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           EN V ENSF+V+ML+K+K S SGAST SA PA          P++TQP T        VA
Sbjct: 60  ENNVVENSFIVIMLSKTKASPSGASTASA-PA----------PSATQPQT--------VA 100

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
            PQ        P A  P P    A A APA  +S  +DVYGQAASNLVAG+ LE+TVQQI
Sbjct: 101 TPQ-----VSAPTASVPVPTSGTATAAAPATAASVQTDVYGQAASNLVAGTTLESTVQQI 155

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           LDMGGGSWDR+TV+RALRAA+NNPERAVEYLYSGIP Q  +PPVA+A A G+    P   
Sbjct: 156 LDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPATGEQAANPLAQ 215

Query: 241 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQI 300
             Q  A  A T GPNANPL+LFPQG+P   + AGAG LDFLRNSQQFQALR MVQANPQI
Sbjct: 216 PQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQFQALRAMVQANPQI 275

Query: 301 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEER 360
           LQPMLQELGKQNP L+RLIQEHQ DFLRLINEPVE GE NV+ QL +AMPQAVTVTPEER
Sbjct: 276 LQPMLQELGKQNPQLVRLIQEHQADFLRLINEPVE-GEENVMEQLEAAMPQAVTVTPEER 334

Query: 361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           EAIERLE MGFDRA+VLEVFFACNKNEELAANYLLDHMHEFED
Sbjct: 335 EAIERLEGMGFDRAMVLEVFFACNKNEELAANYLLDHMHEFED 377

May be involved in nucleotide excision repair.

Arabidopsis thaliana (taxid: 3702)

>sp|Q40742|RAD23_ORYSJ Probable DNA repair protein RAD23 OS=Oryza sativa subsp. japonica GN=RAD23 PE=1 SV=2

 Score =  469 bits (1208), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 255/407 (62%), Positives = 300/407 (73%), Gaps = 23/407 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+ VKTLKG+ F+IEV    KV+DVK+ IET QG  +YPA QQMLIHQGKVLKD TTL+
Sbjct: 1   MKISVKTLKGSTFQIEVDSAQKVADVKRIIETTQGQHIYPAEQQMLIHQGKVLKDDTTLD 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTT-TSQTPAPTV 119
           ENKV ENSF+V+ML + K SSS A   S AP+NQ      APPT T P    SQ P   V
Sbjct: 61  ENKVLENSFLVIMLRQGKGSSSSAPATSKAPSNQ------APPTQTVPAAPASQAP---V 111

Query: 120 APPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQ 179
           AP  +VP +         AP P    +PAPA   SS +D YGQA SNLVAGSNLEAT+Q 
Sbjct: 112 APATTVPVT-------VSAPTPTATASPAPAVAVSSEADNYGQATSNLVAGSNLEATIQS 164

Query: 180 ILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQ 239
           IL+MGGG WDR+ V+ AL AA+NNPERAVEYLYSG+PEQ  + PV   S   Q  NP   
Sbjct: 165 ILEMGGGIWDRDIVLHALSAAFNNPERAVEYLYSGVPEQMDI-PVPPPSI--QPANPTQA 221

Query: 240 TQAQQPAAPAP-TSGPNANPLDLFPQGLPNMGSN-AGAGTLDFLRNSQQFQALRTMVQAN 297
           +QA QPAAP+  +SGPNA+PLDLFPQ LPN  ++ AG G LD LRN+ QF+ L ++VQAN
Sbjct: 222 SQATQPAAPSILSSGPNASPLDLFPQALPNASTDAAGLGNLDALRNNAQFRTLLSLVQAN 281

Query: 298 PQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG-GEGNVLGQLASAMPQAVTVT 356
           PQILQP+LQELGKQNP +++LIQE+Q +FL LINEP EG  E N+L Q   AMPQ + VT
Sbjct: 282 PQILQPLLQELGKQNPQILQLIQENQAEFLHLINEPAEGDDEENLLDQFPEAMPQTIAVT 341

Query: 357 PEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           PEE EAI RLEAMGFDRALVL+VFFACNK+E+LAANYLLDHM+EF+D
Sbjct: 342 PEENEAILRLEAMGFDRALVLDVFFACNKDEQLAANYLLDHMNEFDD 388

May be involved in nucleotide excision repair.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q84L33|RD23A_ARATH Putative DNA repair protein RAD23-1 OS=Arabidopsis thaliana GN=RAD23-1 PE=2 SV=3

 Score =  424 bits (1091), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 236/408 (57%), Positives = 284/408 (69%), Gaps = 42/408 (10%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+ VKTLKG+HFEI V P D +  VKKNIE  QG D YP  QQ+LIH GKVLKD T+L 
Sbjct: 1   MKLTVKTLKGSHFEIRVLPSDTIMAVKKNIEDSQGKDNYPCGQQLLIHNGKVLKDETSLV 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKV E  F+VVML+KSK   SG S   A+     QT+S + P S   TT+S  PA   A
Sbjct: 61  ENKVTEEGFLVVMLSKSK---SGGSAGQAS----VQTSSVSQPVSA--TTSSTKPA---A 108

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
           P  S  +S+P PA+P PA     A            +D YGQAAS LV+GS+LE  VQQI
Sbjct: 109 P--STTQSSPVPASPIPAQEQPAAQ-----------TDTYGQAASTLVSGSSLEQMVQQI 155

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE--QTAVP-PVARASAGGQAGNPP 237
           ++MGGGSWD+ETV RALRAAYNNPERAV+YLYSGIP+  + AVP P A+ +  G A    
Sbjct: 156 MEMGGGSWDKETVTRALRAAYNNPERAVDYLYSGIPQTAEVAVPVPEAQIAGSGAA---- 211

Query: 238 AQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQAN 297
                  P APA + GPN++PLDLFPQ       +   GTL+FLRN+ QFQ LRTMV +N
Sbjct: 212 -------PVAPA-SGGPNSSPLDLFPQETVAAAGSGDLGTLEFLRNNDQFQQLRTMVHSN 263

Query: 298 PQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG--GEGNVLGQLASAMPQAVTV 355
           PQILQPMLQELGKQNP L+RLIQE+Q +FL+L+NEP EG  GEG++  Q    MP A+ V
Sbjct: 264 PQILQPMLQELGKQNPQLLRLIQENQAEFLQLVNEPYEGSDGEGDMFDQPEQEMPHAINV 323

Query: 356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           TP E+EAI+RLEAMGFDRALV+E F AC++NEELAANYLL++  +FED
Sbjct: 324 TPAEQEAIQRLEAMGFDRALVIEAFLACDRNEELAANYLLENSGDFED 371

May be involved in nucleotide excision repair.

Arabidopsis thaliana (taxid: 3702)

>sp|Q84L32|RD23B_ARATH Putative DNA repair protein RAD23-2 OS=Arabidopsis thaliana GN=RAD23-2 PE=2 SV=2

 Score =  407 bits (1045), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 215/405 (53%), Positives = 271/405 (66%), Gaps = 39/405 (9%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+ VKTLKG+HFEI V P D +  VKKNIE  Q  D YP  QQ+LIH GKVLKD TTL 
Sbjct: 1   MKLTVKTLKGSHFEIRVLPTDTIMAVKKNIEDSQSKDNYPCGQQLLIHNGKVLKDETTLV 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKV E  F+VVML+KSK +SS      A P++   T+++         +++   AP+  
Sbjct: 61  ENKVTEEGFLVVMLSKSKTASS------AGPSSTQPTSTTT-----STISSTTLAAPSTT 109

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
              +VP S   P    P                ++ SD YGQAAS LV+GS++E  VQQI
Sbjct: 110 QSIAVPASNSTPVQEQP----------------TAQSDTYGQAASTLVSGSSIEQMVQQI 153

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           ++MGGGSWD+ETV RALRAAYNNPERAV+YLYSGIPE   +P    +  G          
Sbjct: 154 MEMGGGSWDKETVTRALRAAYNNPERAVDYLYSGIPETVTIPATNLSGVGS--------- 204

Query: 241 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQI 300
             ++  AP P+ GPN++PLDLFPQ   +  +    GTL+FLR + QFQ LR+MV +NPQI
Sbjct: 205 -GRELTAPPPSGGPNSSPLDLFPQEAVSDAAGGDLGTLEFLRGNDQFQQLRSMVNSNPQI 263

Query: 301 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNV--LGQLASAMPQAVTVTPE 358
           LQPMLQELGKQNP L+RLIQE+Q +FL+L+NEP EG +G+V    Q    MP +V VTPE
Sbjct: 264 LQPMLQELGKQNPQLLRLIQENQAEFLQLLNEPYEGSDGDVDIFDQPDQEMPHSVNVTPE 323

Query: 359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           E+E+IERLEAMGFDRA+V+E F +C++NEELAANYLL+H  +FED
Sbjct: 324 EQESIERLEAMGFDRAIVIEAFLSCDRNEELAANYLLEHSADFED 368

May be involved in nucleotide excision repair.

Arabidopsis thaliana (taxid: 3702)

>sp|P54727|RD23B_HUMAN UV excision repair protein RAD23 homolog B OS=Homo sapiens GN=RAD23B PE=1 SV=1

 Score =  242 bits (617), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 166/426 (38%), Positives = 235/426 (55%), Gaps = 55/426 (12%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M+V +KTL+   F+I++ PE+ V  +K+ IE+ +G D +P + Q LI+ GK+L D T L+
Sbjct: 1   MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 61  ENKVAENSFVVVMLTKSKVSSS--GASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPT 118
           E K+ E +FVVVM+TK K  S+   A+T  +APA+    TSS   T  Q  T     APT
Sbjct: 61  EYKIDEKNFVVVMVTKPKAVSTPAPATTQQSAPASTTAVTSSTTTTVAQAPTPVPALAPT 120

Query: 119 VAPPQSVPESAPPPAAPAPAPA---PAPAPAPAPAPVS------------SSVSDVYGQA 163
             P    P SA   + PAPA A     PA  PA  PV+            SS S+++  A
Sbjct: 121 STPASITPASATASSEPAPASAAKQEKPAEKPAETPVATSPTATDSTSGDSSRSNLFEDA 180

Query: 164 ASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP---EQTA 220
            S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP   E  A
Sbjct: 181 TSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQA 237

Query: 221 V--PPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTL 278
           V  PP A ++   Q+    A            +SG           G P          L
Sbjct: 238 VVDPPQAASTGAPQSSAVAAAAATTTATTTTTSSG-----------GHP----------L 276

Query: 279 DFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG- 337
           +FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV+   
Sbjct: 277 EFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAG 336

Query: 338 --------EGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEEL 389
                       + +  S     + VTP+E+EAIERL+A+GF   LV++ +FAC KNE L
Sbjct: 337 GQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENL 396

Query: 390 AANYLL 395
           AAN+LL
Sbjct: 397 AANFLL 402

The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, XPA, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the XPC:RAD23B dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. XPC:RAD23B contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. XPC:RAD23B induces a bend in DNA upon binding. XPC:RAD23B stimulates the activity of DNA glycosylases TDG and SMUG1.

Homo sapiens (taxid: 9606)

>sp|P54728|RD23B_MOUSE UV excision repair protein RAD23 homolog B OS=Mus musculus GN=Rad23b PE=1 SV=2

 Score =  239 bits (609), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 162/439 (36%), Positives = 232/439 (52%), Gaps = 74/439 (16%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M+V +KTL+   F+I++ PE+ V  +K+ IE+ +G D +P + Q LI+ GK+L D T L+
Sbjct: 1   MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILSDDTALK 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQP------------ 108
           E K+ E +FVVVM+TK K      +  +A PA   Q +S+  PT+               
Sbjct: 61  EYKIDEKNFVVVMVTKPK------AVTTAVPAT-TQPSSTPSPTAVSSSPAVAAAQAPAP 113

Query: 109 --------TTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAP---APAPAPA-PVSSSV 156
                   T  S  PA T A  +  P  A  P  PA  PA  P   +PAPA + P  SS 
Sbjct: 114 TPALPPTSTPASTAPASTTASSEPAPAGATQPEKPAEKPAQTPVLTSPAPADSTPGDSSR 173

Query: 157 SDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 216
           S+++  A S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP
Sbjct: 174 SNLFEDATSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIP 230

Query: 217 ----EQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSN 272
                Q  V P            PP       P +PA  +                  + 
Sbjct: 231 GDRESQAVVDP------------PPQAVSTGTPQSPAVAAAAATT--------TATTTTT 270

Query: 273 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 332
           +G   L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NE
Sbjct: 271 SGGHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNE 330

Query: 333 PV-EGGE---------------GNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALV 376
           PV E G                G  + +  S     + VTP+E+EAIERL+A+GF   LV
Sbjct: 331 PVQEAGSQGGGGGGGGGGGGGGGGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLV 390

Query: 377 LEVFFACNKNEELAANYLL 395
           ++ +FAC KNE LAAN+LL
Sbjct: 391 IQAYFACEKNENLAANFLL 409

The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, Xpa, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the Xpc:Rad23b dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. Xpc:Rad23b contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. Xpc:Rad23bB induces a bend in DNA upon binding. Xpc:Rad23b stimulates the activity of DNA glycosylases Tdg and Smug1.

Mus musculus (taxid: 10090)

>sp|Q4KMA2|RD23B_RAT UV excision repair protein RAD23 homolog B OS=Rattus norvegicus GN=Rad23b PE=1 SV=1

 Score =  238 bits (607), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 160/431 (37%), Positives = 231/431 (53%), Gaps = 59/431 (13%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M+V +KTL+   F+I++ PE+ V  +K+ IE+ +G D +P + Q LI+ GK+L D T L+
Sbjct: 1   MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILSDDTALK 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGA-------------STVSAAPANQAQTTSSAPPTSTQ 107
           E K+ E +FVVVM+TK K  +S               +  S+  A  AQ  +  P  +  
Sbjct: 61  EYKIDEKNFVVVMVTKPKAVTSAVPATTQQSSSPSTTTVSSSPAAAVAQAPAPTPALAPT 120

Query: 108 PTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAP---APAPAPA-PVSSSVSDVYGQA 163
            T  S TPA T A  +  P  A  P  PA  PA  P   +PAPA + P  SS S+++  A
Sbjct: 121 STPASTTPASTTASSEPAPTGATQPEKPAEKPAQTPVLTSPAPADSTPGDSSRSNLFEDA 180

Query: 164 ASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP----EQT 219
            S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP     Q 
Sbjct: 181 TSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQA 237

Query: 220 AVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLD 279
            V P            PP       P +PA  +                  + +G   L+
Sbjct: 238 VVDP------------PPQAVSTGTPQSPAVAAAAATT--------TATTTTTSGGHPLE 277

Query: 280 FLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG-- 337
           FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV+    
Sbjct: 278 FLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGG 337

Query: 338 -------------EGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACN 384
                         G  + +  S     + VTP+E+EAIERL+A+GF   LV++ +FAC 
Sbjct: 338 QGGGGGGGGGGGGGGGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACE 397

Query: 385 KNEELAANYLL 395
           KNE LAAN+LL
Sbjct: 398 KNENLAANFLL 408

The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, Xpa, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the XPC:RAD23B dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. XPC:RAD23B contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. Xpc:Rad22b induces a bend in DNA upon binding. Xpc:Rad23b stimulates the activity of DNA glycosylases Tdg and Smug1.

Rattus norvegicus (taxid: 10116)

>sp|Q29RK4|RD23B_BOVIN UV excision repair protein RAD23 homolog B OS=Bos taurus GN=RAD23B PE=2 SV=1

 Score =  229 bits (585), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 158/431 (36%), Positives = 226/431 (52%), Gaps = 66/431 (15%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M V +KTL+   F+I++ P++ V  +K+ IE+ +G D +P + Q LI+ GK+L D T L+
Sbjct: 1   MLVTLKTLQQQTFKIDIDPDETVRALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPT----------- 109
           E K+ E +FVVVM+TK K      +  + APA   Q+ S+A  T +  T           
Sbjct: 61  EYKIDEKNFVVVMVTKPK------AVTTPAPATTQQSNSAATTTVSSSTAPAVTQAPAPA 114

Query: 110 --------TTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSV----S 157
                     S TPAPT A  +  P SA     PA  P   P      +  S+S     S
Sbjct: 115 PASAPTPTPVSVTPAPTTASSEPAPASAAKQEKPAERPVETPVATTPTSTDSTSGDSSRS 174

Query: 158 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP- 216
           +++  A S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP 
Sbjct: 175 NLFEDATSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPG 231

Query: 217 ---EQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNA 273
               Q  V P   AS G    +  A            +SG           G P      
Sbjct: 232 DRESQAVVDPPPAASTGAPQSSVAAAAATTTATTTTTSSG-----------GHP------ 274

Query: 274 GAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP 333
               L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEP
Sbjct: 275 ----LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEP 330

Query: 334 VEGGEGNVLGQLASAMPQA---------VTVTPEEREAIERLEAMGFDRALVLEVFFACN 384
           V+   G   G    +   A         + VTP+E+EAIERL+A+GF   LV++ +FAC 
Sbjct: 331 VQEAGGQGGGGGGGSGGIAEAGGGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACE 390

Query: 385 KNEELAANYLL 395
           KNE LAAN+LL
Sbjct: 391 KNENLAANFLL 401

The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, XPA, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the XPC:RAD23B dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. XPC:RAD23B contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. XPC:RAD23B induces a bend in DNA upon binding. XPC:RAD23B stimulates the activity of DNA glycosylases TDG and SMUG1.

Bos taurus (taxid: 9913)

>sp|P54725|RD23A_HUMAN UV excision repair protein RAD23 homolog A OS=Homo sapiens GN=RAD23A PE=1 SV=1

 Score =  211 bits (537), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 156/415 (37%), Positives = 227/415 (54%), Gaps = 71/415 (17%)

Query: 3   VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN 62
           + +KTL+   F+I ++P++ V  +K+ IE  +G D +P + Q LI+ GK+L D   + + 
Sbjct: 5   ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 64

Query: 63  KVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPP 122
           ++ E +FVVVM+TK+K   +G  T SA P         A PT+   ++TS  PAPT    
Sbjct: 65  RIDEKNFVVVMVTKTK---AGQGT-SAPP--------EASPTAAPESSTSFPPAPTSG-- 110

Query: 123 QSVPESAPPPAA---PAPAPAPAPAPAPAPAPVSSSVSDVYGQ---AASNLVAGSNLEAT 176
                S PPPAA    +P+   AP  +P     S   S   G+   AAS LV GS  E  
Sbjct: 111 ----MSHPPPAAREDKSPSEESAPTTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETM 166

Query: 177 VQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNP 236
           + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP           S   + G+ 
Sbjct: 167 LTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP----------GSPEPEHGSV 213

Query: 237 PAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQA 296
                ++QPA  A                       AG   L+FLR+  QFQ +R ++Q 
Sbjct: 214 QESQVSEQPATEA-----------------------AGENPLEFLRDQPQFQNMRQVIQQ 250

Query: 297 NPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP------VEGGEGNVLGQLASAMP 350
           NP +L  +LQ+LG++NP L++ I  HQ  F++++NEP      +   EG V G +    P
Sbjct: 251 NPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEPPGELADISDVEGEV-GAIGEEAP 309

Query: 351 QA--VTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           Q   + VTP+E+EAIERL+A+GF  +LV++ +FAC KNE LAAN+LL     F+D
Sbjct: 310 QMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLS--QNFDD 362

Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.

Homo sapiens (taxid: 9606)

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	403
225452017	381	PREDICTED: putative DNA repair protein R	0.945	1.0	0.766	1e-171
255551362	381	uv excision repair protein rad23, putati	0.945	1.0	0.759	1e-169
224079274	385	predicted protein [Populus trichocarpa]	0.942	0.987	0.745	1e-161
363807216	400	uncharacterized protein LOC100813881 [Gl	0.987	0.995	0.758	1e-160
5640111	389	RAD23 protein [Solanum lycopersicum var.	0.945	0.979	0.732	1e-160
356575534	402	PREDICTED: putative DNA repair protein R	0.990	0.992	0.735	1e-159
297832888	417	hypothetical protein ARALYDRAFT_477488 [	0.982	0.949	0.735	1e-159
358248820	392	uncharacterized protein LOC100809066 [Gl	0.970	0.997	0.754	1e-158
224127650	384	predicted protein [Populus trichocarpa]	0.935	0.981	0.734	1e-158
15232924	419	putative DNA repair protein RAD23-3 [Ara	0.957	0.921	0.697	1e-158

>gi|225452017|ref|XP_002283656.1| PREDICTED: putative DNA repair protein RAD23-3 isoform 1 [Vitis vinifera] gi|296087286|emb|CBI33660.3| unnamed protein product [Vitis vinifera]

 Score =  607 bits (1565), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 309/403 (76%), Positives = 337/403 (83%), Gaps = 22/403 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+FVKTLKGTHFEIEVKPED V+DVKKNIE V G+DVYPA+QQMLIHQGKVLKD TTL+
Sbjct: 1   MKIFVKTLKGTHFEIEVKPEDTVADVKKNIELVHGTDVYPAAQQMLIHQGKVLKDATTLD 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           EN+VAE+SFVV+ML+K+KVS+ GAST SAAP +QAQ  SS+PPTS QP+T  Q  AP VA
Sbjct: 61  ENQVAESSFVVIMLSKNKVSAGGASTTSAAPTSQAQPVSSSPPTSNQPSTAPQ--APVVA 118

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
            P+ +PE                 PAPA AP  SS SD+YGQAASNLVAG+NLE T+QQI
Sbjct: 119 LPEVIPE-----------------PAPAVAPSISSDSDIYGQAASNLVAGNNLEVTIQQI 161

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           LDMGGGSWDR+TV+RALRAAYNNPERAVEYLYSGIPEQ   PP AR  A G A N P Q 
Sbjct: 162 LDMGGGSWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEGPPAARPPASGLAVNLPTQA 221

Query: 241 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQI 300
             Q P     +SGPNANPLDLFPQGLP+MGSNA AGTLDFLRNS QFQALR MVQANPQI
Sbjct: 222 -PQGPQTTVASSGPNANPLDLFPQGLPSMGSNASAGTLDFLRNSPQFQALRAMVQANPQI 280

Query: 301 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEER 360
           LQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVE GEGNVLGQL + +PQAVT+TPEER
Sbjct: 281 LQPMLQELGKQNPHLMRLIQEHQADFLRLINEPVE-GEGNVLGQLGT-VPQAVTITPEER 338

Query: 361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           E+IERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE+
Sbjct: 339 ESIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFEE 381

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255551362|ref|XP_002516727.1| uv excision repair protein rad23, putative [Ricinus communis] gi|223544100|gb|EEF45625.1| uv excision repair protein rad23, putative [Ricinus communis]

 Score =  599 bits (1544), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 306/403 (75%), Positives = 335/403 (83%), Gaps = 22/403 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MKVFVKTLKGT+FEI+VKPED V DVK NIE  QG+DVYPASQQMLIHQGKVLKD TTLE
Sbjct: 1   MKVFVKTLKGTNFEIDVKPEDTVEDVKNNIEIAQGADVYPASQQMLIHQGKVLKDGTTLE 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKVAENSF+V+ML+K KVS SG ST S+AP +QAQ  S+ PP++TQP+TT+Q PA T  
Sbjct: 61  ENKVAENSFIVIMLSKRKVSPSGGSTASSAPPSQAQPASTLPPSATQPSTTAQAPAVTAE 120

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
            PQS  ES                  P   PVSS  +D+YGQAASNLVAGSNLEATVQQI
Sbjct: 121 LPQSAAES-----------------TPVVNPVSSE-TDIYGQAASNLVAGSNLEATVQQI 162

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           LDMGGGSWDRETV RALRAA+NNPERAVEYLYSGIPEQ  V P+ RA + GQA  P A  
Sbjct: 163 LDMGGGSWDRETVARALRAAFNNPERAVEYLYSGIPEQPEVQPLPRAPSSGQAAIPSA-- 220

Query: 241 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQI 300
            AQ+PAAP  + G NANPLDLFPQGLP +GS   AGTLDFLRNSQQFQALR MVQANPQI
Sbjct: 221 TAQEPAAPT-SGGANANPLDLFPQGLPTIGSTTSAGTLDFLRNSQQFQALRAMVQANPQI 279

Query: 301 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEER 360
           LQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVE G+GN+LGQLASA+PQ+V+VTPEER
Sbjct: 280 LQPMLQELGKQNPHLMRLIQEHQADFLRLINEPVE-GDGNLLGQLASAVPQSVSVTPEER 338

Query: 361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           EAIERLEAMGFDRA+VLEVFFACNKNEELAANYLLDHMH+FE+
Sbjct: 339 EAIERLEAMGFDRAIVLEVFFACNKNEELAANYLLDHMHDFEE 381

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224079274|ref|XP_002305813.1| predicted protein [Populus trichocarpa] gi|222848777|gb|EEE86324.1| predicted protein [Populus trichocarpa]

 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 304/408 (74%), Positives = 336/408 (82%), Gaps = 28/408 (6%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MKVFVKTLKGT+FEIEVKPED V+DVKKNIE+VQG+DVYPA+QQML++QGKVLKD TTL+
Sbjct: 1   MKVFVKTLKGTNFEIEVKPEDTVADVKKNIESVQGADVYPAAQQMLVYQGKVLKDDTTLD 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKV+E+SF VVML+KSKVSS G ST  AAPA+QA   SS P   TQP+ TSQ P P  A
Sbjct: 61  ENKVSESSFFVVMLSKSKVSSGGPSTAPAAPASQAPPASSLPSNVTQPSITSQAPVPAAA 120

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSD--VYGQAASNLVAGSNLEATVQ 178
            PQS  ES+P                   A V+S++ D  +YGQAASNLVAGSNLEAT+Q
Sbjct: 121 LPQSAAESSP-------------------AVVTSALLDTNMYGQAASNLVAGSNLEATIQ 161

Query: 179 QILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAG---GQAGN 235
           +ILDMGGG W+RETV+RALRAA+NNPERA++YLYSGIPEQ  VPPVA+   G   G A N
Sbjct: 162 EILDMGGGDWNRETVVRALRAAFNNPERAIDYLYSGIPEQAEVPPVAQVVQGPASGNAVN 221

Query: 236 PPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQ 295
           PPA   A QP   AP SGPNANPLDLFPQG  + GSNAG G LDFLRNSQQFQALR MVQ
Sbjct: 222 PPAL--APQPVV-APNSGPNANPLDLFPQGHHSTGSNAGTGNLDFLRNSQQFQALRAMVQ 278

Query: 296 ANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTV 355
           ANPQILQPMLQELGKQNP+LMRLIQEHQ DFLRLINEPVE GEGNVLGQLASAMPQAVTV
Sbjct: 279 ANPQILQPMLQELGKQNPYLMRLIQEHQADFLRLINEPVE-GEGNVLGQLASAMPQAVTV 337

Query: 356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           TPEEREAIERLEAMGFDRA+VLEV+FACNKNEELAANYLLDHMHEF++
Sbjct: 338 TPEEREAIERLEAMGFDRAIVLEVYFACNKNEELAANYLLDHMHEFDE 385

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807216|ref|NP_001242098.1| uncharacterized protein LOC100813881 [Glycine max] gi|255641670|gb|ACU21107.1| unknown [Glycine max]

 Score =  570 bits (1469), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 307/405 (75%), Positives = 333/405 (82%), Gaps = 7/405 (1%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MKVFVKTLKGTHFEIEV P D +S+VKKNIETVQG+DVYPA+QQMLIHQGKVLKD TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVNPSDTLSEVKKNIETVQGADVYPAAQQMLIHQGKVLKDGTTLE 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKVAE+SF+V+ML+K+K SS   ST S AP+ +     SA PTST  +T  Q PA T A
Sbjct: 61  ENKVAESSFIVIMLSKTKSSSGEGSTTSTAPSAK----PSATPTSTSVSTAPQAPASTGA 116

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
               V      PA      APAPAPAP  +  S   SD+YGQAASNLVAGSNLE T+QQI
Sbjct: 117 SATPVTAPTAAPAPAPAPAAPAPAPAPIFSGSSVPESDIYGQAASNLVAGSNLEGTIQQI 176

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           LDMGGGSWDR+TV+R LRAAYNNPERAVEYLYSGIPEQ   PPV    A  Q  NPPA T
Sbjct: 177 LDMGGGSWDRDTVVRTLRAAYNNPERAVEYLYSGIPEQAEAPPVTGVPASAQPSNPPADT 236

Query: 241 -QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNA-GAGTLDFLRNSQQFQALRTMVQANP 298
            QA QPA+  P+SGPNANPLDLFPQGLPN+GS A GAG+LDFLRNSQQFQALR MVQANP
Sbjct: 237 PQAAQPAS-VPSSGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANP 295

Query: 299 QILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPE 358
           QILQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVEGGEGN+LGQLA  MPQAVTVTPE
Sbjct: 296 QILQPMLQELGKQNPHLMRLIQEHQVDFLRLINEPVEGGEGNILGQLAGTMPQAVTVTPE 355

Query: 359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           ER+AIERLEAMGFDRA VLEV+FACNKNEELAANYLLDHMHEF++
Sbjct: 356 ERQAIERLEAMGFDRATVLEVYFACNKNEELAANYLLDHMHEFDE 400

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|5640111|emb|CAB51544.1| RAD23 protein [Solanum lycopersicum var. cerasiforme]

 Score =  569 bits (1467), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 301/411 (73%), Positives = 326/411 (79%), Gaps = 30/411 (7%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+FVKTLKGTHFEIEVKPED V+DVKKNIE+VQG DVYPA+QQMLIHQGKVLKD TTLE
Sbjct: 1   MKIFVKTLKGTHFEIEVKPEDSVADVKKNIESVQGQDVYPAAQQMLIHQGKVLKDTTTLE 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKVAENSFVV+ML+K+KVSS+G S++SAA +N AQ   S    + Q   T  TP  T A
Sbjct: 61  ENKVAENSFVVIMLSKNKVSSTGTSSISAALSNTAQPDGS----TDQARQTITTPQATAA 116

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
            PQS  ESA                       +SSV+DVY QAASNLVAGSNLE TVQQI
Sbjct: 117 LPQSASESA--------------PTPAPVPAAASSVTDVYDQAASNLVAGSNLETTVQQI 162

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAV--------PPVARASAGGQ 232
           LDMGGGSWDR+TV+RALRAAYNNPERAV+YLYSGIPEQT +         P   A A  Q
Sbjct: 163 LDMGGGSWDRDTVVRALRAAYNNPERAVDYLYSGIPEQTEIPPVARAPAAPAVTAPASAQ 222

Query: 233 AGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRT 292
           A NP AQ  +Q      P+SGPNANPLDLFPQGL N GSNAGAG LDFLRNS QFQALR 
Sbjct: 223 AINPAAQDASQ---LAVPSSGPNANPLDLFPQGLTNAGSNAGAGNLDFLRNSPQFQALRA 279

Query: 293 MVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQA 352
           MVQANPQILQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVE GEGNVLGQ A A+PQA
Sbjct: 280 MVQANPQILQPMLQELGKQNPHLMRLIQEHQPDFLRLINEPVE-GEGNVLGQTAGAIPQA 338

Query: 353 VTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           VTVTPEEREAIERLEAMGFDRALVLEV+FACNKNEELAANYLLDH+HEF++
Sbjct: 339 VTVTPEEREAIERLEAMGFDRALVLEVYFACNKNEELAANYLLDHLHEFDE 389

Source: Solanum lycopersicum var. cerasiforme

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575534|ref|XP_003555895.1| PREDICTED: putative DNA repair protein RAD23-3-like isoform 1 [Glycine max]

 Score =  567 bits (1462), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 298/405 (73%), Positives = 334/405 (82%), Gaps = 6/405 (1%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MKVFVKTLKGTHFEIEV P+D VS+VKKNIETVQG+DVYPA+QQMLIHQGKVL+D TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVTPQDTVSEVKKNIETVQGADVYPAAQQMLIHQGKVLRDATTLE 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKVAEN+F+V+ML+KSK +S   ST S A + +A  TS+ P  ST P + +       A
Sbjct: 61  ENKVAENTFIVIMLSKSKSTSGEGSTTSTALSTKAPQTSTVP-ASTPPVSVAPQAPAPAA 119

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
                     P ++P+PAPAPAPAP  +   V  S  D+YGQAASNLVAGSNLE T+QQI
Sbjct: 120 TGALPASVTAPVSSPSPAPAPAPAPISSGTAVEGS--DIYGQAASNLVAGSNLEGTIQQI 177

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           LDMGGGSWDR+TV+RALRAAYNNPERAVEYLY+GIPEQ   P VARA    Q  NPPA  
Sbjct: 178 LDMGGGSWDRDTVVRALRAAYNNPERAVEYLYTGIPEQAEAPLVARAPVSAQPTNPPADA 237

Query: 241 -QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNA-GAGTLDFLRNSQQFQALRTMVQANP 298
            Q  QPAA   ++GPNANPLDLFPQGLPN+GS A GAG+LDFLRNSQQFQALR MVQANP
Sbjct: 238 PQTAQPAA-VTSAGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANP 296

Query: 299 QILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPE 358
           QILQPMLQELGKQNPHLMRLI++HQ DFLRLINEP EGGEGN+LGQ+AS MPQAVTVTPE
Sbjct: 297 QILQPMLQELGKQNPHLMRLIRDHQADFLRLINEPAEGGEGNILGQMASGMPQAVTVTPE 356

Query: 359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           ER+AIERLEAMGFDRA+VLEV+FACNKNEELAANYLLDHMHEFE+
Sbjct: 357 ERQAIERLEAMGFDRAIVLEVYFACNKNEELAANYLLDHMHEFEE 401

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297832888|ref|XP_002884326.1| hypothetical protein ARALYDRAFT_477488 [Arabidopsis lyrata subsp. lyrata] gi|297330166|gb|EFH60585.1| hypothetical protein ARALYDRAFT_477488 [Arabidopsis lyrata subsp. lyrata]

 Score =  566 bits (1460), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 312/424 (73%), Positives = 344/424 (81%), Gaps = 28/424 (6%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+FVKTLKGTHFEIEVK ED V+DVKKNIETVQG+DVYPA++QMLIHQGKVLKD TT+E
Sbjct: 1   MKIFVKTLKGTHFEIEVKLEDSVADVKKNIETVQGADVYPAAKQMLIHQGKVLKDETTIE 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKVAENSF+VVML KSK +S+GAS+ SA          S PP+++QP+ + QTPA   A
Sbjct: 61  ENKVAENSFIVVMLNKSKPASTGASSASAG----TSQAKSTPPSTSQPSISPQTPASVAA 116

Query: 121 PPQSVPESAPPP-------------AAPAPAPAPAPAPAPAPAPVSS---SVSDVYGQAA 164
           P    P  APPP               P P P PA  P+  PAP S+   S  DVYGQAA
Sbjct: 117 PVAPAPTRAPPPAPTPAPVAATETVTTPIPEPVPATIPSSTPAPDSAPAGSQGDVYGQAA 176

Query: 165 SNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPV 224
           SNL AGSNLE+T+QQILDMGGG+WDRETV+RALRAA+NNPERAVEYLY+GIPEQ  VPPV
Sbjct: 177 SNLAAGSNLESTIQQILDMGGGTWDRETVVRALRAAFNNPERAVEYLYTGIPEQAEVPPV 236

Query: 225 ARASAG-GQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRN 283
           ARA A  GQ  NP AQTQ  QPAA AP SGPNANPLDLFPQGLPN+G N GAGTLDFLRN
Sbjct: 237 ARAPASFGQPANPSAQTQ--QPAA-APASGPNANPLDLFPQGLPNVGGNPGAGTLDFLRN 293

Query: 284 SQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG--EGNV 341
           SQQFQALR MVQANPQ+LQPMLQELGKQNP+LMRLIQ+HQ DFLRLINEPVEGG   GN+
Sbjct: 294 SQQFQALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLINEPVEGGGESGNL 353

Query: 342 LGQLASAM--PQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH 399
           LGQ+A+ M  PQA+ VTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH
Sbjct: 354 LGQMAAGMPQPQAIQVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH 413

Query: 400 EFED 403
           EFE+
Sbjct: 414 EFEE 417

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248820|ref|NP_001240201.1| uncharacterized protein LOC100809066 [Glycine max] gi|255644546|gb|ACU22776.1| unknown [Glycine max]

 Score =  564 bits (1454), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 305/404 (75%), Positives = 331/404 (81%), Gaps = 13/404 (3%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MKVFVKTLKGTHFEIEV P D +S+VKKNIETVQG+DVYPA+QQMLIHQGKVLKD TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVNPSDTLSEVKKNIETVQGADVYPAAQQMLIHQGKVLKDGTTLE 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKVAENSF+V+ML+K+K SS   ST S AP+ +A    SA PTST  +   Q PA T A
Sbjct: 61  ENKVAENSFIVIMLSKTKSSSGEGSTTSTAPSVKA----SATPTSTSVSAAPQAPASTGA 116

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
            P  V   A P +A APAP  + +  P         SD+YGQAASNLVAGSNLE T+QQI
Sbjct: 117 TPTPVTAPAAPASAAAPAPISSGSAVPE--------SDIYGQAASNLVAGSNLEGTIQQI 168

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           LDMGGGSWDR+TV+RALRAAYNNPERAVEYLYSGIPEQ   PPV R  A  Q  NPPA  
Sbjct: 169 LDMGGGSWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEAPPVTREPASAQPANPPAAA 228

Query: 241 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNA-GAGTLDFLRNSQQFQALRTMVQANPQ 299
                 A  P+SGPNANPLDLFPQGLPN+GS A GAG+LDFLRNSQQFQALR MVQANPQ
Sbjct: 229 PQAAQPASVPSSGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANPQ 288

Query: 300 ILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEE 359
           ILQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVEGGEGN+LGQLASAMPQAVTVTPEE
Sbjct: 289 ILQPMLQELGKQNPHLMRLIQEHQVDFLRLINEPVEGGEGNILGQLASAMPQAVTVTPEE 348

Query: 360 REAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           R+AIERLEAMGFDRA VLEV+FACNKNEELAANYLLDHMHEF++
Sbjct: 349 RQAIERLEAMGFDRATVLEVYFACNKNEELAANYLLDHMHEFDE 392

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127650|ref|XP_002329330.1| predicted protein [Populus trichocarpa] gi|222870784|gb|EEF07915.1| predicted protein [Populus trichocarpa]

 Score =  563 bits (1450), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 301/410 (73%), Positives = 333/410 (81%), Gaps = 33/410 (8%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVS-DVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTL 59
           MKVFVKTLKGT+FEIEVKPED V  +VKKNIE VQG+DVYPA+QQMLI+QGKVLKD TTL
Sbjct: 1   MKVFVKTLKGTNFEIEVKPEDTVVVEVKKNIENVQGADVYPAAQQMLIYQGKVLKDDTTL 60

Query: 60  EENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQ----TTSSAPPT--STQPTTTSQ 113
           +E+KVAENSF+VVML+KSKVSS G ST +AAP N +     T ++APPT  S QPT+   
Sbjct: 61  DESKVAENSFIVVMLSKSKVSSGGPSTATAAPPNVSSGGPSTATAAPPTLVSAQPTS--- 117

Query: 114 TPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNL 173
                     S+P +   P++ + A  PA A + A         D+YGQAASNLVAGSNL
Sbjct: 118 ----------SLPSNVTQPSSTSQAAVPAAAFSDA---------DMYGQAASNLVAGSNL 158

Query: 174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQA 233
           EAT+QQILDMGGGSW+RETV+RALRAA+NNPERAVEYLYSGIPEQ  VPPVA+  A G A
Sbjct: 159 EATIQQILDMGGGSWNRETVVRALRAAFNNPERAVEYLYSGIPEQAEVPPVAQGPASGVA 218

Query: 234 GNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTM 293
            NPPAQ Q         + GPNANPLDLFPQGLP+ GSNAGAG LDFLRNSQQFQALR M
Sbjct: 219 VNPPAQAQQPAAPP---SGGPNANPLDLFPQGLPSTGSNAGAGNLDFLRNSQQFQALRAM 275

Query: 294 VQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAV 353
           VQANPQILQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVE GEGNVLGQLASA+PQ V
Sbjct: 276 VQANPQILQPMLQELGKQNPHLMRLIQEHQPDFLRLINEPVE-GEGNVLGQLASAVPQTV 334

Query: 354 TVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFED 403
           TVTPEEREAI+RL AMGFDRALVLEVFFACNKNEELAANYLLDHMHEF++
Sbjct: 335 TVTPEEREAIDRLVAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFDE 384

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232924|ref|NP_186903.1| putative DNA repair protein RAD23-3 [Arabidopsis thaliana] gi|55976503|sp|Q84L31.2|RD23C_ARATH RecName: Full=Putative DNA repair protein RAD23-3; AltName: Full=RAD23-like protein 3; Short=AtRAD23-3 gi|6957717|gb|AAF32461.1| putative RAD23 [Arabidopsis thaliana] gi|14517454|gb|AAK62617.1| AT3g02540/F16B3_17 [Arabidopsis thaliana] gi|21360453|gb|AAM47342.1| AT3g02540/F16B3_17 [Arabidopsis thaliana] gi|30409724|dbj|BAC76392.1| RAD23-like protein [Arabidopsis thaliana] gi|110735092|gb|ABG89116.1| Rad23-1 [synthetic construct] gi|332640303|gb|AEE73824.1| putative DNA repair protein RAD23-3 [Arabidopsis thaliana]

 Score =  562 bits (1449), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 304/436 (69%), Positives = 343/436 (78%), Gaps = 50/436 (11%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+FVKTLKGTHFEIEVKPED V DVKKNIE+VQG+DVYPA++QMLIHQGKVLKD TT+E
Sbjct: 1   MKIFVKTLKGTHFEIEVKPEDSVVDVKKNIESVQGADVYPAAKQMLIHQGKVLKDETTIE 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAP--- 117
           ENKVAENSF+V+M+ KSK +S+ AS+ SA   +QA+   S PP+++QP+ + QTPA    
Sbjct: 61  ENKVAENSFIVIMMNKSKPASAAASSASAG-TSQAK---SIPPSTSQPSISPQTPASVSA 116

Query: 118 -------------------------TVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPV 152
                                    TV  P  +PE       P PA   +  PAP  APV
Sbjct: 117 PVAPAPTRPPPPAPTPTPAPVAATETVTTP--IPE-------PVPATISSSTPAPDSAPV 167

Query: 153 SSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY 212
            S   DVYGQAASNL AGSNLE+T+QQILDMGGG+WDRETV+ ALRAA+NNPERAVEYLY
Sbjct: 168 GSQ-GDVYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLY 226

Query: 213 SGIPEQTAVPPVARA-SAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGS 271
           +GIPEQ  VPPVAR  ++ GQ  NPPAQTQ  QPAA AP SGPNANPLDLFPQGLPN+G 
Sbjct: 227 TGIPEQAEVPPVARPPASAGQPANPPAQTQ--QPAA-APASGPNANPLDLFPQGLPNVGG 283

Query: 272 NAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLIN 331
           N GAGTLDFLRNSQQFQALR MVQANPQ+LQPMLQELGKQNP+LMRLIQ+HQ DFLRLIN
Sbjct: 284 NPGAGTLDFLRNSQQFQALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLIN 343

Query: 332 EPVEGG--EGNVLGQLASAM--PQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNE 387
           EPVEGG   GN+LGQ+A+ M  PQA+ VT EEREAIERLEAMGF+RALVLEVFFACNKNE
Sbjct: 344 EPVEGGGESGNLLGQMAAGMPQPQAIQVTHEEREAIERLEAMGFERALVLEVFFACNKNE 403

Query: 388 ELAANYLLDHMHEFED 403
           ELAANYLLDHMHEFE+
Sbjct: 404 ELAANYLLDHMHEFEE 419

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

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	403
TAIR|locus:2076944	419	RAD23C "RADIATION SENSITIVE23C	0.605	0.582	0.76	1.6e-128
TAIR|locus:2177376	378	RAD23D "RADIATION SENSITIVE23D	0.607	0.648	0.760	4e-123
TAIR|locus:2200522	368	RAD23A "RADIATION SENSITIVE23A	0.585	0.641	0.580	4.3e-94
UNIPROTKB|D4AD39	363	Rad23a "RAD23a homolog (S. cer	0.317	0.352	0.460	3e-55
UNIPROTKB|A3KMV2	362	RAD23A "UV excision repair pro	0.322	0.359	0.446	3.8e-55
MGI|MGI:105126	363	Rad23a "RAD23a homolog (S. cer	0.317	0.352	0.453	3.8e-55
UNIPROTKB|P54725	363	RAD23A "UV excision repair pro	0.317	0.352	0.453	4.9e-55
UNIPROTKB|F1SD96	380	RAD23A "Uncharacterized protei	0.317	0.336	0.453	1e-54
ZFIN|ZDB-GENE-040808-59	362	rad23aa "RAD23 homolog Aa (S.	0.344	0.383	0.440	1e-54
UNIPROTKB|F1PTL1	362	RAD23A "Uncharacterized protei	0.322	0.359	0.439	1e-54

TAIR|locus:2076944 RAD23C "RADIATION SENSITIVE23C" [Arabidopsis thaliana (taxid:3702)]

 Score = 952 (340.2 bits), Expect = 1.6e-128, Sum P(2) = 1.6e-128
 Identities = 190/250 (76%), Positives = 206/250 (82%)

Query:   158 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE 217
             DVYGQAASNL AGSNLE+T+QQILDMGGG+WDRETV+ ALRAA+NNPERAVEYLY+GIPE
Sbjct:   172 DVYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLYTGIPE 231

Query:   218 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 277
             Q  VPPVAR                            NANPLDLFPQGLPN+G N GAGT
Sbjct:   232 QAEVPPVARPPASAGQPANPPAQTQQPAAAPASGP--NANPLDLFPQGLPNVGGNPGAGT 289

Query:   278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG 337
             LDFLRNSQQFQALR MVQANPQ+LQPMLQELGKQNP+LMRLIQ+HQ DFLRLINEPVEGG
Sbjct:   290 LDFLRNSQQFQALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLINEPVEGG 349

Query:   338 --EGNVLGQLASAMPQ--AVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANY 393
                GN+LGQ+A+ MPQ  A+ VT EEREAIERLEAMGF+RALVLEVFFACNKNEELAANY
Sbjct:   350 GESGNLLGQMAAGMPQPQAIQVTHEEREAIERLEAMGFERALVLEVFFACNKNEELAANY 409

Query:   394 LLDHMHEFED 403
             LLDHMHEFE+
Sbjct:   410 LLDHMHEFEE 419

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0043130 "ubiquitin binding" evidence=IDA

GO:0070628 "proteasome binding" evidence=IDA

TAIR|locus:2177376 RAD23D "RADIATION SENSITIVE23D" [Arabidopsis thaliana (taxid:3702)]

 Score = 947 (338.4 bits), Expect = 4.0e-123, Sum P(2) = 4.0e-123
 Identities = 187/246 (76%), Positives = 201/246 (81%)

Query:   158 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE 217
             DVYGQAASNLVAG+ LE+TVQQILDMGGGSWDR+TV+RALRAA+NNPERAVEYLYSGIP 
Sbjct:   133 DVYGQAASNLVAGTTLESTVQQILDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPA 192

Query:   218 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 277
             Q  +PPVA+                            NANPL+LFPQG+P   + AGAG 
Sbjct:   193 QAEIPPVAQAPATGEQAANPLAQPQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGN 252

Query:   278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG 337
             LDFLRNSQQFQALR MVQANPQILQPMLQELGKQNP L+RLIQEHQ DFLRLINEPVEG 
Sbjct:   253 LDFLRNSQQFQALRAMVQANPQILQPMLQELGKQNPQLVRLIQEHQADFLRLINEPVEGE 312

Query:   338 EGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH 397
             E NV+ QL +AMPQAVTVTPEEREAIERLE MGFDRA+VLEVFFACNKNEELAANYLLDH
Sbjct:   313 E-NVMEQLEAAMPQAVTVTPEEREAIERLEGMGFDRAMVLEVFFACNKNEELAANYLLDH 371

Query:   398 MHEFED 403
             MHEFED
Sbjct:   372 MHEFED 377

GO:0003684 "damaged DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0006289 "nucleotide-excision repair" evidence=IEA;ISS

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0009409 "response to cold" evidence=IEP

GO:0043130 "ubiquitin binding" evidence=IDA

GO:0070628 "proteasome binding" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0007067 "mitosis" evidence=RCA

TAIR|locus:2200522 RAD23A "RADIATION SENSITIVE23A" [Arabidopsis thaliana (taxid:3702)]

 Score = 716 (257.1 bits), Expect = 4.3e-94, Sum P(2) = 4.3e-94
 Identities = 144/248 (58%), Positives = 177/248 (71%)

Query:   158 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE 217
             D YGQAAS LV+GS++E  VQQI++MGGGSWD+ETV RALRAAYNNPERAV+YLYSGIPE
Sbjct:   131 DTYGQAASTLVSGSSIEQMVQQIMEMGGGSWDKETVTRALRAAYNNPERAVDYLYSGIPE 190

Query:   218 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 277
                +P                                N++PLDLFPQ   +  +    GT
Sbjct:   191 TVTIP----------ATNLSGVGSGRELTAPPPSGGPNSSPLDLFPQEAVSDAAGGDLGT 240

Query:   278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG 337
             L+FLR + QFQ LR+MV +NPQILQPMLQELGKQNP L+RLIQE+Q +FL+L+NEP EG 
Sbjct:   241 LEFLRGNDQFQQLRSMVNSNPQILQPMLQELGKQNPQLLRLIQENQAEFLQLLNEPYEGS 300

Query:   338 EGNV--LGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLL 395
             +G+V    Q    MP +V VTPEE+E+IERLEAMGFDRA+V+E F +C++NEELAANYLL
Sbjct:   301 DGDVDIFDQPDQEMPHSVNVTPEEQESIERLEAMGFDRAIVIEAFLSCDRNEELAANYLL 360

Query:   396 DHMHEFED 403
             +H  +FED
Sbjct:   361 EHSADFED 368

GO:0003684 "damaged DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0006284 "base-excision repair" evidence=ISS

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0043130 "ubiquitin binding" evidence=IDA

GO:0070628 "proteasome binding" evidence=IDA

UNIPROTKB|D4AD39 Rad23a "RAD23a homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 312 (114.9 bits), Expect = 3.0e-55, Sum P(3) = 3.0e-55
 Identities = 64/139 (46%), Positives = 92/139 (66%)

Query:   273 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 332
             AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct:   227 AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 286

Query:   333 P------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIERLEAMGFDRALVLEVFFACN 384
             P      +   EG V G L    PQ   + VTP+E+EAIERL+A+GF  +LV++ +FAC 
Sbjct:   287 PPGELADISDVEGEV-GALGEEAPQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACE 345

Query:   385 KNEELAANYLLDHMHEFED 403
             KNE LAAN+LL     F+D
Sbjct:   346 KNENLAANFLLSQ--NFDD 362

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

UNIPROTKB|A3KMV2 RAD23A "UV excision repair protein RAD23 homolog A" [Bos taurus (taxid:9913)]

 Score = 311 (114.5 bits), Expect = 3.8e-55, Sum P(3) = 3.8e-55
 Identities = 63/141 (44%), Positives = 93/141 (65%)

Query:   271 SNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLI 330
             + AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++
Sbjct:   224 TEAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQML 283

Query:   331 NEP------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIERLEAMGFDRALVLEVFFA 382
             NEP      +   EG V G +    PQ   + VTP+E+EAIERL+A+GF  +LV++ +FA
Sbjct:   284 NEPPGELVDISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFA 342

Query:   383 CNKNEELAANYLLDHMHEFED 403
             C KNE LAAN+LL     F+D
Sbjct:   343 CEKNENLAANFLLSQ--NFDD 361

GO:0005634 "nucleus" evidence=IEA

GO:0045070 "positive regulation of viral genome replication" evidence=IEA

GO:0032434 "regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

MGI|MGI:105126 Rad23a "RAD23a homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 310 (114.2 bits), Expect = 3.8e-55, Sum P(3) = 3.8e-55
 Identities = 63/139 (45%), Positives = 92/139 (66%)

Query:   273 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 332
             AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct:   227 AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 286

Query:   333 P------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIERLEAMGFDRALVLEVFFACN 384
             P      +   EG V G +    PQ   + VTP+E+EAIERL+A+GF  +LV++ +FAC 
Sbjct:   287 PPGELADISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACE 345

Query:   385 KNEELAANYLLDHMHEFED 403
             KNE LAAN+LL     F+D
Sbjct:   346 KNENLAANFLLSQ--NFDD 362

GO:0000502 "proteasome complex" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=ISO

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

GO:0031593 "polyubiquitin binding" evidence=ISO

GO:0032434 "regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0045070 "positive regulation of viral genome replication" evidence=ISO

UNIPROTKB|P54725 RAD23A "UV excision repair protein RAD23 homolog A" [Homo sapiens (taxid:9606)]

 Score = 310 (114.2 bits), Expect = 4.9e-55, Sum P(3) = 4.9e-55
 Identities = 63/139 (45%), Positives = 92/139 (66%)

Query:   273 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 332
             AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct:   227 AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 286

Query:   333 P------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIERLEAMGFDRALVLEVFFACN 384
             P      +   EG V G +    PQ   + VTP+E+EAIERL+A+GF  +LV++ +FAC 
Sbjct:   287 PPGELADISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACE 345

Query:   385 KNEELAANYLLDHMHEFED 403
             KNE LAAN+LL     F+D
Sbjct:   346 KNENLAANFLLSQ--NFDD 362

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0032434 "regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0031593 "polyubiquitin binding" evidence=IDA

GO:0045070 "positive regulation of viral genome replication" evidence=IMP

GO:0006289 "nucleotide-excision repair" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F1SD96 RAD23A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 310 (114.2 bits), Expect = 1.0e-54, Sum P(3) = 1.0e-54
 Identities = 63/139 (45%), Positives = 92/139 (66%)

Query:   273 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 332
             AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct:   244 AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 303

Query:   333 P------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIERLEAMGFDRALVLEVFFACN 384
             P      +   EG V G +    PQ   + VTP+E+EAIERL+A+GF  +LV++ +FAC 
Sbjct:   304 PPGELADISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACE 362

Query:   385 KNEELAANYLLDHMHEFED 403
             KNE LAAN+LL     F+D
Sbjct:   363 KNENLAANFLLSQ--NFDD 379

GO:0045070 "positive regulation of viral genome replication" evidence=IEA

GO:0032434 "regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

ZFIN|ZDB-GENE-040808-59 rad23aa "RAD23 homolog Aa (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 309 (113.8 bits), Expect = 1.0e-54, Sum P(3) = 1.0e-54
 Identities = 67/152 (44%), Positives = 99/152 (65%)

Query:   263 PQGLP-NMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQE 321
             P  LP +     G   L+FLR+  QFQ++R ++Q NP +L  +LQ+LG++NP L++ I +
Sbjct:   212 PAQLPTDTQPTEGENPLEFLRSQPQFQSMRQVIQQNPSLLPALLQQLGQENPELLQQISQ 271

Query:   322 HQTDFLRLINEPVEGGEGNV--------LGQLAS-AMPQA-VTVTPEEREAIERLEAMGF 371
             HQ  F++++N PV  GEG +        LG +   A P + + VT +E+EAIERL+A+GF
Sbjct:   272 HQELFIQMLNAPVGEGEGELGEGGEFADLGAIGDEAAPGSFIQVTQQEKEAIERLKALGF 331

Query:   372 DRALVLEVFFACNKNEELAANYLLDHMHEFED 403
               ALV++ +FAC KNE LAAN+LL+    FED
Sbjct:   332 SEALVVQAYFACEKNENLAANFLLNQ--NFED 361

GO:0005634 "nucleus" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

UNIPROTKB|F1PTL1 RAD23A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 307 (113.1 bits), Expect = 1.0e-54, Sum P(3) = 1.0e-54
 Identities = 62/141 (43%), Positives = 92/141 (65%)

Query:   271 SNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLI 330
             +  G   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++
Sbjct:   224 TEGGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQML 283

Query:   331 NEP------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIERLEAMGFDRALVLEVFFA 382
             NEP      +   EG V G +    PQ   + VTP+E+EAIERL+A+GF  +LV++ +FA
Sbjct:   284 NEPPGELADISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFA 342

Query:   383 CNKNEELAANYLLDHMHEFED 403
             C KNE LAAN+LL     F+D
Sbjct:   343 CEKNENLAANFLLSQ--NFDD 361

GO:0045070 "positive regulation of viral genome replication" evidence=IEA

GO:0032434 "regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003684 "damaged DNA binding" 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)
Q40742	RAD23_ORYSJ	No assigned EC number	0.6265	0.9528	0.9795	yes	no
Q29RK4	RD23B_BOVIN	No assigned EC number	0.3665	0.9057	0.8946	yes	no
P54727	RD23B_HUMAN	No assigned EC number	0.3896	0.9205	0.9070	yes	no
P54728	RD23B_MOUSE	No assigned EC number	0.3690	0.9057	0.8774	yes	no
O74803	RHP23_SCHPO	No assigned EC number	0.3405	0.8808	0.9646	yes	no
Q84L30	RD23D_ARATH	No assigned EC number	0.7047	0.9354	0.9973	no	no
Q84L31	RD23C_ARATH	No assigned EC number	0.6972	0.9578	0.9212	yes	no
Q4KMA2	RD23B_RAT	No assigned EC number	0.3712	0.9230	0.8963	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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00038207001	SubName- Full=Chromosome chr14 scaffold_9, whole genome shotgun sequence; (381 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00036762001	SubName- Full=Chromosome chr4 scaffold_83, whole genome shotgun sequence; (440 aa)				•	•		•		0.736
	GSVIVG00023710001	SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (758 aa)						•	•		0.441
	GSVIVG00022868001	SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (379 aa)						•	•		0.402

---

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	403
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	1e-106
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	5e-34
smart00213	72	smart00213, UBQ, Ubiquitin homologues	6e-20
pfam09280	59	pfam09280, XPC-binding, XPC-binding domain	7e-20
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	5e-18
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	1e-17
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	4e-10
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	6e-10
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	7e-10
pfam00627	37	pfam00627, UBA, UBA/TS-N domain	2e-09
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	2e-09
smart00165	37	smart00165, UBA, Ubiquitin associated domain	8e-09
cd01803	76	cd01803, Ubiquitin, Ubiquitin	1e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	3e-08
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-08
cd00194	38	cd00194, UBA, Ubiquitin Associated domain	4e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	6e-08
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	1e-07
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-07
cd00194	38	cd00194, UBA, Ubiquitin Associated domain	2e-07
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-07
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-07
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	3e-07
pfam00627	37	pfam00627, UBA, UBA/TS-N domain	3e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-07
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	4e-07
PRK10672	361	PRK10672, PRK10672, rare lipoprotein A; Provisiona	7e-07
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	1e-06
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	1e-06
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	1e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-06
smart00165	37	smart00165, UBA, Ubiquitin associated domain	3e-06
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	3e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-06
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	4e-06
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	5e-06
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	6e-06
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	7e-06
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	8e-06
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	1e-05
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	1e-05
PRK06302	155	PRK06302, PRK06302, acetyl-CoA carboxylase biotin	1e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-05
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	2e-05
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	2e-05
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	3e-05
PLN02983	274	PLN02983, PLN02983, biotin carboxyl carrier protei	3e-05
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	3e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-05
PRK06302	155	PRK06302, PRK06302, acetyl-CoA carboxylase biotin	6e-05
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	6e-05
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	8e-05
pfam10152	147	pfam10152, DUF2360, Predicted coiled-coil domain-c	8e-05
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	8e-05
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	8e-05
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	9e-05
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	1e-04
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	2e-04
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	2e-04
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	2e-04
cd01812	71	cd01812, BAG1_N, Ubiquitin-like domain of BAG1	2e-04
PRK05641	153	PRK05641, PRK05641, putative acetyl-CoA carboxylas	2e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	2e-04
PRK11901	327	PRK11901, PRK11901, hypothetical protein; Reviewed	2e-04
PRK09111	598	PRK09111, PRK09111, DNA polymerase III subunits ga	2e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	3e-04
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	3e-04
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	3e-04
TIGR02813	2582	TIGR02813, omega_3_PfaA, polyketide-type polyunsat	3e-04
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	3e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	4e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	4e-04
PRK11633	226	PRK11633, PRK11633, cell division protein DedD; Pr	4e-04
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	4e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	5e-04
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	5e-04
pfam12526	115	pfam12526, DUF3729, Protein of unknown function (D	5e-04
PRK14960	702	PRK14960, PRK14960, DNA polymerase III subunits ga	5e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	6e-04
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	6e-04
PRK11633	226	PRK11633, PRK11633, cell division protein DedD; Pr	6e-04
PHA03269	566	PHA03269, PHA03269, envelope glycoprotein C; Provi	6e-04
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	7e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	7e-04
COG4982	866	COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein]	7e-04
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	7e-04
COG3147	226	COG3147, DedD, Uncharacterized protein conserved i	8e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	9e-04
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	9e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.001
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.001
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	0.001
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	0.001
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	0.001
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	0.001
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	0.001
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	0.001
pfam12200	124	pfam12200, DUF3597, Domain of unknown function (DU	0.001
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	0.001
PRK11892	464	PRK11892, PRK11892, pyruvate dehydrogenase subunit	0.001
PRK05704	407	PRK05704, PRK05704, dihydrolipoamide succinyltrans	0.001
PRK05704	407	PRK05704, PRK05704, dihydrolipoamide succinyltrans	0.001
pfam04652	315	pfam04652, DUF605, Vta1 like	0.001
PRK12438	991	PRK12438, PRK12438, hypothetical protein; Provisio	0.001
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.001
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.002
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.002
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.002
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	0.002
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	0.002
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	0.002
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.002
PRK11892	464	PRK11892, PRK11892, pyruvate dehydrogenase subunit	0.002
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	0.002
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	0.002
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.003
pfam04652	315	pfam04652, DUF605, Vta1 like	0.003
PRK06975	656	PRK06975, PRK06975, bifunctional uroporphyrinogen-	0.003
COG5373	931	COG5373, COG5373, Predicted membrane protein [Func	0.003
PRK12373	400	PRK12373, PRK12373, NADH dehydrogenase subunit E;	0.003
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	0.004
PRK11901	327	PRK11901, PRK11901, hypothetical protein; Reviewed	0.004
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	0.004
PRK11892	464	PRK11892, PRK11892, pyruvate dehydrogenase subunit	0.004
PRK14959	624	PRK14959, PRK14959, DNA polymerase III subunits ga	0.004

>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score =  317 bits (815), Expect = e-106
 Identities = 162/408 (39%), Positives = 229/408 (56%), Gaps = 38/408 (9%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M +  KTL+   F+I+++P++ V ++K+ IE  QG D YP +QQ LI+ GK+L D  T++
Sbjct: 1   MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVK 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           E K+ E  FVVVM++K K                  T   APP +T  +  + TP+P  +
Sbjct: 61  EYKIKEKDFVVVMVSKPK----------------TGTGKVAPPAATPTSAPTPTPSPPAS 104

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
           P      +AP  A    +P+   A A AP   S+SV      AAS LV GS  E T+++I
Sbjct: 105 PASG-MSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERETTIEEI 163

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           ++MG   ++RE V RALRAA+NNP+RAVEYL +GIPE    P   + +A   A       
Sbjct: 164 MEMG---YEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAASTAAATTETP 220

Query: 241 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQI 300
           Q       A   G             P   +  G   L+FLRN  QFQ LR +VQ NPQ+
Sbjct: 221 QHGSVFEQAAQGGTEQ----------PATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQL 270

Query: 301 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG--GEGNVLGQLASAMPQA------ 352
           L P+LQ++G++NP L++ I +H   FL+++NEPV     E ++ G + +           
Sbjct: 271 LPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGELASESDMEGGVGAIAEAGLPQMNQ 330

Query: 353 VTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE 400
           + VTPEE+EAIERL A+GFDR LV++ +FAC+KNEELAANYLL    +
Sbjct: 331 IQVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQNFD 378

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 378

>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23

 Score =  121 bits (305), Expect = 5e-34
 Identities = 43/78 (55%), Positives = 55/78 (70%), Gaps = 1/78 (1%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          MK+  KTLK   F IEV P+D V+++K+ IE  +G D YP  QQ LI+ GK+LKD TTLE
Sbjct: 1  MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCD-YPPEQQKLIYSGKILKDDTTLE 59

Query: 61 ENKVAENSFVVVMLTKSK 78
          E K+ E  FVVVM++K K
Sbjct: 60 EYKIDEKDFVVVMVSKPK 77

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL). Length = 77

>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues

 Score = 83.1 bits (206), Expect = 6e-20
 Identities = 29/75 (38%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++ VKTL G    +EVKP D VS++K+ I  + G    P  QQ LI++GKVL+D  TL 
Sbjct: 1  IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGI---PPEQQRLIYKGKVLEDDRTLA 57

Query: 61 ENKVAENSFVVVMLT 75
          +  + + S + ++L 
Sbjct: 58 DYGIQDGSTIHLVLR 72

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression. Length = 72

>gnl|CDD|192241 pfam09280, XPC-binding, XPC-binding domain

 Score = 82.3 bits (204), Expect = 7e-20
 Identities = 36/59 (61%), Positives = 48/59 (81%)

Query: 278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG 336
           L FLRN+ QFQ LR MVQ NP++L P+LQ+LG+ NP L++LIQ++Q +FLRL+NE  EG
Sbjct: 1   LAFLRNNPQFQQLRQMVQQNPELLPPLLQQLGQSNPQLLQLIQQNQEEFLRLLNEGAEG 59

Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair. Length = 59

>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL

 Score = 77.3 bits (191), Expect = 5e-18
 Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 3/72 (4%)

Query: 4  FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENK 63
           VKTL G  FE+EV P+D V+++K  I   +G    P  QQ LI+ GK+LKD  TL +  
Sbjct: 1  TVKTLTGKTFELEVSPDDTVAELKAKIAAKEG---VPPEQQRLIYAGKILKDDKTLSDYG 57

Query: 64 VAENSFVVVMLT 75
          + + S + ++L 
Sbjct: 58 IQDGSTLHLVLR 69

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways. Length = 69

>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family

 Score = 76.5 bits (189), Expect = 1e-17
 Identities = 30/69 (43%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 6  KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVA 65
          KTL G    +EV P D VS++K+ IE  +G    P  QQ LI  GKVL+D TTL E  + 
Sbjct: 1  KTLDGKTITLEVDPSDTVSELKEKIEDKEG---IPVDQQRLIFSGKVLEDDTTLSEYGIQ 57

Query: 66 ENSFVVVML 74
          + S + ++L
Sbjct: 58 DGSTLHLVL 66

This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites. Length = 69

>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins

 Score = 55.2 bits (133), Expect = 4e-10
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 4  FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENK 63
           VK   G   E+ V     V+D+K+ +    G    P  QQ L+  GK+L D  TLE+  
Sbjct: 1  KVKLNDGKTVELLVPSGTTVADLKEKLAKKLG---LPPEQQRLLVNGKILPDSLTLEDYG 57

Query: 64 VAENSFVVVMLT 75
          + +   +V++  
Sbjct: 58 LQDGDELVLVPR 69

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate. Length = 69

>gnl|CDD|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein

 Score = 54.9 bits (133), Expect = 6e-10
 Identities = 28/78 (35%), Positives = 39/78 (50%), Gaps = 7/78 (8%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVY-PASQQMLIHQGKVLKDVTTL 59
          +++ VKTL        V+ E  V D+K+ I      +V  P  QQ LI+ G+VLKD  TL
Sbjct: 1  IEIKVKTLDSQTHTFTVEEEITVLDLKEKIA----EEVGIPVEQQRLIYSGRVLKDDETL 56

Query: 60 EENKVAENSFVVVMLTKS 77
           E KV +     + L K 
Sbjct: 57 SEYKVEDGH--TIHLVKR 72

Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules. Length = 72

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 60.7 bits (148), Expect = 7e-10
 Identities = 31/97 (31%), Positives = 43/97 (44%), Gaps = 4/97 (4%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAP 139
           S++  +  +AA A  A   ++AP            PA         P +A   AA   AP
Sbjct: 40  STAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAP 99

Query: 140 -APAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEA 175
            A A A APA A V   V+ + G AA+  VA  N++A
Sbjct: 100 PAAAAAAAPAAAAVEDEVTPLRGAAAA--VA-KNMDA 133

Length = 1228

>gnl|CDD|201355 pfam00627, UBA, UBA/TS-N domain

 Score = 52.5 bits (127), Expect = 2e-09
 Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 3/38 (7%)

Query: 174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL 211
           E  ++Q+ +MG   + RE   +ALRA   N ERAVEYL
Sbjct: 3   EELIKQLREMG---FSREEAKKALRATNGNVERAVEYL 37

This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280. Length = 37

>gnl|CDD|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDDKTAA 57

Query: 61 ENKVAENSFVVVMLT 75
          + K+   S + ++L 
Sbjct: 58 DYKLEGGSVLHLVLA 72

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Length = 76

>gnl|CDD|197551 smart00165, UBA, Ubiquitin associated domain

 Score = 50.6 bits (122), Expect = 8e-09
 Identities = 17/37 (45%), Positives = 21/37 (56%)

Query: 359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLL 395
           + E I++L  MGF R   L+   A N N E AA YLL
Sbjct: 1   DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37

Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin. Length = 37

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 51.4 bits (123), Expect = 1e-08
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains). Length = 76

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 55.7 bits (135), Expect = 3e-08
 Identities = 24/83 (28%), Positives = 33/83 (39%)

Query: 85  STVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPA 144
              +AAP   A   ++A              AP  APP +   +APP  A A A A APA
Sbjct: 38  PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPA 97

Query: 145 PAPAPAPVSSSVSDVYGQAASNL 167
             PA A  ++  +       + L
Sbjct: 98  APPAAAAAAAPAAAAVEDEVTPL 120

Length = 1228

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 55.4 bits (134), Expect = 3e-08
 Identities = 43/158 (27%), Positives = 55/158 (34%), Gaps = 39/158 (24%)

Query: 100 SAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDV 159
           +  P +  P+  +  PA   AP  + P +A  PA PA AP PAPAPAPAPAP S + +  
Sbjct: 391 AGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPA-PAAAPQPAPAPAPAPAPPSPAGNAP 449

Query: 160 YGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQT 219
            G A S   A +    + Q                                     P   
Sbjct: 450 AGGAPSPPPAAA---PSAQP-----------------------------------APAPA 471

Query: 220 AVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNAN 257
           A P    A A      P        PAAPA  +G +  
Sbjct: 472 AAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDA 509

Length = 824

>gnl|CDD|238116 cd00194, UBA, Ubiquitin Associated domain

 Score = 48.6 bits (117), Expect = 4e-08
 Identities = 14/36 (38%), Positives = 19/36 (52%)

Query: 361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLD 396
           E +E+L  MGF R    +   A N N E A  +LL+
Sbjct: 3   EKLEQLLEMGFSREEARKALRATNNNVERAVEWLLE 38

The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins. Length = 38

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 54.5 bits (132), Expect = 6e-08
 Identities = 19/69 (27%), Positives = 27/69 (39%)

Query: 83  GASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPA 142
           G  + +A  A  A   ++A   +  P   +        P  + P + P PAA A A A  
Sbjct: 37  GPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAP 96

Query: 143 PAPAPAPAP 151
            AP  A A 
Sbjct: 97  AAPPAAAAA 105

Length = 1228

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 53.3 bits (128), Expect = 1e-07
 Identities = 41/196 (20%), Positives = 56/196 (28%), Gaps = 16/196 (8%)

Query: 77  SKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPA--- 133
              +++ A     APA  A   ++  P +      +   A   A   +   +   PA   
Sbjct: 373 GPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEA 432

Query: 134 ------------APAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQIL 181
                         APAPAPAPA APA A   ++       AA+         A      
Sbjct: 433 LAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPA 492

Query: 182 DMGGGSWDRETVIRALRAAY-NNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           D     W+      A  A    +   A     S     TA P  A  +        PA  
Sbjct: 493 DDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPR 552

Query: 241 QAQQPAAPAPTSGPNA 256
            A           P A
Sbjct: 553 AAAATEPVVAPRPPRA 568

Length = 700

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 52.6 bits (127), Expect = 2e-07
 Identities = 17/74 (22%), Positives = 27/74 (36%)

Query: 75  TKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAA 134
                +++ A+  ++APA      + A P    P   +    P  A   +   +   P A
Sbjct: 42  AAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPA 101

Query: 135 PAPAPAPAPAPAPA 148
            A A APA A    
Sbjct: 102 AAAAAAPAAAAVED 115

Length = 1228

>gnl|CDD|238116 cd00194, UBA, Ubiquitin Associated domain

 Score = 46.7 bits (112), Expect = 2e-07
 Identities = 19/41 (46%), Positives = 26/41 (63%), Gaps = 3/41 (7%)

Query: 173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 213
            E  ++Q+L+MG   + RE   +ALRA  NN ERAVE+L  
Sbjct: 1   DEEKLEQLLEMG---FSREEARKALRATNNNVERAVEWLLE 38

The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins. Length = 38

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 53.0 bits (127), Expect = 2e-07
 Identities = 49/187 (26%), Positives = 59/187 (31%), Gaps = 10/187 (5%)

Query: 83   GASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPA 142
            G     A P   A   + APP +       +   P VA      ES P P  PA  PA  
Sbjct: 2752 GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAV 2811

Query: 143  PAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMG-----GGSWDRETVIRAL 197
             APA A  P +S    +    ++   A           L +G     GG   R    R+ 
Sbjct: 2812 LAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSP 2871

Query: 198  RAAYNNP-----ERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTS 252
             A    P      R      S   E  A+PP            PP Q Q Q P  P P  
Sbjct: 2872 AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQP 2931

Query: 253  GPNANPL 259
             P   P 
Sbjct: 2932 PPPPPPR 2938

Length = 3151

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 52.4 bits (126), Expect = 2e-07
 Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 78  KVSSSGASTVSAAPAN----QAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPA 133
           K +++  +   A        +A   ++AP                 A   + P +A PPA
Sbjct: 365 KPAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPA 424

Query: 134 APAPAPAPAPAPAPAPAPVSSSVSDV-YGQAASNLVA 169
             A   A APA APA AP + +++     QAA   VA
Sbjct: 425 PVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVA 461

Length = 618

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 52.6 bits (127), Expect = 3e-07
 Identities = 21/87 (24%), Positives = 31/87 (35%), Gaps = 1/87 (1%)

Query: 95  AQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSS 154
           A     +    T     +   A   A   +    A P  AP  A APA  P PA A  ++
Sbjct: 34  ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAA 93

Query: 155 SVSDVYGQAASNL-VAGSNLEATVQQI 180
           +       AA+    A + +E  V  +
Sbjct: 94  AAPAAPPAAAAAAAPAAAAVEDEVTPL 120

Length = 1228

>gnl|CDD|201355 pfam00627, UBA, UBA/TS-N domain

 Score = 45.9 bits (110), Expect = 3e-07
 Identities = 14/37 (37%), Positives = 18/37 (48%)

Query: 358 EEREAIERLEAMGFDRALVLEVFFACNKNEELAANYL 394
            + E I++L  MGF R    +   A N N E A  YL
Sbjct: 1   IDEELIKQLREMGFSREEAKKALRATNGNVERAVEYL 37

This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280. Length = 37

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 51.9 bits (125), Expect = 4e-07
 Identities = 46/229 (20%), Positives = 62/229 (27%), Gaps = 55/229 (24%)

Query: 79  VSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPA 138
             ++      A     A  + +    +    +     AP+  P  +   +  P AAPAPA
Sbjct: 424 APAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPA 483

Query: 139 PAPAPAPAPAPAPVSSS---------------------------------------VSDV 159
           P  APAPA APA  ++                                        V  V
Sbjct: 484 PPAAPAPAAAPAAPAAPAAPAGADDAATLRERWPEILAAVPKRSRKTWAILLPEATVLGV 543

Query: 160 YGQA----------ASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVE 209
            G            A    +  N E  V  + +  GG W  E V+     A         
Sbjct: 544 RGDTLVLGFSTGGLARRFASPGNAEVLVTALAEELGGDWQVEAVVGPAPGAAGGEGPPAP 603

Query: 210 YLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANP 258
                          AR +A      P A   A   AAPA  S   A  
Sbjct: 604 ------ASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPG 646

Length = 824

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 52.0 bits (125), Expect = 4e-07
 Identities = 26/95 (27%), Positives = 37/95 (38%)

Query: 81  SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPA 140
           ++ A   + A         +A P +      +  PAP  AP  +    A PPAA  PAP 
Sbjct: 367 AAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPV 426

Query: 141 PAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEA 175
            APA A   A  +++ + V    A    A     A
Sbjct: 427 AAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVA 461

Length = 618

>gnl|CDD|236733 PRK10672, PRK10672, rare lipoprotein A; Provisional

 Score = 50.4 bits (121), Expect = 7e-07
 Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 81  SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTP-----APTVAPPQSVPESAPPPAAP 135
            + +   + AP       S++   S  PT    T      APT   P  +  S P P AP
Sbjct: 205 GTPSVQPAPAPQGDVLPVSNSTLKSEDPTGAPVTSSGFLGAPTTLAPGVLEGSEPTPTAP 264

Query: 136 APAPAPAPAPAPAPAPVSSSVS 157
           + APA APA A   A  +SS +
Sbjct: 265 SSAPATAPAAAAPQAAATSSSA 286

Length = 361

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.9 bits (120), Expect = 1e-06
 Identities = 17/67 (25%), Positives = 22/67 (32%)

Query: 96  QTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSS 155
                 P    Q    + +   T AP  +V     P   P PA AP  APA      +S 
Sbjct: 362 AAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQ 421

Query: 156 VSDVYGQ 162
           +     Q
Sbjct: 422 LLAARQQ 428

Length = 647

>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like

 Score = 45.2 bits (108), Expect = 1e-06
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM-LIHQGKVLKDVTTL 59
          +++ +K   G    I+VKP   +S +       +G    PA QQ+ LI  G+ L    T+
Sbjct: 1  IRIKLKGKDGKEVFIKVKPTTTLSKLINAYRKKRG---IPADQQVRLIFDGERLDPNDTV 57

Query: 60 EENKVAENSFVVVML 74
           +  + +   + V++
Sbjct: 58 ADYDIEDGDTIDVVI 72

The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localisation, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45). Length = 72

>gnl|CDD|176397 cd01802, AN1_N, ubiquitin-like domain of AN1

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 3/66 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++F++TL GT FE+ V P + V  VK  I+ ++G    P +QQ LI     L+D   L 
Sbjct: 28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEG---IPVAQQHLIWNNMELEDEYCLN 84

Query: 61 ENKVAE 66
          +  ++E
Sbjct: 85 DYNISE 90

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown. Length = 103

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.6 bits (119), Expect = 2e-06
 Identities = 35/184 (19%), Positives = 50/184 (27%), Gaps = 4/184 (2%)

Query: 81  SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPA 140
           ++ A+  + A    A   ++    S  P      P            S      PA A  
Sbjct: 616 AAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGG 675

Query: 141 PAPA---PAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDR-ETVIRA 196
            APA   PAPAPA  ++       Q A    A                 +         A
Sbjct: 676 AAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAA 735

Query: 197 LRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNA 256
                  PE       +G P Q   PP    +A   A  PP+    ++  A       + 
Sbjct: 736 DDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDD 795

Query: 257 NPLD 260
               
Sbjct: 796 EDRR 799

Length = 824

>gnl|CDD|197551 smart00165, UBA, Ubiquitin associated domain

 Score = 43.6 bits (104), Expect = 3e-06
 Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 3/39 (7%)

Query: 173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL 211
            E  + Q+L+MG   + RE  ++ALRAA  N ERA EYL
Sbjct: 1   DEEKIDQLLEMG---FSREEALKALRAANGNVERAAEYL 36

Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin. Length = 37

>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 48.0 bits (114), Expect = 3e-06
 Identities = 23/79 (29%), Positives = 30/79 (37%)

Query: 74  LTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPA 133
           L  + V+ + A  ++      A      PP ST     +    P   PP + P   P   
Sbjct: 18  LAIAAVAGASAVAIALPATANADPAPPPPPPSTAAAAPAPAAPPPPPPPAAPPAPQPDDP 77

Query: 134 APAPAPAPAPAPAPAPAPV 152
             AP P PA   AP P PV
Sbjct: 78  NAAPPPPPADPNAPPPPPV 96

This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. Length = 297

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 48.4 bits (116), Expect = 4e-06
 Identities = 24/68 (35%), Positives = 31/68 (45%)

Query: 88  SAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAP 147
           +A  A  A   ++AP  +  P      P+P    P     S PP AAP+  PAPAPA AP
Sbjct: 415 AAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAP 474

Query: 148 APAPVSSS 155
            P    + 
Sbjct: 475 EPTAAPAP 482

Length = 824

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 47.7 bits (114), Expect = 4e-06
 Identities = 16/67 (23%), Positives = 19/67 (28%)

Query: 82  SGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAP 141
               T S  PA       +  P        SQ    T A P     + P  AAP P    
Sbjct: 183 DTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAAPLPTDQA 242

Query: 142 APAPAPA 148
             +   A
Sbjct: 243 GVSTPAA 249

Length = 331

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 48.2 bits (115), Expect = 5e-06
 Identities = 19/75 (25%), Positives = 32/75 (42%)

Query: 79  VSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPA 138
            ++   S  +AA  + +Q++++A P++ Q  T      PTV+          PP+    A
Sbjct: 387 AAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQA 446

Query: 139 PAPAPAPAPAPAPVS 153
             PA        PVS
Sbjct: 447 VRPAQFKEEKKIPVS 461

Length = 614

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 48.0 bits (115), Expect = 6e-06
 Identities = 23/99 (23%), Positives = 33/99 (33%), Gaps = 1/99 (1%)

Query: 70  VVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESA 129
           + + L     S+S  +     P       +  PP      T      P   P  +   S 
Sbjct: 506 IKLNLESQSGSASNTAKTPPPPQKSPPPPAPTPPLPQPTATAPPPTPPPPPPTATQASSN 565

Query: 130 PPPAAPAP-APAPAPAPAPAPAPVSSSVSDVYGQAASNL 167
            P   PA  +P P     P P+P   S  +   +AA NL
Sbjct: 566 APAQIPADSSPPPPIPEEPTPSPTKDSSPEEIDKAAKNL 604

Length = 620

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.9 bits (114), Expect = 7e-06
 Identities = 35/150 (23%), Positives = 42/150 (28%), Gaps = 31/150 (20%)

Query: 106 TQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAAS 165
             P T +  P    AP  + P +A P  A  PA   A   A A A   ++       A  
Sbjct: 372 AGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPE 431

Query: 166 NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVP-PV 224
                                         AL AA     R      +  P   A P   
Sbjct: 432 ------------------------------ALAAARQASARGPGGAPAPAPAPAAAPAAA 461

Query: 225 ARASAGGQAGNPPAQTQAQQPAAPAPTSGP 254
           AR +A G      A   A   AAPA    P
Sbjct: 462 ARPAAAGPRPVAAAAAAAPARAAPAAAPAP 491

Length = 700

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.7 bits (114), Expect = 8e-06
 Identities = 26/100 (26%), Positives = 35/100 (35%), Gaps = 9/100 (9%)

Query: 84  ASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAP 143
            S   +  AN +   +  P  +  P      P+       +   S PP  A  P P PA 
Sbjct: 361 PSAFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAE 420

Query: 144 APAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDM 183
              P+P P +          A+N     NLE   QQIL  
Sbjct: 421 PTEPSPTPPA---------NAANAPPSLNLEELWQQILAK 451

Length = 620

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 46.2 bits (110), Expect = 1e-05
 Identities = 27/89 (30%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 72  VMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPP-QSVPESAP 130
           V L  S  +    +   AAP +   T S  P  +T P          V  P Q+  ++A 
Sbjct: 162 VPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQANVDTAA 221

Query: 131 PPAAPAPAPAPAPAPAP-APAPVSSSVSD 158
            PA  APA     AP P   A VS+  +D
Sbjct: 222 TPAPAAPATPDGAAPLPTDQAGVSTPAAD 250

Length = 331

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 21/112 (18%), Positives = 38/112 (33%)

Query: 71  VVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAP 130
                K   ++      + AP+ + +  ++A     +P   + TP P    P + P    
Sbjct: 365 APQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHT 424

Query: 131 PPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILD 182
           P +AP    A  P          +   +      ++      LEA  +QIL 
Sbjct: 425 PESAPKLTRAAIPVDEKPKYTPPAPPKEEEKALIADGDVLEQLEAIWKQILR 476

Length = 585

>gnl|CDD|235777 PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated

 Score = 44.4 bits (106), Expect = 1e-05
 Identities = 20/42 (47%), Positives = 23/42 (54%)

Query: 112 SQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
           S+  A  VAP      +AP  AAPA A A A APA APA  +
Sbjct: 33  SRAAAAPVAPVAQQAAAAPVAAAPAAAAAAAAAPAAAPAAAA 74

Length = 155

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.5 bits (111), Expect = 2e-05
 Identities = 23/98 (23%), Positives = 32/98 (32%)

Query: 82  SGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAP 141
           +GA   +A  A  A   ++  P +  P   +         P   P  AP P +PA     
Sbjct: 391 AGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPA 450

Query: 142 APAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQ 179
             AP+P PA   S+       AA    A          
Sbjct: 451 GGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAP 488

Length = 824

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.5 bits (111), Expect = 2e-05
 Identities = 41/173 (23%), Positives = 49/173 (28%), Gaps = 18/173 (10%)

Query: 87  VSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPA 146
           V       A       P S+ P   +  PA   AP       AP  AA APA   + APA
Sbjct: 587 VVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAP-AAPAPAGAAAAPAE-ASAAPA 644

Query: 147 PAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPER 206
           P  A        V    AS+   G   +A                    A  A       
Sbjct: 645 PGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAA------- 697

Query: 207 AVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPL 259
                    P Q A  P A   AG          QA Q A+    +  +  PL
Sbjct: 698 ---------PAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPL 741

Length = 824

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 27/94 (28%), Positives = 36/94 (38%), Gaps = 10/94 (10%)

Query: 88  SAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAP 147
           S+A  +Q    S        P  TS T  P   P  + P    P  +  PA A APAPA 
Sbjct: 150 SSAELSQNSGQS-------VPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAV 202

Query: 148 AP---APVSSSVSDVYGQAASNLVAGSNLEATVQ 178
            P   A V+ S ++V   A     A +  +    
Sbjct: 203 DPQQNAVVAPSQANVDTAATPAPAAPATPDGAAP 236

Length = 331

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.4 bits (110), Expect = 2e-05
 Identities = 41/200 (20%), Positives = 55/200 (27%), Gaps = 11/200 (5%)

Query: 95  AQTTSSAPPTSTQPTTTSQTPAPTVAPP-----QSVPESAPPPAAPAPAPAPAPA-PAPA 148
           A T   AP            PAP           +VP       A   A AP  A  A A
Sbjct: 361 AVTGGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAA 420

Query: 149 PAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGG----GSWDRETVIRALRAAYNNP 204
               +   +      A      ++ +A V    +          +R+    A   + + P
Sbjct: 421 TRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAP 480

Query: 205 ERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQ 264
                   +  P   A  P A   A       PA    +   A A    P A P      
Sbjct: 481 ASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAA 540

Query: 265 GLPNMGSNAGAGTLDFLRNS 284
                   A A  LD LRN+
Sbjct: 541 APAARAGGAAAA-LDVLRNA 559

Length = 830

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.9 bits (109), Expect = 3e-05
 Identities = 24/91 (26%), Positives = 36/91 (39%), Gaps = 1/91 (1%)

Query: 76  KSKVSSSGASTVSAAPANQAQT-TSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAA 134
           K   +   A+  +AAP  QA    + A   +   +  +  PA     P + P +A P AA
Sbjct: 378 KKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAA 437

Query: 135 PAPAPAPAPAPAPAPAPVSSSVSDVYGQAAS 165
           PA APA        PA  +     +  + A 
Sbjct: 438 PAAAPAAVALAPAPPAQAAPETVAIPVRVAP 468

Length = 618

>gnl|CDD|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA carboxylase

 Score = 45.2 bits (107), Expect = 3e-05
 Identities = 21/53 (39%), Positives = 24/53 (45%)

Query: 103 PTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSS 155
           P    P    Q P P   PP S P + P P+APA +P P PA  P      SS
Sbjct: 144 PPPPAPVVMMQPPPPHAMPPASPPAAQPAPSAPASSPPPTPASPPPAKAPKSS 196

Length = 274

>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 45.4 bits (108), Expect = 3e-05
 Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 1/71 (1%)

Query: 85  STVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPA 144
           S +    A  A    +A   +    TT + P      P+    S P P A A  P PAPA
Sbjct: 116 SEIDTGGAPPA-AAPAAAAAAKAEKTTPEKPKAAAPTPEPPAASKPTPPAAAKPPEPAPA 174

Query: 145 PAPAPAPVSSS 155
             P P PV+ +
Sbjct: 175 AKPPPTPVARA 185

Length = 418

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.4 bits (108), Expect = 5e-05
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 79  VSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAP-----PQSVPESAPPPA 133
             ++ A + +AA    A   ++A P +      +  P P  AP     P S   +AP   
Sbjct: 393 APAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGG 452

Query: 134 APAPAPAPAPAPAPAPAPVSS 154
           AP+P PA AP+  PAPAP ++
Sbjct: 453 APSPPPAAAPSAQPAPAPAAA 473

Length = 824

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.0 bits (107), Expect = 5e-05
 Identities = 20/97 (20%), Positives = 29/97 (29%), Gaps = 5/97 (5%)

Query: 83  GASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPA 142
                + A A  +   ++               AP  A   +   +  P  APAPAPAP 
Sbjct: 388 AGGAGAPAAAAPSAAAAAPAAAPAPAA-----AAPAAAAAPAPAAAPQPAPAPAPAPAPP 442

Query: 143 PAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQ 179
                APA  + S       +A    A +        
Sbjct: 443 SPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAA 479

Length = 824

>gnl|CDD|235777 PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated

 Score = 42.5 bits (101), Expect = 6e-05
 Identities = 18/44 (40%), Positives = 20/44 (45%)

Query: 113 QTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSV 156
              AP      + P +A P AA A A APA APA A A     V
Sbjct: 38  APVAPVAQQAAAAPVAAAPAAAAAAAAAPAAAPAAAAAEAEGHV 81

Length = 155

>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++ +KTL G       +P++ V  VK  ++  +G DV    Q  LI+ GK + D   L 
Sbjct: 1  MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDV---KQIRLIYSGKQMSDDLKLS 57

Query: 61 ENKVAENSFVVVML 74
          + KV   S + ++L
Sbjct: 58 DYKVVPGSTIHMVL 71

Length = 76

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 44.4 bits (105), Expect = 8e-05
 Identities = 19/68 (27%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 91  PANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPA-APAPAPAPAPAPAPAP 149
           PA   Q  S+A   S  P+ +S    P+     + P   PP      PA  P   P+ AP
Sbjct: 386 PAAAPQP-SAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAP 444

Query: 150 APVSSSVS 157
             V  +  
Sbjct: 445 QAVRPAQF 452

Length = 614

>gnl|CDD|220603 pfam10152, DUF2360, Predicted coiled-coil domain-containing protein (DUF2360)

 Score = 42.0 bits (99), Expect = 8e-05
 Identities = 19/58 (32%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 95  AQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPV 152
              T    P       T+  P P   P ++   S PPP APA  PA     APA   V
Sbjct: 51  EDVTVQTTPPPPASAITNGGPPPP-PPARAEAASPPPPEAPAEPPAEPEPEAPAENTV 107

This is the conserved 140 amino acid region of a family of proteins conserved from nematodes to humans. One C. elegans member is annotated as a Daf-16-dependent longevity protein 1 but this could not be confirmed. The function is unknown. Length = 147

>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 44.4 bits (106), Expect = 8e-05
 Identities = 19/53 (35%), Positives = 24/53 (45%)

Query: 116 APTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLV 168
           A   A       +    AA APAPAPA A APA A  +++ +      AS  V
Sbjct: 197 AAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPGKAPHASPAV 249

Length = 547

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 44.3 bits (105), Expect = 8e-05
 Identities = 24/74 (32%), Positives = 28/74 (37%), Gaps = 10/74 (13%)

Query: 84  ASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAP 143
                A P+      + A P           P P  APP      A P AA  PAPAPAP
Sbjct: 378 ERGAPAPPSAAWGAPTPAAP---------AAPPPAAAPPVPPAAPARPAAAR-PAPAPAP 427

Query: 144 APAPAPAPVSSSVS 157
             A AP   S+  +
Sbjct: 428 PAAAAPPARSADPA 441

Length = 576

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 43.9 bits (104), Expect = 9e-05
 Identities = 27/84 (32%), Positives = 33/84 (39%), Gaps = 4/84 (4%)

Query: 92  ANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPA---PAPAPAPAPA 148
            + A T + A P  T PT  SQTPA   AP  +V        AP+ A    A  PAPA  
Sbjct: 170 TDPATTPAPAAPVDTTPTN-SQTPAVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAP 228

Query: 149 PAPVSSSVSDVYGQAASNLVAGSN 172
             P  ++         S   A  N
Sbjct: 229 ATPDGAAPLPTDQAGVSTPAADPN 252

Length = 331

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 33/147 (22%), Positives = 45/147 (30%), Gaps = 21/147 (14%)

Query: 122 PQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQIL 181
           P +  E+A P     PA   A APA AP   +++       A +   A +          
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAA-----APAPAAAPAAAASAPAAPPAA 420

Query: 182 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ 241
                             A   P  A        P   A+ P   A A  +    P +  
Sbjct: 421 APPA---------PVAAPAAAAPAAAPA----AAPAAVALAPAPPAQAAPETVAIPVRVA 467

Query: 242 ---AQQPAAPAPTSGPNANPLDLFPQG 265
              A   AAPAP + P A  L    +G
Sbjct: 468 PEPAVASAAPAPAAAPAAARLTPTEEG 494

Length = 618

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 33/127 (25%), Positives = 51/127 (40%), Gaps = 22/127 (17%)

Query: 76  KSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTP--APTVAP---PQSVPESAP 130
            + V+ + A+   AA    A +  +APP +  P   +     AP  AP   P +V  +  
Sbjct: 391 AAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPA 450

Query: 131 PPAAPAP--------------APAPAPAPAPAPAPVSSSVS---DVYGQAASNLVAGSNL 173
           PPA  AP                + APAPA APA    + +   DV+      L A   +
Sbjct: 451 PPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTEEGDVWHATVQQLAAAEAI 510

Query: 174 EATVQQI 180
            A  +++
Sbjct: 511 TALAREL 517

Length = 618

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 38/202 (18%), Positives = 59/202 (29%), Gaps = 23/202 (11%)

Query: 77  SKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPA 136
           S   S  A+  + A    A   S  P         ++  A T +PP +      P  A  
Sbjct: 362 SAFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEP 421

Query: 137 PAPAPAPAPAPAPAPVSSSVSDVYGQAASN---------------LVAGSNLEATVQ--- 178
             P+P P    A AP S ++ +++ Q  +                LV+  +  A +    
Sbjct: 422 TEPSPTPPANAANAPPSLNLEELWQQILAKLELPSTRMLLSQQAELVSLDSNRAVIAVSP 481

Query: 179 QILDMGGGSWDRETVIR-ALRAAYNNPERAV-EYLYSGIPEQTAVPPVARASAGGQAGNP 236
             L M      R+ ++  A         +   E            PP  + S    A  P
Sbjct: 482 NWLGMVQS---RKPLLEQAFAKVLGRSIKLNLESQSGSASNTAKTPPPPQKSPPPPAPTP 538

Query: 237 PAQTQAQQPAAPAPTSGPNANP 258
           P          P P   P    
Sbjct: 539 PLPQPTATAPPPTPPPPPPTAT 560

Length = 620

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 43.3 bits (103), Expect = 2e-04
 Identities = 28/116 (24%), Positives = 38/116 (32%), Gaps = 13/116 (11%)

Query: 73  MLT---KSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESA 129
           ML     + +        SAAPA  AQ T++       P   +  P P  AP Q+     
Sbjct: 356 MLAFHPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPL 415

Query: 130 PPPAAPA----------PAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEA 175
           P   +                 A    PA A  +  V+    + AS   A S LE 
Sbjct: 416 PETTSQLLAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEK 471

Length = 647

>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 42.9 bits (102), Expect = 2e-04
 Identities = 19/48 (39%), Positives = 23/48 (47%)

Query: 119 VAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASN 166
           VA       +AP  AAPA A A APAPAPA A   ++ +     A   
Sbjct: 194 VAAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPGK 241

Length = 547

>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 23/86 (26%), Positives = 30/86 (34%), Gaps = 4/86 (4%)

Query: 85  STVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAP-PQSVPESAPPPAAPAPAPAPAP 143
           + ++       +   S     T   T +  P P   P P+  P   P  +A AP P  AP
Sbjct: 361 ADLTQRLNRLEKEVRSLRSAPTAAATAAGAPLPDFDPRPRGPPAPEPARSAEAP-PLVAP 419

Query: 144 APAPAPAPVSSSVSDVYGQAASNLVA 169
           A APA         DV       L A
Sbjct: 420 AAAPAGLA--LRWRDVLAALKMQLRA 443

Length = 504

>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V VK    +H ++ +  +    D+KK +  V G        Q LI +GK   D  TL+
Sbjct: 1  IRVRVKHGGESH-DLSISSQATFGDLKKMLAPVTG---VEPRDQKLIFKGKERDDAETLD 56

Query: 61 ENKVAENSFVVVM 73
           + V + S V+++
Sbjct: 57 MSGVKDGSKVMLL 69

BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP). Length = 71

>gnl|CDD|235540 PRK05641, PRK05641, putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 18/43 (41%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 115 PAPTVAPPQSVPESAPPPAAP-APAPAPAPAPAPAPAPVSSSV 156
               V      P  AP PA P AP P    APAPAPA    +V
Sbjct: 44  DLSAVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPAPASAGENV 86

Length = 153

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 31/178 (17%), Positives = 50/178 (28%), Gaps = 11/178 (6%)

Query: 84   ASTVSAAPA-NQAQTTSSAPPTSTQPT----TTSQTPAPTVAPPQSVPESAPPPAAPAPA 138
            A  V   P   +    ++  P  + P              VA PQ           P   
Sbjct: 861  AEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVI 920

Query: 139  PAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALR 198
             AP             +V+    + A  +V   +  A +++  +        E V+    
Sbjct: 921  AAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAE------TAEVVVAEPE 974

Query: 199  AAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNA 256
                     V  + + +   TAV P    +   +A        A    APAP   P A
Sbjct: 975  VVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVEHNHATAPMTRAPAPEYVPEA 1032

Length = 1068

>gnl|CDD|237015 PRK11901, PRK11901, hypothetical protein; Reviewed

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 19/77 (24%), Positives = 29/77 (37%)

Query: 81  SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPA 140
               ST+  APA  A +  +  P + +   T      T  P  +  ++A     PA +  
Sbjct: 168 QGNTSTLPTAPATVAPSKGAKVPATAETHPTPPQKPATKKPAVNHHKTATVAVPPATSGK 227

Query: 141 PAPAPAPAPAPVSSSVS 157
           P    A A A  S+  S
Sbjct: 228 PKSGAASARALSSAPAS 244

Length = 327

>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated

 Score = 43.0 bits (102), Expect = 2e-04
 Identities = 21/94 (22%), Positives = 28/94 (29%), Gaps = 7/94 (7%)

Query: 73  MLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPP 132
            L +   S  G               ++A          +               +A P 
Sbjct: 386 RLQEGPPSPGGGGGGPPGGGGAPGAPAAAAAPGAAAAAPAAGGPAAAL-------AAVPD 438

Query: 133 AAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASN 166
           AA A A  PAPA AP PA   +S  D+   A   
Sbjct: 439 AAAAAAAPPAPAAAPQPAVRLNSFEDIVALAEEK 472

Length = 598

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 42.7 bits (101), Expect = 3e-04
 Identities = 17/88 (19%), Positives = 28/88 (31%), Gaps = 1/88 (1%)

Query: 79  VSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVP-ESAPPPAAPAP 137
            + +  +  + A    A   +     +  P       A   + P     +  P P  P  
Sbjct: 688 AAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDD 747

Query: 138 APAPAPAPAPAPAPVSSSVSDVYGQAAS 165
            P PA APA  P P + + +     A  
Sbjct: 748 PPDPAGAPAQPPPPPAPAPAAAPAAAPP 775

Length = 824

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.8 bits (101), Expect = 3e-04
 Identities = 42/163 (25%), Positives = 50/163 (30%), Gaps = 37/163 (22%)

Query: 91  PANQAQTTSSAPP-TSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAP 149
           PA  A+  + A   T  +P   +   AP VA   + P  A  PAA A APA  PA AP P
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAP-VAQAAAAPAPAAAPAAAASAPAAPPAAAP-P 423

Query: 150 APVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVE 209
           APV          AA    A +   A                                  
Sbjct: 424 APV----------AAPAAAAPAAAPAAAPA------------------------AVALAP 449

Query: 210 YLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTS 252
              +    +T   PV  A     A   PA   A   A   PT 
Sbjct: 450 APPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTE 492

Length = 618

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 40/202 (19%), Positives = 54/202 (26%), Gaps = 41/202 (20%)

Query: 70  VVVMLTKSKVSSSGASTVSAAPANQAQTTSSA---PPTSTQPTTTSQTPAPTVAPPQSVP 126
               L     +++ A+   A PA  A   ++              ++  A   A  +   
Sbjct: 406 AGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDE 465

Query: 127 ESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGG 186
             A PPA    A APA    P  A   +  +     A    V  +   A           
Sbjct: 466 RDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAAS-------- 517

Query: 187 SWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARA-----------SAG----- 230
                       AA   PE          P   A  P ARA           +AG     
Sbjct: 518 -----REDAPAAAAPPAPEARP-------PTPAAAAPAARAGGAAAALDVLRNAGMRVSS 565

Query: 231 --GQAGNPPAQTQAQQPAAPAP 250
             G      A+  A   AAP P
Sbjct: 566 DRGARAAAAAKPAAAPAAAPKP 587

Length = 830

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.8 bits (101), Expect = 3e-04
 Identities = 31/81 (38%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 103 PTSTQPTTTSQTPAPTVAPPQSV--PESAPPPAAPAPA-PAPAPAPAPAPAPVSSSVSDV 159
           P        + TPA   APP +   P     PA PA A PAPAPAP  A AP + S    
Sbjct: 382 PAPPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPARSADP- 440

Query: 160 YGQAASNLVAGSNLEATVQQI 180
              AAS   AG    A V  +
Sbjct: 441 -AAAAS---AGDRWRAFVAFV 457

Length = 576

>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid synthase PfaA

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 46/210 (21%), Positives = 73/210 (34%), Gaps = 24/210 (11%)

Query: 48   HQGKVLKDVTTLEENKVAENSFVVVMLT------KSKVSSSGASTVSAAPANQAQTTSSA 101
            HQ + LK        +   N   +  L       KS V+ +    V+ + A  A    + 
Sbjct: 1096 HQAETLKVHEQYLNLQTDSNIVKLSPLATQAPVIKSVVTQAPVVQVTISVAPAAPVLPAV 1155

Query: 102  --PPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDV 159
              PP  +     S   A  +AP   VP + P   +    P+ A A AP  +   S++  V
Sbjct: 1156 VSPPVVSAAPAQSVATAVAMAPVAEVPIAVPVQQSVDYMPSVAQAAAPQASVNDSAIQQV 1215

Query: 160  YGQ--AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYN-----NPE------- 205
              +  A         LE  +    D+G  S  R  ++ +++   N     NPE       
Sbjct: 1216 MMEVVAEKTGYPTEMLELEMDMEADLGIDSIKRVEILGSVQEIINDLPELNPEDLAELRT 1275

Query: 206  --RAVEYLYSGIPEQTAVPPVARASAGGQA 233
                V Y+ S +    A  PV  A +    
Sbjct: 1276 LGEIVNYMQSKVSAAVASAPVNTAVSSTDL 1305

Members of the seed for this alignment are involved in omega-3 polyunsaturated fatty acid biosynthesis, such as the protein PfaA from the eicosapentaenoic acid biosynthesis operon in Photobacterium profundum strain SS9. PfaA is encoded together with PfaB, PfaC, and PfaD, and the functions of the individual polypeptides have not yet been described. More distant homologs of PfaA, also included with the reach of this model, appear to be involved in polyketide-like biosynthetic mechanisms of polyunsaturated fatty acid biosynthesis, an alternative to the more familiar iterated mechanism of chain extension and desaturation, and in most cases are encoded near genes for homologs of PfaB, PfaC, and/or PfaD. Length = 2582

>gnl|CDD|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 14/61 (22%), Positives = 18/61 (29%)

Query: 91  PANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPA 150
              ++           QP  T+  P P   P Q+     P   AP      AP      A
Sbjct: 113 QVPRSTVQIQQQAQQQQPPATTAQPQPVTPPRQTTAPVQPQTPAPVRTQPAAPVTQAVEA 172

Query: 151 P 151
           P
Sbjct: 173 P 173

Length = 256

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.2 bits (99), Expect = 4e-04
 Identities = 35/161 (21%), Positives = 50/161 (31%), Gaps = 18/161 (11%)

Query: 89  AAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAP-APAPAP 147
           A  A +  +              +  PA    P        P  AA A APA  APA AP
Sbjct: 432 ALAAARQASARGPGGAPAPAPAPAAAPAAAARPA--AAGPRPVAAAAAAAPARAAPAAAP 489

Query: 148 APAPVSSSV-SDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPER 206
           APA        ++  + AS   A            D     W  E++     A  ++   
Sbjct: 490 APADDDPPPWEELPPEFASPAPAQP----------DAAPAGWVAESIPDPATADPDDAFE 539

Query: 207 AVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAA 247
            +    +  P     P  A A+    A  PP  + +  P  
Sbjct: 540 TL----APAPAAAPAPRAAAATEPVVAPRPPRASASGLPDM 576

Length = 700

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 42.6 bits (100), Expect = 4e-04
 Identities = 37/185 (20%), Positives = 53/185 (28%), Gaps = 14/185 (7%)

Query: 74   LTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPA 133
            LT+  V+S   S  S           +A          + +PA  + PP S   +APPP 
Sbjct: 2783 LTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPP 2842

Query: 134  APAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETV 193
               P P+     + AP        DV  +  S   A          +  +   +  R T 
Sbjct: 2843 PGPPPPSLPLGGSVAPG------GDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTE 2896

Query: 194  IRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSG 253
              AL           +      P      P        Q   PP     +     APT+ 
Sbjct: 2897 SFALPPDQPERPPQPQ-----APPPPQPQPQPPPPPQPQ---PPPPPPPRPQPPLAPTTD 2948

Query: 254  PNANP 258
            P    
Sbjct: 2949 PAGAG 2953

Length = 3151

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.1 bits (99), Expect = 4e-04
 Identities = 17/83 (20%), Positives = 23/83 (27%), Gaps = 2/83 (2%)

Query: 77  SKVSSSGASTVSAAPANQAQTTS-SAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAP 135
            K   +              T   +AP  S     +      + A   S P+SA  PA  
Sbjct: 364 QKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPA-G 422

Query: 136 APAPAPAPAPAPAPAPVSSSVSD 158
            P       PA  P    S+   
Sbjct: 423 TPPTVSVDPPAAVPVNPPSTAPQ 445

Length = 614

>gnl|CDD|236940 PRK11633, PRK11633, cell division protein DedD; Provisional

 Score = 41.1 bits (97), Expect = 4e-04
 Identities = 22/73 (30%), Positives = 24/73 (32%), Gaps = 9/73 (12%)

Query: 89  AAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPP-------AAPAPAPAP 141
           A  A  A   S  P T   P T  +     V PP+  P   P P           PAP P
Sbjct: 74  AVRAGDAAAPSLDPATVAPPNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAPKP 133

Query: 142 APAPAPA--PAPV 152
            P P      AP 
Sbjct: 134 EPKPVVEEKAAPT 146

Length = 226

>gnl|CDD|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 39.8 bits (93), Expect = 4e-04
 Identities = 28/58 (48%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 95  AQTTSSAPPT-STQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAP 151
           A  T  APP   T PT  S  PA    PP S P   P PAA  PAPA AP P+  P P
Sbjct: 80  APLTPPAPPEPVTPPTAQSPAPAVPTPPPTSTPAVPPAPAAAVPAPAAAPPPSDPPQP 137

Length = 141

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.9 bits (99), Expect = 5e-04
 Identities = 22/95 (23%), Positives = 35/95 (36%), Gaps = 1/95 (1%)

Query: 73  MLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPP 132
           +L  + +S    ++  A P      +    P       T Q       PP       P P
Sbjct: 359 LLPSAFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVP 418

Query: 133 AAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNL 167
           A P   P+P P    A AP S ++ +++ Q  + L
Sbjct: 419 AEP-TEPSPTPPANAANAPPSLNLEELWQQILAKL 452

Length = 620

>gnl|CDD|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 20/50 (40%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 106 TQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPA-PAPAPAPAPVSS 154
           T P        PT   P     + PP + PA  PAPA   PAPA AP  S
Sbjct: 83  TPPAPPEPVTPPTAQSPAPAVPTPPPTSTPAVPPAPAAAVPAPAAAPPPS 132

Length = 141

>gnl|CDD|152960 pfam12526, DUF3729, Protein of unknown function (DUF3729)

 Score = 39.3 bits (92), Expect = 5e-04
 Identities = 18/68 (26%), Positives = 20/68 (29%), Gaps = 1/68 (1%)

Query: 84  ASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAP 143
              V         T          P   S+  AP   P   VP  A PP+  AP      
Sbjct: 40  PPPVGDPRPPVVDTPPPVSAVWVLPPP-SEPAAPPPDPEPPVPGPAGPPSPLAPPAPARK 98

Query: 144 APAPAPAP 151
            P P P P
Sbjct: 99  PPLPPPRP 106

This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with pfam01443, pfam01661, pfam05417, pfam01660, pfam00978. There is a single completely conserved residue L that may be functionally important. Length = 115

>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.0 bits (98), Expect = 5e-04
 Identities = 24/80 (30%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 73  MLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPP 132
           +L    V  +G + V      Q       P ++ QP      PA     P+  PE  P P
Sbjct: 366 ILVSEPVQQNGQAEVGLNSQAQ-TAQEITPVSAVQPVEVISQPAMVEPEPEPEPEPEPEP 424

Query: 133 AA-PAPAPAPAPAPAPAPAP 151
              P P P P P P P P P
Sbjct: 425 EPEPEPEPEPEPEPEPEPQP 444

Length = 702

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.9 bits (99), Expect = 6e-04
 Identities = 26/152 (17%), Positives = 39/152 (25%), Gaps = 12/152 (7%)

Query: 107 QPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASN 166
           Q                    ++  P   A  PA   APA   AP  +  +    +A++ 
Sbjct: 583 QVEAVVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAA 642

Query: 167 LVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVAR 226
              G        + + +   S   +        A            +      A  P A 
Sbjct: 643 PAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGA------------APAAPPPAPAPAAP 690

Query: 227 ASAGGQAGNPPAQTQAQQPAAPAPTSGPNANP 258
           A+  G A   PA   A  P A          P
Sbjct: 691 AAPAGAAPAQPAPAPAATPPAGQADDPAAQPP 722

Length = 824

>gnl|CDD|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional

 Score = 40.8 bits (96), Expect = 6e-04
 Identities = 16/58 (27%), Positives = 19/58 (32%), Gaps = 2/58 (3%)

Query: 94  QAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAP 151
           Q Q     PP +T        P  T AP Q  P++  P      AP      AP    
Sbjct: 122 QQQAQQQQPPATTAQPQPVTPPRQTTAPVQ--PQTPAPVRTQPAAPVTQAVEAPKVEA 177

Length = 256

>gnl|CDD|236940 PRK11633, PRK11633, cell division protein DedD; Provisional

 Score = 40.4 bits (95), Expect = 6e-04
 Identities = 18/72 (25%), Positives = 24/72 (33%), Gaps = 1/72 (1%)

Query: 88  SAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAP 147
               A QA   +  P  + +        AP++ P    P + P    PAP   P P P  
Sbjct: 55  MMPAATQA-LPTQPPEGAAEAVRAGDAAAPSLDPATVAPPNTPVEPEPAPVEPPKPKPVE 113

Query: 148 APAPVSSSVSDV 159
            P P       V
Sbjct: 114 KPKPKPKPQQKV 125

Length = 226

>gnl|CDD|165527 PHA03269, PHA03269, envelope glycoprotein C; Provisional

 Score = 41.6 bits (97), Expect = 6e-04
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 3/92 (3%)

Query: 70  VVVMLTKSKVSSSGASTVSAAPANQAQTTSSA--PPTSTQPTTTSQT-PAPTVAPPQSVP 126
           +++++T + ++   A+  +  P  +  T+++   P  +  P   +   P P VAP  +  
Sbjct: 6   IILIITIACINLIIANLNTNIPIPELHTSAATQKPDPAPAPHQAASRAPDPAVAPTSAAS 65

Query: 127 ESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSD 158
                  AP PA +    PAPAP   +S   D
Sbjct: 66  RKPDLAQAPTPAASEKFDPAPAPHQAASRAPD 97

Length = 566

>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 41.3 bits (98), Expect = 7e-04
 Identities = 15/44 (34%), Positives = 17/44 (38%), Gaps = 2/44 (4%)

Query: 116 APTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDV 159
           A   A P +    A   AA     A APA A A A     V +V
Sbjct: 81  AAAAAAPAAAAAPAAAAAAAPAPAAAAPAAAAAAA--GGGVVEV 122

Length = 547

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 32/188 (17%), Positives = 56/188 (29%), Gaps = 6/188 (3%)

Query: 73  MLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPP 132
           ML          +    A        +S   +S Q      +P  T   P S P   PP 
Sbjct: 137 MLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSPEETARAPSSPPAEPPPS 196

Query: 133 AAPAPAPAPAPAPAP--APAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDR 190
             PA A    P  +   + +  S + +     A     + S+  ++       G      
Sbjct: 197 TPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGP----E 252

Query: 191 ETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAP 250
                   A    P R  E      P     P  + +S   ++ +P   +    PA  +P
Sbjct: 253 NECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSP 312

Query: 251 TSGPNANP 258
            +  +++ 
Sbjct: 313 RASSSSSS 320

Length = 1352

>gnl|CDD|227315 COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein]

 Score = 41.4 bits (97), Expect = 7e-04
 Identities = 23/54 (42%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 109 TTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPA---PAPAPVSSSVSDV 159
           T   + PA   A P +   SAP PAA APAP  A APA   P P       SD 
Sbjct: 5   TDAKEEPAKEEATPPAPAASAPAPAAAAPAPVAAAAPAAAGPRPDDEPFKASDA 58

Length = 866

>gnl|CDD|176403 cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1 and hPLIC2

 Score = 37.4 bits (87), Expect = 7e-04
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 8/69 (11%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM--LIHQGKVLKDVTT 58
          +KV VKT K    EIE+  +  V D K+ +     S  + A+Q+   LI  GK+LKD  T
Sbjct: 1  IKVTVKTPKDKE-EIEIAEDASVKDFKEAV-----SKKFKANQEQLVLIFAGKILKDTDT 54

Query: 59 LEENKVAEN 67
          L ++ + + 
Sbjct: 55 LTQHNIKDG 63

hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein. Length = 71

>gnl|CDD|225689 COG3147, DedD, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 40.3 bits (94), Expect = 8e-04
 Identities = 21/70 (30%), Positives = 26/70 (37%), Gaps = 2/70 (2%)

Query: 89  AAPANQAQTTSSAP--PTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPA 146
           AA +   Q  +  P   T       +QTP P   P Q    + P    P P P P   PA
Sbjct: 85  AAASVDPQPVAQPPVESTPAGVPVAAQTPKPVKPPKQPPAGAVPAKPTPKPEPKPVAEPA 144

Query: 147 PAPAPVSSSV 156
            AP   +  V
Sbjct: 145 AAPTGQAFVV 154

Length = 226

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.5 bits (97), Expect = 9e-04
 Identities = 39/189 (20%), Positives = 55/189 (29%), Gaps = 13/189 (6%)

Query: 91   PANQAQTTS-SAPPTSTQPTT--TSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAP 147
            PA  ++     APP S +P      +      APP  +P     P  P P+P+PA     
Sbjct: 2580 PAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPD 2639

Query: 148  APAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNN---- 203
               P +    +      +         A  +        S  +    RA R    +    
Sbjct: 2640 PHPPPTVPPPERPRDDPAPGRVSRPRRAR-RLGRAAQASSPPQRPRRRAARPTVGSLTSL 2698

Query: 204  -----PERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANP 258
                 P    E     +   T +PP   A+       P A      PA PA   GP    
Sbjct: 2699 ADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPA 2758

Query: 259  LDLFPQGLP 267
                  G P
Sbjct: 2759 RPPTTAGPP 2767

Length = 3151

>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 41.0 bits (97), Expect = 9e-04
 Identities = 13/41 (31%), Positives = 16/41 (39%)

Query: 115 PAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSS 155
            A       +   +A    APAPA A APA A   A  +  
Sbjct: 200 AAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPG 240

Length = 547

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.5 bits (97), Expect = 0.001
 Identities = 46/195 (23%), Positives = 59/195 (30%), Gaps = 11/195 (5%)

Query: 77   SKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPA 136
             +VS    +      A  +         + +PT  S T      PP   PE AP     A
Sbjct: 2659 GRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSA 2718

Query: 137  -PAP---------APAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGG 186
             P P         +PA   APAP  V +  +   G A       +              G
Sbjct: 2719 TPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAG 2778

Query: 187  SWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPA 246
               R T       + +       +  +  P     P  A   A   AG  P  T A QP 
Sbjct: 2779 PPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSA-QPT 2837

Query: 247  APAPTSGPNANPLDL 261
            AP P  GP    L L
Sbjct: 2838 APPPPPGPPPPSLPL 2852

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.5 bits (97), Expect = 0.001
 Identities = 34/171 (19%), Positives = 48/171 (28%), Gaps = 15/171 (8%)

Query: 79   VSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPA 138
              ++      A PA  A     A P +         P  T  PP   P +AP    P   
Sbjct: 2724 GPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRL 2783

Query: 139  PAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALR 198
              PA A          S  D     A+ L   + L                         
Sbjct: 2784 TRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASP---------------AGPL 2828

Query: 199  AAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPA 249
                + +        G P  +     + A  G     PP+++ A +PAAPA
Sbjct: 2829 PPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPA 2879

Length = 3151

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.6 bits (96), Expect = 0.001
 Identities = 18/96 (18%), Positives = 30/96 (31%), Gaps = 2/96 (2%)

Query: 71  VVMLTKSKVSSSGASTVSAAPANQAQTTSSAP--PTSTQPTTTSQTPAPTVAPPQSVPES 128
                ++  + + A     APA      S+    P    P TTSQ  A      ++   +
Sbjct: 377 PAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQGAT 436

Query: 129 APPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAA 164
               + PA A    P  +      S   +    + A
Sbjct: 437 KAKKSEPAAASRARPVNSALERLASVRPAPSALEKA 472

Length = 647

>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 20/79 (25%), Positives = 25/79 (31%), Gaps = 1/79 (1%)

Query: 95  AQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVP-ESAPPPAAPAPAPAPAPAPAPAPAPVS 153
           A    ++      P T +  PAP   PP +     AP    P P PA  PAP P     +
Sbjct: 21  AAVAGASAVAIALPATANADPAPPPPPPSTAAAAPAPAAPPPPPPPAAPPAPQPDDPNAA 80

Query: 154 SSVSDVYGQAASNLVAGSN 172
                    A        N
Sbjct: 81  PPPPPADPNAPPPPPVDPN 99

This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. Length = 297

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 17/66 (25%), Positives = 23/66 (34%), Gaps = 3/66 (4%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAP 139
           S + A   + APA   Q  +   P+     T +       A P     +AP P   A   
Sbjct: 189 SQTPAVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAPATPDG---AAPLPTDQAGVS 245

Query: 140 APAPAP 145
            PA  P
Sbjct: 246 TPAADP 251

Length = 331

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 46/195 (23%), Positives = 58/195 (29%), Gaps = 14/195 (7%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESA---PPPAAPA 136
           ++ G + V A    +A   S       QP           AP    P  A   P P A A
Sbjct: 442 AADGDAPVPAKANARASADSRCDERDAQPPAD---SGSASAPASDAPPDAAFEPAPRAAA 498

Query: 137 PAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRA 196
           P+ A   A   A AP ++S  D    AA                    GG+     V+R 
Sbjct: 499 PSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAAAPAARAGGAAAALDVLR- 557

Query: 197 LRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNA 256
                 N    V           A P  A A+A   A  P    Q   P A A T     
Sbjct: 558 ------NAGMRVSSDRGARAAAAAKPAAAPAAAPKPAA-PRVAVQVPTPRARAATGDAPP 610

Query: 257 NPLDLFPQGLPNMGS 271
           N      Q   + G+
Sbjct: 611 NGAARAEQAAESRGA 625

Length = 830

>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 41.0 bits (97), Expect = 0.001
 Identities = 15/50 (30%), Positives = 18/50 (36%)

Query: 104 TSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
            +      +  PA       +    AP PAA A   A APA A AP    
Sbjct: 194 VAAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPGKAP 243

Length = 547

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 16/71 (22%), Positives = 24/71 (33%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAP 139
             + A   +A  A      ++ PP +  P   +    P  A P   P      A PA + 
Sbjct: 379 RGAPAPPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPARSA 438

Query: 140 APAPAPAPAPA 150
            PA A +    
Sbjct: 439 DPAAAASAGDR 449

Length = 576

>gnl|CDD|221459 pfam12200, DUF3597, Domain of unknown function (DUF3597)

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 127 ESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDV 159
            +A P  A APA APA A A APA    + + V
Sbjct: 14  AAAAPAPAAAPATAPAAAAAAAPAATPPAAASV 46

This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. Length = 124

>gnl|CDD|176393 cd01798, parkin_N, amino-terminal ubiquitin-like of parkin protein

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 3  VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
          V+V+T  G  F +EV P+  +  +K+ +   QG    P  Q  +I  GK L++ TT++E
Sbjct: 1  VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGV---PPDQLRVIFAGKELRNTTTIQE 56

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain. Length = 70

>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta; Provisional

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 13/52 (25%), Positives = 16/52 (30%)

Query: 100 SAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAP 151
           SA      P   ++  A   A   +       PA  APA   A   A    P
Sbjct: 83  SASDAGAAPAAAAEAAAAAPAAAAAAAAKKAAPAPAAPAAPAAEVAADPDIP 134

Length = 464

>gnl|CDD|235571 PRK05704, PRK05704, dihydrolipoamide succinyltransferase; Validated

 Score = 40.6 bits (96), Expect = 0.001
 Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 23/95 (24%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAP--------PQSVPES--- 128
           +++GA+  +AA A  A    +    +     ++   +P              +V  +   
Sbjct: 80  AAAGAAAAAAAAAAAAAAAPAQAQAAAAAEQSNDALSPAARKLAAENGLDASAVKGTGKG 139

Query: 129 ------------APPPAAPAPAPAPAPAPAPAPAP 151
                       A   AAPA   A APA APAP  
Sbjct: 140 GRVTKEDVLAALAAAAAAPAAPAAAAPAAAPAPLG 174

Length = 407

>gnl|CDD|235571 PRK05704, PRK05704, dihydrolipoamide succinyltransferase; Validated

 Score = 40.6 bits (96), Expect = 0.001
 Identities = 25/96 (26%), Positives = 35/96 (36%), Gaps = 25/96 (26%)

Query: 81  SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAP------------PQSVP-- 126
             GA+  +AA A  A   ++A P   Q    ++     ++P              +V   
Sbjct: 77  DEGAAAGAAAAAAAAAAAAAAAPAQAQAAAAAEQSNDALSPAARKLAAENGLDASAVKGT 136

Query: 127 -----------ESAPPPAAPAPAPAPAPAPAPAPAP 151
                       +A   AA APA   A APA APAP
Sbjct: 137 GKGGRVTKEDVLAALAAAAAAPAAPAAAAPAAAPAP 172

Length = 407

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 4/80 (5%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAP 139
           S S   + S    +      S P   + P+ +S  PAP+     + P S   P  P+P P
Sbjct: 183 SPSDPPSSSPGVPS----FPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPP 238

Query: 140 APAPAPAPAPAPVSSSVSDV 159
            PA  P P    V    +  
Sbjct: 239 GPAAPPPPPVQQVPPLSTAK 258

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|171499 PRK12438, PRK12438, hypothetical protein; Provisional

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 7/66 (10%)

Query: 77  SKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPA 136
            +V   G   V+ AP   A +   APP    P      P   V PP++    A PP  P 
Sbjct: 892 DQVFGPGTGRVATAPGGDAAS---APPPGAGP----PAPPQAVPPPRTTQPPAAPPRGPD 944

Query: 137 PAPAPA 142
             PA  
Sbjct: 945 VPPAAV 950

Length = 991

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 18/73 (24%), Positives = 23/73 (31%), Gaps = 2/73 (2%)

Query: 77  SKVSSSGASTVSAAPANQA--QTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAA 134
            K+S SG +     P+ QA         P    P T +    P     Q    +  P A 
Sbjct: 37  KKLSQSGVAEFPWDPSPQAPPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAAN 96

Query: 135 PAPAPAPAPAPAP 147
           P    A    PA 
Sbjct: 97  PPATFALPAGPAG 109

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 27/84 (32%), Positives = 28/84 (33%), Gaps = 2/84 (2%)

Query: 89   AAPANQAQTTSSA-PPTSTQPTTTSQTPA-PTVAPPQSVPESAPPPAAPAPAPAPAPAPA 146
            A PA    T S A PP   +     Q P  P   P    P    PP  P P P P  AP 
Sbjct: 2887 ARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPT 2946

Query: 147  PAPAPVSSSVSDVYGQAASNLVAG 170
              PA        V       LV G
Sbjct: 2947 TDPAGAGEPSGAVPQPWLGALVPG 2970

Length = 3151

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 26/109 (23%), Positives = 35/109 (32%), Gaps = 6/109 (5%)

Query: 100 SAPPTSTQPTTTSQTPAPTVAPPQ-SVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSD 158
              P  TQP    Q  A   A P  S   +A  P+AP  A  PA  P        ++V  
Sbjct: 378 HIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPV 437

Query: 159 VYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERA 207
                A   V  +  +   ++I      S         LR      E+A
Sbjct: 438 NPPSTAPQAVRPAQFKEE-KKIPVSKVSS----LGPSTLRPIQEKAEQA 481

Length = 614

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 1/69 (1%)

Query: 74  LTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQS-VPESAPPP 132
              +  ++S + + S+A A  +   S+  P  T PT +   PA     P S  P++  P 
Sbjct: 391 QPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAVRPA 450

Query: 133 AAPAPAPAP 141
                   P
Sbjct: 451 QFKEEKKIP 459

Length = 614

>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 3/64 (4%)

Query: 97  TTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPA---PAPAPAPAPVS 153
           T  + P  +      ++    T   P++   +  PPAA  P P  A   P PAPA  P  
Sbjct: 120 TGGAPPAAAPAAAAAAKAEKTTPEKPKAAAPTPEPPAASKPTPPAAAKPPEPAPAAKPPP 179

Query: 154 SSVS 157
           + V+
Sbjct: 180 TPVA 183

Length = 418

>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 39.8 bits (94), Expect = 0.002
 Identities = 16/50 (32%), Positives = 22/50 (44%)

Query: 111 TSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVY 160
            +       A P +   +A   AAPAPAPA A APA A    +++     
Sbjct: 194 VAAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPGKAP 243

Length = 547

>gnl|CDD|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 38.3 bits (89), Expect = 0.002
 Identities = 18/62 (29%), Positives = 22/62 (35%)

Query: 90  APANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAP 149
           AP           P + Q    +    P  + P   P  A    APA AP P+  P P  
Sbjct: 80  APLTPPAPPEPVTPPTAQSPAPAVPTPPPTSTPAVPPAPAAAVPAPAAAPPPSDPPQPPR 139

Query: 150 AP 151
           AP
Sbjct: 140 AP 141

Length = 141

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 25/103 (24%), Positives = 33/103 (32%), Gaps = 2/103 (1%)

Query: 75  TKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAA 134
           +    S S  +  S A          + P    PT    +P P+ AP  S          
Sbjct: 86  STPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPG 145

Query: 135 PAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATV 177
           P PA +P  A A   A  S + S    QAA  L +        
Sbjct: 146 PPPAASPPAAGASPAAVASDAAS--SRQAALPLSSPEETARAP 186

Length = 1352

>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta; Provisional

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 15/43 (34%), Positives = 18/43 (41%)

Query: 116 APTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSD 158
               A       +AP  AA A A   APAPA   AP +   +D
Sbjct: 88  GAAPAAAAEAAAAAPAAAAAAAAKKAAPAPAAPAAPAAEVAAD 130

Length = 464

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 27/70 (38%), Positives = 27/70 (38%), Gaps = 6/70 (8%)

Query: 91  PANQAQTTSSAPPTSTQPTTTSQTPA-PTVAPPQSVPESAPPPAAPA-----PAPAPAPA 144
           PA  A      P    QP    Q P  P VAP      SAP PA  A     P  AP P 
Sbjct: 121 PAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPE 180

Query: 145 PAPAPAPVSS 154
           P   PAPV  
Sbjct: 181 PVAEPAPVMD 190

Length = 333

>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 1/69 (1%)

Query: 84  ASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPT-VAPPQSVPESAPPPAAPAPAPAPA 142
           A   +AAPA      ++AP   ++P   +  PAP  V   + +        A A APA  
Sbjct: 52  APPAAAAPAAAQPPPAAAPAAVSRPAAPAAEPAPWLVEHAKRLTAQREQLVARAAAPAAP 111

Query: 143 PAPAPAPAP 151
            A APA   
Sbjct: 112 EAQAPAAPA 120

Length = 484

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 84  ASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSV--PESAPPPAAPAPAPAP 141
               + APAN++++T +   ++  P + ++  +PT   P S   P   PPPA+P P+PAP
Sbjct: 73  PGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAP 132

Query: 142 APAPAPAPAPVSSSVSD 158
             +    P         
Sbjct: 133 DLSEMLRPVGSPGPPPA 149

Length = 1352

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 3/81 (3%)

Query: 79  VSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPA 138
            SS   S++  AP++     S  PP S +  T    P    APP    +  PP +   P 
Sbjct: 204 PSSPSDSSLPPAPSS---FQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPT 260

Query: 139 PAPAPAPAPAPAPVSSSVSDV 159
           P  A A       ++     +
Sbjct: 261 PPSASATPAPIGGITLDDDAI 281

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|235899 PRK06975, PRK06975, bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 19/68 (27%), Positives = 23/68 (33%), Gaps = 3/68 (4%)

Query: 89  AAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPA 148
           A  A Q  T + AP   T    +      T  P  +    APPP  PA  P P       
Sbjct: 266 ADAAAQPATAAPAPSRMTDTNDSKS---VTSQPAAAAAAPAPPPNPPATPPEPPARRGRG 322

Query: 149 PAPVSSSV 156
            A +   V
Sbjct: 323 SAALWFVV 330

Length = 656

>gnl|CDD|227665 COG5373, COG5373, Predicted membrane protein [Function unknown]

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 19/73 (26%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 84  ASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVP--ESAPPPAAPAPAPAP 141
           A       A +A   +  P  +    +    P    AP Q      +  P A PAP+ AP
Sbjct: 48  AKAAEQMAAPEAAEAAPLPAAAESIASPEVPPPVPPAPAQEGEAPAAEQPSAVPAPSAAP 107

Query: 142 APAPAPAPAPVSS 154
           APA    P+  ++
Sbjct: 108 APAEPVEPSLAAN 120

Length = 931

>gnl|CDD|237082 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional

 Score = 39.0 bits (91), Expect = 0.003
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 1/70 (1%)

Query: 89  AAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPA 148
             P+  A+  S+   T+    T +  P       ++ PE+ P     A  PAP  A   A
Sbjct: 241 VPPSEAARPKSADAETNAALKTPATAPKAAAKNAKA-PEAQPVSGTAAAEPAPKEAAKAA 299

Query: 149 PAPVSSSVSD 158
            A    ++ D
Sbjct: 300 AAAAKPALED 309

Length = 400

>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.1 bits (91), Expect = 0.004
 Identities = 13/63 (20%), Positives = 22/63 (34%)

Query: 89  AAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPA 148
           A     ++  ++  P +  P   +Q         +S+  +    A  A AP P   P P 
Sbjct: 341 ALGGAPSEGVAAVAPPAPAPADLTQRLNRLEKEVRSLRSAPTAAATAAGAPLPDFDPRPR 400

Query: 149 PAP 151
             P
Sbjct: 401 GPP 403

Length = 504

>gnl|CDD|237015 PRK11901, PRK11901, hypothetical protein; Reviewed

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 19/88 (21%), Positives = 24/88 (27%)

Query: 85  STVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPA 144
             V+AA  N    TS+ P        +     P  A     P   P    PA        
Sbjct: 158 GQVNAASQNAQGNTSTLPTAPATVAPSKGAKVPATAETHPTPPQKPATKKPAVNHHKTAT 217

Query: 145 PAPAPAPVSSSVSDVYGQAASNLVAGSN 172
            A  PA      S      A +    S+
Sbjct: 218 VAVPPATSGKPKSGAASARALSSAPASH 245

Length = 327

>gnl|CDD|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 18/52 (34%), Positives = 21/52 (40%)

Query: 102 PPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
           PP   +P T     +P  A P   P S P       A  PAPA AP P+   
Sbjct: 84  PPAPPEPVTPPTAQSPAPAVPTPPPTSTPAVPPAPAAAVPAPAAAPPPSDPP 135

Length = 141

>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta; Provisional

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 16/51 (31%), Positives = 22/51 (43%)

Query: 109 TTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDV 159
           + +    AP  A   +    A   AA A   APAPA   APA   ++  D+
Sbjct: 83  SASDAGAAPAAAAEAAAAAPAAAAAAAAKKAAPAPAAPAAPAAEVAADPDI 133

Length = 464

>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau; Provisional

 Score = 38.9 bits (90), Expect = 0.004
 Identities = 23/77 (29%), Positives = 31/77 (40%), Gaps = 9/77 (11%)

Query: 88  SAAPANQAQTTSSAPPTSTQPTTTS-QTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPA 146
           +           +AP     P++ +  TPAP+ AP   VP    PPA P     P PAP 
Sbjct: 396 TIPTPGTQGPQGTAPAAGMTPSSAAPATPAPSAAPSPRVPWDDAPPAPPRSGIPPRPAPR 455

Query: 147 --------PAPAPVSSS 155
                    AP  V+S+
Sbjct: 456 MPEASPVPGAPDSVASA 472

Length = 624

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	403
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	100.0
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	100.0
PF09280	59	XPC-binding: XPC-binding domain; InterPro: IPR0153	99.8
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.75
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.73
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.72
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.71
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.7
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.7
PTZ00044	76	ubiquitin; Provisional	99.7
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.68
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.68
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.67
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.67
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.66
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.66
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.65
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.65
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.64
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.63
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.63
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.62
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.61
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.57
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.55
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.53
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.53
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.43
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.42
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.41
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.39
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.37
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.28
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.26
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.23
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.15
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.0
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	98.88
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	98.85
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	98.84
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.83
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	98.8
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	98.78
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	98.76
PLN02560	308	enoyl-CoA reductase	98.75
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	98.73
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	98.69
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.65
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	98.62
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.6
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	98.58
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.36
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.35
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.15
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.12
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	98.08
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.04
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	97.78
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	97.46
KOG4495	110	consensus RNA polymerase II transcription elongati	97.46
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	97.36
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.35
COG5417	81	Uncharacterized small protein [Function unknown]	97.05
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	97.04
KOG4583	391	consensus Membrane-associated ER protein involved	96.94
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	96.94
KOG0418	200	consensus Ubiquitin-protein ligase [Posttranslatio	96.91
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	96.88
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	96.68
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	96.62
KOG0013	231	consensus Uncharacterized conserved protein [Funct	96.61
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	96.61
KOG1639	297	consensus Steroid reductase required for elongatio	96.57
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	96.54
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	96.54
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	96.53
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	96.44
KOG0944	763	consensus Ubiquitin-specific protease UBP14 [Postt	96.22
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	96.21
smart00727	41	STI1 Heat shock chaperonin-binding motif.	96.07
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	96.06
KOG0944	763	consensus Ubiquitin-specific protease UBP14 [Postt	96.04
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	95.91
PF13019	162	Telomere_Sde2: Telomere stability and silencing	95.86
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	95.65
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	95.58
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	95.46
KOG0418	200	consensus Ubiquitin-protein ligase [Posttranslatio	95.36
smart00546	43	CUE Domain that may be involved in binding ubiquit	95.06
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	94.95
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	94.92
smart00546	43	CUE Domain that may be involved in binding ubiquit	94.67
PF09288	55	UBA_3: Fungal ubiquitin-associated domain ; InterP	93.69
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	93.32
PF11626	87	Rap1_C: TRF2-interacting telomeric protein/Rap1 -	92.41
PF09288	55	UBA_3: Fungal ubiquitin-associated domain ; InterP	92.38
PF14453	57	ThiS-like: ThiS-like ubiquitin	92.38
PRK06437	67	hypothetical protein; Provisional	92.05
KOG0012	380	consensus DNA damage inducible protein [Replicatio	91.98
PF11626	87	Rap1_C: TRF2-interacting telomeric protein/Rap1 -	91.85
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	91.38
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	91.25
PF06972	60	DUF1296: Protein of unknown function (DUF1296); In	90.68
PF07499	47	RuvA_C: RuvA, C-terminal domain; InterPro: IPR0111	89.85
PRK08364	70	sulfur carrier protein ThiS; Provisional	89.82
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	89.59
PRK06488	65	sulfur carrier protein ThiS; Validated	89.08
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	88.67
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	88.36
cd07922	81	CarBa CarBa is the A subunit of 2-aminophenol 1,6-	87.27
PF12754	309	Blt1: Cell-cycle control medial ring component; In	87.22
PF11547	53	E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro	84.95
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	84.42
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	84.27
PF06972	60	DUF1296: Protein of unknown function (DUF1296); In	83.0
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	82.99
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	82.72
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	82.68
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	82.63
PRK05863	65	sulfur carrier protein ThiS; Provisional	81.92
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	81.77
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	81.61
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	80.83
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	80.52
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	80.03
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	80.02

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=100.00  E-value=6e-90  Score=693.88  Aligned_cols=363  Identities=43%  Similarity=0.727  Sum_probs=256.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|++.+++++|||||+||+|+|+++|++|+|+++++|+||++|+|..
T Consensus         1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k~k~~   80 (378)
T TIGR00601         1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSKPKTG   80 (378)
T ss_pred             CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEeccCCCC
Confidence            99999999999999999999999999999999988555899999999999999999999999999999999999998875


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCcc
Q 015628           81 SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAP-APAPAPAPAPAPAPVSSSVSDV  159 (403)
Q Consensus        81 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~p~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  159 (403)
                      +...+.+...+.+++.+           +.+++. +|+..+. .++++++.+.++.+ .++ ++...+.   +++.. ..
T Consensus        81 ~~~~~~~~~~~~~~p~~-----------~~~~~~-~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~~~~---~~~~~-~~  142 (378)
T TIGR00601        81 TGKSAPPAATPTSAPTP-----------TPSPPA-SPASGMS-AAPASAVEEKSPSEESAT-ATAPESP---STSVP-SS  142 (378)
T ss_pred             CCCCCCCCCCCCCCCCC-----------CCCCCC-CCCCCCC-CCCCCCCccccccCCCCC-CCCCCCC---Ccccc-cc
Confidence            33222111011010111           000000 0000000 00000000000000 000 0100000   00000 00


Q ss_pred             cccccccccCCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCCCCCCCccccccCCCCCCCCCCc
Q 015628          160 YGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQ  239 (403)
Q Consensus       160 ~~~~~s~l~~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~~~~~~~~~~~~~~~~~~~~~~~  239 (403)
                      ...+.|+|++|+++|++|++||+||   |+|+||++||||||||||||||||++|||++++...+    ...    +...
T Consensus       143 ~~~~~s~l~~g~~~e~~I~~i~eMG---f~R~qV~~ALRAafNNPdRAVEYL~tGIP~~~~~~~~----~~~----~~~~  211 (378)
T TIGR00601       143 GSDAASTLVVGSERETTIEEIMEMG---YEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEP----VQQ----TAAS  211 (378)
T ss_pred             CCCcccccccchHHHHHHHHHHHhC---CCHHHHHHHHHHHhCCHHHHHHHHHhCCCcccccccc----CCC----cccc
Confidence            1145789999999999999999999   9999999999999999999999999999998652111    000    1000


Q ss_pred             cccCCCCCCCCCCCCCCCCCCCcCCCCCCCC------CCCCCCchHHhhCcHHHHHHHHHHHhCccchHHHHHHHHhhCH
Q 015628          240 TQAQQPAAPAPTSGPNANPLDLFPQGLPNMG------SNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNP  313 (403)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~------~~~~~~~l~~Lr~~pqf~~lR~~vq~NP~lL~~~lq~i~~~nP  313 (403)
                       .     + ....+.+..+ |||++++.++.      .+.|+++|++||++|||++||++||+||++|++|||||+++||
T Consensus       212 -~-----~-~~~~~~~~~~-~lf~~a~~~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLqql~~~nP  283 (378)
T TIGR00601       212 -T-----A-AATTETPQHG-SVFEQAAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENP  283 (378)
T ss_pred             -c-----c-cccCCCCCCc-chhhhhhcccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHHHHHhhCH
Confidence             0     0 0111112222 89998864321      1124568999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcHHHHHHHhcCCCCC--CCCccc---ccccc-cCC--ccccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCC
Q 015628          314 HLMRLIQEHQTDFLRLINEPVEG--GEGNVL---GQLAS-AMP--QAVTVTPEEREAIERLEAMGFDRALVLEVFFACNK  385 (403)
Q Consensus       314 ~l~~lI~~n~e~Fl~~l~~~~~~--~~g~~~---~~~~~-~~~--~~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~  385 (403)
                      +|+++|++||++||+||+++++.  ++++..   ++... ..+  ..|+||+||++||+|||+|||+|+.||||||||||
T Consensus       284 ~l~q~I~~n~e~Fl~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~lT~eE~~AIeRL~~LGF~r~~viqaY~ACdK  363 (378)
T TIGR00601       284 QLLQQISQHPEQFLQMLNEPVGELAGESDMEGGVGAIAEAGLPQMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFACDK  363 (378)
T ss_pred             HHHHHHHHCHHHHHHHhcCcccccccccccccccccccccCcccccccccCHHHHHHHHHHHHcCCCHHHHHHHHHhcCC
Confidence            99999999999999999998522  111111   11111 111  26899999999999999999999999999999999


Q ss_pred             CHHHHHHHHhccCCC
Q 015628          386 NEELAANYLLDHMHE  400 (403)
Q Consensus       386 ne~~a~~~L~~~~~d  400 (403)
                      |||+||||||++.+|
T Consensus       364 NEelAAn~Lf~~~~~  378 (378)
T TIGR00601       364 NEELAANYLLSQNFD  378 (378)
T ss_pred             cHHHHHHHHHhhcCC
Confidence            999999999999876

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]

Probab=100.00  E-value=3e-90  Score=667.11  Aligned_cols=339  Identities=58%  Similarity=0.880  Sum_probs=268.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|++|+|+|.+++||.+||++|+...|.+ +|++.|||||+||+|+|++++.+|+|+++++|+||++|+|..
T Consensus         1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~d-yP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~k~~   79 (340)
T KOG0011|consen    1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPD-YPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKDKSA   79 (340)
T ss_pred             CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCC-CchhhheeeecceeccCCcchhhhccccCceEEEEEecCccc
Confidence            8999999999999999999999999999999999988 999999999999999999999999999999999999999831


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 015628           81 SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVY  160 (403)
Q Consensus        81 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (403)
                      . ...    ++.+      +++       ...+  ..+.++++     +.+.   ...++ ++        ..++....+
T Consensus        80 ~-t~~----ap~s------~~~-------~~~p--~~~~ap~~-----s~a~---~~s~~-~~--------~~~~~~~~~  122 (340)
T KOG0011|consen   80 S-TQV----APQS------SAA-------THLP--KAAEAPPS-----SAAE---DASPA-TP--------AQTSQEDTY  122 (340)
T ss_pred             c-cCC----CCCC------ccc-------cCCC--ccCCCCCc-----cccc---cCCCC-cc--------ccccccchh
Confidence            1 110    0000      000       0000  00000000     0000   00000 00        011223456


Q ss_pred             ccccccccCCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCCCCCCCccccccCCCCCCCCCCcc
Q 015628          161 GQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT  240 (403)
Q Consensus       161 ~~~~s~l~~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~~~~~~~~~~~~~~~~~~~~~~~~  240 (403)
                      +.+.++|++|.++|.+|.+||+||   |+||+|+|||||||||||||||||++|||+....+.+...+...         
T Consensus       123 ~~aas~Lv~G~~~e~~V~~Im~MG---y~re~V~~AlRAafNNPeRAVEYLl~GIP~~~~~~~~~~~~~~~---------  190 (340)
T KOG0011|consen  123 EIAASTLVVGSEYEQTVQQIMEMG---YDREEVERALRAAFNNPERAVEYLLNGIPEDAEVPEPEKSTAAA---------  190 (340)
T ss_pred             hhhhhhhhccchhHHHHHHHHHhC---ccHHHHHHHHHHhhCChhhhHHHHhcCCcccccCCcccCCcccC---------
Confidence            788899999999999999999999   99999999999999999999999999999986655543211100         


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCchHHhhCcHHHHHHHHHHHhCccchHHHHHHHHhhCHHHHHHHH
Q 015628          241 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQ  320 (403)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~l~~Lr~~pqf~~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI~  320 (403)
                               +....+.+|.++|++.+....   |+++|+|||++|||++||++||+||+||++|||+|+++||+|+|+|+
T Consensus       191 ---------~~~p~~~~p~~~~~~~~~~~~---~~~~l~fLr~~~qf~~lR~~iqqNP~ll~~~Lqqlg~~nP~L~q~Iq  258 (340)
T KOG0011|consen  191 ---------AELPANAQPLDLFPQGAVEAS---GGDPLEFLRNQPQFQQLRQMIQQNPELLHPLLQQLGKQNPQLLQLIQ  258 (340)
T ss_pred             ---------CCCCCCCChhhcCCccchhhh---cCCchhhhhccHHHHHHHHHHhhCHHHHHHHHHHHhhhCHHHHHHHH
Confidence                     000002356788887654443   34899999999999999999999999999999999999999999999


Q ss_pred             HcHHHHHHHhcCCCCCCCCcccccccccCC-ccccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015628          321 EHQTDFLRLINEPVEGGEGNVLGQLASAMP-QAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH  399 (403)
Q Consensus       321 ~n~e~Fl~~l~~~~~~~~g~~~~~~~~~~~-~~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~  399 (403)
                      +||++||+|||++++|+++++.++.+..++ +.|++|+||.+||+|||+|||+|..|||||||||||||+||||||+|+|
T Consensus       259 ~nqe~Fl~mlnep~~~~~~~~~~~~~~~~~~~~I~vtpee~eAIeRL~alGF~ralViqayfACdKNEelAAN~Ll~~~f  338 (340)
T KOG0011|consen  259 ENQEAFLQLLNEPVEGGDGGGTGAPAAEGPGHQIQVTPEEKEAIERLEALGFPRALVIQAYFACDKNEELAANYLLSHSF  338 (340)
T ss_pred             HHHHHHHHHhhcccccccccccccccccCCcceEecCHHHHHHHHHHHHhCCcHHHHHHHHHhcCccHHHHHHHHHhhcc
Confidence            999999999999998766666666655555 7899999999999999999999999999999999999999999999995


Q ss_pred             CC
Q 015628          400 EF  401 (403)
Q Consensus       400 d~  401 (403)
                      ||
T Consensus       339 ~d  340 (340)
T KOG0011|consen  339 ED  340 (340)
T ss_pred             CC
Confidence            54

>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array

Probab=99.80  E-value=9.3e-20  Score=137.76  Aligned_cols=57  Identities=60%  Similarity=1.068  Sum_probs=54.1

Q ss_pred             hHHhhCcHHHHHHHHHHHhCccchHHHHHHHHhhCHHHHHHHHHcHHHHHHHhcCCC
Q 015628          278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV  334 (403)
Q Consensus       278 l~~Lr~~pqf~~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI~~n~e~Fl~~l~~~~  334 (403)
                      |++||++|+|++||++||+||++|+++||+|+++||+|+++|++||++|++||+++.
T Consensus         1 L~~Lr~~Pqf~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~n~e~Fl~ll~~~~   57 (59)
T PF09280_consen    1 LEFLRNNPQFQQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQNPEEFLRLLNEPA   57 (59)
T ss_dssp             CGGGTTSHHHHHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHHTHHHHHHHHHSTS
T ss_pred             ChHHHcChHHHHHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHHCHHHHHHHHcCCC
Confidence            578999999999999999999999999999999999999999999999999999874

They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.75  E-value=3.9e-18  Score=134.58  Aligned_cols=73  Identities=27%  Similarity=0.403  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+++|+++.++|++++||.+||++|+++.|   +|+++|+|+|+||.|+|+.+|++|||+++++|+|+++.
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~g---i~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~   73 (74)
T cd01807           1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLN---VPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRP   73 (74)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcC
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999873

GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.73  E-value=1.4e-17  Score=131.80  Aligned_cols=75  Identities=55%  Similarity=0.790  Sum_probs=72.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCC--CCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVY--PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~i--p~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+++.++|++++||.+||++|++..|   +  ++++|||+|+|++|+|+.+|++|||++|++|++++++++
T Consensus         1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~---i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~~~   77 (77)
T cd01805           1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKG---CDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSKPK   77 (77)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhC---CCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEecCC
Confidence            89999999999999999999999999999999999   7  999999999999999999999999999999999998864

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).

>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF

Probab=99.72  E-value=1.8e-17  Score=132.63  Aligned_cols=74  Identities=22%  Similarity=0.354  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCcE-EEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTH-FEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~-~~ie-V~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|++ +.|+ +++++||.+||++|++..|   +|+++|||+|+||+|+|+.+|++|||+++++|+|+++..
T Consensus         1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~g---i~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~~   76 (78)
T cd01797           1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFN---VEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQD   76 (78)
T ss_pred             CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhC---CCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            899999999997 7895 8999999999999999999   999999999999999999999999999999999999753

NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.71  E-value=2.6e-17  Score=130.04  Aligned_cols=71  Identities=18%  Similarity=0.328  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+||++.|+.+.++|++++||.+||++|++..|   +++++|||||+|++|+|+++|++|||++|++||+..
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~---~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTG---TRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhC---CChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence            78999999999999999999999999999999999   999999999999999999999999999999999864

UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.70  E-value=5.2e-17  Score=128.22  Aligned_cols=73  Identities=27%  Similarity=0.369  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+.  +++.++|++++||.+||.+|+++.|   +|+++|+|+|+||.|+|+.+|++|+|+++++|+++++.++
T Consensus         1 mqi~vk~~--~~~~l~v~~~~tV~~lK~~i~~~~g---ip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~G   73 (74)
T cd01793           1 MQLFVRAQ--NTHTLEVTGQETVSDIKAHVAGLEG---IDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLG   73 (74)
T ss_pred             CEEEEECC--CEEEEEECCcCcHHHHHHHHHhhhC---CCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            89999984  7899999999999999999999999   9999999999999999999999999999999999998754

Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.

>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=99.70  E-value=1.6e-16  Score=162.11  Aligned_cols=76  Identities=29%  Similarity=0.440  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      ++|+||+.++ ++.|.|..+.||.+||++|...++   +++++++|||+||||+|+.+|..|||++|.+||||++.....
T Consensus        16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~---a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~~~~   91 (493)
T KOG0010|consen   16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFG---APPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQPRP   91 (493)
T ss_pred             eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcC---CChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccCCCC
Confidence            5799999988 899999999999999999999999   899999999999999999999999999999999998755433

>PTZ00044 ubiquitin; Provisional

Probab=99.70  E-value=7.7e-17  Score=127.37  Aligned_cols=74  Identities=28%  Similarity=0.446  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+++.++|++++||.+||++|++..|   +|++.|||+|+|+.|+|+.+|++|+|+++++|||+++.+
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (76)
T PTZ00044          1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEG---IDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLR   74 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEcc
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999864

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.68  E-value=1e-16  Score=128.11  Aligned_cols=73  Identities=23%  Similarity=0.407  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+.+.|+|+++.||.+||++|+++.+   +++++|||+|+||+|+|+ +|++|||+++++|+||....
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~---~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~   74 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLK---VPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVE   74 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhC---CChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecc
Confidence            89999999999999999999999999999999999   999999999999999999 99999999999999998753

midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.68  E-value=1.2e-16  Score=134.38  Aligned_cols=75  Identities=33%  Similarity=0.546  Sum_probs=72.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+++.|+|++++||.+||++|+++.|   +|+++|||+|+||+|+|+.+|++|+|+++++|+|+++.++
T Consensus        28 M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~g---ip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l~G  102 (103)
T cd01802          28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEG---IPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAMRG  102 (103)
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhC---CChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEecCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998653

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.67  E-value=3.1e-16  Score=123.28  Aligned_cols=74  Identities=36%  Similarity=0.557  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +|++.|||+|+|+.|.|+.+|++|+|+++++|+|+++.+
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g---~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~   74 (76)
T cd01806           1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALR   74 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhC---CChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEcc
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999764

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.

>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2

Probab=99.67  E-value=1.5e-16  Score=127.54  Aligned_cols=74  Identities=28%  Similarity=0.401  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEE--EeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkL--iy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+.+.++|+++.||.+||++|+...|   +++++|||  +|+|++|+|+.+|++|||+++++|+|++++-
T Consensus         3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~---i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~~   78 (80)
T cd01792           3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIG---VPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQNC   78 (80)
T ss_pred             eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhC---CCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEcc
Confidence            78999999999999999999999999999999999   99999999  9999999999999999999999999999863

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>cd01803 Ubiquitin Ubiquitin

Probab=99.66  E-value=3e-16  Score=123.40  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+..+|   +|++.|+|+|+|+.|+|+.+|++|+|+++++|+|+++.+.
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~g   75 (76)
T cd01803           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (76)
T ss_pred             CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhC---CCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEccC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998643

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)

>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2

Probab=99.66  E-value=2.5e-16  Score=124.33  Aligned_cols=72  Identities=22%  Similarity=0.271  Sum_probs=69.5

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+||++.|+++.|+|++++||.+||++|+...|   +|+++|+|+|+||+|+|+.+|++|||+++++|+++++..
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---i~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~   72 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRER---VQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLR   72 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhC---CCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEcc
Confidence            689999999999999999999999999999999   999999999999999999999999999999999998864

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.65  E-value=3e-16  Score=122.95  Aligned_cols=69  Identities=28%  Similarity=0.462  Sum_probs=66.7

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      +.||.++|+++.++|++++||.+||.+|++..|   +|+++|||+|+||+|+|+.+|++|+|+++++|||++
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~g---i~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~   69 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEG---VDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV   69 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhC---CCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence            468999999999999999999999999999999   999999999999999999999999999999999997

DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.65  E-value=5.5e-16  Score=120.62  Aligned_cols=72  Identities=36%  Similarity=0.459  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+..+|   ++++.|+|+|+|++|+|+.+|++|||+++++|+|+.+
T Consensus         1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~   72 (72)
T cd01809           1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVG---IPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR   72 (72)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999864

Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.

>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein

Probab=99.64  E-value=4.2e-16  Score=121.61  Aligned_cols=70  Identities=30%  Similarity=0.546  Sum_probs=67.6

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+||++.|+++.++|++++||.+||++|+++.|   +|+++|+|+|+||.|+|+.+|++|||+++++|||+.|
T Consensus         1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---i~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~   70 (70)
T cd01798           1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQG---VPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR   70 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHC---CCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence            689999999999999999999999999999999   9999999999999999999999999999999999864

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.

>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2

Probab=99.63  E-value=8.2e-16  Score=120.35  Aligned_cols=71  Identities=32%  Similarity=0.428  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+.+|+ +.|+|++++||.+||++|++..|   ++.++|+|+|+||+|.|+.+|++|||+++++|||+++
T Consensus         1 ~~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~---i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~   71 (71)
T cd01808           1 IKVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFK---ANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             CEEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhC---CCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence            68999999997 58999999999999999999999   9999999999999999999999999999999999874

hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.

>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein

Probab=99.63  E-value=6.7e-16  Score=123.49  Aligned_cols=73  Identities=21%  Similarity=0.207  Sum_probs=64.7

Q ss_pred             CEEEEEeCCCcE--EEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccc--cCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTH--FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENK--VAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~--~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~g--I~~~s~I~v~v   74 (403)
                      |+|+||+.+|++  |.|++++++||.+||++|+...+.. +++++|||||+||+|+|+.+|++|+  |+++.+|||+.
T Consensus         2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~-~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~   78 (79)
T cd01790           2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSK-PLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC   78 (79)
T ss_pred             eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCC-CChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence            589999999999  5556689999999999999987521 5689999999999999999999996  99999999985

Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.

>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade

Probab=99.62  E-value=1.2e-15  Score=118.21  Aligned_cols=68  Identities=38%  Similarity=0.613  Sum_probs=65.7

Q ss_pred             EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         6 Ktl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+++|+.|.|+|++++||.+||++|+...+   +|++.|+|+|+|++|+|+.+|++|||+++++|+|++++
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~---~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~   68 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETG---IPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKP   68 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHT---STGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccc---cccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEec
Confidence            689999999999999999999999999999   99999999999999999999999999999999999875

There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.61  E-value=1.7e-15  Score=120.03  Aligned_cols=70  Identities=29%  Similarity=0.414  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEe---CCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy---~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+|| ++|++|.|+|++++||.+||++|++.+|   +|+++|||+|   +||+|+|+.+|++|+|++|++|+||.
T Consensus         1 ~~i~vk-~~g~~~~v~v~~~~Tv~~lK~~i~~~tg---vp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lmG   73 (74)
T cd01813           1 VPVIVK-WGGQEYSVTTLSEDTVLDLKQFIKTLTG---VLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMMG   73 (74)
T ss_pred             CEEEEE-ECCEEEEEEECCCCCHHHHHHHHHHHHC---CCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEEe
Confidence            689999 8999999999999999999999999999   9999999996   99999999999999999999999985

The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.

>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain

Probab=99.57  E-value=4.9e-15  Score=116.23  Aligned_cols=68  Identities=34%  Similarity=0.435  Sum_probs=64.4

Q ss_pred             EEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCC-CcccccccCCCcEEEEE
Q 015628            3 VFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVM   73 (403)
Q Consensus         3 I~VKtl-~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~-~tLsd~gI~~~s~I~v~   73 (403)
                      |+||+. +|+++.++|++++||.+||.+|+++.|   +|+++|+|+|+||.|+|+ .+|++|||+++++|++-
T Consensus         1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~g---ip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l~   70 (71)
T cd01796           1 ITVYTARSETTFSLDVDPDLELENFKALCEAESG---IPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhC---CCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEEe
Confidence            689999 999999999999999999999999999   999999999999999987 68999999999999873

DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.55  E-value=1.5e-14  Score=112.38  Aligned_cols=70  Identities=29%  Similarity=0.421  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+||+. |+.+.++|++++||.+||++|+..+|   +|+++|||+|+|+.|.|+.+|++|||++|++|+||.
T Consensus         1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~   70 (71)
T cd01812           1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTG---VEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhC---CChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence            68999986 99999999999999999999999999   999999999999999999999999999999999984

BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).

>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=7.6e-15  Score=109.34  Aligned_cols=70  Identities=36%  Similarity=0.548  Sum_probs=68.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      |.|.||+++|+.+.|++++.++|..+|++|+++.|   +|+.+|||||.||.+.|+++-.+|++.-|++||++
T Consensus         1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeG---IPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcC---CCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence            88999999999999999999999999999999999   99999999999999999999999999999999974

>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120

Probab=99.53  E-value=2.7e-14  Score=113.36  Aligned_cols=68  Identities=26%  Similarity=0.396  Sum_probs=65.1

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         8 l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      ++|+++.|+|++++||.+||++|+..+|   +|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+++.+.
T Consensus         5 l~g~~~~l~v~~~~TV~~lK~~i~~~~g---ip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~g   72 (76)
T cd01800           5 LNGQMLNFTLQLSDPVSVLKVKIHEETG---MPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERG   72 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHC---CCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCC
Confidence            5799999999999999999999999999   9999999999999999999999999999999999998654

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.

>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]

Probab=99.43  E-value=1.7e-14  Score=119.51  Aligned_cols=76  Identities=37%  Similarity=0.583  Sum_probs=73.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |.++++++.|++.+++|++++||..||.+|....|   +|++.|+|||+||+|+|..||++|||...++||++.+..+.
T Consensus         1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~G---i~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~GG   76 (128)
T KOG0003|consen    1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
T ss_pred             CcEEEEEeeCceEEEEecccchHHHHHHHhccccC---CCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHhcC
Confidence            78999999999999999999999999999999999   99999999999999999999999999999999999988765

>smart00213 UBQ Ubiquitin homologues

Probab=99.42  E-value=4.4e-13  Score=101.24  Aligned_cols=64  Identities=42%  Similarity=0.649  Sum_probs=61.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCc
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS   68 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s   68 (403)
                      |+|+||+.+ +.+.++|+++.||.+||.+|+..+|   +++++|+|+|+|+.|.|+.+|++|||++|+
T Consensus         1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~---~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213        1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTG---IPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHC---CCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            899999998 7899999999999999999999999   999999999999999999999999999875

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.41  E-value=1.2e-12  Score=106.63  Aligned_cols=75  Identities=16%  Similarity=0.265  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+|++.+|+.+.+.|.+++||..||++++++.|   +++++|+|+|+|+.|.|+.|+.+|+|.++++|+|+++..+
T Consensus        12 i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~g---i~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~G   86 (87)
T cd01763          12 INLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQG---LSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTG   86 (87)
T ss_pred             EEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhC---CCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEeccc
Confidence            67999999999999999999999999999999999   9999999999999999999999999999999999988653

Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.

>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]

Probab=99.39  E-value=3.1e-13  Score=119.45  Aligned_cols=78  Identities=35%  Similarity=0.546  Sum_probs=74.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+|+++.++++.++|+.++||..+|.+|+...|   ||+++|||||.|+.|.|..+|+||+|+..++|+|+++.++..
T Consensus         1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~eg---Ip~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg~   77 (156)
T KOG0004|consen    1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGA   77 (156)
T ss_pred             CccchhhccccceeeeecccccHHHHHHhhhcccC---CCchhhhhhhhhcccccCCccccccccccceEEEEEEecCCc
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999977654


Q ss_pred             C
Q 015628           81 S   81 (403)
Q Consensus        81 ~   81 (403)
                      .
T Consensus        78 k   78 (156)
T KOG0004|consen   78 K   78 (156)
T ss_pred             c
Confidence            4

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.37  E-value=5.9e-13  Score=105.33  Aligned_cols=59  Identities=25%  Similarity=0.257  Sum_probs=51.0

Q ss_pred             EeC-CCCcHHHHHHHHHHHhCCCCC-CCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628           16 EVK-PEDKVSDVKKNIETVQGSDVY-PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus        16 eV~-~~~TV~dLK~kI~~~~g~~~i-p~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      +|+ .++||.+||++|+++.+.. + ++++|||||+||+|+|+++|++|||+++++|||+.+
T Consensus        15 ~~~~~~~TV~~LK~kI~~~~~eg-i~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~~   75 (75)
T cd01815          15 DVSPGGYQVSTLKQLIAAQLPDS-LPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILRK   75 (75)
T ss_pred             CcCCccCcHHHHHHHHHHhhccC-CCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEeC
Confidence            344 4689999999999996422 5 589999999999999999999999999999999863

BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.28  E-value=6.2e-12  Score=106.21  Aligned_cols=77  Identities=17%  Similarity=0.236  Sum_probs=63.2

Q ss_pred             EEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCC--CCCC--CCCcEEEeCCeecCCCCcccccc------cCCCcEE
Q 015628            2 KVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGS--DVYP--ASQQMLIHQGKVLKDVTTLEENK------VAENSFV   70 (403)
Q Consensus         2 kI~VKtl~g~~~-~ieV~~~~TV~dLK~kI~~~~g~--~~ip--~~~QkLiy~GkiL~D~~tLsd~g------I~~~s~I   70 (403)
                      .|.||..+|..+ ...+.+++||.+||++|++..+.  ..+|  +++|||||+||+|+|+++|++|+      +....++
T Consensus         6 e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~Tm   85 (113)
T cd01814           6 EIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVITM   85 (113)
T ss_pred             EEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceEE
Confidence            577887788553 45678999999999999977642  1244  99999999999999999999999      7777899


Q ss_pred             EEEEecCC
Q 015628           71 VVMLTKSK   78 (403)
Q Consensus        71 ~v~v~k~k   78 (403)
                      ||+++.+.
T Consensus        86 Hvvlr~~~   93 (113)
T cd01814          86 HVVVQPPL   93 (113)
T ss_pred             EEEecCCC
Confidence            99987544

NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.26  E-value=1.6e-11  Score=93.91  Aligned_cols=68  Identities=43%  Similarity=0.663  Sum_probs=64.4

Q ss_pred             EEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            4 FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         4 ~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      +||..+|+.+.+.+.++.||.+||++|+..+|   +++++|+|+|+|+.|+|+.+|.+|+|++++.|+|+.
T Consensus         1 ~v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~---~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769           1 TVKTLTGKTFELEVSPDDTVAELKAKIAAKEG---VPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             CeEccCCCEEEEEECCCChHHHHHHHHHHHHC---cChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence            37888899999999999999999999999999   999999999999999999999999999999999875

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=99.23  E-value=2.4e-11  Score=96.57  Aligned_cols=65  Identities=18%  Similarity=0.274  Sum_probs=58.9

Q ss_pred             EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecC-CCCcccccccC-CCcEEEEEE
Q 015628            6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVA-ENSFVVVML   74 (403)
Q Consensus         6 Ktl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~-D~~tLsd~gI~-~~s~I~v~v   74 (403)
                      |...|.++.|+|++++||.+||.+|+.+.|   +|++.||| |.|+.|. |+.+|++|||+ +|+++++.+
T Consensus         8 ~~~~~~t~~l~v~~~~TV~~lK~kI~~~~g---ip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799           8 AQSHTVTIWLTVRPDMTVAQLKDKVFLDYG---FPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             cccCCCeEEEEECCCCcHHHHHHHHHHHHC---cCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            445688999999999999999999999999   99999999 9999985 67899999999 789999875

HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.

>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins

Probab=99.15  E-value=1.3e-10  Score=90.63  Aligned_cols=71  Identities=24%  Similarity=0.391  Sum_probs=65.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~-~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+|++.+|+.+.+.|.++++|..|++++++..+   ++. ..++|+|.|+.|+++.|+++|||+++++|.|++
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~---i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKG---IPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHT---TTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhC---CCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            78999999999999999999999999999999999   889 999999999999999999999999999999875

SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.00  E-value=9.1e-10  Score=90.87  Aligned_cols=63  Identities=21%  Similarity=0.237  Sum_probs=57.6

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCC-CCcccccccCCCcEEEEEEecC
Q 015628           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKD-VTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus        12 ~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D-~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      ...++|++++||++||.+|...++   +++.+|||+|.|+.|.| .++|++|||..++.|.|.+..|
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~---V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~LlideP   79 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFS---VAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADEP   79 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhc---CCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecCC
Confidence            457889999999999999999999   99999999999999976 5799999999999999998643

The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,

>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []

Probab=98.88  E-value=3.1e-09  Score=72.99  Aligned_cols=36  Identities=50%  Similarity=0.723  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHH
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL  211 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL  211 (403)
                      .++.|+.|++||   |+|++|++||+++.||.++||+||
T Consensus         2 ~~~~v~~L~~mG---f~~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    2 DEEKVQQLMEMG---FSREQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHHHHT---S-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHhC
Confidence            478999999999   999999999999999999999998

The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....

>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B

Probab=98.85  E-value=1.5e-08  Score=82.12  Aligned_cols=71  Identities=25%  Similarity=0.316  Sum_probs=59.2

Q ss_pred             EEEEEeCC-CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEE-EeCCe-----ec-CCCCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLK-GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQGK-----VL-KDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~-g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkL-iy~Gk-----iL-~D~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.|+.-. ....+..+++++||.+||++|+..+|   ++++.|+| +|.|+     .| +|+++|++|++++|..|||+
T Consensus         3 ~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G---~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVv   79 (84)
T cd01789           3 TVNITSSADSFSFEKKYSRGLTIAELKKKLELVVG---TPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVI   79 (84)
T ss_pred             EEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHC---CCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEE
Confidence            56676533 34455669999999999999999999   99999999 58888     45 67789999999999999998


Q ss_pred             Ee
Q 015628           74 LT   75 (403)
Q Consensus        74 v~   75 (403)
                      -.
T Consensus        80 D~   81 (84)
T cd01789          80 DV   81 (84)
T ss_pred             eC
Confidence            54

Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.

>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A

Probab=98.84  E-value=2.3e-08  Score=85.28  Aligned_cols=75  Identities=20%  Similarity=0.284  Sum_probs=55.4

Q ss_pred             EEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCC----CCCCCCcEEEeCCeecCCCCcccccccCCCc------EE
Q 015628            2 KVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSD----VYPASQQMLIHQGKVLKDVTTLEENKVAENS------FV   70 (403)
Q Consensus         2 kI~VKtl~g~-~~~ieV~~~~TV~dLK~kI~~~~g~~----~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s------~I   70 (403)
                      .|+++..+|+ +-.+.+++++||.+||++|......+    ...+..+||||.||+|+|+++|++|++..++      ++
T Consensus         4 ~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~vm   83 (111)
T PF13881_consen    4 ELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTVM   83 (111)
T ss_dssp             EEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EEE
T ss_pred             EEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEEE
Confidence            5777778998 77889999999999999999876533    1235578999999999999999999998766      45


Q ss_pred             EEEEec
Q 015628           71 VVMLTK   76 (403)
Q Consensus        71 ~v~v~k   76 (403)
                      ||+++.
T Consensus        84 Hlvvrp   89 (111)
T PF13881_consen   84 HLVVRP   89 (111)
T ss_dssp             EEEE-S
T ss_pred             EEEecC
Confidence            555543

>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=98.83  E-value=2.7e-08  Score=75.51  Aligned_cols=72  Identities=39%  Similarity=0.585  Sum_probs=68.2

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      ++++++.|+.+.+++....+|..+|.+|....|   ++...|+|+|.|+.|.|+.+|.+|+|..++.++++.+.+
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~---~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~   73 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEG---IPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLR   73 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcC---CCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecC
Confidence            678889999999999999999999999999999   999999999999999999999999999999999988764

>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]

Probab=98.80  E-value=6e-09  Score=114.31  Aligned_cols=70  Identities=26%  Similarity=0.400  Sum_probs=67.4

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      .|+|||++.++.++.|...+||++||..|.++..   |+.+.|||||.|++|.|++++.+|+| +|.+|||+-|
T Consensus         4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~n---i~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlver   73 (1143)
T KOG4248|consen    4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVN---IPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVER   73 (1143)
T ss_pred             ceeeeecccceeEEEechHHHHHHHHHHHHHhcc---cccccceeeecceeeccchhhhhccC-CCeEEEeecc
Confidence            4899999999999999999999999999999999   99999999999999999999999999 8999999977

>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []

Probab=98.78  E-value=1.1e-08  Score=70.18  Aligned_cols=36  Identities=39%  Similarity=0.641  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHH
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYL  394 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L  394 (403)
                      +.+.|++|++|||+++.|++||.+|++|.+.|++||
T Consensus         2 ~~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    2 DEEKVQQLMEMGFSREQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence            457799999999999999999999999999999998

The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....

>cd00194 UBA Ubiquitin Associated domain

Probab=98.76  E-value=1.4e-08  Score=69.75  Aligned_cols=37  Identities=38%  Similarity=0.532  Sum_probs=34.9

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhc
Q 015628          360 REAIERLEAMGFDRALVLEVFFACNKNEELAANYLLD  396 (403)
Q Consensus       360 ~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~  396 (403)
                      .+.|++|++|||+++.|++|+..|++|.+.|++|||+
T Consensus         2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~~   38 (38)
T cd00194           2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWLLE   38 (38)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            3579999999999999999999999999999999985

The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.

>PLN02560 enoyl-CoA reductase

Probab=98.75  E-value=2.2e-08  Score=99.58  Aligned_cols=70  Identities=33%  Similarity=0.440  Sum_probs=61.5

Q ss_pred             CEEEEEeCCCcEE---EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeC---C----eecCCCCcccccccCCCcEE
Q 015628            1 MKVFVKTLKGTHF---EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G----KVLKDVTTLEENKVAENSFV   70 (403)
Q Consensus         1 MkI~VKtl~g~~~---~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~---G----kiL~D~~tLsd~gI~~~s~I   70 (403)
                      |+|+||..+|+.+   +|+|+++.||++||++|+++.+.  +++++|||++.   |    +.|+|+++|++|||+++++|
T Consensus         1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~--~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstL   78 (308)
T PLN02560          1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKK--YYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTV   78 (308)
T ss_pred             CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCC--CChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceE
Confidence            8999999889887   79999999999999999999872  47999999972   3    48899999999999999986


Q ss_pred             EE
Q 015628           71 VV   72 (403)
Q Consensus        71 ~v   72 (403)
                      ++
T Consensus        79 y~   80 (308)
T PLN02560         79 VF   80 (308)
T ss_pred             EE
Confidence            54

>smart00165 UBA Ubiquitin associated domain

Probab=98.73  E-value=1.7e-08  Score=69.03  Aligned_cols=36  Identities=47%  Similarity=0.629  Sum_probs=34.4

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHh
Q 015628          360 REAIERLEAMGFDRALVLEVFFACNKNEELAANYLL  395 (403)
Q Consensus       360 ~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~  395 (403)
                      .+.|++|++|||++++|++|+..|++|.+.|++|||
T Consensus         2 ~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L~   37 (37)
T smart00165        2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL   37 (37)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence            467999999999999999999999999999999997

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

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=98.69  E-value=5.4e-08  Score=82.26  Aligned_cols=73  Identities=22%  Similarity=0.287  Sum_probs=61.7

Q ss_pred             CEEEEEeCCC-cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCccccccc-------CCCcEEEE
Q 015628            1 MKVFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-------AENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g-~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI-------~~~s~I~v   72 (403)
                      |-++++.+.. .++.+++.++.||.+||++|+....   .|++.|+|+..+.+|+|+++|++||+       ....+|-+
T Consensus         1 MdvFlmIrR~KTTiF~dakes~tVlelK~~iegI~k---~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgL   77 (119)
T cd01788           1 MDVFLMIRRHKTTIFTDAKESTTVYELKRIVEGILK---RPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGL   77 (119)
T ss_pred             CceEEEEEecceEEEeecCCcccHHHHHHHHHHHhc---CChhHheeecCceeecccccHHHcCccccccccCCCCeEEE
Confidence            4555554444 4577899999999999999999999   99999999977889999999999999       56778877


Q ss_pred             EEec
Q 015628           73 MLTK   76 (403)
Q Consensus        73 ~v~k   76 (403)
                      .+++
T Consensus        78 a~r~   81 (119)
T cd01788          78 AFRS   81 (119)
T ss_pred             EEec
Confidence            7774

Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.

>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A

Probab=98.65  E-value=8.4e-08  Score=77.98  Aligned_cols=72  Identities=24%  Similarity=0.320  Sum_probs=57.5

Q ss_pred             EEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeC----C---eec-CCCCcccccccCCCcEEE
Q 015628            2 KVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ----G---KVL-KDVTTLEENKVAENSFVV   71 (403)
Q Consensus         2 kI~VKtl~g--~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~----G---kiL-~D~~tLsd~gI~~~s~I~   71 (403)
                      +|+|.....  +.+++.++.++||.+||.+|+..+|   +++..|+|.|.    +   ..| +|+.+|.+||+++|..||
T Consensus         3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~G---i~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~   79 (87)
T PF14560_consen    3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTG---IPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIH   79 (87)
T ss_dssp             EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHT---S-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEE
T ss_pred             EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhC---CCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEE
Confidence            577776554  4888999999999999999999999   99999999765    2   123 567899999999999999


Q ss_pred             EEEec
Q 015628           72 VMLTK   76 (403)
Q Consensus        72 v~v~k   76 (403)
                      |.=..
T Consensus        80 V~D~~   84 (87)
T PF14560_consen   80 VVDTN   84 (87)
T ss_dssp             EEE-T
T ss_pred             EEeCC
Confidence            98543

>cd00194 UBA Ubiquitin Associated domain

Probab=98.62  E-value=6.2e-08  Score=66.52  Aligned_cols=37  Identities=51%  Similarity=0.788  Sum_probs=35.0

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      ++.|+.|++||   |+|++|++||+++.+|.++|++||+.
T Consensus         2 ~~~v~~L~~mG---f~~~~~~~AL~~~~~d~~~A~~~L~~   38 (38)
T cd00194           2 EEKLEQLLEMG---FSREEARKALRATNNNVERAVEWLLE   38 (38)
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            56899999999   99999999999999999999999973

The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=98.60  E-value=1.1e-07  Score=75.67  Aligned_cols=70  Identities=23%  Similarity=0.263  Sum_probs=55.3

Q ss_pred             CEEEEEeCC-CcEEEEEeC-CCCcHHHHHHHHHHHhCCCCCCCCCcEE--EeCCeecCCCCcccccccCCCcEEEE
Q 015628            1 MKVFVKTLK-GTHFEIEVK-PEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~-g~~~~ieV~-~~~TV~dLK~kI~~~~g~~~ip~~~QkL--iy~GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      +.|.++..+ .....++++ ++.||.+||+.|+...+.  +++++|||  ++.|++|.|+.+|.+|||++|++|+|
T Consensus         1 ~~i~~~~~~~k~~~~~~~~~~~aTV~dlk~~i~~~~~~--~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801           1 LEILDAKRSDKPIGKLKVSSGDATIADLKKLIAKSSPQ--LTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             CeeeccccCcCceeecccCCCCccHHHHHHHHHHHcCC--CCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            356666555 333334444 889999999999988652  67899988  48999999999999999999998775

Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.

>smart00165 UBA Ubiquitin associated domain

Probab=98.58  E-value=8.4e-08  Score=65.52  Aligned_cols=36  Identities=53%  Similarity=0.850  Sum_probs=34.4

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHH
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  212 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~  212 (403)
                      ++.|+.|++||   |++++|.+||+...||.++|++||+
T Consensus         2 ~~~v~~L~~mG---f~~~~a~~aL~~~~~d~~~A~~~L~   37 (37)
T smart00165        2 EEKIDQLLEMG---FSREEALKALRAANGNVERAAEYLL   37 (37)
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence            57899999999   9999999999999999999999995

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

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.36  E-value=1.9e-06  Score=61.76  Aligned_cols=67  Identities=31%  Similarity=0.457  Sum_probs=60.6

Q ss_pred             EEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         5 VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+..++..+.+.+..+.||.+||++|..++|   +++..++|+++|+.+.+...+.+|++.+++.|+++.
T Consensus         2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196           2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLG---LPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             eEecCCCEEEEEcCCCCcHHHHHHHHHHHHC---cChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            3444688889999999999999999999999   889999999999999999888899999999998874

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.

>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway

Probab=98.35  E-value=8.1e-07  Score=71.48  Aligned_cols=69  Identities=28%  Similarity=0.359  Sum_probs=43.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeC---Ceec--CCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---GKVL--KDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~---GkiL--~D~~tLsd~gI~~~s~I~v~   73 (403)
                      |-|.||+.+| .+.|+|++++||.+||++|.+..+   ++...|.|..+   .+.|  .++++|+++||+.||.|+|-
T Consensus         5 milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~---~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~   78 (80)
T PF11543_consen    5 MILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLS---IPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK   78 (80)
T ss_dssp             -EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS------TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred             EEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcC---CCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence            6788898777 678999999999999999999999   88888888532   2344  46789999999999999763

Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.

>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]

Probab=98.15  E-value=5.1e-06  Score=85.44  Aligned_cols=71  Identities=23%  Similarity=0.371  Sum_probs=66.2

Q ss_pred             EEEEEeCCCcEEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            2 KVFVKTLKGTHFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         2 kI~VKtl~g~~~~ie-V~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      .|.|| +.|+.+.++ ++.++|+..||.+|...+|   +++++||++++|+.|.|+-.+..++||++.+|++|.+.
T Consensus         5 ~v~VK-W~gk~y~v~~l~~d~t~~vlKaqlf~LTg---V~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~   76 (473)
T KOG1872|consen    5 TVIVK-WGGKKYPVETLSTDETPSVLKAQLFALTG---VPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTA   76 (473)
T ss_pred             eEeee-ecCccccceeccCCCchHHHHHHHHHhcC---CCccceeEEEecccccccccccccccCCCCEEEeeccc
Confidence            36677 899999998 9999999999999999999   99999999999999999999999999999999999764

>cd01811 OASL_repeat1 2'-5' oligoadenylate synthetase-like protein, repeat 1 of 2

Probab=98.12  E-value=1.4e-05  Score=62.72  Aligned_cols=71  Identities=18%  Similarity=0.313  Sum_probs=62.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeC---C--eecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G--KVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~---G--kiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      ++|+||-+.+..+.+.|+|..+|..||++|....+   + ...|||.|.   |  ..|.+.++|.+|||-.+-.|.|+-.
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~---~-~g~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lleT   76 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRN---C-SGLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLET   76 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhC---c-ccceEEEeecCCcccccccccccHhhhcceeccEEEEEec
Confidence            58999999999999999999999999999999999   5 469999983   3  4578999999999998888877754

OASL_repeat1 (2'-5' oligoadenylate synthetase-like protein) belongs to a family of interferon-induced 2'-5' oligoadenylate synthetases which are important for the antiviral activity of interferons. While each member of this famliy has a conserved N-terminal OAS catalytic domain, only OASL has two tandem ubiquitin-like repeats located at the C-terminus and this CD represents one of those repeats.

>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]

Probab=98.08  E-value=1.6e-06  Score=66.04  Aligned_cols=69  Identities=19%  Similarity=0.308  Sum_probs=61.4

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      .+.+...-|++..|.+++++||+++|+.|+.++|   ..++++.|--.+.+++|..+|++|.|++|-.+.+.
T Consensus         3 ev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtG---T~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely   71 (73)
T KOG3493|consen    3 EVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY   71 (73)
T ss_pred             eehhhhhcCceEEEEeCCcccccCHHHHHHHhhC---CChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence            4667777899999999999999999999999999   77888888777789999999999999999877664

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=98.04  E-value=7.2e-06  Score=80.43  Aligned_cols=74  Identities=27%  Similarity=0.394  Sum_probs=64.2

Q ss_pred             CEEEEEeC---CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTL---KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl---~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |.|.|+..   .-..+.|+|+.+..|.+||+.++.+.|   +|+++.|+||.||.|.|+.++..+.+...+.+|+|+-++
T Consensus         1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~g---vp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~lRP   77 (446)
T KOG0006|consen    1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQG---VPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIMLLRP   77 (446)
T ss_pred             CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhC---CChhheEEEEeccccccCceeecccccccchhhhhccCc
Confidence            66777754   224588999999999999999999999   999999999999999999999999998889999885443

>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=97.78  E-value=0.00024  Score=72.91  Aligned_cols=59  Identities=20%  Similarity=0.148  Sum_probs=50.1

Q ss_pred             EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628           14 EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus        14 ~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      .++.....|-.+|..+|.++.|   ++-.-.|.|.+||+|.-.+||.+-|++.+-.+.|++.
T Consensus        53 l~k~sL~i~Gselqa~iakklg---i~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~~  111 (568)
T KOG2561|consen   53 LKKCSLHITGSELQALIAKKLG---IKENHVKCIINGKILSCRKTLAEQGLKINQELMVAVG  111 (568)
T ss_pred             hhhcccccccHHHHHHHHHHcC---CchhhhheeeccceeecccchhhhhhhhhhHHHHHhc
Confidence            4555667778899999999999   8888889999999999999999999988776666554

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=97.46  E-value=0.00014  Score=74.39  Aligned_cols=42  Identities=31%  Similarity=0.460  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015628          358 EEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH  399 (403)
Q Consensus       358 ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~  399 (403)
                      +-...|++|++|||+|++|..|+.|+-.|.+.|++||+..--
T Consensus       155 ~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~tGIP  196 (378)
T TIGR00601       155 ERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIP  196 (378)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHHhCCC
Confidence            344669999999999999999999999999999999997633

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG4495 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription]

Probab=97.46  E-value=0.00017  Score=59.39  Aligned_cols=61  Identities=23%  Similarity=0.351  Sum_probs=49.6

Q ss_pred             EEEEEe-CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEe-CC-eecCCCCcccccccC
Q 015628            2 KVFVKT-LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-QG-KVLKDVTTLEENKVA   65 (403)
Q Consensus         2 kI~VKt-l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy-~G-kiL~D~~tLsd~gI~   65 (403)
                      .++++. ....++.++.+++.||.+||.+++....   -|+..|+|+. .. .+|+|.++|+++|..
T Consensus         2 ~~f~~VrR~kttif~da~es~tV~elK~~l~gi~~---~Pvn~qrL~kmd~eqlL~D~ktL~d~gft   65 (110)
T KOG4495|consen    2 DVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILK---RPVNEQRLYKMDTEQLLDDGKTLGDCGFT   65 (110)
T ss_pred             ceeeeeeecceeEEeecCccccHHHHHHHHHHHHh---CCCcchheeecCHHHHhhccchhhhcccc
Confidence            344443 3445678899999999999999999998   8999999976 33 678999999999874

>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]

Probab=97.36  E-value=0.001  Score=55.25  Aligned_cols=72  Identities=14%  Similarity=0.234  Sum_probs=64.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      +|.|+.-++....+.|..+..+..|++.-+++.|   +.....|++|+|+.+.+..|=.+++..+++.|-++...
T Consensus        22 ~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~G---l~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q   93 (99)
T KOG1769|consen   22 NLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQG---LSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQ   93 (99)
T ss_pred             EEEEecCCCCEEEEEeecCChHHHHHHHHHHHcC---CccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeec
Confidence            4566665667778899999999999999999999   88999999999999999999999999999999998754

>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi

Probab=97.35  E-value=0.00045  Score=57.65  Aligned_cols=60  Identities=17%  Similarity=0.228  Sum_probs=46.7

Q ss_pred             EEEEEeCCC-cEEEEEeC--CCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCccccc
Q 015628            2 KVFVKTLKG-THFEIEVK--PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN   62 (403)
Q Consensus         2 kI~VKtl~g-~~~~ieV~--~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~   62 (403)
                      .|+||..++ ..+.++|.  .+.||..||+.|.+..+.+ ..-.++||||+||+|.|...|...
T Consensus         2 ~l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~-~s~~rLRlI~~Gr~L~d~t~l~~~   64 (97)
T PF10302_consen    2 YLTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPE-PSRRRLRLIYAGRLLNDHTDLSSE   64 (97)
T ss_pred             eEEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCC-CccccEEeeecCcccCccchhhhh
Confidence            366776553 34677777  7899999999999998422 556788999999999998877654

They contain a characteristic GFDRL sequence motif.

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.05  E-value=0.0026  Score=50.12  Aligned_cols=71  Identities=11%  Similarity=0.244  Sum_probs=57.5

Q ss_pred             EEEE--EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCC--CCCcEEEeCCeecCCCCcccccccCCCcEEEE
Q 015628            2 KVFV--KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP--ASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         2 kI~V--Ktl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip--~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      +|+|  +..+|.+|.+.+....+|+.|-..+.+....+-.+  -..+|..-++++|.++..|.+|+|.+|+.+.+
T Consensus         6 kVTvD~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei   80 (81)
T COG5417           6 KVTVDFTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI   80 (81)
T ss_pred             EEEEEeEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence            4444  66789999999999999999998888776533122  23568889999999999999999999998875

>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []

Probab=97.04  E-value=0.0013  Score=52.39  Aligned_cols=71  Identities=18%  Similarity=0.271  Sum_probs=50.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC---CcEEE-eCCeecCCCCcccccccCCCcEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS---QQMLI-HQGKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~---~QkLi-y~GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      +|+|...+|+.+.+.+..+.+|.+|...|.+..+.......   ..+|. -+|..|+++.+|.++||.+|+.|++
T Consensus         4 rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L   78 (79)
T PF08817_consen    4 RVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGDVLVL   78 (79)
T ss_dssp             EEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred             EEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence            57777655688999999999999999999998873212222   35666 6899999999999999999999986

Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.

>KOG4583 consensus Membrane-associated ER protein involved in stress response (contains ubiquitin-like domain) [Posttranslational modification, protein turnover, chaperones]

Probab=96.94  E-value=0.00028  Score=70.03  Aligned_cols=74  Identities=20%  Similarity=0.199  Sum_probs=56.4

Q ss_pred             EEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCC--cEEEEEEec
Q 015628            2 KVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAEN--SFVVVMLTK   76 (403)
Q Consensus         2 kI~VKtl~g--~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~--s~I~v~v~k   76 (403)
                      .++||..+.  +.+.|+.+..+||++||..++..+..+ --..+|||||+||.|.|...|+|+-+|..  .++||+...
T Consensus        11 ~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPsk-pl~~dqrliYsgkllld~qcl~d~lrkq~k~Hv~hlvcns   88 (391)
T KOG4583|consen   11 TLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSK-PLELDQRLIYSGKLLLDHQCLTDWLRKQVKEHVKHLVCNS   88 (391)
T ss_pred             EEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCC-CchhhHHHHhhccccccchhHHHHHHHHHHHHHHHHhcCC
Confidence            467776665  446778888999999999999988654 23568999999999999999999866543  355555543

>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast

Probab=96.94  E-value=0.0058  Score=48.66  Aligned_cols=68  Identities=22%  Similarity=0.299  Sum_probs=57.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCC-cEEE--eCCeecCCC--CcccccccCCCcEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQ-QMLI--HQGKVLKDV--TTLEENKVAENSFVVV   72 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~-QkLi--y~GkiL~D~--~tLsd~gI~~~s~I~v   72 (403)
                      +|.||..+|+.+...+..++||.+|...|.....   .+... .+|+  |-.+.|.++  ++|.++|+..+..|+|
T Consensus         8 ~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~---~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    8 RIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLF---SPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             EEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHH---CTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcchHHHHHHHHHHhcC---CCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence            6899999999999999999999999999998877   33443 6776  678888654  6999999999998876

The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....

>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.91  E-value=0.0036  Score=57.57  Aligned_cols=94  Identities=20%  Similarity=0.233  Sum_probs=62.6

Q ss_pred             HHHHHHHhCccchHHHHHHHHhhCHH---HHHHHHHcHHHHHHHhcCCCCCCCCcccccccccCCccccCCHHHHHHHHH
Q 015628          289 ALRTMVQANPQILQPMLQELGKQNPH---LMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIER  365 (403)
Q Consensus       289 ~lR~~vq~NP~lL~~~lq~i~~~nP~---l~~lI~~n~e~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~ee~~ai~r  365 (403)
                      -||..+-+    ||.+|..-.-.+|+   ++++.-+|.+.|..-.-.=-..  .      .+   ......+.+...|++
T Consensus       104 TlrtvLis----lQalL~~pEp~dPqDavva~qy~~n~~~F~~TAr~WT~~--f------A~---~~~~~~~~~~~~v~~  168 (200)
T KOG0418|consen  104 TLRTVLIS----LQALLCAPEPKDPQDAVVAEQYVDNYEMFYKTARYWTTE--F------AG---GRLPDDPWDKKKVDS  168 (200)
T ss_pred             hHHHHHHH----HHHHHcCCCCCChHHHHHHHHHhhhHHHHHHHHHHHHHH--H------hC---CCCCCCchhHHHHHH
Confidence            34555444    44444443444444   5556667888887653210000  0      00   023456677888999


Q ss_pred             HHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          366 LEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       366 L~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      |++|||+|..++.+|...+||.+.|.+.||+.
T Consensus       169 l~~mGf~~~~~i~~L~~~~w~~~~a~~~~~s~  200 (200)
T KOG0418|consen  169 LIEMGFSELEAILVLSGSDWNLADATEQLLSG  200 (200)
T ss_pred             HHHhcccHHHHHHHhhccccchhhhhHhhccC
Confidence            99999999999999999999999999999873

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=96.88  E-value=0.0058  Score=48.74  Aligned_cols=68  Identities=13%  Similarity=0.135  Sum_probs=56.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecCC---CCcccccccCCCcEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVV   72 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~D---~~tLsd~gI~~~s~I~v   72 (403)
                      +|.||..+|+.+...+..++||.+|.+.|....+   ......+|+  |-.|.|.+   +++|.++|+....+|+|
T Consensus         6 ~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~---~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v   78 (80)
T smart00166        6 RLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALT---DGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL   78 (80)
T ss_pred             EEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHccc---CCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence            6899999999999999999999999999966555   445567775  67788864   47999999988887765

Present in FAF1 and Shp1p.

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=96.68  E-value=0.012  Score=46.58  Aligned_cols=67  Identities=28%  Similarity=0.392  Sum_probs=53.6

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecCC---CCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~D---~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.||..+|+.+...+..++||.+|.+-|.....    .....+|+  |-.|.|.|   +.+|.++|+. .+.+++.
T Consensus         4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~----~~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~-~s~~~~~   75 (77)
T cd01767           4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGP----PAEPFTLMTSFPRRVLTDLDYELTLQEAGLV-NEVVFQR   75 (77)
T ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCC----CCCCEEEEeCCCCccCCCCCccCcHHHcCCc-cceEEEE
Confidence            6899999999999999999999999999977654    24556776  66788865   7899999999 4555443

The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.

>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs)

Probab=96.62  E-value=0.0033  Score=44.12  Aligned_cols=40  Identities=33%  Similarity=0.356  Sum_probs=34.4

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      ++.|+.|.+|= -.|+++.++++|++.-+|.|+||++|+.|
T Consensus         2 ~~~v~~L~~mF-P~~~~~~I~~~L~~~~~~ve~ai~~LL~~   41 (42)
T PF02845_consen    2 EEMVQQLQEMF-PDLDREVIEAVLQANNGDVEAAIDALLEM   41 (42)
T ss_dssp             HHHHHHHHHHS-SSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            67899999992 12899999999999999999999999865

CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.61  E-value=0.0041  Score=58.30  Aligned_cols=65  Identities=25%  Similarity=0.395  Sum_probs=55.6

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCc--EEEEEEec
Q 015628            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS--FVVVMLTK   76 (403)
Q Consensus         9 ~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s--~I~v~v~k   76 (403)
                      .++.|.+.+...+||.++|.++....|   +.+..|+++|+|++|.|...|..|+|..+.  +|-++|..
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg---~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqviVlq  221 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEG---VDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQVIVLQ  221 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhc---cchhhheeeccCCceeccccceeeeecCCCEEEEEEEecc
Confidence            466788888899999999999999999   668899999999999999999999999994  44444433

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=96.61  E-value=0.013  Score=46.75  Aligned_cols=67  Identities=19%  Similarity=0.358  Sum_probs=55.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecCC---CCcccccccCCCcEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVV   72 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~D---~~tLsd~gI~~~s~I~v   72 (403)
                      +|.||..+|+.+...+..++||.+|.+.|....+   . ....+|+  |-.|.+.+   +++|.++|+.+..+|+|
T Consensus         6 ~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~---~-~~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           6 RIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTG---N-GGPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCC---C-CCCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence            6899999999999999999999999999986654   1 2556776  77899964   47999999998888776

SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]

Probab=96.57  E-value=0.0044  Score=59.50  Aligned_cols=70  Identities=19%  Similarity=0.233  Sum_probs=54.0

Q ss_pred             CEEEEEeCCCc-EE-EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE----eCCeecCCCCcccccccCCCcEEEE
Q 015628            1 MKVFVKTLKGT-HF-EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI----HQGKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g~-~~-~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi----y~GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      |+|+++..++. .. ..+.+...||.|++++|..+..+  +.+.++|+.    -+||.|.|+.+|++|+..++.+|+|
T Consensus         1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k--~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~v   76 (297)
T KOG1639|consen    1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLK--ITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIYV   76 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhc--cCccchhheeeccCCCccccchhHHHHhccCCCCEEEE
Confidence            88999887763 23 36778889999999888877654  556555443    4799999999999999999866644

>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A

Probab=96.54  E-value=0.0058  Score=43.16  Aligned_cols=40  Identities=25%  Similarity=0.298  Sum_probs=33.3

Q ss_pred             HHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          361 EAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       361 ~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      +.|.+++++ |.++..|++-+.+|+||.+.|++..|++..+
T Consensus         2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~~~   42 (43)
T PF14555_consen    2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDGEA   42 (43)
T ss_dssp             HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS-S
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence            568888887 9999999999999999999999999987543

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=96.54  E-value=0.015  Score=46.68  Aligned_cols=64  Identities=22%  Similarity=0.315  Sum_probs=52.4

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecCC-CCcccccccCCC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAEN   67 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~D-~~tLsd~gI~~~   67 (403)
                      +|.||..+|+.+...++.++||.+|.+.|....+.  .......|+  |-.|.|.| +.+|++.|+.+.
T Consensus         6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~--~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s   72 (79)
T cd01770           6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPE--FAARPFTLMTAFPVKELSDESLTLKEANLLNA   72 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCC--CCCCCEEEecCCCCcccCCCCCcHHHCCCcCc
Confidence            68899999999999999999999999999987642  223556775  77888865 779999999863

p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]

Probab=96.53  E-value=0.003  Score=65.96  Aligned_cols=43  Identities=26%  Similarity=0.392  Sum_probs=38.9

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHhccCCCCC
Q 015628          360 REAIERLEAMGFDRALVLEVFFACNK-NEELAANYLLDHMHEFE  402 (403)
Q Consensus       360 ~~ai~rL~~lGF~~~~~~~a~~ac~~-ne~~a~~~L~~~~~d~~  402 (403)
                      +-+|++|.+|||+...+.+|+++.+. |-|-|-||||+|+.|-|
T Consensus       559 qs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqHMdDPd  602 (749)
T COG5207         559 QSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQHMDDPD  602 (749)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhhccCcc
Confidence            44699999999999999999999976 89999999999988754

>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=96.44  E-value=0.0097  Score=62.15  Aligned_cols=45  Identities=40%  Similarity=0.534  Sum_probs=39.9

Q ss_pred             cccCCHHHHHH--HHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhc
Q 015628          352 AVTVTPEEREA--IERLEAMGF-DRALVLEVFFACNKNEELAANYLLD  396 (403)
Q Consensus       352 ~~~lt~ee~~a--i~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~  396 (403)
                      .-.+.+|++-+  +++|.+||| +|+..++|+++.++|.+.|+..||.
T Consensus       445 ~~~~~pe~r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverll~  492 (493)
T KOG0010|consen  445 QQTVPPEERYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERLLG  492 (493)
T ss_pred             cCCCCchHHHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhc
Confidence            34577777777  899999998 8999999999999999999999974

>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]

Probab=96.22  E-value=0.0028  Score=68.01  Aligned_cols=43  Identities=40%  Similarity=0.652  Sum_probs=39.7

Q ss_pred             ccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCC
Q 015628          171 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  216 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP  216 (403)
                      +..+..|..|++||   |.|.|++.||++..||.+|||||+++-+-
T Consensus       633 ~~~e~~v~si~smG---f~~~qa~~aL~~~n~nveravDWif~h~d  675 (763)
T KOG0944|consen  633 EVDEESVASIVSMG---FSRNQAIKALKATNNNVERAVDWIFSHMD  675 (763)
T ss_pred             CCChhHheeeeeec---CcHHHHHHHHHhcCccHHHHHHHHHhccc
Confidence            45688999999999   99999999999999999999999998754

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=96.21  E-value=0.034  Score=45.06  Aligned_cols=68  Identities=19%  Similarity=0.372  Sum_probs=59.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecCC---CCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~D---~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.||..+|+.+.-.+..+.+|.+|-..|.. .|   .+.+..+|+  |--|.|..   +.+|.+.|+.+..+|+|-
T Consensus         7 ~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g---~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq   79 (82)
T cd01773           7 RLMLRYPDGKREQIALPEQAKLLALVRHVQS-KG---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ   79 (82)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cC---CCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEe
Confidence            6899999999999999999999999999988 56   678889997  77888742   579999999999998874

Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>smart00727 STI1 Heat shock chaperonin-binding motif

Probab=96.07  E-value=0.0067  Score=42.18  Aligned_cols=36  Identities=47%  Similarity=0.652  Sum_probs=29.8

Q ss_pred             HHhhCcHHHHHHHHHHHhCccchHHHHHHHHhhCHHHHHHH
Q 015628          279 DFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLI  319 (403)
Q Consensus       279 ~~Lr~~pqf~~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI  319 (403)
                      ..|+ +|+|+++.+-+++||+++..+++.    ||++++.|
T Consensus         6 ~~l~-~P~~~~~l~~~~~nP~~~~~~~~~----nP~~~~~i   41 (41)
T smart00727        6 LRLQ-NPQVQSLLQDMQQNPDMLAQMLQE----NPQLLQLI   41 (41)
T ss_pred             HHHc-CHHHHHHHHHHHHCHHHHHHHHHh----CHHhHhhC
Confidence            3444 999999999999999998887764    99988764

>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly

Probab=96.06  E-value=0.023  Score=44.04  Aligned_cols=63  Identities=17%  Similarity=0.210  Sum_probs=46.3

Q ss_pred             eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEE
Q 015628            7 TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         7 tl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      ..+++.+.|.|.++.++.++-+....++|   +..++-.|.|++|.|+-+.++.-.|+-+|..+.+
T Consensus         3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~---l~~~~~~L~h~~k~ldlslp~R~snL~n~akLeL   65 (65)
T PF11470_consen    3 CYNFRRFKVKVTPNTTLNQVLEEACKKFG---LDPSSYDLKHNNKPLDLSLPFRLSNLPNNAKLEL   65 (65)
T ss_dssp             -TTS-EEEE---TTSBHHHHHHHHHHHTT-----GGG-EEEETTEEESSS-BHHHH---SS-EEEE
T ss_pred             ccCCcEEEEEECCCCCHHHHHHHHHHHcC---CCccceEEEECCEEeccccceeecCCCCCCEEeC
Confidence            35788999999999999999999999999   8889999999999999999999999999988764

TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.

>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]

Probab=96.04  E-value=0.008  Score=64.67  Aligned_cols=45  Identities=29%  Similarity=0.553  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHHhccCCCCC
Q 015628          358 EEREAIERLEAMGFDRALVLEVFFAC-NKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       358 ee~~ai~rL~~lGF~~~~~~~a~~ac-~~ne~~a~~~L~~~~~d~~  402 (403)
                      -++..|.+|++|||+.+.|.+|++.. +.+.|.|-||||+|+.|.|
T Consensus       570 ~d~s~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl~~HMdDpd  615 (763)
T KOG0944|consen  570 ADRSVISQLVEMGFPEEACRRALYYTGNSGAEAASNWLMEHMDDPD  615 (763)
T ss_pred             hhHHHHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHHHHhccCcc
Confidence            35678999999999999999999999 7888999999999998865

>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs)

Probab=95.91  E-value=0.018  Score=40.35  Aligned_cols=37  Identities=32%  Similarity=0.475  Sum_probs=33.0

Q ss_pred             HHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          361 EAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       361 ~ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      +.|+.|++|  .++++.+..+|.+|++|.+.|.+.||+.
T Consensus         3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~   41 (42)
T PF02845_consen    3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM   41 (42)
T ss_dssp             HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            468999999  6899999999999999999999999974

CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=95.86  E-value=0.052  Score=49.33  Aligned_cols=76  Identities=18%  Similarity=0.240  Sum_probs=54.5

Q ss_pred             CEEEEEeCCC----cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCc-EEEe-CCeec--CCCCcccccccCCCc----
Q 015628            1 MKVFVKTLKG----THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQ-MLIH-QGKVL--KDVTTLEENKVAENS----   68 (403)
Q Consensus         1 MkI~VKtl~g----~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~Q-kLiy-~GkiL--~D~~tLsd~gI~~~s----   68 (403)
                      |+|+|++++|    .++.+.+..+.||.+|+.+|....+   ++...+ .|.+ .++.|  .++..++++.-...+    
T Consensus         1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~---~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~~~~   77 (162)
T PF13019_consen    1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLP---IPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDSDFI   77 (162)
T ss_pred             CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcC---CCccceeEEEEeCCCeeCCCccccHHhhccCcCCCCce
Confidence            7899999999    5889999999999999999999998   776663 3443 34444  456667776544432    


Q ss_pred             EEEEEEecCCC
Q 015628           69 FVVVMLTKSKV   79 (403)
Q Consensus        69 ~I~v~v~k~k~   79 (403)
                      +|.|+++..+.
T Consensus        78 ~l~l~~rl~GG   88 (162)
T PF13019_consen   78 TLRLSLRLRGG   88 (162)
T ss_pred             EEEEEEeccCC
Confidence            45555555443

>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]

Probab=95.65  E-value=0.016  Score=57.87  Aligned_cols=42  Identities=31%  Similarity=0.476  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      -...|.+|++|||+|++|+.|+.|.=+|.|.|+.||+..--+
T Consensus       135 ~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~GIP~  176 (340)
T KOG0011|consen  135 YEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLNGIPE  176 (340)
T ss_pred             hHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhcCCcc
Confidence            345699999999999999999999999999999999975433

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=95.58  E-value=0.079  Score=43.07  Aligned_cols=69  Identities=16%  Similarity=0.175  Sum_probs=55.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeC--CeecC--------CCCcccccccCCCcEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GKVLK--------DVTTLEENKVAENSFV   70 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~--GkiL~--------D~~tLsd~gI~~~s~I   70 (403)
                      .+|.||..+|+.+.-.+..++||.+|..-|.. .+   ..+....|+++  -|.|.        .+.||.+.||.+..+|
T Consensus         5 ~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~---~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L   80 (85)
T cd01774           5 VKIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LK---ETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVL   80 (85)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CC---CCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEE
Confidence            37899999999999999999999999999964 34   45678888854  48885        3679999999988777


Q ss_pred             EEE
Q 015628           71 VVM   73 (403)
Q Consensus        71 ~v~   73 (403)
                      +|-
T Consensus        81 ~V~   83 (85)
T cd01774          81 FVQ   83 (85)
T ss_pred             EEe
Confidence            653

Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=95.46  E-value=0.095  Score=42.12  Aligned_cols=68  Identities=22%  Similarity=0.274  Sum_probs=57.8

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecC--C-CCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--D-VTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~--D-~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.||..+|+.+.-.+..++++.+|..-|... |   ++....+|+  |--|.+.  | +.+|.+.|+....+|+|-
T Consensus         6 ~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~---~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~Ve   78 (80)
T cd01771           6 KLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-G---YPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLILE   78 (80)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-C---CCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEEE
Confidence            78999999999999999999999999999764 6   667788886  7788885  2 569999999988888763

Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.36  E-value=0.022  Score=52.53  Aligned_cols=47  Identities=26%  Similarity=0.292  Sum_probs=43.6

Q ss_pred             ccccCCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          165 SNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       165 s~l~~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      ..+..+..+.+.|.+|.+||   |+|+.++.+|+-..-|-.+|-|+|++|
T Consensus       154 ~~~~~~~~~~~~v~~l~~mG---f~~~~~i~~L~~~~w~~~~a~~~~~s~  200 (200)
T KOG0418|consen  154 GRLPDDPWDKKKVDSLIEMG---FSELEAILVLSGSDWNLADATEQLLSG  200 (200)
T ss_pred             CCCCCCchhHHHHHHHHHhc---ccHHHHHHHhhccccchhhhhHhhccC
Confidence            33778888999999999999   999999999999999999999999886

>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs)

Probab=95.06  E-value=0.062  Score=37.74  Aligned_cols=39  Identities=26%  Similarity=0.406  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHc--CCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          173 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       173 ~e~~v~~i~~M--G~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .++.|..|.+|  .   ++++.|++.|++.-+|.|+|++.|+.|
T Consensus         2 ~~~~v~~L~~mFP~---l~~~~I~~~L~~~~g~ve~~i~~LL~~   42 (43)
T smart00546        2 NDEALHDLKDMFPN---LDEEVIKAVLEANNGNVEATINNLLEG   42 (43)
T ss_pred             hHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            36789999999  5   799999999999999999999999876

CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)

>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]

Probab=94.95  E-value=0.09  Score=43.12  Aligned_cols=69  Identities=16%  Similarity=0.183  Sum_probs=59.0

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |.|...+|..+.+.|..+.+...|.+..+.+.|+   ..+..|++|+|+.++-++|-.+++..+++.|-++.
T Consensus        27 Lkvv~qd~telfFkiKktT~f~klm~af~~rqGK---~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~   95 (103)
T COG5227          27 LKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGK---NMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVT   95 (103)
T ss_pred             eEEecCCCCEEEEEEeccchHHHHHHHHHHHhCc---CcceeEEEEcceecCCCCChhhcCCccchHHHHHH
Confidence            4444556788888999999999999999999994   47899999999999999999999999998776543

>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]

Probab=94.92  E-value=0.066  Score=50.28  Aligned_cols=70  Identities=19%  Similarity=0.211  Sum_probs=53.6

Q ss_pred             EEEEEeCCC-cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEE-EeCC-----eecC-CCCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQG-----KVLK-DVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g-~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkL-iy~G-----kiL~-D~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.|.+... ..++..+..+.||.+||.|++-.+|   .+++.++| +|.|     ..|. ++..|..|+..+|-.|||+
T Consensus         3 ~v~Iss~~~~~~~Ekr~~~~ltl~q~K~KLe~~~G---~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihvi   79 (234)
T KOG3206|consen    3 RVVISSSLNDFRTEKRLSNSLTLAQFKDKLELLTG---TEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVI   79 (234)
T ss_pred             EEEEecccccchhhhhcCCcCcHHHHHhhhhhhhC---CCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEE
Confidence            455543222 2245567789999999999999999   89999999 5665     2454 4779999999999999988


Q ss_pred             E
Q 015628           74 L   74 (403)
Q Consensus        74 v   74 (403)
                      =
T Consensus        80 D   80 (234)
T KOG3206|consen   80 D   80 (234)
T ss_pred             e
Confidence            4

>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs)

Probab=94.67  E-value=0.088  Score=36.95  Aligned_cols=37  Identities=35%  Similarity=0.442  Sum_probs=32.9

Q ss_pred             HHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          361 EAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       361 ~ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      +.|+.|.+|  .+++..+...|.+|++|.+.|.+.||+.
T Consensus         4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~   42 (43)
T smart00546        4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG   42 (43)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            468999999  4579999999999999999999999874

CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)

>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle

Probab=93.69  E-value=0.061  Score=40.18  Aligned_cols=37  Identities=27%  Similarity=0.526  Sum_probs=25.3

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhC-----CCHHHHHHHHhc
Q 015628          360 REAIERLEAMGFDRALVLEVFFACN-----KNEELAANYLLD  396 (403)
Q Consensus       360 ~~ai~rL~~lGF~~~~~~~a~~ac~-----~ne~~a~~~L~~  396 (403)
                      .+.|+|++.|||+++.||+||..-+     .+.+...|..++
T Consensus        10 ~~lVd~F~~mGF~~dkVvevlrrlgik~~n~~dn~t~~~ilE   51 (55)
T PF09288_consen   10 KDLVDQFENMGFERDKVVEVLRRLGIKSMNGVDNETENKILE   51 (55)
T ss_dssp             HHHHHHHHHHT--HHHHHHHHHHS--SS--SS--HHHHHHHH
T ss_pred             HHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCccchhHHHHHH
Confidence            4679999999999999999998754     234566666554

This domain is predominantly found in fungi []. ; PDB: 1TTE_A.

>PF15044 CLU_N: Mitochondrial function, CLU-N-term

Probab=93.32  E-value=0.12  Score=41.19  Aligned_cols=56  Identities=23%  Similarity=0.351  Sum_probs=45.6

Q ss_pred             eCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCccccc-ccCCCcEEEEEE
Q 015628           17 VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN-KVAENSFVVVML   74 (403)
Q Consensus        17 V~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~-gI~~~s~I~v~v   74 (403)
                      |.++++|.+||+.|......  ..-....|.|+|+.|+|...|+++ |++++..|.|+.
T Consensus         1 v~~~d~v~dvrq~L~~~~~t--~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lve   57 (76)
T PF15044_consen    1 VSPTDTVQDVRQVLAESPET--CYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELVE   57 (76)
T ss_pred             CChhhHHHHHHHHHHhCccc--cceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEEe
Confidence            56889999999999877542  445677889999999998888888 588888888774

>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []

Probab=92.41  E-value=0.18  Score=41.08  Aligned_cols=35  Identities=29%  Similarity=0.637  Sum_probs=30.8

Q ss_pred             HHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          363 IERLEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       363 i~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      |+++.++||++..|++|+.+|-.|..+|..|++..
T Consensus         1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~   35 (87)
T PF11626_consen    1 IKHYEELGYSREFVTHALYATSGDPELARRFVLNF   35 (87)
T ss_dssp             -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred             CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            67789999999999999999999999999988765

The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.

>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle

Probab=92.38  E-value=0.15  Score=38.18  Aligned_cols=23  Identities=35%  Similarity=0.679  Sum_probs=19.4

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHH
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRA  199 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrA  199 (403)
                      ...|+++++||   |+|+.|+.|||-
T Consensus        10 ~~lVd~F~~mG---F~~dkVvevlrr   32 (55)
T PF09288_consen   10 KDLVDQFENMG---FERDKVVEVLRR   32 (55)
T ss_dssp             HHHHHHHHHHT-----HHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CcHHHHHHHHHH
Confidence            56899999999   999999999995

This domain is predominantly found in fungi []. ; PDB: 1TTE_A.

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=92.38  E-value=0.42  Score=36.11  Aligned_cols=56  Identities=20%  Similarity=0.293  Sum_probs=40.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+|.   |+.  +++..+.|+.+||+++..         +.=.+||+|-..+++..     +++||.|+++.|
T Consensus         1 M~I~vN---~k~--~~~~~~~tl~~lr~~~k~---------~~DI~I~NGF~~~~d~~-----L~e~D~v~~Ikk   56 (57)
T PF14453_consen    1 MKIKVN---EKE--IETEENTTLFELRKESKP---------DADIVILNGFPTKEDIE-----LKEGDEVFLIKK   56 (57)
T ss_pred             CEEEEC---CEE--EEcCCCcCHHHHHHhhCC---------CCCEEEEcCcccCCccc-----cCCCCEEEEEeC
Confidence            666665   544  677788899999987632         22377999998887654     567899988753

>PRK06437 hypothetical protein; Provisional

Probab=92.05  E-value=1  Score=34.81  Aligned_cols=54  Identities=22%  Similarity=0.327  Sum_probs=43.1

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         9 ~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      .++...++++...||.+|-+.    .+   ++.....+..+|+++.     .++-|++||.|.++-
T Consensus         9 g~~~~~~~i~~~~tv~dLL~~----Lg---i~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv~   62 (67)
T PRK06437          9 GHINKTIEIDHELTVNDIIKD----LG---LDEEEYVVIVNGSPVL-----EDHNVKKEDDVLILE   62 (67)
T ss_pred             CCcceEEEcCCCCcHHHHHHH----cC---CCCccEEEEECCEECC-----CceEcCCCCEEEEEe
Confidence            445577888888999988765    46   7788888899999997     556788999998774

>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]

Probab=91.98  E-value=0.23  Score=50.29  Aligned_cols=69  Identities=14%  Similarity=0.135  Sum_probs=59.8

Q ss_pred             CEEEEEeC--CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCC--CcccccccCCCcEEEE
Q 015628            1 MKVFVKTL--KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV--TTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl--~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~--~tLsd~gI~~~s~I~v   72 (403)
                      |.++|.+.  ..++|.|+|..+..+..|+..++...|   +..+..-|||++++|.+.  ..|..||++.+++|.+
T Consensus         1 M~~tvs~~l~~~~~~~i~v~~dg~L~nl~aL~~~d~g---~~~~~~~li~n~~~l~s~~s~~l~Q~g~~~~dsl~l   73 (380)
T KOG0012|consen    1 MSLTVSVALNFEKKFPIPVTTDGELNNLAALCWKDTG---IVYDPSDLIYNPRPLVSNESQGLTQIGLKDGDSLAL   73 (380)
T ss_pred             CeEEEEEEecceeeeccccccccchhhHHHHHHHHhC---cccchhhcccCCCccccchhhhhhhcccccceeEec
Confidence            67777655  667899999999999999999999999   999999999999999765  5899999999888743

>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []

Probab=91.85  E-value=0.3  Score=39.76  Aligned_cols=35  Identities=29%  Similarity=0.469  Sum_probs=31.1

Q ss_pred             HHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          177 VQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       177 v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      |+.+.+.|   |.++.|..||++.-.+|..|..|++++
T Consensus         1 i~~~~~~g---~~~~~v~~aL~~tSgd~~~a~~~vl~~   35 (87)
T PF11626_consen    1 IKHYEELG---YSREFVTHALYATSGDPELARRFVLNF   35 (87)
T ss_dssp             -HHHHHHT---B-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred             CchHHHhC---CCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            56688899   999999999999999999999999887

The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=91.38  E-value=0.75  Score=36.52  Aligned_cols=66  Identities=11%  Similarity=0.166  Sum_probs=45.3

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC--CCcEEEeCCeecCCCCcccccccCCCcEEE
Q 015628            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGSDVYPA--SQQMLIHQGKVLKDVTTLEENKVAENSFVV   71 (403)
Q Consensus         1 MkI~VKtl~------g-~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~--~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~   71 (403)
                      |+|+|+...      | ....+++....||.+|++.|......  +..  ....+..+|+...+     ++-|++|+.|.
T Consensus         2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~--l~~~~~~~~vavN~~~v~~-----~~~l~dgDeVa   74 (82)
T PLN02799          2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPS--LEEVRSCCVLALNEEYTTE-----SAALKDGDELA   74 (82)
T ss_pred             eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChh--HHHHhhCcEEEECCEEcCC-----CcCcCCCCEEE
Confidence            788888543      4 45677888889999999999776421  111  12345678887653     34578899998


Q ss_pred             EE
Q 015628           72 VM   73 (403)
Q Consensus        72 v~   73 (403)
                      ++
T Consensus        75 i~   76 (82)
T PLN02799         75 II   76 (82)
T ss_pred             Ee
Confidence            87

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=91.25  E-value=0.94  Score=35.32  Aligned_cols=57  Identities=11%  Similarity=0.142  Sum_probs=41.1

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCC-CCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628           12 HFEIEVKPEDKVSDVKKNIETVQGS-DVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus        12 ~~~ieV~~~~TV~dLK~kI~~~~g~-~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      ...++++...||.+|.+.+...++. .........+..+|+...     .++-|++|+.|.++
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~-----~~~~l~~gD~v~i~   74 (80)
T cd00754          17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVR-----LDTPLKDGDEVAII   74 (80)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcC-----CCcccCCCCEEEEe
Confidence            4667887789999999999987541 001123456677999887     34568899999887

MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.

>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function

Probab=90.68  E-value=0.72  Score=34.98  Aligned_cols=41  Identities=29%  Similarity=0.370  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .-.+|++|-+.-|+ +..+++-+.|+-++++||.||+-|++-
T Consensus         5 ~rk~VQ~iKEiv~~-hse~eIya~L~ecnMDpnea~qrLL~q   45 (60)
T PF06972_consen    5 SRKTVQSIKEIVGC-HSEEEIYAMLKECNMDPNEAVQRLLSQ   45 (60)
T ss_pred             HHHHHHHHHHHhcC-CCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence            46799999998655 899999999999999999999999863

>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction

Probab=89.85  E-value=0.45  Score=34.20  Aligned_cols=37  Identities=22%  Similarity=0.463  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHH
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  212 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~  212 (403)
                      .++.+.-|+..|   |.+.++.+|++....+|+.-+|.++
T Consensus         3 ~~d~~~AL~~LG---y~~~e~~~av~~~~~~~~~~~e~~i   39 (47)
T PF07499_consen    3 LEDALEALISLG---YSKAEAQKAVSKLLEKPGMDVEELI   39 (47)
T ss_dssp             HHHHHHHHHHTT---S-HHHHHHHHHHHHHSTTS-HHHHH
T ss_pred             HHHHHHHHHHcC---CCHHHHHHHHHHhhcCCCCCHHHHH
Confidence            578899999999   9999999999998766666677665

The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=89.82  E-value=2.1  Score=33.21  Aligned_cols=53  Identities=26%  Similarity=0.458  Sum_probs=40.4

Q ss_pred             CCc--EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            9 KGT--HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         9 ~g~--~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      +|+  ...++++...||.+|.+.+    +   ++.....+..+|+++..     +.-+++||.|.++
T Consensus        10 ng~~~~~~~~~~~~~tv~~ll~~l----~---~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii   64 (70)
T PRK08364         10 IGRGIEKEIEWRKGMKVADILRAV----G---FNTESAIAKVNGKVALE-----DDPVKDGDYVEVI   64 (70)
T ss_pred             eccccceEEEcCCCCcHHHHHHHc----C---CCCccEEEEECCEECCC-----CcCcCCCCEEEEE
Confidence            454  5677888889999998765    5   66667777899999854     4557889988876

>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain

Probab=89.59  E-value=1.8  Score=33.82  Aligned_cols=65  Identities=22%  Similarity=0.204  Sum_probs=47.8

Q ss_pred             EEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCC-CCCcEEEe----CC--eecCCCCcccccccCCCcEEEE
Q 015628            5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-ASQQMLIH----QG--KVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         5 VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip-~~~QkLiy----~G--kiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      |+.++|...+++|+.+.|+.+|=..|+...+   +. .+-.=|.|    +|  .-|+.+++|.++..+......+
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~---l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~~~~~~~l   72 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLG---LKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKKNNPPFTL   72 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHT---TSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBTSSSSEEE
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcC---CCCccEEEEEEeecCCCcceeccCcccHHHHcCCCCCCEEE
Confidence            6788999999999999999999999999999   43 23335666    23  3467788999987773333333

The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=89.08  E-value=1.6  Score=33.20  Aligned_cols=60  Identities=13%  Similarity=0.258  Sum_probs=41.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+|   +|+.+.+  + ..||.+|.+.+    +   +......+-++++++. .....+.-+++||.|-++-
T Consensus         1 m~i~~---Ng~~~~~--~-~~tl~~Ll~~l----~---~~~~~vavavN~~iv~-~~~~~~~~L~dgD~Ieiv~   60 (65)
T PRK06488          1 MKLFV---NGETLQT--E-ATTLALLLAEL----D---YEGNWLATAVNGELVH-KEARAQFVLHEGDRIEILS   60 (65)
T ss_pred             CEEEE---CCeEEEc--C-cCcHHHHHHHc----C---CCCCeEEEEECCEEcC-HHHcCccccCCCCEEEEEE
Confidence            55655   4777666  3 35899988765    5   5555666779999886 2334556788999998874

>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis

Probab=88.67  E-value=1.8  Score=34.99  Aligned_cols=37  Identities=16%  Similarity=0.169  Sum_probs=34.3

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCe
Q 015628           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK   51 (403)
Q Consensus        12 ~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~Gk   51 (403)
                      ++.|.|.+..+..+|+++|.++.+   +|.+..+|.|+..
T Consensus        12 tIaIrvp~~~~y~~L~~ki~~kLk---l~~e~i~LsYkde   48 (80)
T cd06406          12 TVAIQVARGLSYATLLQKISSKLE---LPAEHITLSYKSE   48 (80)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhC---CCchhcEEEeccC
Confidence            889999999999999999999999   9999999999753

PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain

>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain

Probab=88.36  E-value=1.6  Score=35.76  Aligned_cols=47  Identities=17%  Similarity=0.275  Sum_probs=38.6

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEe
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH   48 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy   48 (403)
                      .+++|+.+|+.+.+.+.+++.+.+|+..|.++.|.+..+.....|.|
T Consensus         2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Y   48 (86)
T cd06409           2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSY   48 (86)
T ss_pred             cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEE
Confidence            46788999999999999999999999999999993322225667777

The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is

>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol

Probab=87.27  E-value=4.6  Score=32.64  Aligned_cols=51  Identities=27%  Similarity=0.486  Sum_probs=36.8

Q ss_pred             hHHHHHHHHhhCHHHHHHHHHcHHHHHHHhcCCCCCCCCcccccccccCCccccCCHHHHHHHH-----HHHHcCCChHH
Q 015628          301 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIE-----RLEAMGFDRAL  375 (403)
Q Consensus       301 L~~~lq~i~~~nP~l~~lI~~n~e~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~ee~~ai~-----rL~~lGF~~~~  375 (403)
                      ++.++++|+ ++|.+.+...++|+.|+.-                       ..||+||+++|.     .|..+|-.--.
T Consensus         6 ~nrli~~L~-~dp~~rerF~~DPea~~~~-----------------------~gLt~eE~~aL~~~D~~~L~~lGvhp~L   61 (81)
T cd07922           6 VNRLIQELF-KDPGLIERFQDDPSAVFEE-----------------------YGLTPAERAALREGTFGALTSIGVHPIL   61 (81)
T ss_pred             HHHHHHHHh-cCHHHHHHHHHCHHHHHHH-----------------------cCCCHHHHHHHHccCHHHHHHcCCCHHH
Confidence            356778876 6999999999999988642                       357999999963     35555544433

CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.

>PF12754 Blt1: Cell-cycle control medial ring component; InterPro: IPR024737 During size-dependent cell cycle transitions controlled by the ubiquitous cyclin-dependent kinase Cdk1, Blt1 has been shown to co-localise with Cdr2 in the medial interphase nodes, as well as with Mid1 which was previously shown to localise to similar interphase structures

Probab=87.22  E-value=0.18  Score=50.16  Aligned_cols=60  Identities=25%  Similarity=0.390  Sum_probs=0.0

Q ss_pred             EEEEEeCCCcEEEEEeC---C--CCcHHHHHHHHHH----------HhCCCCCCCCCcE-----EEeCCeecCCCCcccc
Q 015628            2 KVFVKTLKGTHFEIEVK---P--EDKVSDVKKNIET----------VQGSDVYPASQQM-----LIHQGKVLKDVTTLEE   61 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~---~--~~TV~dLK~kI~~----------~~g~~~ip~~~Qk-----Liy~GkiL~D~~tLsd   61 (403)
                      .|++|.+..-.+.|.+.   +  +.+|.+||..++.          +.+   +|.+++|     |+|+.|.+.|.++|.+
T Consensus        80 tV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~---vp~dKik~~~~~lL~~kkPv~~~ktl~e  156 (309)
T PF12754_consen   80 TVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETR---VPLDKIKNFRCRLLYKKKPVGDSKTLAE  156 (309)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhccccccccccc---CCHHHhhhhhhhheecCccCCCcCcHHH
Confidence            46667666655555433   2  5789999999999          777   9999999     9999999999999887


Q ss_pred             ccc
Q 015628           62 NKV   64 (403)
Q Consensus        62 ~gI   64 (403)
                      ..-
T Consensus       157 ~l~  159 (309)
T PF12754_consen  157 VLA  159 (309)
T ss_dssp             ---
T ss_pred             HHh
Confidence            743

Physical interactions between Blt1-Mid1, Blt1-Cdr2 and Cdr2-Mid1 were detected, indicating that medial cortical nodes are formed by the ordered, Cdr2-dependent assembly of multiple interacting proteins during interphase[].; PDB: 2LO0_A.

>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin

Probab=84.95  E-value=1.9  Score=31.34  Aligned_cols=35  Identities=26%  Similarity=0.378  Sum_probs=28.5

Q ss_pred             HHHHHH--cCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          363 IERLEA--MGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       363 i~rL~~--lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      |++-..  -|=+|+..|+-+...+-|.++|+|-|++.
T Consensus        13 I~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsR   49 (53)
T PF11547_consen   13 INQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLSR   49 (53)
T ss_dssp             HHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhcc
Confidence            555444  38999999999999999999999999987

Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.

>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=84.42  E-value=1.2  Score=46.46  Aligned_cols=41  Identities=22%  Similarity=0.385  Sum_probs=37.6

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCC
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  217 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~  217 (403)
                      ...|.+|+.||   |++-..+.||++.-||-|.|.++|+--++.
T Consensus       430 ~~~la~Lv~mG---F~e~~A~~ALe~~gnn~~~a~~~L~~s~~n  470 (568)
T KOG2561|consen  430 GISLAELVSMG---FEEGKARSALEAGGNNEDTAQRLLSASVAN  470 (568)
T ss_pred             hhhHHHHHHhc---cccchHHHHHHhcCCcHHHHHHHHHHhCCC
Confidence            35799999999   999999999999999999999999987664

>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function

Probab=84.27  E-value=4.6  Score=31.29  Aligned_cols=68  Identities=16%  Similarity=0.215  Sum_probs=53.3

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE-eCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-HQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         8 l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi-y~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      .+|+...++.+.+..+.-+..+--+..|...-|++...|- -+|.+|+-++.++|||+.++-++++.++
T Consensus         3 VNGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLK   71 (76)
T PF10790_consen    3 VNGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLK   71 (76)
T ss_pred             eCCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEee
Confidence            3578888888888888777777777766433667766664 5788999899999999999998888764

>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function

Probab=83.00  E-value=3.2  Score=31.51  Aligned_cols=38  Identities=18%  Similarity=0.443  Sum_probs=33.2

Q ss_pred             HHHHHHHHHc-C-CChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          360 REAIERLEAM-G-FDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       360 ~~ai~rL~~l-G-F~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      +.-|+-|++. | +++.++.-.|.-|+-|.+.|++.|+.+
T Consensus         6 rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q   45 (60)
T PF06972_consen    6 RKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ   45 (60)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence            4568888886 4 699999999999999999999999974

>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A

Probab=82.99  E-value=5.5  Score=32.73  Aligned_cols=62  Identities=13%  Similarity=0.213  Sum_probs=42.0

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eC--C-eecCC-CCcccccccCCCcEEEEEEec
Q 015628           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQ--G-KVLKD-VTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus        11 ~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~--G-kiL~D-~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      ..++..++..+||..+++.+.+.+.   + ....||-  |.  + ..|.+ +.||.+.+|.+|-.|++=.+.
T Consensus        14 ~~~t~~FSk~DTI~~v~~~~rklf~---i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn   81 (88)
T PF14836_consen   14 SVLTKQFSKTDTIGFVEKEMRKLFN---I-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERN   81 (88)
T ss_dssp             EEEEEEE-TTSBHHHHHHHHHHHCT-----TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--
T ss_pred             cHhHhhccccChHHHHHHHHHHHhC---C-CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeec
Confidence            3577788999999999999999998   8 6677883  32  2 24655 579999999999877776654

>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal

Probab=82.72  E-value=6.7  Score=30.87  Aligned_cols=57  Identities=19%  Similarity=0.284  Sum_probs=41.2

Q ss_pred             CcE-EEEEeCCC-CcHHHHHHHHHHHhCCCCCC--CCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628           10 GTH-FEIEVKPE-DKVSDVKKNIETVQGSDVYP--ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus        10 g~~-~~ieV~~~-~TV~dLK~kI~~~~g~~~ip--~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      |+. ..+++..+ .||.+|++.|.++++.  +-  .....+..+|+.+.+     +.-|++|+.|.++
T Consensus        14 g~~~~~~~~~~~~~tv~~L~~~L~~~~p~--l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~   74 (80)
T TIGR01682        14 GTDEETLELPDESTTVGELKEHLAKEGPE--LAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFI   74 (80)
T ss_pred             CCCeEEEECCCCCcCHHHHHHHHHHhCch--hhhhccceEEEECCEEcCC-----CcCcCCCCEEEEe
Confidence            443 57888876 8999999999888641  11  123456678888775     4578899999887

The C-terminal Gly-Gly of this model is critical to function.

>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown

Probab=82.68  E-value=4  Score=35.50  Aligned_cols=60  Identities=17%  Similarity=0.174  Sum_probs=42.7

Q ss_pred             EeCC-CCcHHHHHHHHHHHhCCC-------CCCCCCcEEEeC-----------------Ceec---CCCCcccccccCCC
Q 015628           16 EVKP-EDKVSDVKKNIETVQGSD-------VYPASQQMLIHQ-----------------GKVL---KDVTTLEENKVAEN   67 (403)
Q Consensus        16 eV~~-~~TV~dLK~kI~~~~g~~-------~ip~~~QkLiy~-----------------GkiL---~D~~tLsd~gI~~~   67 (403)
                      .|+. +.||.+|++.|.+.....       .+..+..||++.                 ..+|   +++++|.+|||.+.
T Consensus        21 ~vdL~~~Tv~~l~~~v~~~I~t~~~~~Pfrn~~yDtlKIy~~AHg~Kt~nLvInle~De~~iL~~~~~~~tL~~~gv~nE  100 (122)
T PF10209_consen   21 NVDLKDTTVKDLKEQVKQDIKTRPGLPPFRNVKYDTLKIYTKAHGSKTNNLVINLEDDEDWILDVSDDDKTLKELGVENE  100 (122)
T ss_pred             cCCcccCcHHHHHHHHHHHHhcCCCCCCceeeecceEEEEecCCCCCcCCceeeccCCcceeeecCCCCCcHHHcCCCcc
Confidence            4786 899999999988775321       133455666642                 1467   67889999999998


Q ss_pred             cEEEEEEe
Q 015628           68 SFVVVMLT   75 (403)
Q Consensus        68 s~I~v~v~   75 (403)
                      .-|-+...
T Consensus       101 TEiSfF~~  108 (122)
T PF10209_consen  101 TEISFFNM  108 (122)
T ss_pred             ceeeeeCH
Confidence            88877654

>smart00295 B41 Band 4

Probab=82.63  E-value=10  Score=34.39  Aligned_cols=61  Identities=21%  Similarity=0.204  Sum_probs=44.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCcEEEe--C-C---eecCCCCcccccccC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIH--Q-G---KVLKDVTTLEENKVA   65 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~-~~QkLiy--~-G---kiL~D~~tLsd~gI~   65 (403)
                      .|.|..++|....|.++.+.||.+|...|+.+.|   +.. ...-|.+  . +   .-|+...+|.+...+
T Consensus         5 ~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~---l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~   72 (207)
T smart00295        5 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLG---IRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVK   72 (207)
T ss_pred             EEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhC---CCccceeEEEEEcCCCCcCeeCCCccCHHHhcCC
Confidence            5788899999999999999999999999999999   632 1223332  1 1   345656677776654

1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=81.92  E-value=4.3  Score=30.95  Aligned_cols=60  Identities=17%  Similarity=0.240  Sum_probs=42.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+|.   |+.+.+  ....||.+|-+.    .+   ++.....+.++++++..+.- ..+ +++||.|-++-
T Consensus         1 m~i~vN---G~~~~~--~~~~tl~~ll~~----l~---~~~~~vav~~N~~iv~r~~~-~~~-L~~gD~ieIv~   60 (65)
T PRK05863          1 MIVVVN---EEQVEV--DEQTTVAALLDS----LG---FPEKGIAVAVDWSVLPRSDW-ATK-LRDGARLEVVT   60 (65)
T ss_pred             CEEEEC---CEEEEc--CCCCcHHHHHHH----cC---CCCCcEEEEECCcCcChhHh-hhh-cCCCCEEEEEe
Confidence            556554   766554  567788877664    46   77888899999998865432 235 89999998774

>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer

Probab=81.77  E-value=4.6  Score=31.02  Aligned_cols=60  Identities=15%  Similarity=0.150  Sum_probs=46.3

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus        12 ~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      ...+.+....||.+|.+.+..+++.- .......+..+|+.+.+  .-.+.-+++++.|.++-
T Consensus        13 ~~~~~~~~~~tv~~ll~~l~~~~p~~-~~~~~~~v~vN~~~v~~--~~~~~~l~~gD~V~i~p   72 (77)
T PF02597_consen   13 EEEIEVPEGSTVRDLLEALAERYPEL-ALRDRVAVAVNGEIVPD--DGLDTPLKDGDEVAILP   72 (77)
T ss_dssp             EEEEEESSTSBHHHHHHHHCHHTGGG-HTTTTEEEEETTEEEGG--GTTTSBEETTEEEEEEE
T ss_pred             CeEEecCCCCcHHHHHHHHHhhcccc-ccCccEEEEECCEEcCC--ccCCcCcCCCCEEEEEC
Confidence            56788889999999999998886421 12256788899999988  35566788999998874

ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....

>smart00666 PB1 PB1 domain

Probab=81.61  E-value=6.5  Score=30.72  Aligned_cols=45  Identities=16%  Similarity=0.178  Sum_probs=36.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~G   50 (403)
                      +|.|+. ++..+.+.+..+.|..+|+.+|..+++   +.....+|-|..
T Consensus         3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~---~~~~~~~l~Y~D   47 (81)
T smart00666        3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFG---LDNQSFTLKYQD   47 (81)
T ss_pred             cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhC---CCCCCeEEEEEC
Confidence            455654 677888999999999999999999998   665677888864

Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.

>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium)

Probab=80.83  E-value=6.4  Score=31.74  Aligned_cols=70  Identities=14%  Similarity=0.128  Sum_probs=45.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCcEEEeCCee-----cCCCCcccc----cccCCCcEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQGKV-----LKDVTTLEE----NKVAENSFV   70 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~-~~QkLiy~Gki-----L~D~~tLsd----~gI~~~s~I   70 (403)
                      |+|.+. .+|..+.+.+.++.++.+|+++|.++++   +.. ....|-|..-.     |..+.-|.+    |.....++|
T Consensus         1 ~~vK~~-~~~d~~r~~l~~~~~~~~L~~~i~~r~~---~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~~~~~~~~v   76 (82)
T cd06407           1 VRVKAT-YGEEKIRFRLPPSWGFTELKQEIAKRFK---LDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVYRSSGSHTI   76 (82)
T ss_pred             CEEEEE-eCCeEEEEEcCCCCCHHHHHHHHHHHhC---CCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHHHHCCCCeE
Confidence            455555 4677889999999999999999999988   543 45667674321     222222333    344455666


Q ss_pred             EEEE
Q 015628           71 VVML   74 (403)
Q Consensus        71 ~v~v   74 (403)
                      .+.+
T Consensus        77 ~l~v   80 (82)
T cd06407          77 RLLV   80 (82)
T ss_pred             EEEe
Confidence            6665

The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte

>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A

Probab=80.52  E-value=4.9  Score=28.12  Aligned_cols=37  Identities=24%  Similarity=0.397  Sum_probs=30.2

Q ss_pred             HHHHHHHHHc-CCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          174 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       174 e~~v~~i~~M-G~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      ++.|.++|+. |   -+++.++.-|+.+.+|.++||..-+.
T Consensus         1 ~e~i~~F~~iTg---~~~~~A~~~L~~~~wdle~Av~~y~~   38 (43)
T PF14555_consen    1 DEKIAQFMSITG---ADEDVAIQYLEANNWDLEAAVNAYFD   38 (43)
T ss_dssp             HHHHHHHHHHH----SSHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred             CHHHHHHHHHHC---cCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4678888886 6   79999999999999999999986653

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=80.03  E-value=8.3  Score=30.76  Aligned_cols=59  Identities=12%  Similarity=0.264  Sum_probs=40.2

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCC---CCC-----CCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628           11 THFEIEVKPEDKVSDVKKNIETVQGSD---VYP-----ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus        11 ~~~~ieV~~~~TV~dLK~kI~~~~g~~---~ip-----~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      ....+++. ..||.+|.+.|.++++.-   .+.     .....+..+|+...++..   .-|++|+.|.++
T Consensus        16 ~~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~   82 (88)
T TIGR01687        16 KSEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIF   82 (88)
T ss_pred             ceEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEe
Confidence            34677776 889999999999886410   010     123556678887765432   568899999887

Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.

>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA

Probab=80.02  E-value=7.3  Score=31.90  Aligned_cols=53  Identities=19%  Similarity=0.285  Sum_probs=38.8

Q ss_pred             EEEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCccc
Q 015628            2 KVFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE   60 (403)
Q Consensus         2 kI~VKtl-~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLs   60 (403)
                      +|+||.. .|..+.|.|.++.+..+|..+|..+++   +. ...+|-|...  .|-.+|.
T Consensus         2 ~ikVKv~~~~Dv~~i~v~~~i~f~dL~~kIrdkf~---~~-~~~~iKykDE--GD~iti~   55 (86)
T cd06408           2 KIRVKVHAQDDTRYIMIGPDTGFADFEDKIRDKFG---FK-RRLKIKMKDD--GDMITMG   55 (86)
T ss_pred             cEEEEEEecCcEEEEEcCCCCCHHHHHHHHHHHhC---CC-CceEEEEEcC--CCCcccc
Confidence            3555544 678899999999999999999999999   63 4556666654  3444443

NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	403
1oqy_A	368	Structure Of The Dna Repair Protein Hhr23a Length =		1e-33
2qsg_X	171	Crystal Structure Of The Rad4-Rad23 Complex Length		3e-13
1uel_A	95	Solution Structure Of Ubiquitin-Like Domain Of Hhr2		1e-11
1p1a_A	85	Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Le		2e-11
1pve_A	72	Solution Structure Of Xpc Binding Domain Of Hhr23b		1e-10
2f4m_B	61	The Mouse Pngase-Hr23 Complex Reveals A Complete Re		3e-10
1ify_A	49	Solution Structure Of The Internal Uba Domain Of Hh		2e-08
2wyq_A	85	The Crystal Structure Of The Ubiquitin-Like (Ubl) D		3e-08
1p98_A	78	High-Resolution Nmr Structure Of The Ubl-Domain Of		3e-08
1dv0_A	47	Refined Nmr Solution Structure Of The C-Terminal Ub		6e-08
1f4i_A	45	Solution Structure Of The Hhr23a Uba(2) Mutant P333		1e-07
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		2e-07
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		9e-07
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		9e-07
1tp4_A	97	Solution Structure Of The Xpc Binding Domain Of Hhr		1e-06
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		2e-06
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		2e-06
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		3e-06
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		4e-06
3jvz_X	81	E2~ubiquitin-Hect Length = 81		4e-06
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		4e-06
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		4e-06
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		4e-06
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		5e-06
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		5e-06
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		5e-06
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		5e-06
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		5e-06
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		5e-06
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		5e-06
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		6e-06
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		6e-06
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		6e-06
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		6e-06
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		6e-06
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		6e-06
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		6e-06
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		6e-06
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		7e-06
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		7e-06
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		7e-06
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		7e-06
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		7e-06
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		7e-06
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		8e-06
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		9e-06
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		1e-05
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		1e-05
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		1e-05
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		1e-05
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		1e-05
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		1e-05
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		1e-05
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		1e-05
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		1e-05
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		2e-05
3h7s_A	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		2e-05
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		2e-05
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		2e-05
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		2e-05
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		2e-05
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-05
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		2e-05
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		2e-05
1ndd_B	76	Structure Of Nedd8 Length = 76		2e-05
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		2e-05
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-05
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		3e-05
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		3e-05
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		3e-05
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		3e-05
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		3e-05
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		3e-05
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		3e-05
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		4e-05
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		4e-05
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		4e-05
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		4e-05
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		4e-05
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		5e-05
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		6e-05
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		8e-05
4hk2_A	78	U7ub25.2540 Length = 78		9e-05
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		1e-04
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		1e-04
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		2e-04
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		5e-04
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		7e-04
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		8e-04
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		8e-04

>pdb|1OQY|A Chain A, Structure Of The Dna Repair Protein Hhr23a Length = 368

Iteration: 1
 Score =  140 bits (353), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 97/254 (38%), Positives = 136/254 (53%), Gaps = 57/254 (22%)
Query: 163 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI-----PE 217
           AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GI     PE
Sbjct: 158 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIPGSPEPE 214
Query: 218 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 277
             +V                                 +  P              AG   
Sbjct: 215 HGSV----------------------------QESQVSEQPAT----------EAAGENP 236
Query: 278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP---- 333
           L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NEP    
Sbjct: 237 LEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEPPGEL 296
Query: 334 --VEGGEGNVLGQLASAMPQA--VTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEEL 389
             +   EG V G +    PQ   + VTP+E+EAIERL+A+GF  +LV++ +FAC KNE L
Sbjct: 297 ADISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACEKNENL 355
Query: 390 AANYLLDHMHEFED 403
           AAN+LL     F+D
Sbjct: 356 AANFLLS--QNFDD 367

>pdb|2QSG|X Chain X, Crystal Structure Of Rad4-Rad23 Bound To A Uv-Damaged Dna Length = 171

Iteration: 1
 Score = 73.2 bits (178), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 46/133 (34%), Positives = 72/133 (54%), Gaps = 24/133 (18%)
Query: 289 ALRTMVQANPQILQPMLQELGKQNPHL---------------MRLIQEHQTDFLRLINEP 333
           +LR +V  NP+ L P+L+ +  + P L               +  + ++  D +   ++ 
Sbjct: 37  SLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEAVGDNMQDVMEGADDM 96
Query: 334 VEGGEGNVLGQLASA-MPQA-------VTVTPEEREAIERLEAMGFDRALVLEVFFACNK 385
           VEG +  V G+ A+A + Q        V  TPE+ +AI RL  +GF+R LV++V+FAC+K
Sbjct: 97  VEGEDIEVTGEAAAAGLGQGEGEGSFQVDYTPEDDQAISRLCELGFERDLVIQVYFACDK 156
Query: 386 NEELAANYLL-DH 397
           NEE AAN L  DH
Sbjct: 157 NEEAAANILFSDH 169

>pdb|1UEL|A Chain A, Solution Structure Of Ubiquitin-Like Domain Of Hhr23b Complexed With Ubiquitin-Interacting Motif Of Proteasome Subunit S5a Length = 95

Iteration: 1
 Score = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/74 (44%), Positives = 52/74 (70%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M+V +KTL+   F+I++ PE+ V  +K+ IE+ +G D +P + Q LI+ GK+L D T L+
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60
Query: 61 ENKVAENSFVVVML 74
          E K+ E +FVVVM+
Sbjct: 61 EYKIDEKNFVVVMV 74

>pdb|1P1A|A Chain A, Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Length = 85

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 33/74 (44%), Positives = 52/74 (70%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M+V +KTL+   F+I++ PE+ V  +K+ IE+ +G D +P + Q LI+ GK+L D T L+
Sbjct: 4  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 63
Query: 61 ENKVAENSFVVVML 74
          E K+ E +FVVVM+
Sbjct: 64 EYKIDEKNFVVVMV 77

>pdb|1PVE|A Chain A, Solution Structure Of Xpc Binding Domain Of Hhr23b Length = 72

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 45/58 (77%)
Query: 278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVE 335
           L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV+
Sbjct: 6   LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQ 63

>pdb|2F4M|B Chain B, The Mouse Pngase-Hr23 Complex Reveals A Complete Remodulation Of The Protein-Protein Interface Compared To Its Yeast Orthologs Length = 61

Iteration: 1
 Score = 63.2 bits (152), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 44/57 (77%)
Query: 278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV 334
           L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV
Sbjct: 4   LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 60

>pdb|1IFY|A Chain A, Solution Structure Of The Internal Uba Domain Of Hhr23a Length = 49

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/50 (56%), Positives = 36/50 (72%), Gaps = 3/50 (6%)
Query: 167 LVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 216
           LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct: 2   LVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 48

>pdb|2WYQ|A Chain A, The Crystal Structure Of The Ubiquitin-Like (Ubl) Domain Of Hhr23a (Human Homologue A Of Rad23) Length = 85

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 48/74 (64%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +KTL+   F+I ++P++ V  +K+ IE  +G D +P + Q LI+ GK+L D   + 
Sbjct: 6  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 65
Query: 61 ENKVAENSFVVVML 74
          + ++ E +FVVVM+
Sbjct: 66 DYRIDEKNFVVVMV 79

>pdb|1P98|A Chain A, High-Resolution Nmr Structure Of The Ubl-Domain Of Hhr23a Length = 78

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 48/74 (64%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +KTL+   F+I ++P++ V  +K+ IE  +G D +P + Q LI+ GK+L D   + 
Sbjct: 3  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 62
Query: 61 ENKVAENSFVVVML 74
          + ++ E +FVVVM+
Sbjct: 63 DYRIDEKNFVVVMV 76

>pdb|1DV0|A Chain A, Refined Nmr Solution Structure Of The C-Terminal Uba Domain Of The Human Homologue Of Rad23a (Hhr23a) Length = 47

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 33/40 (82%)
Query: 358 EEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH 397
           +E+EAIERL+A+GF  +LV++ +FAC KNE LAAN+LL  
Sbjct: 3   QEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQ 42

>pdb|1F4I|A Chain A, Solution Structure Of The Hhr23a Uba(2) Mutant P333e, Deficient In Binding The Hiv-1 Accessory Protein Vpr Length = 45

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 24/40 (60%), Positives = 34/40 (85%)
Query: 358 EEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH 397
           +E+EAIERL+A+GF+ +LV++ +FAC KNE LAAN+LL  
Sbjct: 1   QEKEAIERLKALGFEESLVIQAYFACEKNENLAANFLLSQ 40

>pdb|3V6C|B Chain B, Crystal Structure Of Usp2 In Complex With Mutated Ubiquitin Length = 91

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FV TL GTH  +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 18 MQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 74
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 75 DYNIQKESTLHLVL 88

>pdb|3V6E|B Chain B, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin Length = 91

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FV TL G H  +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 18 MQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 74
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 75 DYNIQKESTLHLVL 88

>pdb|2K25|A Chain A, Automated Nmr Structure Of The Ubb By Fapsy Length = 103

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 9  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 65
Query: 61 ENKVAENSFVVVML 74
          E  + + S + ++L
Sbjct: 66 EYNIQKESTLHLVL 79

>pdb|1TP4|A Chain A, Solution Structure Of The Xpc Binding Domain Of Hhr23a Protein Length = 97

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 44/61 (72%)
Query: 273 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 332
           AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct: 7   AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 66
Query: 333 P 333
           P
Sbjct: 67  P 67

>pdb|2OJR|A Chain A, Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag Length = 111

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92
Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

>pdb|3VDZ|A Chain A, Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-Dse3-Ubiquitin At 2.4 Angstroms Length = 111

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92
Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

>pdb|1YX5|B Chain B, Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Length = 98

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|2K6D|B Chain B, Cin85 Sh3-C Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3JVZ|X Chain X, E2~ubiquitin-Hect Length = 81

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 6  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 62
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 63 DYNIQKESTLHLVL 76

>pdb|3DVG|X Chain X, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 80

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|2KHW|B Chain B, Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex Length = 79

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|4AP4|C Chain C, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 80

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 5  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 61
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 62 DYNIQKESTLHLVL 75

>pdb|3NOB|A Chain A, Structure Of K11-Linked Di-Ubiquitin Length = 78

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 59
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 60 DYNIQKESTLHLVL 73

>pdb|2LD9|A Chain A, Backbone Structure Of Ubiquitin Determined Using Backbone Amide Noes And Backbone N-H And N-C Rdcs Length = 77

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 59 DYNIQKESTLHLVL 72

>pdb|4I6L|B Chain B, Crystal Structure Of Otub1 In Complex With Ubiquitin Variant Length = 76

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ L+   K L+D  TL 
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQKLLFARKQLEDGRTLS 59
Query: 61 ENKVAENSFVVVML 74
          +  + + SF+ ++L
Sbjct: 60 DYNIHKESFLYLVL 73

>pdb|2ZNV|C Chain C, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 77

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1AAR|A Chain A, Structure Of A Diubiquitin Conjugate And A Model For Interaction With Ubiquitin Conjugating Enzyme (E2) Length = 76

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3DVG|Y Chain Y, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 79

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 61 DYNIQRESTLHLVL 74

>pdb|3U30|A Chain A, Crystal Structure Of A Linear-Specific Ubiquitin Fab Bound To Linear Ubiquitin Length = 172

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 77
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 78 DYNIQKESTLHLVL 91

>pdb|2GBR|A Chain A, Crystal Structure Of The 35-36 Moad Insertion Mutant Of Ubiquitin Length = 81

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQG--SDVYPASQQMLIHQGKVLKDVTT 58
          M++FVKTL G    +EV+P D + +VK  I+  +G  +   P  QQ LI  GK L+D  T
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGRWALAIPPDQQRLIFAGKQLEDGRT 60
Query: 59 LEENKVAENSFVVVML 74
          L +  + + S + ++L
Sbjct: 61 LSDYNIQKESTLHLVL 76

>pdb|1XD3|B Chain B, Crystal Structure Of Uchl3-Ubvme Complex Length = 75

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1CMX|B Chain B, Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases Length = 76

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3RUL|A Chain A, New Strategy To Analyze Structures Of Glycopeptide-Target Complexes Length = 79

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3K9O|B Chain B, The Crystal Structure Of E2-25k And Ubb+1 Complex Length = 96

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 59 DYNIQKESTLHLVL 72

>pdb|2ZVN|A Chain A, Nemo Cozi Domain Incomplex With Diubiquitin In P212121 Space Group Length = 154

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 59
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 60 DYNIQKESTLHLVL 73

>pdb|2ZNV|B Chain B, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 76

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

>pdb|2XK5|B Chain B, Crystal Structure Of K6-Linked Diubiquitin Length = 76

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPQQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3U5E|MM Chain m, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 60s Subunit, Ribosome A Length = 128

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|2W9N|A Chain A, Crystal Structure Of Linear Di-Ubiquitin Length = 152

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 77  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 133
Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 134 DYNIQKESTLHLVL 147

>pdb|3B08|A Chain A, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With Linear Di- Ubiquitin Length = 152

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3AI5|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein Length = 307

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 290
Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 291 DYNIQKESTLHLVL 304

>pdb|3LDZ|F Chain F, Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin Length = 73

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3ONS|A Chain A, Crystal Structure Of Human Ubiquitin In A New Crystal Form Length = 72

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|2Y5B|B Chain B, Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde Length = 152

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3MTN|B Chain B, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 85

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 61 DYNIQKWS 68

>pdb|1ZGU|B Chain B, Solution Structure Of The Human Mms2-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  G+ L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGRQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|4HJK|A Chain A, U7ub7 Disulfide Variant Length = 77

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/68 (39%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVK L G    +EV+P D + +VK  I+   G   YP  QQ LI  GK L+D  TL 
Sbjct: 2  MQIFVKCLTGKTNTLEVEPSDTIENVKAKIQDKIG---YPPDQQRLIFAGKQLEDGRTLS 58
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 59 DYNIQKES 66

>pdb|1UD7|A Chain A, Solution Structure Of The Designed Hydrophobic Core Mutant Of Ubiquitin, 1d7 Length = 76

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M+VF+KTL G    IEV+P D V + K  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQVFLKTLTGKTVTIEVEPSDTVENFKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTIHLVL 71

>pdb|2ZCB|A Chain A, Crystal Structure Of Ubiquitin P37aP38A Length = 76

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G     A QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IAADQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3DBH|I Chain I, Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1- Uba3arg190ala-Nedd8ala72arg) Length = 88

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 69
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 70 DYKILGGSVLHLVL 83

>pdb|2O6V|D Chain D, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  G+ L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGRQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

>pdb|1YIW|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin Length = 76

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3DBL|I Chain I, Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1- Uba3arg190wt-Nedd8ala72gln) Length = 88

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 69
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 70 DYKILGGSVLHLVL 83

>pdb|3Q3F|A Chain A, Engineering Domain-Swapped Binding Interfaces By Mutually Exclusive Folding: Insertion Of Ubiquitin Into Position 103 Of Barnase Length = 189

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 2   KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
           ++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL +
Sbjct: 107 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSD 163
Query: 62  NKVAENSFVVVML 74
             + + S + ++L
Sbjct: 164 YNIQKESTLHLVL 176

>pdb|2NVU|I Chain I, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A Trapped Ubiquitin-Like Protein Activation Complex Length = 81

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 6  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 62
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 63 DYKILGGSVLHLVL 76

>pdb|3H7S|A Chain A, Crystal Structures Of K63-Linked Di- And Tri-Ubiquitin Reveal A Highly Extended Chain Architecture Length = 76

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKV 64
          +  +
Sbjct: 58 DYNI 61

>pdb|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant Of Ubiquitin Length = 88

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++F+KTL G  F +E++P D + ++K  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 66
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 67 DYNIQKESTLHLVL 80

>pdb|1C3T|A Chain A, Rotamer Strain As A Determinant Of Protein Structural Specificity Length = 76

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +E++P D V ++K  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQLFVKTLTGKTLTVELEPSDTVENLKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNLQKESTIHLVL 71

>pdb|4F8C|B Chain B, Structure Of The Cif:nedd8 Complex - Yersinia Pseudotuberculosis Cycle Inhibiting Factor In Complex With Human Nedd8 Length = 88

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 58 DYKILGGSVLHLVL 71

>pdb|4II3|B Chain B, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme 1 (uba1) In Complex With Ubiquitin And Atp/mg Length = 96

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 21 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 77
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 78 DYNIQKESTLHLVL 91

>pdb|1YJ1|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin Length = 76

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++FVKTL G    +EV+P D + +VK  I   Q  +  P  QQ LI  GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKI---QDKEXIPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1S1Q|B Chain B, Tsg101(Uev) Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 2  KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
          ++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL +
Sbjct: 2  QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSD 58
Query: 62 NKVAENSFVVVML 74
            + + S + ++L
Sbjct: 59 YNIQKESTLHLVL 71

>pdb|2BKR|B Chain B, Nedd8 Nedp1 Complex Length = 77

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 2  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 58
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 59 DYKILGGSVLHLVL 72

>pdb|1NDD|B Chain B, Structure Of Nedd8 Length = 76

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 58 DYKILGGSVLHLVL 71

>pdb|3GZN|I Chain I, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8 And Mln4924 Length = 82

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 7  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 63
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 64 DYKILGGSVLHLVL 77

>pdb|4HCP|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Nedd8 Length = 78

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 3  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 59
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 60 DYKILGGSVLHLVL 73

>pdb|2O6V|B Chain B, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  G  L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGXQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

>pdb|4A18|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1 Length = 129

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    ++V+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLDVEASDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1OTR|B Chain B, Solution Structure Of A Cue-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1OGW|A Chain A, Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK  +D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQXEDGRTLS 57
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 58 DYNIQKES 65

>pdb|4HCN|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Ubiquitin Length = 98

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 79
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 80 DYNIQKESTLHLVL 93

>pdb|3OLM|D Chain D, Structure And Function Of A Ubiquitin Binding Site Within The Catalytic Domain Of A Hect Ubiquitin Ligase Length = 79

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|1ZW7|A Chain A, Elimination Of The C-Cap In Ubiquitin Structure, Dynamics And Thermodynamic Consequences Length = 82

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+   G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGATITLEVESSDTIDNVKSKIQAAPG---IPPDQQELIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|2JWZ|A Chain A, Mutations In The Hydrophobic Core Of Ubiquitin Differentially Affect Its Recognition By Receptor Proteins Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 58 DYNIQKES 65

>pdb|2FCS|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [l-Gln35]ubiquitin With A Cubic Space Group Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++FVKTL G    +EV+P D + +VK  I   Q  +  P  QQ LI  GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKI---QDKEQIPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3ZF7|SS Chain s, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 128

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L++  TL 
Sbjct: 1  MQIFVKTLTGKTIALEVEASDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEEGRTLA 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3U5G|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome B Length = 152

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|4GSW|A Chain A, Crystal Structure Of Ubiquitin From Entamoeba Histolytica To 2.15 Angstrom Length = 80

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D +  +K  I+  +G    P  QQ LI  GK L++  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEG---IPPDQQRLIFAGKQLEEGKTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|3DQV|A Chain A, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 81

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 5  VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV 64
          VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK   D  T  + K+
Sbjct: 10 VKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQXNDEKTAADYKI 66
Query: 65 AENSFVVVML 74
             S + ++L
Sbjct: 67 XGGSVLHLVL 76

>pdb|3U5C|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome A Length = 152

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 58 DYNIQKES 65

>pdb|4HK2|A Chain A, U7ub25.2540 Length = 78

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVK   G  + +EV+P D + +VK  I+   G    P  QQ LI  GK L+D  TL 
Sbjct: 3  MQIFVKFRTGKTYTLEVEPSDTIENVKAKIQDKLG---IPPDQQWLIFAGKRLEDGRTLS 59
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 60 DYNIQKES 67

>pdb|3N3K|B Chain B, The Catalytic Domain Of Usp8 In Complex With A Usp8 Specific Inhibitor Length = 85

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++ VKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENS 68
          +  +  +S
Sbjct: 61 DYNIHNHS 68

>pdb|2GBM|A Chain A, Crystal Structure Of The 35-36 8 Glycine Insertion Mutant Of Ubiquitin Length = 84

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQ-----GSDVYPASQQMLIHQGKVLKD 55
          M++FVKTL G    +EV+P D + +VK  I+  +     G    P  QQ LI  GK L+D
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGGGGGGGGGIPPDQQRLIFAGKQLED 60
Query: 56 VTTLEENKVAENSFVVVML 74
            TL +  + + S + ++L
Sbjct: 61 GRTLSDYNIQKESTLHLVL 79

>pdb|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1 Length = 76

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P D +  +K+ +E  +G    P  QQ LI+ GK L D  T +
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEG---IPPVQQRLIYAGKQLADDKTAK 57
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIEGGSVLHLVL 71

>pdb|4II2|B Chain B, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1) In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg Length = 83

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FV+TL G    +EV+  D + +V+  I+  +G    P  QQ LI  G+ L+D  TL 
Sbjct: 8  MQIFVRTLTGRTITLEVESSDTIDNVRARIQDREG---IPPDQQRLIFAGRQLEDGRTLA 64
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 65 DYNIQRESTLHLVL 78

>pdb|2KDI|A Chain A, Solution Structure Of A UbiquitinUIM FUSION PROTEIN Length = 114

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 2  KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
          ++F KTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL +
Sbjct: 11 QIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIWAGKQLEDGRTLSD 67
Query: 62 NKVAENSFVVVML 74
            +   S + ++L
Sbjct: 68 YNIQRESTLHLVL 80

>pdb|2GBK|A Chain A, Crystal Structure Of The 9-10 Moad Insertion Mutant Of Ubiquitin Length = 83

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 10/81 (12%)
Query: 1  MKVFVKTLK-------GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVL 53
          M++FVKTL        G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L
Sbjct: 1  MQIFVKTLTQVRELVGGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQL 57
Query: 54 KDVTTLEENKVAENSFVVVML 74
          +D  TL +  + + S + ++L
Sbjct: 58 EDGRTLSDYNIQKESTLHLVL 78

>pdb|2JVC|A Chain A, Nmr Solution Structure Of Ubiquitin Like Protein Length = 82

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    I+V   D V  VK  I   +G    P  QQ LI  GK L+D   + 
Sbjct: 6  MQIFVKTLTGKTITIDVDHADTVGAVKAKIYDKEG---IPPDQQRLIFGGKQLEDSNAMS 62
Query: 61 ENKVAENSFVVVML 74
          +  V + S + ++L
Sbjct: 63 DYNVQKESTLHLVL 76

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	403
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	2e-87
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	9e-38
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	3e-37
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	1e-36
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	2e-32
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	4e-31
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	6e-25
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	5e-24
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	5e-24
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	8e-24
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	5e-23
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	2e-22
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	6e-22
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	2e-21
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	3e-21
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	3e-21
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	8e-21
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	1e-20
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	1e-20
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	2e-20
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	8e-04
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	2e-20
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	4e-20
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	7e-20
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	8e-20
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	1e-19
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	3e-19
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	4e-19
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	1e-18
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	2e-18
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	2e-18
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	5e-18
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	8e-18
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	3e-17
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	8e-17
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	1e-16
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	2e-16
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	6e-16
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	7e-16
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	1e-15
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	2e-15
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	2e-15
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	8e-15
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	3e-14
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	3e-14
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	9e-08
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	6e-14
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	5e-13
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	5e-07
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	7e-13
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	2e-12
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	6e-09
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	2e-11
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	1e-09
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	1e-09
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	2e-09
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	5e-09
1we6_A	111	Splicing factor, putative; structural genomics, ub	5e-09
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	5e-09
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	5e-08
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	2e-07
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	2e-07
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	3e-06
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	3e-06
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	5e-06
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	5e-06
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	9e-06
2uv9_A	1878	Fatty acid synthase alpha subunits; fungal, dehydr	5e-06
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	6e-06
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	1e-05
2uv8_A	1887	Fatty acid synthase subunit alpha (FAS2); fatty ac	2e-05
2uv8_A	1887	Fatty acid synthase subunit alpha (FAS2); fatty ac	3e-04
2uv8_A	1887	Fatty acid synthase subunit alpha (FAS2); fatty ac	6e-04
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	2e-05
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	4e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	4e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	8e-04
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	5e-05
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	6e-05
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	6e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	9e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	1e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	4e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	7e-04
1eys_C	382	Photosynthetic reaction center; membrane protein c	2e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	3e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	5e-04
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	6e-04
3nwa_A	703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	6e-04
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	6e-04
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	7e-04
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	8e-04

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A Length = 368

 Score =  268 bits (686), Expect = 2e-87
 Identities = 131/409 (32%), Positives = 201/409 (49%), Gaps = 55/409 (13%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           + + +KTL+   F+I ++P++ V  +K+ IE  +G D +P + Q LI+ GK+L D   + 
Sbjct: 8   VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 67

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           + ++ E +FVVVM+TK+K                      A PT+   ++TS  PAPT  
Sbjct: 68  DYRIDEKNFVVVMVTKTK------------AGQGTSAPPEASPTAAPESSTSFPPAPTSG 115

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQI 180
                P +    +    +       + + +  SS  S     AAS LV GS  E  + +I
Sbjct: 116 MSHPPPAAREDKSPSEESAPTTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETMLTEI 175

Query: 181 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 240
           + MG   ++RE V+ ALRA+YNNP RAVEYL +GIP                        
Sbjct: 176 MSMG---YERERVVAALRASYNNPHRAVEYLLTGIPG----------------------- 209

Query: 241 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQI 300
             +        S  +  P              AG   L+FLR+  QFQ +R ++Q NP +
Sbjct: 210 SPEPEHGSVQESQVSEQP----------ATEAAGENPLEFLRDQPQFQNMRQVIQQNPAL 259

Query: 301 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVE-------GGEGNVLGQLASAMPQAV 353
           L  +LQ+LG++NP L++ I  HQ  F++++NEP                    +     +
Sbjct: 260 LPALLQQLGQENPQLLQQISRHQEQFIQMLNEPPGELADISDVEGEVGAIGEEAPQMNYI 319

Query: 354 TVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE 402
            VTP+E+EAIERL+A+GF  +LV++ +FAC KNE LAAN+LL    + E
Sbjct: 320 QVTPQEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQNFDDE 368

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 95

 Score =  130 bits (330), Expect = 9e-38
 Identities = 38/93 (40%), Positives = 59/93 (63%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M+V +KTL+   F+I++ PE+ V  +K+ IE+ +G D +P + Q LI+ GK+L D T L+
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 61 ENKVAENSFVVVMLTKSKVSSSGASTVSAAPAN 93
          E K+ E +FVVVM+TK K  S+ A        +
Sbjct: 61 EYKIDEKNFVVVMVTKPKAVSTPAPATLEHHHH 93

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A Length = 85

 Score =  128 bits (325), Expect = 3e-37
 Identities = 29/78 (37%), Positives = 52/78 (66%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +KTL+   F+I ++P++ V  +K+ IE  +G D +P + Q LI+ GK+L D   + 
Sbjct: 6  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 65

Query: 61 ENKVAENSFVVVMLTKSK 78
          + ++ E +FVVVM+TK+K
Sbjct: 66 DYRIDEKNFVVVMVTKTK 83

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 106

 Score =  117 bits (294), Expect = 2e-32
 Identities = 19/101 (18%), Positives = 45/101 (44%), Gaps = 3/101 (2%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           + +  K  K     ++++P + + + K  +           SQ  LI+ GKVL+D  T+ 
Sbjct: 2   VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSIS---CEESQIKLIYSGKVLQDSKTVS 58

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSA 101
           E  + +   VV M+++ K + +  +      ++  +  ++ 
Sbjct: 59  ECGLKDGDQVVFMVSQKKSTKTKVTERDPNSSSVDKLAAAL 99

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score =  112 bits (283), Expect = 4e-31
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV-LKDVTTL 59
          MK  V+ L G+ FE+EV   D +  VK+ IE  Q     P S+Q LI  G V L++  T+
Sbjct: 11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQH---IPVSKQTLIVDGIVILREDLTV 67

Query: 60 EENKVAENSFVVVMLT 75
          E+ ++   S + + ++
Sbjct: 68 EQCQIVPTSDIQLEVS 83

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A Length = 76

 Score = 96.1 bits (240), Expect = 6e-25
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57

Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 58 DYKILGGSVLHLVL 71

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B Length = 88

 Score = 93.9 bits (234), Expect = 5e-24
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57

Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 58 DYKILGGSVLHLVL 71

>1pve_A HHR23B, UV excision repair protein RAD23 homolog B; XPC binding domain, solution structure, nucleotide excision repair, chaps, DNA binding protein; NMR {Homo sapiens} SCOP: a.189.1.1 Length = 72

 Score = 93.4 bits (232), Expect = 5e-24
 Identities = 29/70 (41%), Positives = 47/70 (67%)

Query: 274 GAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP 333
               L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEP
Sbjct: 2   SHMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEP 61

Query: 334 VEGGEGNVLG 343
           V+   G   G
Sbjct: 62  VQEAGGQGGG 71

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 93.6 bits (233), Expect = 8e-24
 Identities = 23/81 (28%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKD-VTTL 59
          + V VK      F +EV   + VS +K  I  V+     P  +  L + G  L D    L
Sbjct: 16 IHVTVKFPSKQ-FTVEVDRTETVSSLKDKIHIVEN---TPIKRMQLYYSGIELADDYRNL 71

Query: 60 EENKVAENSFVVVMLTKSKVS 80
           E  + E S +VV L     +
Sbjct: 72 NEYGITEFSEIVVFLKSINRA 92

>2f4m_B UV excision repair protein RAD23 homolog B; glycoproteins, ubiquitin-dependent protein degradation, NUCL excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: a.189.1.1 PDB: 2f4o_B* Length = 61

 Score = 90.6 bits (225), Expect = 5e-23
 Identities = 27/60 (45%), Positives = 44/60 (73%)

Query: 275 AGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV 334
              L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV
Sbjct: 1   GHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 60

>1dv0_A DNA repair protein HHR23A; helical bundle, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.5.2.1 PDB: 1f4i_A Length = 47

 Score = 88.3 bits (219), Expect = 2e-22
 Identities = 25/45 (55%), Positives = 35/45 (77%)

Query: 358 EEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE 402
           +E+EAIERL+A+GF  +LV++ +FAC KNE LAAN+LL    + E
Sbjct: 3   QEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQNFDDE 47

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Length = 85

 Score = 88.2 bits (219), Expect = 6e-22
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++ VKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60

Query: 61 ENKVAENSFVVVML 74
          +  +  +S + ++L
Sbjct: 61 DYNIHNHSALYLLL 74

>3u5c_F RP14, S2, YS8, 40S ribosomal protein S5; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_F 3o30_D 3o2z_D 3u5g_F 3jyv_G* 2noq_F 1s1h_G 3iz6_F Length = 225

 Score = 89.1 bits (221), Expect = 2e-21
 Identities = 7/74 (9%), Positives = 16/74 (21%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M      ++       V+    V       E VQ         ++         +V    
Sbjct: 1  MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQ---AQTEIKLFNKWSFEEVEVKDAS 57

Query: 61 ENKVAENSFVVVML 74
               +    + + 
Sbjct: 58 LVDYVQVRQPIFVA 71

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ... Length = 76

 Score = 85.8 bits (213), Expect = 3e-21
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p Length = 128

 Score = 87.8 bits (217), Expect = 3e-21
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 3/98 (3%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G       QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPD---QQRLIFAGKQLEDGRTLS 57

Query: 61 ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTT 98
          +  + + S + ++L         +    A+  N  ++ 
Sbjct: 58 DYNIQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSV 95

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} Length = 85

 Score = 85.1 bits (211), Expect = 8e-21
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60

Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKWSTLFLLL 74

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: k.45.1.1 PDB: 3dbr_I 3dbl_I Length = 88

 Score = 84.7 bits (210), Expect = 1e-20
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 69

Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 70 DYKILGGSVLHLVL 83

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Length = 88

 Score = 84.7 bits (210), Expect = 1e-20
 Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++F+KTL G  F +E++P D + ++K  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 66

Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 67 DYNIQKESTLHLVL 80

>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} SCOP: a.5.2.1 Length = 49

 Score = 83.3 bits (206), Expect = 2e-20
 Identities = 28/50 (56%), Positives = 36/50 (72%), Gaps = 3/50 (6%)

Query: 167 LVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 216
           LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct: 2   LVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 48

>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} SCOP: a.5.2.1 Length = 49

 Score = 36.3 bits (84), Expect = 8e-04
 Identities = 11/42 (26%), Positives = 18/42 (42%)

Query: 357 PEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHM 398
            E    +  + +MG++R  V+    A   N   A  YLL  +
Sbjct: 6   SEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 47

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A Length = 90

 Score = 84.2 bits (209), Expect = 2e-20
 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V VKTL        V  +  V + K++I         P+ +Q LI+QG+VL+D   L+
Sbjct: 6  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQ 62

Query: 61 ENKVAENSFVVVMLTKSKVSSSGAST 86
          E  V      +V     +      ++
Sbjct: 63 EYNVGGKVIHLVERAPPQTHLPSGAS 88

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 81

 Score = 83.1 bits (206), Expect = 4e-20
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++ VK L+G    ++V  ++ VS +K+ +         P  QQ L+ +GK L D   L 
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLN---VPVRQQRLLFKGKALADGKRLS 64

Query: 61 ENKVAENSFVVVML 74
          +  +  NS + +++
Sbjct: 65 DYSIGPNSKLNLVV 78

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Length = 98

 Score = 82.9 bits (205), Expect = 7e-20
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score = 83.4 bits (206), Expect = 8e-20
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92

Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S Length = 77

 Score = 81.5 bits (202), Expect = 1e-19
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 1  MKVFVKTLKGTH-FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTL 59
          M + +    G   +E+ V PE  V   K+ I    G    P + Q LI+ GK+LKD  T+
Sbjct: 3  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTV 59

Query: 60 EENKVAENSFVVVMLTK 76
          E   + +   V ++ ++
Sbjct: 60 ESYHIQDGHSVHLVKSQ 76

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 87

 Score = 80.9 bits (200), Expect = 3e-19
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++VFVK   G  +   + P   +  +K+ IE  QG    P  QQ L  QG+VL+D   L 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLG 64

Query: 61 ENKVAENSFVVVMLTKSKVSSSG 83
             + ++  +++   K    SSG
Sbjct: 65 IYGIQDSDTLILSKKKGSGPSSG 87

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A Length = 76

 Score = 80.4 bits (199), Expect = 4e-19
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M VFV+      F +EV  +  +  +K+ +   QG    PA Q  +I  GK L +  T++
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQG---VPADQLRVIFAGKELPNHLTVQ 57

Query: 61 ENKVAENSFVVVML 74
             + + S V ++ 
Sbjct: 58 NCDLEQQSIVHIVQ 71

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score = 79.8 bits (197), Expect = 1e-18
 Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           ++ ++   G   ++ V+  D V  +K+ +   +G        Q     G+ L D    E
Sbjct: 24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG---VEPGSQRWFFSGRPLTDKMKFE 80

Query: 61 ENKVAENSFVVVMLTK 76
          E K+ ++  V V++++
Sbjct: 81 ELKIPKDYVVQVIVSQ 96

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 78.9 bits (195), Expect = 2e-18
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V VKTL        V  +  V + K++I         P+ +Q LI+QG+VL+D   L+
Sbjct: 18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQ 74

Query: 61 ENKVAEN 67
          E  V   
Sbjct: 75 EYNVGGK 81

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A Length = 96

 Score = 79.0 bits (195), Expect = 2e-18
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 5/98 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58

Query: 61 ENKVAENSFVVVMLTK--SKVSSSGASTVSAAPANQAQ 96
          +  + + S + ++L                  P + AQ
Sbjct: 59 DYNIQKESTLHLVLRLRGYADLREDPDRQDHHPGSGAQ 96

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score = 78.3 bits (193), Expect = 5e-18
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           ++F KTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIWAGKQLEDGRTLS 66

Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 67 DYNIQRESTLHLVL 80

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score = 77.4 bits (191), Expect = 8e-18
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           + + +K+ +   +E+ V PE  V   K+ I    G    P + Q LI+ GK+LKD  T+E
Sbjct: 29  LNIHIKSGQDK-WEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTVE 84

Query: 61  ENKVAENSFVVVMLTK 76
              + +   V ++ ++
Sbjct: 85  SYHIQDGHSVHLVKSQ 100

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 100

 Score = 75.8 bits (187), Expect = 3e-17
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           +KV VKT K    +  V     +  +K+ I            Q +LI  GK+LKD  +L 
Sbjct: 23  IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLA 78

Query: 61  ENKVAENSFVVVMLTKSKVSSSG 83
           +  V +   V +++ K +  + G
Sbjct: 79  QCGVRDGLTVHLVI-KRQHRAMG 100

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score = 74.7 bits (184), Expect = 8e-17
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 5/92 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           +KV VKT K    +  V     +  +K+ I            Q +LI  GK+LKD  +L 
Sbjct: 18  IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLA 73

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPA 92
           +  V +   V +++ K +  + G    ++ P+
Sbjct: 74  QCGVRDGLTVHLVI-KRQHRAMGNECPASGPS 104

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score = 73.2 bits (180), Expect = 1e-16
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + V+  KG     EV+    V+ +K+ +    G +        L  +GK L+D   L 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPLG 61

Query: 61 ENKVAENSFVVVML 74
          E  +   S V + L
Sbjct: 62 EYGLKPLSTVFMNL 75

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens} Length = 88

 Score = 72.8 bits (179), Expect = 2e-16
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + V+  KG     EV+    V+ +K+ +    G +        L  +GK L+D   L 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPLG 61

Query: 61 ENKVAENSFVVVML 74
          E  +   S V + L
Sbjct: 62 EYGLKPLSTVFMNL 75

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 74.8 bits (183), Expect = 6e-16
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M+V VKTL+G      ++    V D+K  I        +      L++ G +  +   + 
Sbjct: 1  MQVQVKTLEGETKIYTLEQGTSVLDLKSQI---SQDMGFEIDMMTLVNNGFIAPNTELVT 57

Query: 61 EN 62
          ++
Sbjct: 58 DD 59

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 72.6 bits (178), Expect = 7e-16
 Identities = 28/95 (29%), Positives = 42/95 (44%), Gaps = 5/95 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           +KV VKT K    E  V     V   K+ I     S      Q +LI  GK+LKD  TL 
Sbjct: 33  IKVTVKTPKEKE-EFAVPENSSVQQFKEAISKRFKS---QTDQLVLIFAGKILKDQDTLI 88

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQA 95
           ++ + +   V +++ K   +SS     +AA  +  
Sbjct: 89  QHGIHDGLTVHLVI-KRDPNSSSVDKYAAALEHHH 122

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 96

 Score = 70.9 bits (174), Expect = 1e-15
 Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V VKT +  H E  +     V   KK I          A + +LI  GK+L+D   L 
Sbjct: 18 IRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDILS 73

Query: 61 ENKVAENSFVVVMLTKSKVSSSG 83
          +  + + S V V++      SSG
Sbjct: 74 QRGILDGSTVHVVVRSHSGPSSG 96

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 78

 Score = 69.7 bits (171), Expect = 2e-15
 Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 1  MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
          M + V+T+ G  TH    +    KV ++++ I+ +          Q L ++GK ++D  T
Sbjct: 3  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFH---VEPGLQRLFYRGKQMEDGHT 59

Query: 59 LEENKVAENSFVVVMLTKS 77
          L + +V  N  + +++ +S
Sbjct: 60 LFDYEVRLNDTIQLLVRQS 78

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 70.5 bits (173), Expect = 2e-15
 Identities = 24/70 (34%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          MKV VKT K    E  V     V   K+ I     S      Q +LI  GK+LKD  TL 
Sbjct: 26 MKVTVKTPKEKE-EFAVPENSSVQQFKEEISKRFKS---HTDQLVLIFAGKILKDQDTLS 81

Query: 61 ENKVAENSFV 70
          ++ + +   V
Sbjct: 82 QHGIHDGLTV 91

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 89

 Score = 68.6 bits (168), Expect = 8e-15
 Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 1  MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
          M + V+T+ G  T    +V  +  + ++++ +  +          Q L ++GK L++  T
Sbjct: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD---VRPECQRLFYRGKQLENGYT 64

Query: 59 LEENKVAENSFVVVML 74
          L +  V  N  + +++
Sbjct: 65 LFDYDVGLNDIIQLLV 80

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B Length = 169

 Score = 69.6 bits (170), Expect = 3e-14
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B Length = 152

 Score = 68.9 bits (168), Expect = 3e-14
 Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 58 DYNIQKES 65

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B Length = 152

 Score = 50.0 bits (119), Expect = 9e-08
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 77  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 133

Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 134 DYNIQKESTLHLVL 147

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana} Length = 85

 Score = 65.8 bits (161), Expect = 6e-14
 Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +K+ VK   G    + V P+  V D+K  ++ +          Q LI +GKVL + +TL+
Sbjct: 13 IKLTVK-FGGKSIPLSVSPDCTVKDLKSQLQPITN---VLPRGQKLIFKGKVLVETSTLK 68

Query: 61 ENKVAENSFVVVMLTK 76
          ++ V   + +++M ++
Sbjct: 69 QSDVGSGAKLMLMASQ 84

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 65.8 bits (160), Expect = 5e-13
 Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 77

Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 78 DYNIQKES 85

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 48.5 bits (115), Expect = 5e-07
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 97  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 153

Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 154 DYNIQKESTLHLVL 167

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score = 63.3 bits (154), Expect = 7e-13
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FV+  +      EV  ++ V+ +K ++ +++G        Q+++  G  L+D  TL 
Sbjct: 20 MQLFVRAQEL--HTFEVTGQETVAQIKAHVASLEG---IAPEDQVVLLAGAPLEDEATLG 74

Query: 61 ENKVAENSFVVVML 74
          +  V   + + V  
Sbjct: 75 QCGVEALTTLEVAG 88

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A Length = 159

 Score = 63.4 bits (154), Expect = 2e-12
 Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 5/63 (7%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GKVLKDVTT 58
            + VK L G  F++ +     VS++K  I    G     A QQ L     G  L+D   
Sbjct: 3  WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG---VHAFQQRLAVHPSGVALQDRVP 59

Query: 59 LEE 61
          L  
Sbjct: 60 LAS 62

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A Length = 159

 Score = 53.8 bits (129), Expect = 6e-09
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           + + V+  KG     EV+    V+ +K+ +    G +        L  +GK L+D   L 
Sbjct: 82  LSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPLG 138

Query: 61  ENKVAENSFVVVML 74
           E  +   S V + L
Sbjct: 139 EYGLKPLSTVFMNL 152

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A Length = 115

 Score = 59.8 bits (145), Expect = 2e-11
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 2   KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
                 L G      +   D+VS +K  I    G    PA +Q L ++G  +KD  +L  
Sbjct: 37  DKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATG---MPAGKQKLQYEGIFIKDSNSLAY 93

Query: 62  NKVAENSFVVVML 74
             +A  + + + L
Sbjct: 94  YNMASGAVIHLAL 106

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 93

 Score = 53.8 bits (129), Expect = 1e-09
 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 4/87 (4%)

Query: 1  MKVFVKT--LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
          + + VK+   +    E+       V  +K ++  V          Q LI+ GK+L D   
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPER-PRPEDQRLIYSGKLLLDHQC 66

Query: 59 LEE-NKVAENSFVVVMLTKSKVSSSGA 84
          L +     E   V+ ++   K   S  
Sbjct: 67 LRDLLPKQEKRHVLHLVCNVKSGPSSG 93

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 102

 Score = 54.2 bits (130), Expect = 1e-09
 Identities = 17/97 (17%), Positives = 41/97 (42%), Gaps = 8/97 (8%)

Query: 1   MKVFVKTLKGTH----FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV 56
           M + V  ++       F ++V P+ ++S+ +   E   G    PA +  +++  ++L D 
Sbjct: 8   MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG---VPAEEAQIVYMEQLLTDD 64

Query: 57  T-TLEENKVAENSFVVVMLTKSKVSSSGASTVSAAPA 92
             +L    + +   VV++   +    +   T S   +
Sbjct: 65  HCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTPSGPSS 101

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 56.1 bits (135), Expect = 2e-09
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
            ++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 106 GQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 162

Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 163 DYNIQKESTLHLVL 176

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 52.3 bits (125), Expect = 5e-09
 Identities = 24/91 (26%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTL 59
          + V +K L  T      +PED V  +K      Q       SQ  LI+QG++L+    TL
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ------ESQMKLIYQGRLLQDPARTL 61

Query: 60 EENKVAENSFVVVMLTKSKVSSSGASTVSAA 90
              +  N  +    +    + SG S  S  
Sbjct: 62 SSLNITNNCVIHCHRSPPGAAVSGPSASSGP 92

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 111

 Score = 52.9 bits (127), Expect = 5e-09
 Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 1   MKVFVKT-LKGTHFEIEVKPE-DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
           ++V       G   EI V+   + V  +K+ I         PA++Q L  +   LKD  +
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMS 86

Query: 59  LEENKVAENSFVVVML 74
           L    V     + + L
Sbjct: 87  LAHYNVGAGEILTLSL 102

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 52.1 bits (125), Expect = 5e-09
 Identities = 18/83 (21%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +     T  +++V  +   S++K+ I ++ G    P + Q ++++G  + +  TL 
Sbjct: 18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMYKGL-VPEDKTLR 72

Query: 61 ENKVAENSFVVVMLTKSKVSSSG 83
          E KV   + ++V+ +     SSG
Sbjct: 73 EIKVTSGAKIMVVGSTISGPSSG 95

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1 Length = 96

 Score = 49.5 bits (118), Expect = 5e-08
 Identities = 18/101 (17%), Positives = 36/101 (35%), Gaps = 12/101 (11%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
             V VK  K     +E+  ++     K  +  + G      ++Q ++ +G  LKD     
Sbjct: 8   YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTG---VQPARQKVMVKGGTLKD-DDWG 63

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSA 101
             K+     V++M +   +           P+ +    SS 
Sbjct: 64  NIKMKNGMTVLMMGSADALPE--------EPSAKTSGPSSG 96

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 48.0 bits (114), Expect = 2e-07
 Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 3/63 (4%)

Query: 1  MKVFVKTLKGTH--FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
          + + +K     +    I       V  +K ++  V  S       Q L++ G++L D   
Sbjct: 24 VTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKP-LTKDQRLVYSGRLLPDHLQ 82

Query: 59 LEE 61
          L++
Sbjct: 83 LKD 85

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 3/57 (5%)

Query: 174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAG 230
           E  V  I+ MG   + R+  ++ALRA  N+ ERAV++++S I +  A   ++  S+G
Sbjct: 10  EDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMSGPSSG 63

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 43.2 bits (102), Expect = 3e-06
 Identities = 10/42 (23%), Positives = 22/42 (52%)

Query: 361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE 402
           + +  + +MGF R   L+   A N + E A +++  H+ + +
Sbjct: 11  DCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLD 52

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A Length = 90

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 4/85 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTT 58
          + + VK     +    +  +D V D+K+ ++T+ G  V P  Q++L    +GK  ++   
Sbjct: 8  LPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTG--VLPERQKLLGLKVKGKPAENDVK 65

Query: 59 LEENKVAENSFVVVMLTKSKVSSSG 83
          L   K+  N+ +++M T+    SSG
Sbjct: 66 LGALKLKPNTKIMMMGTRESGPSSG 90

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B* Length = 307

 Score = 47.1 bits (111), Expect = 5e-06
 Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 290

Query: 61  ENKVAENS 68
           +  + + S
Sbjct: 291 DYNIQKES 298

>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1 Length = 73

 Score = 43.3 bits (102), Expect = 5e-06
 Identities = 8/40 (20%), Positives = 24/40 (60%), Gaps = 3/40 (7%)

Query: 174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 213
           +++V  +L  G   +  +   +AL+A+  + E+A +++++
Sbjct: 30  QSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFN 66

>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1 Length = 73

 Score = 42.5 bits (100), Expect = 9e-06
 Identities = 6/40 (15%), Positives = 18/40 (45%)

Query: 361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE 400
            +++ L + GF   +  +   A   + E A +++ ++   
Sbjct: 31  SSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNSGP 70

>2uv9_A Fatty acid synthase alpha subunits; fungal, dehydratase, enoyl reductase, ketoacyl synthase, ketoacyl reductase; 3.1A {Thermomyces lanuginosus} PDB: 2uvb_A* Length = 1878

 Score = 48.0 bits (114), Expect = 5e-06
 Identities = 21/63 (33%), Positives = 25/63 (39%)

Query: 107 QPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASN 166
                   P PT A   S   +     A   APA APAPAPA A  ++ V D    A   
Sbjct: 91  DVEPIEDEPEPTPAAASSADAAPAAAPAAPAAPAAAPAPAPASAGPAAPVQDAPVTATDV 150

Query: 167 LVA 169
           + A
Sbjct: 151 IRA 153

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 44.2 bits (104), Expect = 6e-06
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 3  VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-----ASQQMLIHQGKVLKDVT 57
          + +  + G   E    P D  SD+ K++      D         +   LI+QG+ L    
Sbjct: 20 LRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNV 79

Query: 58 TLEENKVAENSFVVVMLT 75
          TL   K+      V+ L 
Sbjct: 80 TLGALKLPFGKTTVMHLV 97

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A Length = 93

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V V    G    ++   ED V D KK +    G+     ++ +L   G VLKD  +LE
Sbjct: 22 IEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGT---QPNKIVLQKGGSVLKDHISLE 78

Query: 61 ENKV 64
          + +V
Sbjct: 79 DYEV 82

>2uv8_A Fatty acid synthase subunit alpha (FAS2); fatty acid biosynthesis, malonyl/palmitoyl transferase, phosphopantetheine, transferase; HET: GVL FMN; 3.10A {Saccharomyces cerevisiae} PDB: 2vkz_A* 3hmj_A* Length = 1887

 Score = 46.1 bits (109), Expect = 2e-05
 Identities = 15/63 (23%), Positives = 25/63 (39%)

Query: 107 QPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASN 166
            P  +        A  ++   +    A    A APAP  A APA  ++ ++D   +A+  
Sbjct: 91  TPDPSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVKASLL 150

Query: 167 LVA 169
           L  
Sbjct: 151 LHV 153

>2uv8_A Fatty acid synthase subunit alpha (FAS2); fatty acid biosynthesis, malonyl/palmitoyl transferase, phosphopantetheine, transferase; HET: GVL FMN; 3.10A {Saccharomyces cerevisiae} PDB: 2vkz_A* 3hmj_A* Length = 1887

 Score = 42.3 bits (99), Expect = 3e-04
 Identities = 20/48 (41%), Positives = 24/48 (50%)

Query: 106 TQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
                  + PA   AP  +   SAP PAA APAP  A APA A A ++
Sbjct: 94  PSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIA 141

>2uv8_A Fatty acid synthase subunit alpha (FAS2); fatty acid biosynthesis, malonyl/palmitoyl transferase, phosphopantetheine, transferase; HET: GVL FMN; 3.10A {Saccharomyces cerevisiae} PDB: 2vkz_A* 3hmj_A* Length = 1887

 Score = 41.1 bits (96), Expect = 6e-04
 Identities = 12/58 (20%), Positives = 18/58 (31%)

Query: 98  TSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSS 155
           T      + +     +          +   +A  PA  A A   A A   A  PV +S
Sbjct: 91  TPDPSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVKAS 148

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1 Length = 100

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 12/64 (18%), Positives = 28/64 (43%), Gaps = 3/64 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V      G    ++   +D + D+KK I    G+     ++ +L     + KD  +L 
Sbjct: 29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGT---RWNKIVLKKWYTIFKDHVSLG 85

Query: 61 ENKV 64
          + ++
Sbjct: 86 DYEI 89

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 3/71 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + V    +      + V+P+  V+ +K  +    G   +P   Q  +   ++ +D  TL 
Sbjct: 27 VSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYG---FPPVLQQWVIGQRLARDQETLH 83

Query: 61 ENKVAENSFVV 71
           + V +N    
Sbjct: 84 SHGVRQNGDSA 94

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 44.8 bits (105), Expect = 4e-05
 Identities = 28/174 (16%), Positives = 41/174 (23%), Gaps = 25/174 (14%)

Query: 94  QAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
           QAQ       T  Q       P    A   S  +   PP    P+        PA   + 
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70

Query: 154 SSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 213
                   QA +++         +                      AY  P+  V     
Sbjct: 71  QQ----IDQATTSMNDMHLHNVPLVD------------------PNAYMQPQVPV---QM 105

Query: 214 GIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLP 267
           G P Q    P+A  + G  +       +      P         P+       P
Sbjct: 106 GTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPP 159

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 41.0 bits (95), Expect = 8e-04
 Identities = 23/197 (11%), Positives = 45/197 (22%), Gaps = 22/197 (11%)

Query: 88  SAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAP 147
            A        T    P    P         +       P+ A P         PA     
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70

Query: 148 APAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERA 207
                +++          + V   +  A +Q  + +  G+                    
Sbjct: 71  QQIDQATT---SMNDMHLHNVPLVDPNAYMQPQVPVQMGT-------------------P 108

Query: 208 VEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLP 267
           ++     +       P A      +  N            P  T      P  + P    
Sbjct: 109 LQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERM 168

Query: 268 NMGSNAGAGTLDFLRNS 284
            + S     + D++R++
Sbjct: 169 LVPSELSNASPDYIRST 185

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1 Length = 107

 Score = 41.3 bits (96), Expect = 5e-05
 Identities = 18/65 (27%), Positives = 26/65 (40%)

Query: 19  PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK 78
               +S +K+ I       V       LI+ G+ LKD  TL+   +   S V V+     
Sbjct: 43  GGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKSWS 102

Query: 79  VSSSG 83
             SSG
Sbjct: 103 GPSSG 107

>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 83

 Score = 40.2 bits (94), Expect = 6e-05
 Identities = 13/65 (20%), Positives = 26/65 (40%)

Query: 336 GGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLL 395
            G+   L + A+AM         +  A+ +L  MGF      +     + +   A  +L+
Sbjct: 6   SGDAVELFKKANAMLDEDEDERVDEAALRQLTEMGFPENRATKALQLNHMSVPQAMEWLI 65

Query: 396 DHMHE 400
           +H  +
Sbjct: 66  EHAED 70

>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1 Length = 43

 Score = 39.2 bits (91), Expect = 6e-05
 Identities = 15/42 (35%), Positives = 19/42 (45%)

Query: 356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH 397
           T  +  A+E L  MGF           CN + E A N+LLD 
Sbjct: 1   TTPKSLAVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDS 42

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 43.2 bits (101), Expect = 9e-05
 Identities = 15/59 (25%), Positives = 20/59 (33%)

Query: 95  AQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
                S+            + + T A    +    PP   P PAP P PAPA    P +
Sbjct: 6   HHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDT 64

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 42.8 bits (100), Expect = 1e-04
 Identities = 11/58 (18%), Positives = 19/58 (32%)

Query: 96  QTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
           + +    P+++  +  S   A    P      + PPP APA    P      +     
Sbjct: 17  RGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVLQRI 74

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 41.7 bits (97), Expect = 4e-04
 Identities = 11/70 (15%), Positives = 19/70 (27%), Gaps = 2/70 (2%)

Query: 85  STVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPA 144
            +    P+    + +S    +  P      P P   PP +     PP      +      
Sbjct: 18  GSHMVIPSASVTSAASDFLAALHPP--VTVPDPAPPPPPAPAAGNPPDTVTGDSVLQRIL 75

Query: 145 PAPAPAPVSS 154
             P     +S
Sbjct: 76  RGPTGPGTTS 85

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 40.5 bits (94), Expect = 7e-04
 Identities = 11/74 (14%), Positives = 17/74 (22%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAP 139
           ++S        P          PP              +V        + P   + APA 
Sbjct: 31  AASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVLQRILRGPTGPGTTSLAPAV 90

Query: 140 APAPAPAPAPAPVS 153
                P P     +
Sbjct: 91  RYGRQPGPEAPASA 104

>1eys_C Photosynthetic reaction center; membrane protein complex, electron transport; HET: BGL BCL BPH MQ8 HEM CRT LDA PEF; 2.20A {Thermochromatium tepidum} SCOP: a.138.1.2 Length = 382

 Score = 41.8 bits (97), Expect = 2e-04
 Identities = 16/77 (20%), Positives = 22/77 (28%), Gaps = 1/77 (1%)

Query: 83  GASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPA 142
           GA      P       +      + P +    PA         P    P A   PA A  
Sbjct: 298 GAQMAKDYPGLYKTAVTQEALPGSAPASE-AAPAAATEAAPEAPAQEVPAAEAVPAAAEP 356

Query: 143 PAPAPAPAPVSSSVSDV 159
            A   A +   + V +V
Sbjct: 357 GAAEAAGSVEPAPVEEV 373

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 41.8 bits (98), Expect = 3e-04
 Identities = 17/101 (16%), Positives = 26/101 (25%), Gaps = 3/101 (2%)

Query: 75  TKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAA 134
             ++       +  AAP+  A           Q     Q   P      + P    PP  
Sbjct: 348 KDAETEIPAGESSDAAPSADAAQMKEMMAMM-QKMQQQQAAYPP--QGYAPPPQGYPPQG 404

Query: 135 PAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEA 175
             P   P     P   P     +   G   +    G + +A
Sbjct: 405 YPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAAPPQGVDNQA 445

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 41.1 bits (96), Expect = 5e-04
 Identities = 19/92 (20%), Positives = 24/92 (26%), Gaps = 6/92 (6%)

Query: 75  TKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVP------ES 128
              + S +  S  +A                         P P   PPQ  P      + 
Sbjct: 355 PAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQG 414

Query: 129 APPPAAPAPAPAPAPAPAPAPAPVSSSVSDVY 160
            PP   P P     P  AP  AP     +  Y
Sbjct: 415 YPPQGYPPPPQGAPPQGAPPAAPPQGVDNQAY 446

>4ae4_A Ubiquitin-associated protein 1; protein transport, endosomal sorting, tetherin, VPU, HIV-1, monoubiquitin; HET: NHE; 1.65A {Homo sapiens} PDB: 4ae4_B* Length = 118

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 15/49 (30%), Positives = 22/49 (44%)

Query: 354 TVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE 402
            ++P ER+ +E +  MG+    VL    A   N E   +YL  H    E
Sbjct: 3   HMSPSERQCVETVVNMGYSYECVLRAMKAAGANIEQILDYLFAHGQLCE 51

>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane fusion, viral P glycoprotein B, HSV-1, membrane; HET: NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A* 3nwd_A* Length = 703

 Score = 41.1 bits (96), Expect = 6e-04
 Identities = 12/79 (15%), Positives = 17/79 (21%)

Query: 82  SGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAP 141
           +   T   A A QA     A P                   +    + P PA      A 
Sbjct: 6   TSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDNATVAA 65

Query: 142 APAPAPAPAPVSSSVSDVY 160
             A          + +   
Sbjct: 66  GHATLREHLRDIKAENTDA 84

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A Length = 118

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 1  MKVFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTL 59
          M VF+   +  T    + K    V ++K+ +E +      P  +Q L    ++L D  TL
Sbjct: 1  MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKR---PPEEQRLYKDDQLLDDGKTL 57

Query: 60 EENKVAENS 68
           E      +
Sbjct: 58 GECGFTSQT 66

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 40.6 bits (94), Expect = 7e-04
 Identities = 18/60 (30%), Positives = 22/60 (36%)

Query: 108 PTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNL 167
             T  Q P P   PP +    A P +A A A   + A   A     S  S   G   S+L
Sbjct: 22  YMTDLQRPQPPPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGGGFFSSL 81

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1 Length = 116

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)

Query: 5  VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-----ASQQMLIHQGKVLKDVTTL 59
          +  + G   E    P D  SD+ K++      D         +   LI+QG+ L    TL
Sbjct: 21 LILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTL 80

Query: 60 EENKVAENSFVVVMLT 75
             K+      V+ L 
Sbjct: 81 GALKLPFGKTTVMHLV 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	403
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	100.0
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	100.0
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	99.83
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	99.82
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.78
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.76
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.76
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.75
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.75
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.74
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.73
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.73
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.73
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.72
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.72
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.72
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.72
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.72
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.71
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.71
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.7
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.7
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.7
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.7
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.7
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.7
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.7
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.69
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.69
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.69
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.69
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.69
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.69
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.69
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.68
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.68
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.68
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.67
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.67
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.67
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.67
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.67
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.66
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.66
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	99.66
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.66
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.47
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.65
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.65
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.64
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.64
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.64
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.63
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	99.63
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.63
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.62
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.61
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.61
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.61
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.61
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.6
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.6
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.6
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.6
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.6
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.6
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.59
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.59
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.59
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.58
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.58
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.58
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.57
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.56
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.54
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.54
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.53
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.53
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.53
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.52
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.5
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.47
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.44
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	99.41
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.4
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.4
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.39
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.36
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.35
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.34
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.33
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.27
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.26
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	99.26
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	99.25
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	99.25
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.24
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	99.23
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.22
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	99.21
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.2
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.16
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	99.16
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	99.16
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	99.16
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.14
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.14
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	99.12
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	99.1
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	99.06
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.06
2dna_A	67	Unnamed protein product; ubiquitin associated doma	99.06
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	99.05
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.04
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.04
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	99.01
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	98.99
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	98.99
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	98.98
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	98.98
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	98.97
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	98.97
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	98.97
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	98.96
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	98.96
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	98.95
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	98.94
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	98.94
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	98.93
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	98.92
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	98.92
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	98.91
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	98.89
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	98.89
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	98.87
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	98.86
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	98.86
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	98.84
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	98.83
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	98.82
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	98.82
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	98.81
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	98.78
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	98.77
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	98.76
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	98.75
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	98.72
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	98.71
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	98.71
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	98.68
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	98.65
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	98.62
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	98.61
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	98.61
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	98.55
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	98.52
2dna_A	67	Unnamed protein product; ubiquitin associated doma	98.48
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.46
2pjh_A	80	Protein NPL4, nuclear protein localization protein	98.46
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	98.43
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	98.42
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	98.41
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	98.41
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	98.35
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	98.34
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	98.26
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	98.25
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	98.23
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	98.21
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	98.18
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	98.17
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	98.11
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	98.09
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	98.07
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	98.03
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	97.96
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	97.92
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	97.75
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	97.75
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	97.72
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	97.68
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	97.65
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	97.6
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	97.54
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	97.52
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	97.39
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	97.27
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	97.2
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.19
2cos_A	54	Serine/threonine protein kinase LATS2; UBA domain,	97.18
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	97.0
2pwq_A	216	Ubiquitin conjugating enzyme; structural genomics	96.92
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	96.91
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	96.54
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	96.25
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	96.15
1tte_A	215	Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiq	96.05
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	95.96
2dam_A	67	ETEA protein; KIAA0887, UBA-like domain, structura	95.41
2dal_A	62	Protein KIAA0794; FAS associted factor 1, UBA-like	95.17
2cos_A	54	Serine/threonine protein kinase LATS2; UBA domain,	94.95
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	94.95
1v92_A	46	NSFL1 cofactor P47; 3-helix bundle, recombination;	94.69
2pwq_A	216	Ubiquitin conjugating enzyme; structural genomics	94.6
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	94.6
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	94.43
4fp9_B	335	Mterf domain-containing protein 2; modification en	94.24
2dhy_A	67	CUE domain-containing protein 1; structural genomi	94.02
2dhy_A	67	CUE domain-containing protein 1; structural genomi	93.92
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	93.88
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	93.79
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	93.78
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	93.67
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	92.8
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	92.77
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	92.75
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	92.56
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	92.43
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	92.35
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	91.88
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	90.89
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	90.76
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	90.75
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	90.7
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	90.25
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	89.84
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	88.25
2qho_B	53	E3 ubiquitin-protein ligase EDD1; protein-protein	87.84
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	87.8
2dzl_A	66	Protein FAM100B; UBA-like domain, structural genom	87.73
3mva_O	343	Transcription termination factor, mitochondrial; a	86.8
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	86.68
1ip9_A	85	BEM1 protein; ubiquitin alpha/beta roll, signaling	85.93
1ufz_A	83	Hypothetical protein BAB28515; HBS1-like domain, s	85.92
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	85.56
4dbg_B	162	Ring finger protein 31; ubiquitin fold, ubiquitina	85.3
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	85.02
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	84.72
1p3q_Q	54	VPS9P, vacuolar protein sorting-associated protein	84.7
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	83.92
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	82.5
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	82.25
3e21_A	45	HFAF1, FAS-associated factor 1; UBA, alternative s	82.21
1q02_A	52	Sequestosome 1; helical bundle, protein binding; N	81.9
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	81.46
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	81.21
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	80.72
2llw_A	71	Heat shock protein STI1; DP domain, alpha helix, c	80.64
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	80.07

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A

Probab=100.00  E-value=1.3e-75  Score=588.58  Aligned_cols=353  Identities=37%  Similarity=0.633  Sum_probs=247.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.++++..+++++|||||+||+|+|+++|++|+|+++++|++|+.|.+..
T Consensus         8 M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~~~   87 (368)
T 1oqy_A            8 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKAG   87 (368)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCCSS
T ss_pred             EEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCCCC
Confidence            89999999999999999999999999999999532212999999999999999999999999999999998887776654


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 015628           81 SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQS-VPESAPPPAAPAPAPAPAPAPAPAPAPVSSSVSDV  159 (403)
Q Consensus        81 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~-~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (403)
                      +...+.++..+.+++++  + ++     ..+.+.+.++...+.+ .+.++...+.++.    +|..++.. .+.......
T Consensus        88 ~~~~~~~~~~~~~~~~~--~-~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~p~~~~~~-~~~~~~~~~  154 (368)
T 1oqy_A           88 QGTSAPPEASPTAAPES--S-TS-----FPPAPTSGMSHPPPAAREDKSPSEESAPTT----SPESVSGS-VPSSGSSGR  154 (368)
T ss_dssp             SCCCCCSSCCCCCSSSC--C-CS-----CCCSSSCCCCCCCSSSSCCCCCSCSCCCCS----STTCSCCC-SCSCCCSCC
T ss_pred             CCCCCCcccCCCCCccc--c-CC-----CCCCCCCCCCCCCccccccCCccccCCCCC----CCCccccc-ccccccccc
Confidence            43111111111110100  0 00     0000000000000000 0000000000000    11110000 011111234


Q ss_pred             cccccccccCCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCCCCCCCccccccCCCCCCCCCCc
Q 015628          160 YGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQ  239 (403)
Q Consensus       160 ~~~~~s~l~~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~~~~~~~~~~~~~~~~~~~~~~~  239 (403)
                      ++.+.|+||+|+.++.+|++||+||   |+|++|++|||++|||||||||||++|||++.....+        ...+   
T Consensus       155 ~~~~~s~l~~g~~~~~~i~~l~~MG---f~~~~~~~AL~a~~nn~~~A~e~L~~gip~~~~~~~~--------~~~~---  220 (368)
T 1oqy_A          155 EEDAASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIPGSPEPEHG--------SVQE---  220 (368)
T ss_dssp             CCCCCTTTCCTTTHHHHHHHHHTTT---CCSHHHHHHHHHSCSSTTHHHHTTTTSSTTCSSCCCC--------CCCC---
T ss_pred             cccccccccCCcchHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCcccccccC--------Cccc---
Confidence            5667899999999999999999999   9999999999999999999999999999987432210        0000   


Q ss_pred             cccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCchHHhhCcHHHHHHHHHHHhCccchHHHHHHHHhhCHHHHHHH
Q 015628          240 TQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLI  319 (403)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~l~~Lr~~pqf~~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI  319 (403)
                      ..   +   .+..                ++++++.++|+|||++|||++||++||+||++|++|||+|+++||+|+++|
T Consensus       221 ~~---~---~~~~----------------~~~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~l~~~lq~l~~~nP~l~~~I  278 (368)
T 1oqy_A          221 SQ---V---SEQP----------------ATEAAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQI  278 (368)
T ss_dssp             CC---S---SCCC----------------CSSCCSCCTTHHHHHSHHHHHHHHSTTTCTTHHHHHHTTTTTTCHHHHHHH
T ss_pred             cc---c---cccc----------------CccccccchHHHHhcChHHHHHHHHHHhChHHHHHHHHHHHhhCHHHHHHH
Confidence            00   0   0000                111234678999999999999999999999999999999999999999999


Q ss_pred             HHcHHHHHHHhcCCCCCC-CCc----ccccc--cccCCccccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHH
Q 015628          320 QEHQTDFLRLINEPVEGG-EGN----VLGQL--ASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAAN  392 (403)
Q Consensus       320 ~~n~e~Fl~~l~~~~~~~-~g~----~~~~~--~~~~~~~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~  392 (403)
                      ++||++||+||+++++++ .+.    +.+..  .......|+||+||+++|+||++|||+|++||+||++||||+++|+|
T Consensus       279 ~~n~~~Fl~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~t~ee~eaI~rL~~mGF~~~~a~~al~a~~~n~e~A~~  358 (368)
T 1oqy_A          279 SRHQEQFIQMLNEPPGELADISDVEGEVGAIGEEAPQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACEKNENLAAN  358 (368)
T ss_dssp             HHHHHHHHHHHHSCCCCSCSSCCCSSSSCCCSCCCTTCSSCCCCTTTHHHHHHHHHHTCCSHHHHHHTSSSSSCSSHHHH
T ss_pred             HHCHHHHHHHHcCcccccccccccccccccccccCCccccccCCCcCHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHH
Confidence            999999999999886421 110    00000  01123478999999999999999999999999999999999999999


Q ss_pred             HHhccCCCCC
Q 015628          393 YLLDHMHEFE  402 (403)
Q Consensus       393 ~L~~~~~d~~  402 (403)
                      |||+|++|+|
T Consensus       359 ~L~~~~~d~~  368 (368)
T 1oqy_A          359 FLLSQNFDDE  368 (368)
T ss_dssp             HHHHHHCCCC
T ss_pred             HHhhCcCcCC
Confidence            9999988754

>1pve_A HHR23B, UV excision repair protein RAD23 homolog B; XPC binding domain, solution structure, nucleotide excision repair, chaps, DNA binding protein; NMR {Homo sapiens} SCOP: a.189.1.1

Probab=99.83  E-value=2.3e-21  Score=150.27  Aligned_cols=62  Identities=44%  Similarity=0.880  Sum_probs=58.7

Q ss_pred             CCchHHhhCcHHHHHHHHHHHhCccchHHHHHHHHhhCHHHHHHHHHcHHHHHHHhcCCCCC
Q 015628          275 AGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG  336 (403)
Q Consensus       275 ~~~l~~Lr~~pqf~~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI~~n~e~Fl~~l~~~~~~  336 (403)
                      .+++++||++|+|++||++||+||++|++||++|+++||+|+++|++||++|++||+++.++
T Consensus         3 ~~~l~~Lr~~Pqf~qlR~~vqqNP~lL~~lLqqL~~~NPqL~q~I~~n~e~Fl~ll~e~~~~   64 (72)
T 1pve_A            3 HMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQE   64 (72)
T ss_dssp             TCTTGGGTTCTTTTTHHHHHTTCGGGHHHHHHHHHTTCHHHHHHHHTTHHHHHHHHHSCSCC
T ss_pred             CchHHHHHcChHHHHHHHHHHHCHHHHHHHHHHHHhHCHHHHHHHHHCHHHHHHHHcCCccC
Confidence            45789999999999999999999999999999999999999999999999999999998653

>2f4m_B UV excision repair protein RAD23 homolog B; glycoproteins, ubiquitin-dependent protein degradation, NUCL excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: a.189.1.1 PDB: 2f4o_B*

Probab=99.82  E-value=1.6e-20  Score=141.34  Aligned_cols=59  Identities=46%  Similarity=0.935  Sum_probs=56.5

Q ss_pred             CchHHhhCcHHHHHHHHHHHhCccchHHHHHHHHhhCHHHHHHHHHcHHHHHHHhcCCC
Q 015628          276 GTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV  334 (403)
Q Consensus       276 ~~l~~Lr~~pqf~~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI~~n~e~Fl~~l~~~~  334 (403)
                      +++++||++|+|++||++||+||++|+++|++|+++||+|+++|++|||+|++||++++
T Consensus         2 ~~l~~Lr~~Pqf~~lR~~vq~NP~~L~~lLqql~~~nP~l~~~I~~n~e~Fl~ll~e~~   60 (61)
T 2f4m_B            2 HPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV   60 (61)
T ss_dssp             CGGGGGTTCHHHHHHHHHHHHCGGGHHHHHHHHHHHCHHHHHHHHHSHHHHHHHHTSCC
T ss_pred             chHHHHHcChHHHHHHHHHHHCHHHHHHHHHHHHhHCHHHHHHHHHCHHHHHHHHcccC
Confidence            46899999999999999999999999999999999999999999999999999998763

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.78  E-value=2.8e-19  Score=149.52  Aligned_cols=77  Identities=25%  Similarity=0.402  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||||+||+|+|+.+|++|||++|++|+|++++++..
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~~~~   78 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSIS---CEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQKKST   78 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTT---SCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC----
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCCCCC
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999876644

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.76  E-value=4.4e-18  Score=139.22  Aligned_cols=78  Identities=45%  Similarity=0.705  Sum_probs=73.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHH---hCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETV---QGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~---~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+.|.++|++++||.+||++|+..   .|   +|+++|||+|+||.|+|+++|++|||++|++|+|+++++
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~~   77 (95)
T 1uel_A            1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDA---FPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKP   77 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTT---CCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSC
T ss_pred             CEEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCC---CChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeCC
Confidence            899999999999999999999999999999999   67   999999999999999999999999999999999999876


Q ss_pred             CCCC
Q 015628           78 KVSS   81 (403)
Q Consensus        78 k~~~   81 (403)
                      +..+
T Consensus        78 ~~~~   81 (95)
T 1uel_A           78 KAVS   81 (95)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5443

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B

Probab=99.76  E-value=2.3e-18  Score=138.98  Aligned_cols=80  Identities=34%  Similarity=0.492  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++|+|+++++|+|+++.++..
T Consensus         1 M~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl~Gg~   77 (88)
T 4fbj_B            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGG   77 (88)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBCC---
T ss_pred             CEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHC---cChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEECCCCC
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999987755


Q ss_pred             CCC
Q 015628           81 SSG   83 (403)
Q Consensus        81 ~~~   83 (403)
                      ...
T Consensus        78 ~~~   80 (88)
T 4fbj_B           78 GLR   80 (88)
T ss_dssp             ---
T ss_pred             CCC
Confidence            433

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A

Probab=99.75  E-value=2.3e-18  Score=138.85  Aligned_cols=75  Identities=28%  Similarity=0.380  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.++|   +|+++|||+|+||.|+|+.+|++|+| ++++|||+++.+..
T Consensus         6 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---ip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~~~   80 (90)
T 4dwf_A            6 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAPPQ   80 (90)
T ss_dssp             EEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCCC-
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCCCC
Confidence            79999999999999999999999999999999999   99999999999999999999999999 89999999986543

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.75  E-value=3.2e-18  Score=134.61  Aligned_cols=74  Identities=24%  Similarity=0.320  Sum_probs=71.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++|+|+++++|+|+++.+
T Consensus         5 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl~   78 (79)
T 3phx_B            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLR   78 (79)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCB
T ss_pred             EEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcC---CCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            78999999999999999999999999999999999   999999999999999999999999999999999999865

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A

Probab=99.74  E-value=7.1e-18  Score=134.17  Aligned_cols=76  Identities=36%  Similarity=0.640  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHH---hCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETV---QGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~---~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+.|.++|++++||.+||++|+..   .|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++++
T Consensus         6 m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~~   82 (85)
T 2wyq_A            6 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDA---FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKT   82 (85)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTT---CCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC--
T ss_pred             EEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccC---CCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcCC
Confidence            789999999999999999999999999999998   67   999999999999999999999999999999999999876


Q ss_pred             CC
Q 015628           78 KV   79 (403)
Q Consensus        78 k~   79 (403)
                      ++
T Consensus        83 ~~   84 (85)
T 2wyq_A           83 KA   84 (85)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.73  E-value=4.5e-18  Score=140.62  Aligned_cols=74  Identities=27%  Similarity=0.459  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCcEEEE--EeCCCCcHHHHHHHH-HHHhCCCCCCCCCcEEEeCCeecCCCCccccccc-CCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEI--EVKPEDKVSDVKKNI-ETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~i--eV~~~~TV~dLK~kI-~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI-~~~s~I~v~v~k   76 (403)
                      |+|+||+++|++|.+  +|++++||.+||++| +...|   +|+++|||||+||+|+|+.+|++|+| ++|++|+||+++
T Consensus        20 m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~g---ip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~lmvsk   96 (98)
T 4a20_A           20 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKA---SHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   96 (98)
T ss_dssp             EEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSC---SCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcC---CChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEEEEeC
Confidence            789999999998777  566999999999999 77778   99999999999999999999999999 999999999987


Q ss_pred             C
Q 015628           77 S   77 (403)
Q Consensus        77 ~   77 (403)
                      +
T Consensus        97 p   97 (98)
T 4a20_A           97 N   97 (98)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.73  E-value=7.9e-18  Score=136.36  Aligned_cols=74  Identities=39%  Similarity=0.646  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.++|   +|+++|||+|+||.|+|+.+|++|||++|++|+|+++.+
T Consensus        18 m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~rlr   91 (91)
T 3v6c_B           18 MQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   91 (91)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhC---CChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEecC
Confidence            79999999999999999999999999999999999   999999999999999999999999999999999998764

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.73  E-value=6.6e-18  Score=135.49  Aligned_cols=72  Identities=36%  Similarity=0.517  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCee-cCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV-LKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~Gki-L~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +|+++|||+|+||. |+|+++|++|+|+++++|+|+++
T Consensus        11 ~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i~lv~~   83 (84)
T 2kk8_A           11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQH---IPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVS   83 (84)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEEC
T ss_pred             eEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHC---cChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEc
Confidence            89999999999999999999999999999999999   99999999999999 99999999999999999999875

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A

Probab=99.72  E-value=9.3e-18  Score=136.84  Aligned_cols=71  Identities=27%  Similarity=0.379  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+||++.|+++.|+|++++||.+||++|+++.|   +|+++|||+|+||+|+|+.+|++|+|++|++|+|+-
T Consensus        22 IqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~G---ip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~~   92 (93)
T 3plu_A           22 IEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIG---TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   92 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhC---CCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEEe
Confidence            68999999999999999999999999999999999   999999999999999999999999999999999863

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A

Probab=99.72  E-value=2e-17  Score=134.80  Aligned_cols=77  Identities=36%  Similarity=0.589  Sum_probs=73.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|+.|.|+|++++||.+||++|++.+|   +|+++|||+|+|+.|+|+.+|++|+|+++++|+|+++.+...
T Consensus         2 m~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~g---ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~~gG~   78 (96)
T 3k9o_B            2 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYA   78 (96)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC--
T ss_pred             cEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhC---CChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCC
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999877643

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.72  E-value=5.3e-18  Score=137.21  Aligned_cols=73  Identities=29%  Similarity=0.457  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEEEeC--CCCcHHHHHHHH-HHHhCCCCCCCCCcEEEeCCeecCCCCccccccc-CCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVK--PEDKVSDVKKNI-ETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~--~~~TV~dLK~kI-~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI-~~~s~I~v~v~k   76 (403)
                      |+|+||+++|++|.|+|+  +++||.+||++| +...|   +|+++|||||+||+|+|+.+|++|+| .++++|+|++++
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKA---SHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSC---SSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcC---CChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            899999999999988755  999999999999 88889   99999999999999999999999999 699999999875

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.72  E-value=3e-17  Score=136.86  Aligned_cols=76  Identities=26%  Similarity=0.324  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|+ |.|+|++++||.+||++|+.++|   +++++|||+|+||+|+|+++|++|+|+++++|+|+++++...
T Consensus        18 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~~~   93 (106)
T 1wx7_A           18 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRA   93 (106)
T ss_dssp             EEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHT---CCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCCCCS
T ss_pred             EEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHC---cChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCCCC
Confidence            78999999886 79999999999999999999999   999999999999999999999999999999999999876543

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.72  E-value=2.2e-17  Score=135.83  Aligned_cols=75  Identities=36%  Similarity=0.577  Sum_probs=72.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+++   +|+++|||+|+||+|+|+++|++|+|+++++|+|+++.+.
T Consensus        23 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl~G   97 (98)
T 4hcn_B           23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   97 (98)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCSC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhC---CChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998764

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A

Probab=99.71  E-value=3.4e-17  Score=126.76  Aligned_cols=75  Identities=36%  Similarity=0.550  Sum_probs=71.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+.+|++|+|+++++|+|+++.+.
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~---i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~G   75 (76)
T 1ndd_A            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRG   75 (76)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC-
T ss_pred             CEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHC---cChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998653

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: d.15.1.1 PDB: 3dbr_I 3dbl_I

Probab=99.71  E-value=1.7e-17  Score=132.61  Aligned_cols=75  Identities=36%  Similarity=0.546  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+.+|++|+|+++++|+|+++.+.
T Consensus        13 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl~G   87 (88)
T 3dbh_I           13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRG   87 (88)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCCCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHC---cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            78999999999999999999999999999999999   9999999999999999999999999999999999998654

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.70  E-value=2.5e-17  Score=137.57  Aligned_cols=77  Identities=19%  Similarity=0.364  Sum_probs=73.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|+.|.|+|++++||.+||++|+.+.|   +++++|||+|+||.|+|+++|++|||++|++|||++++++..
T Consensus        24 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~~~~~  100 (106)
T 1ttn_A           24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG---VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQN  100 (106)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTC---CCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSSCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHC---cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCCC
Confidence            78999999999999999999999999999999999   999999999999999999999999999999999999876654

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.70  E-value=3.1e-17  Score=128.54  Aligned_cols=73  Identities=22%  Similarity=0.349  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCcEE-EEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHF-EIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~-~ie-V~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+++|+.+ .++ |++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|||+++++|+|+++.
T Consensus         3 m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~g---ip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i~l~~r~   77 (78)
T 2faz_A            3 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFH---VEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   77 (78)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             EEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHC---cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeC
Confidence            8999999999985 899 9999999999999999999   99999999999999999999999999999999999875

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...

Probab=99.70  E-value=5.7e-17  Score=125.47  Aligned_cols=75  Identities=37%  Similarity=0.601  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+.+|+.+.++|++++||.+||++|++..|   +|+++|||+|+||.|+|+.+|++|+|+++++|+|+++.++
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~---i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~G   75 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRG   75 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998653

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.70  E-value=1.6e-17  Score=137.53  Aligned_cols=71  Identities=17%  Similarity=0.281  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+||++.|+++.|+|++++||.+||++|+++.|   +|+++|||||+||+|+|+.+|++|+|+++++|+|+.
T Consensus        29 m~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~G---ip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHC---CCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhC---CCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEe
Confidence            78999999999999999999999999999999999   999999999999999999999999999999999864

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=4.5e-17  Score=128.08  Aligned_cols=73  Identities=27%  Similarity=0.424  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+.+|++|||++|++|+|+++.
T Consensus         8 m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~---i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A            8 MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLN---VPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             EEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTC---CCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            78999999999999999999999999999999999   99999999999999999999999999999999999875

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=99.70  E-value=3.5e-17  Score=129.88  Aligned_cols=76  Identities=36%  Similarity=0.546  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|+++.|+|++++||.+||++|+++++   +|+++|||+|+||.|+|+.+|++|+|+++++|+|+++.+..
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~---ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~GG   79 (85)
T 3n3k_B            4 MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGG   79 (85)
T ss_dssp             CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC--
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999987653

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.70  E-value=7.4e-17  Score=129.61  Aligned_cols=77  Identities=19%  Similarity=0.293  Sum_probs=72.5

Q ss_pred             CEEEEEeCCC-cEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKG-THFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g-~~~~i-eV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++| +++.| +|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
T Consensus         8 m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~g---ip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~g   84 (89)
T 1wy8_A            8 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD---VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPDS   84 (89)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSC---CCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECCCC
T ss_pred             EEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHC---cChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeCCC
Confidence            7999999999 79999 59999999999999999999   9999999999999999999999999999999999998765


Q ss_pred             CC
Q 015628           79 VS   80 (403)
Q Consensus        79 ~~   80 (403)
                      ..
T Consensus        85 G~   86 (89)
T 1wy8_A           85 GP   86 (89)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} SCOP: d.15.1.1

Probab=99.69  E-value=5.7e-17  Score=128.45  Aligned_cols=76  Identities=37%  Similarity=0.577  Sum_probs=73.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|+++.|+|++++||.+||++|+++++   +|+++|||+|+||.|+|+.+|++|+|+++++|+|+++.+..
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~---i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~GG   79 (85)
T 3mtn_B            4 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRGG   79 (85)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCCCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHC---cChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECcCC
Confidence            79999999999999999999999999999999999   99999999999999999999999999999999999987653

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.69  E-value=4.4e-17  Score=130.79  Aligned_cols=71  Identities=30%  Similarity=0.411  Sum_probs=68.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++||| +|++|||++|
T Consensus        18 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~~i-~g~~i~lv~R   88 (88)
T 4eew_A           18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVER   88 (88)
T ss_dssp             EEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEEC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCEECCCCCcHHHcCC-CCcEEEEEEC
Confidence            78999999999999999999999999999999999   99999999999999999999999999 8999999875

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.69  E-value=6.5e-17  Score=131.55  Aligned_cols=77  Identities=19%  Similarity=0.214  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHh--CCCCCCCCCcEEEeCCeecCCCCccccc--ccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQ--GSDVYPASQQMLIHQGKVLKDVTTLEEN--KVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~--~~~ieV~~~~TV~dLK~kI~~~~--g~~~ip~~~QkLiy~GkiL~D~~tLsd~--gI~~~s~I~v~v   74 (403)
                      |+|+||+.+|+  .+.|+|++++||.+||++|+..+  +   +++++|||||+||+|+|+.+|++|  +|+++++|||++
T Consensus         8 m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~---i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv~   84 (93)
T 1wgd_A            8 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPER---PRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVC   84 (93)
T ss_dssp             CEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTC---CCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEEC
T ss_pred             EEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCC---CChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEEe
Confidence            79999999998  67788889999999999999998  8   999999999999999999999999  999999999998


Q ss_pred             ecCCCC
Q 015628           75 TKSKVS   80 (403)
Q Consensus        75 ~k~k~~   80 (403)
                      +.+...
T Consensus        85 ~~~gg~   90 (93)
T 1wgd_A           85 NVKSGP   90 (93)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.69  E-value=3.9e-17  Score=131.65  Aligned_cols=75  Identities=24%  Similarity=0.310  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
T Consensus         5 m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~g   79 (88)
T 2hj8_A            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG   79 (88)
T ss_dssp             EEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTC---SCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC---
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhC---CChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCC
Confidence            78999999999999999999999999999999999   9999999999999999999999999999999999998654

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.69  E-value=7.6e-17  Score=128.86  Aligned_cols=76  Identities=29%  Similarity=0.446  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|+.+.++|++++||.+||++|++..+   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+..
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---i~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~GG   83 (87)
T 1wh3_A            8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSG   83 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTC---CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhC---CChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            78999999999999999999999999999999999   99999999999999999999999999999999999987653

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=99.69  E-value=7.2e-17  Score=130.18  Aligned_cols=75  Identities=33%  Similarity=0.604  Sum_probs=69.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+++.++|++++||.+||++|++..|   +|+++|||+|+||.|+|+.+|++|+|+++++|+|+++.+.
T Consensus        10 ~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r~~G   84 (88)
T 1sif_A           10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   84 (88)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC----
T ss_pred             eEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHC---cChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999988664

>2uyz_B Small ubiquitin-related modifier 1; sumoylation, cell division, nuclear protein, ubiquitin-like modifier, UBL conjugation pathway; 1.4A {Homo sapiens} SCOP: d.15.1.1 PDB: 2vrr_B 2iy0_B 2iy1_B 2g4d_B 2las_A 2io2_B 1z5s_B 3uip_B* 1tgz_B* 2bf8_B

Probab=99.69  E-value=4.3e-17  Score=128.14  Aligned_cols=75  Identities=19%  Similarity=0.268  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+++.++|++++||.+||++|+++.|   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.++
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~g---i~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~G   78 (79)
T 2uyz_B            4 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   78 (79)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHC---CCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            78999999999999999999999999999999999   9999999999999999999999999999999999998653

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.68  E-value=1e-16  Score=130.83  Aligned_cols=74  Identities=27%  Similarity=0.300  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCC-CcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~-~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|+.|.|+|++++||.+||++|+..     . +++|||||+||.|+|+ ++|++|+|+++++|||++++++.
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~-----~-~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~~~   81 (95)
T 1wia_A            8 INVRLKFLNDTEELAVARPEDTVGTLKSKYFPG-----Q-ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGA   81 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHSSS-----T-TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhh-----C-cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCCC
Confidence            789999999999999999999999999999776     3 7899999999999999 99999999999999999987654


Q ss_pred             C
Q 015628           80 S   80 (403)
Q Consensus        80 ~   80 (403)
                      .
T Consensus        82 ~   82 (95)
T 1wia_A           82 A   82 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.68  E-value=3.8e-17  Score=136.64  Aligned_cols=77  Identities=22%  Similarity=0.234  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC---------------CCcEEEeCCeecC-CCCccccccc
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA---------------SQQMLIHQGKVLK-DVTTLEENKV   64 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~---------------~~QkLiy~GkiL~-D~~tLsd~gI   64 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+++.+   +++               +.|+|||+||+|. |+++|++|||
T Consensus         8 M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~---i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dygI   84 (105)
T 1v2y_A            8 MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ---LKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGI   84 (105)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHH---HHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTC
T ss_pred             EEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhC---CCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHcCC
Confidence            89999999999999999999999999999999998   766               4679999999996 5699999999


Q ss_pred             CCCcEEEEEEecCCCC
Q 015628           65 AENSFVVVMLTKSKVS   80 (403)
Q Consensus        65 ~~~s~I~v~v~k~k~~   80 (403)
                      +++++|||+++.+...
T Consensus        85 ~~g~~l~lv~~lr~~~  100 (105)
T 1v2y_A           85 RNRDEVSFIKKLGQKS  100 (105)
T ss_dssp             CSSEEEEEEECSCSCC
T ss_pred             CCCCEEEEEehhccCC
Confidence            9999999999887653

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.68  E-value=1.2e-16  Score=130.71  Aligned_cols=75  Identities=31%  Similarity=0.370  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCC-CcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~-~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++| ++.|+|++++||.+||++|+.+.|   +|+++|||+|+||+|+|+ ++|++|+|+++++|+|+++.+..
T Consensus        16 ~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~gg   91 (94)
T 2kan_A           16 IHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVEN---TPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSINR   91 (94)
T ss_dssp             EEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSS---SCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCCSS
T ss_pred             EEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHC---cCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCCCC
Confidence            6899999988 899999999999999999999999   999999999999999999 99999999999999999987654

>1wyw_B Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 1y8r_C* 2asq_A 2pe6_B 1a5r_A 2kqs_A 3kyc_D* 3rzw_C

Probab=99.67  E-value=9e-17  Score=132.05  Aligned_cols=75  Identities=19%  Similarity=0.268  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+++.|+|++++||.+||++|+.+.|   +|+++|||||+|+.|+|+.+|++|+|+++++|+|+++.++
T Consensus        22 m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~g---ip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~~G   96 (97)
T 1wyw_B           22 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   96 (97)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSSC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecCC
Confidence            78999999999999999999999999999999999   9999999999999999999999999999999999998754

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.67  E-value=2.1e-16  Score=123.08  Aligned_cols=71  Identities=30%  Similarity=0.517  Sum_probs=68.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+ +|+.+.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+.+|++|||++|++|+|+.+
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~---i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~   75 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   75 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhC---CCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEc
Confidence            6899999 999999999999999999999999999   9999999999999999999999999999999999864

>1wju_A NEDD8 ultimate buster-1; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.67  E-value=1.7e-16  Score=131.43  Aligned_cols=73  Identities=19%  Similarity=0.132  Sum_probs=65.5

Q ss_pred             EEEEEeCC----CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            2 KVFVKTLK----GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         2 kI~VKtl~----g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      .|.|+..+    +++|.|+|++++||.+||++|+++.|   +|+++|||||+||+|+|+++|++|+|+++++|+||+ .+
T Consensus        17 ti~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~g---ip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti~vl~-lr   92 (100)
T 1wju_A           17 TIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG---LQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLE-LK   92 (100)
T ss_dssp             EEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTT---CCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEEC-CC
T ss_pred             EEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHC---cCHHHeEEEeCCeECCCCCcHHHcCCCCCCEEEEEE-EC
Confidence            36677766    77899999999999999999999999   999999999999999999999999999999995554 44


Q ss_pred             C
Q 015628           78 K   78 (403)
Q Consensus        78 k   78 (403)
                      .
T Consensus        93 g   93 (100)
T 1wju_A           93 Q   93 (100)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3vdz_A Ubiquitin-40S ribosomal protein S27A; gadolinium, MRI contrast agent, peptide-based contrast agent lanthanide binding TAG; 2.40A {Synthetic construct} PDB: 2ojr_A

Probab=99.67  E-value=1.8e-16  Score=133.51  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+.|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
T Consensus        36 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~G  110 (111)
T 3vdz_A           36 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  110 (111)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECCCC
T ss_pred             EEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhC---CChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            79999999999999999999999999999999999   9999999999999999999999999999999999998754

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.67  E-value=2.8e-16  Score=128.92  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+.+|+.+.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+.+|++|||+++++|+|+++.+.
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~g---i~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~g   75 (98)
T 1yx5_B            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (98)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998764

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.66  E-value=2.4e-16  Score=130.70  Aligned_cols=76  Identities=20%  Similarity=0.334  Sum_probs=69.9

Q ss_pred             CEEEEEeCCC----cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCC-CcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKG----THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g----~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~-~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+..+    ++|.|+|++++||.+||++|+.++|   +|+++|||+|+||.|+|+ ++|++|+|+++++|+|+++
T Consensus         8 m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~~   84 (102)
T 1v5o_A            8 MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG---VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQK   84 (102)
T ss_dssp             EEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTC---CCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBC
T ss_pred             EEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHC---cChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEEC
Confidence            7899999754    7999999999999999999999999   999999999999999988 6999999999999999987


Q ss_pred             cCCC
Q 015628           76 KSKV   79 (403)
Q Consensus        76 k~k~   79 (403)
                      .+..
T Consensus        85 ~~gg   88 (102)
T 1v5o_A           85 DNVG   88 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.66  E-value=1.1e-16  Score=130.74  Aligned_cols=75  Identities=27%  Similarity=0.322  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+. |+.|.|+|++++||.+||++|+...+   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+..
T Consensus        18 m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~g   92 (96)
T 1wx8_A           18 IRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSG   92 (96)
T ss_dssp             EEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTC---SCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSSC
T ss_pred             EEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCCC
Confidence            78999998 99999999999999999999999999   99999999999999999999999999999999999887653

>1dv0_A DNA repair protein HHR23A; helical bundle, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.5.2.1 PDB: 1f4i_A

Probab=99.66  E-value=1.5e-17  Score=119.35  Aligned_cols=47  Identities=53%  Similarity=0.905  Sum_probs=42.9

Q ss_pred             CHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCCC
Q 015628          356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       356 t~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~~  402 (403)
                      |+||.++|+||++|||+|.+||+||++|+||+++|+||||+++.|++
T Consensus         1 ~~~e~eaI~rL~~mGF~~~~a~~Al~a~~~n~e~A~~~Lf~~~~d~~   47 (47)
T 1dv0_A            1 GSQEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQNFDDE   47 (47)
T ss_dssp             --CCHHHHTTTTTTTCCHHHHHHHHTTTTSCHHHHHHHTTSCCCCCC
T ss_pred             CcchHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCcCCCC
Confidence            68899999999999999999999999999999999999999987753

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.66  E-value=2.9e-16  Score=130.04  Aligned_cols=74  Identities=30%  Similarity=0.353  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+. |+.+.|+|++++||.+||++|+...|   +|+++|||+|+||+|+|+++|++|||++|++|+|+++++.
T Consensus        26 m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~l~~~~~~   99 (101)
T 2klc_A           26 MKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFK---SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQN   99 (101)
T ss_dssp             EEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHT---CCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCSS
T ss_pred             EEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHC---cChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCC
Confidence            78999998 88999999999999999999999999   9999999999999999999999999999999999987654

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A

Probab=99.47  E-value=7.5e-18  Score=131.29  Aligned_cols=75  Identities=27%  Similarity=0.408  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+.+|+++.++|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+.+|++|||++|++|+|+++.++
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlrg   75 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQG---VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   75 (76)
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998653

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.65  E-value=3.2e-16  Score=134.94  Aligned_cols=76  Identities=29%  Similarity=0.329  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||++ |+.|.|+|++++||.+||++|+.++|   +++++|||||+||+|+|+++|++|+|+++++|+|+++++...
T Consensus        33 m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~gg~  108 (125)
T 1j8c_A           33 IKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFK---SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPNS  108 (125)
T ss_dssp             EEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHC---SCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC-----
T ss_pred             EEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHC---cCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCCCC
Confidence            78999998 99999999999999999999999999   999999999999999999999999999999999999876543

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.65  E-value=2.4e-16  Score=130.42  Aligned_cols=75  Identities=27%  Similarity=0.324  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|+ +.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+..
T Consensus        23 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~~   97 (100)
T 1yqb_A           23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   97 (100)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             EEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHC---cChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCCC
Confidence            78999999886 79999999999999999999999   99999999999999999999999999999999999986553

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.64  E-value=7e-16  Score=131.14  Aligned_cols=76  Identities=21%  Similarity=0.232  Sum_probs=65.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCC---CC--CCCCcEEEeCCeecCCCCcccccccCCCc--EEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSD---VY--PASQQMLIHQGKVLKDVTTLEENKVAENS--FVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~---~i--p~~~QkLiy~GkiL~D~~tLsd~gI~~~s--~I~v~   73 (403)
                      |+|+||+++|+++.|+|++++||.+||++|+...+++   .+  ++++|||||.||+|+|+.+|++|+|+.++  +|||+
T Consensus        17 m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlhLv   96 (116)
T 1wgh_A           17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   96 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEE
Confidence            7899999999999999999999999999999943221   13  69999999999999999999999998775  45556


Q ss_pred             Eec
Q 015628           74 LTK   76 (403)
Q Consensus        74 v~k   76 (403)
                      ++.
T Consensus        97 lr~   99 (116)
T 1wgh_A           97 ARE   99 (116)
T ss_dssp             ECS
T ss_pred             ccC
Confidence            554

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.64  E-value=3.9e-16  Score=127.25  Aligned_cols=73  Identities=22%  Similarity=0.342  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+  |+.+.|+|++++||.+||++|+++.|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
T Consensus        20 m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~G   92 (93)
T 2l7r_A           20 MQLFVRA--QELHTFEVTGQETVAQIKAHVASLEG---IAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLG   92 (93)
T ss_dssp             CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHT---CCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCCC
T ss_pred             EEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhC---cChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            7999997  89999999999999999999999999   9999999999999999999999999999999999988653

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.64  E-value=1e-15  Score=138.26  Aligned_cols=77  Identities=35%  Similarity=0.549  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|+++.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+++|++|+|+++++|||+++.++..
T Consensus         1 MqI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl~GG~   77 (169)
T 3l0w_B            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG   77 (169)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC---CCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCCC--
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHC---cCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEecccc
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999977643

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.63  E-value=5.4e-16  Score=127.40  Aligned_cols=72  Identities=21%  Similarity=0.276  Sum_probs=67.4

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~-~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+|| +.|+.| .|+|++++||.+||++|++.+|   +|+++|||+|+||+|+|+ +|++|+|+++++|+||.+..
T Consensus         8 m~i~Vk-~~g~~~~~l~v~~~~TV~~lK~~I~~~tg---ip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~~~   80 (96)
T 1wgg_A            8 YSVTVK-WGKEKFEGVELNTDEPPMVFKAQLFALTG---VQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             EEEEEE-ETTEEEEEEEEESSSCHHHHHHHHHHHTC---CCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCC
T ss_pred             EEEEEE-ECCEEEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecch
Confidence            689999 578999 6999999999999999999999   999999999999999999 99999999999999997643

>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.63  E-value=2.3e-16  Score=114.18  Aligned_cols=49  Identities=57%  Similarity=1.000  Sum_probs=47.1

Q ss_pred             cccCCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCC
Q 015628          166 NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  217 (403)
Q Consensus       166 ~l~~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~  217 (403)
                      +|++|+.+++.|++|++||   |+|++|++|||+++||++||||||++|||+
T Consensus         1 ~~~~~~~~~~~i~~L~~MG---F~~~~a~~AL~~~~~n~e~A~e~L~~gip~   49 (49)
T 1ify_A            1 TLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIPG   49 (49)
T ss_dssp             CCCCSHHHHHHHHHHHHTT---CCHHHHHHHHHTTTSCSHHHHHHHHHCCCC
T ss_pred             CCCCCccCHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHhCCCC
Confidence            4789999999999999999   999999999999999999999999999995

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.63  E-value=8.5e-16  Score=128.48  Aligned_cols=74  Identities=23%  Similarity=0.152  Sum_probs=68.4

Q ss_pred             CEEEEEeCCC---cEEEEEeC--------C-CCcHHHHHHHHHHHh--CCCCCCCCC-cEEEeCCeecCCCCcccccccC
Q 015628            1 MKVFVKTLKG---THFEIEVK--------P-EDKVSDVKKNIETVQ--GSDVYPASQ-QMLIHQGKVLKDVTTLEENKVA   65 (403)
Q Consensus         1 MkI~VKtl~g---~~~~ieV~--------~-~~TV~dLK~kI~~~~--g~~~ip~~~-QkLiy~GkiL~D~~tLsd~gI~   65 (403)
                      |+|+||+.++   ++|.|+|+        + ++||.+||++|+.+.  |   +|+++ |||||+||+|+|+++|++|+|+
T Consensus        13 ~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~g---ip~~~~qrLi~~Gk~L~D~~tL~~y~i~   89 (107)
T 1x1m_A           13 WHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQES---VPDPELIDLIYCGRKLKDDQTLDFYGIQ   89 (107)
T ss_dssp             CCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTT---CCCSSSEEEEETTEECCTTCBHHHHTCC
T ss_pred             eEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccC---CChhhcEEEEECCeECCCCCcHHHcCCC
Confidence            7899999999   89999954        4 499999999999999  8   99999 9999999999999999999999


Q ss_pred             CCcEEEEEEecC
Q 015628           66 ENSFVVVMLTKS   77 (403)
Q Consensus        66 ~~s~I~v~v~k~   77 (403)
                      ++++|||+++.+
T Consensus        90 ~g~~i~lv~~~~  101 (107)
T 1x1m_A           90 PGSTVHVLRKSW  101 (107)
T ss_dssp             TTCEEEEEESSC
T ss_pred             CCCEEEEEeCCC
Confidence            999999998754

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=127.80  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
T Consensus        36 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~G  110 (111)
T 2ojr_A           36 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  110 (111)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHC---CCTTTEEEEETTEECCSSCBTTTTTCCTTCEEEEEECCCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHC---cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            78999999999999999999999999999999999   9999999999999999999999999999999999998654

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=2.5e-15  Score=127.22  Aligned_cols=76  Identities=33%  Similarity=0.522  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      ++|+||+++|+.+.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+..
T Consensus        10 ~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~GG   85 (114)
T 2kdi_A           10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG   85 (114)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCSS
T ss_pred             EEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHC---cChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCC
Confidence            58999999999999999999999999999999999   99999999999999999999999999999999999987654

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.61  E-value=4.2e-16  Score=129.23  Aligned_cols=72  Identities=29%  Similarity=0.517  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+ +|+.|.|+|++++||.+||++|++++|   +|+++|||+|+||.|+|+.+|++|||++|++|+|+++.
T Consensus        29 i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~~gI~~g~tI~lv~~~  100 (101)
T 3m63_B           29 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ  100 (101)
T ss_dssp             CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHS---CCSTTCCEEETTEECCTTSBTTTTTCCTTEEEEECCCC
T ss_pred             EEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHC---cChHHEEEEECCEECCCcCcHHHCCCCCCCEEEEEeCC
Confidence            5688897 899999999999999999999999999   99999999999999999999999999999999999764

>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics, apoptosis, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.61  E-value=2.4e-15  Score=121.95  Aligned_cols=73  Identities=29%  Similarity=0.408  Sum_probs=67.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCC-----CcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCC-CCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPE-----DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKD-VTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~-----~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D-~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+||+ .|+.|.|+|+++     +||.+||++|+..+|   +|+++|||+|+||.|+| +++|++|+|+++++|+|+.
T Consensus         8 ~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~g---ip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~   83 (92)
T 1wxv_A            8 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIG---VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIG   83 (92)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTC---CCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEES
T ss_pred             EEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHC---cCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEe
Confidence            6899997 588999999985     999999999999999   99999999999999998 6689999999999999997


Q ss_pred             ecC
Q 015628           75 TKS   77 (403)
Q Consensus        75 ~k~   77 (403)
                      +..
T Consensus        84 ~~~   86 (92)
T 1wxv_A           84 KKN   86 (92)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            543

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.61  E-value=1.5e-15  Score=130.62  Aligned_cols=79  Identities=16%  Similarity=0.261  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCC--CCCCC--CCcEEEeCCeecCCCCcccccccCCC------cE
Q 015628            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGS--DVYPA--SQQMLIHQGKVLKDVTTLEENKVAEN------SF   69 (403)
Q Consensus         1 MkI~VKtl~g~~~-~ieV~~~~TV~dLK~kI~~~~g~--~~ip~--~~QkLiy~GkiL~D~~tLsd~gI~~~------s~   69 (403)
                      |+|+||+++|+.| .+++++++||.+||++|+...+.  ..+|+  ++|||||+||+|+|+++|++|+|.++      .+
T Consensus        17 ~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~~~~~~~v~t   96 (126)
T 1se9_A           17 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTT   96 (126)
T ss_dssp             EEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEE
T ss_pred             EEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcHHHcCCCcCCccCCcEE
Confidence            6899999999998 69999999999999999765431  12776  79999999999999999999999998      56


Q ss_pred             EEEEEecCCC
Q 015628           70 VVVMLTKSKV   79 (403)
Q Consensus        70 I~v~v~k~k~   79 (403)
                      |||+++.+..
T Consensus        97 mhlVlrl~g~  106 (126)
T 1se9_A           97 MHVIIQAPVT  106 (126)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEeccCCc
Confidence            8888776643

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.60  E-value=1.2e-15  Score=131.42  Aligned_cols=74  Identities=20%  Similarity=0.253  Sum_probs=65.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHH------HhCCCCC--CCCCcEEEeCCeecCCCCcccccccCCCcE--E
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIET------VQGSDVY--PASQQMLIHQGKVLKDVTTLEENKVAENSF--V   70 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~------~~g~~~i--p~~~QkLiy~GkiL~D~~tLsd~gI~~~s~--I   70 (403)
                      |+|+||+++|+++.|+|++++||.+||++|+.      +.+   +  ++++|||||+||+|+|+++|++|+|+++++  |
T Consensus        18 m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~---ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tl   94 (125)
T 2gow_A           18 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEE---QVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVM   94 (125)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCC---TTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEE
T ss_pred             EEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccC---CCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEE
Confidence            68999999999999999999999999999998      445   5  489999999999999999999999998875  5


Q ss_pred             EEEEecC
Q 015628           71 VVMLTKS   77 (403)
Q Consensus        71 ~v~v~k~   77 (403)
                      +|+++.+
T Consensus        95 hlv~r~~  101 (125)
T 2gow_A           95 HLVARET  101 (125)
T ss_dssp             EEEECSC
T ss_pred             EEEecCC
Confidence            5555543

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A

Probab=99.60  E-value=2e-15  Score=122.37  Aligned_cols=72  Identities=25%  Similarity=0.409  Sum_probs=68.3

Q ss_pred             CEEEEEeCCCcEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE---eCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~i-eV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi---y~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||. .|++|.| +|++++||.+||++|++++|   +|+++|||+   |+||+|+|+.+|++|+|+++++|+||.+.
T Consensus         8 m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~g---ip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~~   83 (90)
T 1v5t_A            8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTG---VLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTR   83 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTC---CCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCC
T ss_pred             EEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHC---cCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEecC
Confidence            7899995 8899999 99999999999999999999   999999999   99999999999999999999999999753

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.60  E-value=8.4e-16  Score=127.19  Aligned_cols=71  Identities=20%  Similarity=0.239  Sum_probs=64.2

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHh-CCCCCCCCCcEEEeCCeecCCCCccccc--ccCCCcEEEEE
Q 015628            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQ-GSDVYPASQQMLIHQGKVLKDVTTLEEN--KVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~--~~~ieV~~~~TV~dLK~kI~~~~-g~~~ip~~~QkLiy~GkiL~D~~tLsd~--gI~~~s~I~v~   73 (403)
                      |+|+||+++|+  .+.|+|++++||.+||++|+.+. |.  .|+++|||||+||+|+|+++|++|  +|+++++|+|+
T Consensus        24 m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~--pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~tihLv   99 (99)
T 2kdb_A           24 VTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSK--PLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV   99 (99)
T ss_dssp             EEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTC--CCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEEEEC
T ss_pred             EEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCC--CChhhEEEEECCEECCCCCCHHHHhcCCCCCCEEEeC
Confidence            78999999998  67899999999999999999874 51  446999999999999999999999  99999999874

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=99.60  E-value=1.9e-15  Score=134.08  Aligned_cols=76  Identities=24%  Similarity=0.292  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|||+|+|+.|+|+.+|++|+|+++++|+|+++.++.
T Consensus        82 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---ip~~~q~L~~~G~~L~d~~tL~~y~i~~g~~l~l~~rl~GG  157 (159)
T 3rt3_B           82 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGG  157 (159)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC--
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHC---CCHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            78999999999999999999999999999999999   99999999999999999999999999999999999987753

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A

Probab=99.60  E-value=1.1e-15  Score=130.02  Aligned_cols=72  Identities=22%  Similarity=0.290  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccC-------CCcEEEE
Q 015628            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVA-------ENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g~-~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~-------~~s~I~v   72 (403)
                      |.++|+.+.++ ++.|+|++++||.+||++|+.+.|   +|+++|||||+||+|+|+++|++|||+       .+++|+|
T Consensus         1 M~mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~eg---IP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L   77 (118)
T 2fnj_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK---RPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGL   77 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEE
T ss_pred             CcEEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhC---CCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEE
Confidence            78888887776 589999999999999999999999   999999999999999999999999999       6999999


Q ss_pred             EEe
Q 015628           73 MLT   75 (403)
Q Consensus        73 ~v~   75 (403)
                      +++
T Consensus        78 ~lr   80 (118)
T 2fnj_B           78 AFR   80 (118)
T ss_dssp             EEB
T ss_pred             Eec
Confidence            998

>4ajy_B Transcription elongation factor B polypeptide 2; E3 ubiquitin ligase, transcription factor, hypoxic signaling transcription; 1.73A {Homo sapiens} PDB: 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A 3ztc_A* 3ztd_A* 3zun_A* 1lm8_B 4b95_A* 2fnj_B 4b9k_A* 4awj_A*

Probab=99.60  E-value=1.4e-15  Score=129.18  Aligned_cols=73  Identities=22%  Similarity=0.286  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCC-------CcEEEE
Q 015628            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAE-------NSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g~-~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~-------~s~I~v   72 (403)
                      |.|+|+...++ ++.++|++++||.+||++|+.+.|   +|+++|||||+||+|+|+++|++|||++       +++|+|
T Consensus         1 m~vFl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~g---iPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~L   77 (118)
T 4ajy_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK---RPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGL   77 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEE
T ss_pred             CceEEEEecCCEEEEEEcCCCChHHHHHHHHHHHHC---CCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEE
Confidence            78888887777 688999999999999999999999   9999999999999999999999999999       999999


Q ss_pred             EEec
Q 015628           73 MLTK   76 (403)
Q Consensus        73 ~v~k   76 (403)
                      +++.
T Consensus        78 vlr~   81 (118)
T 4ajy_B           78 AFRA   81 (118)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9985

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.59  E-value=1.8e-15  Score=127.09  Aligned_cols=76  Identities=24%  Similarity=0.324  Sum_probs=72.1

Q ss_pred             CEEEEEeC---CCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTL---KGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl---~g~~~~ieV~~-~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+.   +|+.+.++|++ ++||.+||++|+..+|   +|+++|||+|+|++|+|+.+|++|+|+++++|+|+++.
T Consensus        28 i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~g---ip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r~  104 (111)
T 1we6_A           28 ATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRE  104 (111)
T ss_dssp             EEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTT---CCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSS
T ss_pred             EEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHC---CCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEEc
Confidence            68999998   89999999998 9999999999999999   99999999999999999999999999999999999987


Q ss_pred             CCC
Q 015628           77 SKV   79 (403)
Q Consensus        77 ~k~   79 (403)
                      +..
T Consensus       105 ~GG  107 (111)
T 1we6_A          105 RSG  107 (111)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.59  E-value=4.4e-15  Score=119.13  Aligned_cols=70  Identities=24%  Similarity=0.436  Sum_probs=66.4

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      +++++++|+.|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++
T Consensus        14 ~~~~~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~l~~s   83 (85)
T 2kd0_A           14 KLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITN---VLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             EEEEEETTEEEEEEECTTSBHHHHHHHHHHHHC---CCTTTCEEEETTEECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             EEEEEECCEEEEEEECCCCcHHHHHHHHHHHHC---cChHHEEEEECCeECCCcCCHHHCCCCCCCEEEEEEe
Confidence            567778999999999999999999999999999   9999999999999999999999999999999999864

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.59  E-value=3.6e-15  Score=134.20  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=71.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+++.|+|++++||.+||++|+.++|   +|+++|||+|+|+.|+|+.+|++|+|+++++|+|+++.+
T Consensus        21 m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~   94 (172)
T 3u30_A           21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   94 (172)
T ss_dssp             EEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cChHHEEEEECCccccccCCHhHcCCcccceeeeeeccc
Confidence            79999999999999999999999999999999999   999999999999999999999999999999999999764

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.58  E-value=1.7e-15  Score=124.02  Aligned_cols=71  Identities=23%  Similarity=0.365  Sum_probs=65.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+|| +.|++|.|+|++++||.+||++|+.++|   +|+++|||+|+||+| |+.+|++|+|+++++|+||.++
T Consensus        18 ~~i~Vk-~~g~~~~i~v~~~~TV~~LK~~I~~~tg---ip~~~QrL~~~Gk~L-dd~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           18 VDLKII-WNKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMYKGLVP-EDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             EEEEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHC---SCSTTCCCBSSSBCC-SSSBHHHHCCCTTEEEEECCSS
T ss_pred             EEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCeeC-CcCcHHHCCCCCCCEEEEEecc
Confidence            678998 6789999999999999999999999999   999999999999999 5559999999999999998754

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.58  E-value=3e-15  Score=137.44  Aligned_cols=77  Identities=35%  Similarity=0.543  Sum_probs=73.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+|++|+|+.+|++|+|+++++|+|+++.+...
T Consensus       106 MqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~g---Ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~LvlrlrGG~  182 (189)
T 3q3f_A          106 GQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG  182 (189)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCCCCC
T ss_pred             eeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccC---CCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCCC
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999876543

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=99.58  E-value=4.7e-15  Score=131.49  Aligned_cols=73  Identities=30%  Similarity=0.420  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE-e-CCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-H-QGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi-y-~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+++|++|.++|++++||.+||++|+...|   +|+++|||+ | +|+.|+|+.+|++|+|+++++|+|+++.
T Consensus         3 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~~   77 (159)
T 3rt3_B            3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG---VHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   77 (159)
T ss_dssp             CEEEEEETTSCEEEEECCTTCCHHHHHHHHHHHHC---CCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEECC
T ss_pred             eEEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHhC---CCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEccC
Confidence            89999999999999999999999999999999999   999999999 9 7999999999999999999999999873

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.57  E-value=6.9e-15  Score=122.72  Aligned_cols=73  Identities=19%  Similarity=0.250  Sum_probs=68.4

Q ss_pred             CEEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCccccccc-CCCcEEEEEEec
Q 015628            1 MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g--~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI-~~~s~I~v~v~k   76 (403)
                      |+|+|++..+  .++.|+|++++||.+||++|++++|   +|++.|||||+|++|+|+++|.+||| ++|++|+|++-.
T Consensus        25 l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~G---ipp~~QRli~ggkll~D~~TL~~ygI~~~G~t~hL~l~~  100 (105)
T 4dbg_A           25 LWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYG---FPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLS  100 (105)
T ss_dssp             EEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEECC
T ss_pred             EEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhC---CCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEEe
Confidence            6899999885  6899999999999999999999999   99999999999999999999999999 599999999853

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p

Probab=99.56  E-value=2.7e-16  Score=135.58  Aligned_cols=76  Identities=36%  Similarity=0.555  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|++|.|+|++++||.+||.+|+...|   +|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+++.++.
T Consensus         1 M~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~~rl~GG   76 (128)
T 3u5e_m            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (128)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhC---cChHHEEEEECCEECCCCCchhhhccCCCCEEEEEEEcCCC
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999987654

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B

Probab=99.54  E-value=1.9e-14  Score=125.68  Aligned_cols=73  Identities=38%  Similarity=0.627  Sum_probs=70.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+..+|   +|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+.+.
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g---ip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~   73 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   73 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHC---cChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeec
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999864

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.4e-14  Score=122.50  Aligned_cols=73  Identities=25%  Similarity=0.282  Sum_probs=67.1

Q ss_pred             EEEEE-eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            2 KVFVK-TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         2 kI~VK-tl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      .|+|+ ...++.+.++++++.||++||++|+...+   +|++.|+|||+||+|+|+.+|++|||++|.+|||+++..
T Consensus        17 tvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~---iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~   90 (118)
T 2daf_A           17 TVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLG---IPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFST   90 (118)
T ss_dssp             EEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHT---CCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEES
T ss_pred             EEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhC---CChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecC
Confidence            45555 55688999999999999999999999999   999999999999999999999999999999999999763

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B

Probab=99.53  E-value=2.5e-14  Score=124.82  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|+.+.++|++++||.+||++|+.+.|   +|+++|+|+|+||.|+|+++|++|+|+++++|+|+++.++
T Consensus        77 ~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g---i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~r~~G  151 (152)
T 3b08_A           77 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  151 (152)
T ss_dssp             EEEEEEESSSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC
T ss_pred             cceeeeecCCCEEEEEeCCCCcHHHHHHHHHHHhC---cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            68999999999999999999999999999999999   9999999999999999999999999999999999998764

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.53  E-value=1.4e-14  Score=130.31  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |.|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|+|+|+|+.|+|+++|.+|+|+++++|+|+++.++
T Consensus        97 ~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~q~L~~~g~~L~D~~tL~~y~i~~g~tl~l~~rlrg  171 (172)
T 3u30_A           97 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  171 (172)
T ss_dssp             EEEEEEESSCCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCCEEETTEECCTTSBSGGGTCCTTCEEEECC----
T ss_pred             ccceeecccCcceeEEecCCCCHHHHHHHHHHHhC---CCceeEEEEECCccCCCCCcHHHhCCCCCCEEEEEEecCC
Confidence            57899999999999999999999999999999999   9999999999999999999999999999999999998654

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A

Probab=99.53  E-value=3e-14  Score=120.44  Aligned_cols=76  Identities=24%  Similarity=0.338  Sum_probs=69.6

Q ss_pred             CEEEEEeC----------CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEE
Q 015628            1 MKVFVKTL----------KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFV   70 (403)
Q Consensus         1 MkI~VKtl----------~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I   70 (403)
                      ++|+|+..          +|+++.|+|++++||.+||++|+...|   +|+++|||+|+|+.|+|+.+|++|+|+++++|
T Consensus        26 i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~~i  102 (115)
T 1we7_A           26 VSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATG---MPAGKQKLQYEGIFIKDSNSLAYYNMASGAVI  102 (115)
T ss_dssp             EEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSS---CCTTTEEEEETTEEECTTSBHHHHTCCSSCEE
T ss_pred             EEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHC---CChHHEEEEECCEECCCCCCHHHCCCCCCCEE
Confidence            35777764          578999999999999999999999999   99999999999999999999999999999999


Q ss_pred             EEEEecCCC
Q 015628           71 VVMLTKSKV   79 (403)
Q Consensus        71 ~v~v~k~k~   79 (403)
                      +|+++.+..
T Consensus       103 ~lv~rl~GG  111 (115)
T 1we7_A          103 HLALKERSG  111 (115)
T ss_dssp             EEEECCCSC
T ss_pred             EEEEEcCCC
Confidence            999987654

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=99.52  E-value=1.3e-15  Score=135.31  Aligned_cols=77  Identities=35%  Similarity=0.549  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      |+|+||+++|+++.|+|++++||.+||.+|+...|   +|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+++.+...
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GGg   77 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG   77 (152)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCCC
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999876543

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=1.5e-14  Score=117.01  Aligned_cols=69  Identities=20%  Similarity=0.265  Sum_probs=63.2

Q ss_pred             CEEEEEeCCCcEE--EE-EeCCCCcHHHHHHHHHHH-hCCCCCCCCCcEEEeC--CeecCCCCcccccccCCCcEEEE
Q 015628            1 MKVFVKTLKGTHF--EI-EVKPEDKVSDVKKNIETV-QGSDVYPASQQMLIHQ--GKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g~~~--~i-eV~~~~TV~dLK~kI~~~-~g~~~ip~~~QkLiy~--GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      |+|+||+++|+.+  .| +|++++||.+||++|++. .|   +++++|||+|.  ||+|+|+++|++|+|+++++|+|
T Consensus        11 M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~---i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           11 YEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQ---WYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             EEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSS---SCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             EEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcC---CChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            7999999998775  58 999999999999999995 67   99999999976  99999999999999999999765

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=4.6e-14  Score=116.92  Aligned_cols=71  Identities=20%  Similarity=0.314  Sum_probs=65.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEe--CCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy--~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |.+++++++|+++.|+|++++||.+||.+|++++|   +|+++|||+|  .|+ |+|+.+|++|+|+.+++|||++.
T Consensus         9 m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tg---Ipp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~   81 (100)
T 2dzm_A            9 MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQ---IPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTP   81 (100)
T ss_dssp             EEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHC---CCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCS
T ss_pred             eEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHC---CChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEec
Confidence            56777889999999999999999999999999999   9999999996  566 99999999999999999998764

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.44  E-value=1.5e-13  Score=134.67  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=69.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|+.+.|+|++++||.+||++|+.+.|   +|+++|||+|+||+|+|+++|++|+|+++++|+|+++.+
T Consensus       234 MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~G---Ip~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRLr  307 (307)
T 3ai5_A          234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  307 (307)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC---
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            78999999999999999999999999999999999   999999999999999999999999999999999998753

>2lbc_A Ubiquitin carboxyl-terminal hydrolase 13; tandem UBA of USP13; NMR {Homo sapiens}

Probab=99.41  E-value=7.4e-13  Score=113.93  Aligned_cols=41  Identities=29%  Similarity=0.471  Sum_probs=38.2

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCC-CC
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH-EF  401 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~-d~  401 (403)
                      +.|++|++|||+|+.|++||.+|++|++.|++|||++.. |.
T Consensus        80 ~~v~~L~~MGF~~~~a~~AL~~~~~~~e~A~e~L~~~~~~d~  121 (126)
T 2lbc_A           80 EIVAIITSMGFQRNQAIQALRATNNNLERALDWIFSHPEFEE  121 (126)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHTSCHHHHHHHHHTCCSSCC
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCCcc
Confidence            569999999999999999999999999999999999877 53

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.40  E-value=3.2e-13  Score=112.89  Aligned_cols=71  Identities=20%  Similarity=0.234  Sum_probs=65.6

Q ss_pred             CEEEEEeCCCcEEEEEeC-CCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCe-----------e----cCCCCccccccc
Q 015628            1 MKVFVKTLKGTHFEIEVK-PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-----------V----LKDVTTLEENKV   64 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~-~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~Gk-----------i----L~D~~tLsd~gI   64 (403)
                      |+|+||+.+|+. .|+|+ +++||.+||++|+.+++   +|++.|+|+|.|+           .    ++|+++|++|||
T Consensus         8 M~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~g---ip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi   83 (107)
T 1wf9_A            8 TMLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQ---IPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNL   83 (107)
T ss_dssp             EEEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSC---CCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCC
T ss_pred             EEEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHhC---cCcccCEEEECCccccccCccccccccccCCCCCCHHHCCC
Confidence            789999999965 79999 99999999999999999   9999999999988           3    588999999999


Q ss_pred             CCCcEEEEEEe
Q 015628           65 AENSFVVVMLT   75 (403)
Q Consensus        65 ~~~s~I~v~v~   75 (403)
                      ++|++|||+..
T Consensus        84 ~~G~~L~l~~~   94 (107)
T 1wf9_A           84 AHGSMVYLAYE   94 (107)
T ss_dssp             CTTCEEECCCS
T ss_pred             CCCCEEEEEeC
Confidence            99999998865

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.40  E-value=2e-13  Score=109.96  Aligned_cols=73  Identities=15%  Similarity=0.070  Sum_probs=64.0

Q ss_pred             EEEEE--eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEe-------CCeecCCCCcccccccCCCcEEEE
Q 015628            2 KVFVK--TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-------QGKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         2 kI~VK--tl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy-------~GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      +|.|.  ..+.+.+++.+++++||.+||.+|+.++|   +|+++|||||       .|+.|+|+++|++|+|++|++|||
T Consensus         4 ~v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~~G---ip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihl   80 (86)
T 4b6w_A            4 KVSLTHSASRMRVPEKRYGLAQTIESIKENVFTHFA---TPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHV   80 (86)
T ss_dssp             EEEEEETTCSCCEEEEEEETTSBHHHHHHHHHTTSC---CCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEE
T ss_pred             EEEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHHHC---CCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEE
Confidence            44554  34567789999999999999999999999   9999999997       589999999999999999999999


Q ss_pred             EEecC
Q 015628           73 MLTKS   77 (403)
Q Consensus        73 ~v~k~   77 (403)
                      +-+.|
T Consensus        81 vd~~P   85 (86)
T 4b6w_A           81 VDLQP   85 (86)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            97643

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.39  E-value=8.9e-13  Score=108.13  Aligned_cols=70  Identities=17%  Similarity=0.195  Sum_probs=62.2

Q ss_pred             CEEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeC--Ce---ec-CCCCcccccccCCCcEEEE
Q 015628            1 MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GK---VL-KDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g--~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~--Gk---iL-~D~~tLsd~gI~~~s~I~v   72 (403)
                      ++|+|+...+  +.++++|++++||.+||++|+.++|   +|+++|||+|.  |+   .| +|+++|++|+|++|++|+|
T Consensus        16 v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~G---iP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihl   92 (95)
T 2kjr_A           16 IKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTG---GCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHV   92 (95)
T ss_dssp             EEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHC---SCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEE
T ss_pred             EEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHC---cCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEE
Confidence            3677887655  4789999999999999999999999   99999999997  55   34 8999999999999999998


Q ss_pred             E
Q 015628           73 M   73 (403)
Q Consensus        73 ~   73 (403)
                      +
T Consensus        93 v   93 (95)
T 2kjr_A           93 V   93 (95)
T ss_dssp             E
T ss_pred             E
Confidence            7

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.36  E-value=6.4e-14  Score=128.28  Aligned_cols=71  Identities=21%  Similarity=0.257  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|++|.|+|++++||.+||.+|+...|   +|+++|+|||+|++|+|+.+|+     ++++|+|+++.+..
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keG---IP~~qQRLIf~GK~LeD~~TLs-----~~STLhLvlRLrGG   71 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMG---FEIDMMTLVNNGFIAPNTELVT-----DDVTYYLSLKLLGG   71 (189)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhC---cChhHEEEEecCeECCCCCccc-----CCCEEEEEEecCCC
Confidence            89999999999999999999999999999999999   9999999999999999999998     88999999987653

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.35  E-value=1.7e-12  Score=106.88  Aligned_cols=71  Identities=11%  Similarity=0.040  Sum_probs=62.2

Q ss_pred             EEEEEeCC--CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCC---ee----cCCCCcccccccCCCcEEEE
Q 015628            2 KVFVKTLK--GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         2 kI~VKtl~--g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~G---ki----L~D~~tLsd~gI~~~s~I~v   72 (403)
                      +|+|+...  ++.++++|++++||.+||++|+.++|   +|+++|||+|.|   +.    ++|+++|++|+|++|++|+|
T Consensus        16 ~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~G---ip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ihl   92 (97)
T 2kj6_A           16 HLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCG---TSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLHI   92 (97)
T ss_dssp             EEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHC---CCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEEE
T ss_pred             EEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHC---cCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEEE
Confidence            56777543  35789999999999999999999999   999999999988   33    58899999999999999999


Q ss_pred             EEe
Q 015628           73 MLT   75 (403)
Q Consensus        73 ~v~   75 (403)
                      +-.
T Consensus        93 vd~   95 (97)
T 2kj6_A           93 IDL   95 (97)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            854

>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B, tubulin folding cofactor B, microtubule, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.34  E-value=2e-12  Score=105.57  Aligned_cols=73  Identities=22%  Similarity=0.209  Sum_probs=63.5

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCC---ee----cCCCCcccccccCCCcEEEE
Q 015628            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g~-~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~G---ki----L~D~~tLsd~gI~~~s~I~v   72 (403)
                      ++|+|+..... .++++|++++||.+||++|+.++|   +|+++|||+|.|   +.    ++|+++|.+|||+++++|||
T Consensus         8 v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~g---ip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v   84 (95)
T 1v6e_A            8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVG---SPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHV   84 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTC---SCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEE
T ss_pred             EEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHC---CCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEE
Confidence            36778875553 689999999999999999999999   999999999986   54    58999999999999999998


Q ss_pred             EEec
Q 015628           73 MLTK   76 (403)
Q Consensus        73 ~v~k   76 (403)
                      +-..
T Consensus        85 ~d~~   88 (95)
T 1v6e_A           85 IDHS   88 (95)
T ss_dssp             BCCS
T ss_pred             EECC
Confidence            8643

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.33  E-value=1.8e-12  Score=103.89  Aligned_cols=71  Identities=17%  Similarity=0.304  Sum_probs=63.6

Q ss_pred             CEEEEEeCCCcEEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeC--CeecC---CCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GKVLK---DVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ie-V~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~--GkiL~---D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+||+.+|+. .|+ |++++||.+||.+|+++.|   +++++|+|+|+  +|.|.   |+++|++|||++|++|+|..
T Consensus         1 m~i~vr~~~G~~-~v~~l~~~~Tv~~Lk~~I~~~~g---i~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~   76 (86)
T 2kzr_A            1 WRVRCKAKGGTH-LLQGLSSRTRLRELQGQIAAITG---IAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEE   76 (86)
T ss_dssp             CCEEEEETTEEE-EECSCCTTCBHHHHHHHHHHHTC---CCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCC
T ss_pred             CEEEEEcCCCCE-EeeecCCCCCHHHHHHHHHHHhC---CCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEe
Confidence            899999999964 477 9999999999999999999   99999999987  48874   68899999999999998875


Q ss_pred             e
Q 015628           75 T   75 (403)
Q Consensus        75 ~   75 (403)
                      .
T Consensus        77 ~   77 (86)
T 2kzr_A           77 D   77 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=99.27  E-value=7.5e-12  Score=102.40  Aligned_cols=76  Identities=14%  Similarity=0.206  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+.+|+.+.+.|.+++++..||++++++.|   +++..+||+|.|+.|.++.|+++|++.++++|+|+++....
T Consensus         8 i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~g---i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~GG   83 (94)
T 2io1_B            8 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG---LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   83 (94)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCEES
T ss_pred             EEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhC---CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            68999999999999999999999999999999999   99999999999999999999999999999999999987654

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.26  E-value=4.3e-12  Score=125.39  Aligned_cols=71  Identities=18%  Similarity=0.288  Sum_probs=65.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE---eCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi---y~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+|| ++|++|.|+|++++||.+||++|++++|   +|+++||||   |+||+|+|+.+|++|+|++|++|+||.+
T Consensus         6 i~i~Vk-~~g~~~~v~v~~~~Tv~~lK~~I~~~tg---Vpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs   79 (320)
T 3shq_A            6 VVVIVK-WSGKEYPVDLTDQDTVEVLRHEIFRKTQ---VRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGS   79 (320)
T ss_dssp             EEEEEE-ETTEEEEEEEETTSBHHHHHHHHHHHHC---CCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECC
T ss_pred             EEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEcc
Confidence            578999 6899999999999999999999999999   999999999   8999999999999999999999999964

>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.26  E-value=6.5e-12  Score=88.13  Aligned_cols=40  Identities=23%  Similarity=0.327  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  215 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GI  215 (403)
                      .++.|++|++||   |+|++|++||++++||+++|++||++||
T Consensus         4 ~e~~i~~L~~MG---F~~~~a~~AL~~~~~n~e~A~~~L~~~~   43 (43)
T 2g3q_A            4 KSLAVEELSGMG---FTEEEAHNALEKCNWDLEAATNFLLDSA   43 (43)
T ss_dssp             HHHHHHHHHTTT---SCHHHHHHHHHHHTSCHHHHHHHHHTCC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCcCHHHHHHHHHcCC
Confidence            368999999999   9999999999999999999999999986

>1vej_A Riken cDNA 4931431F19; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.25  E-value=1.1e-11  Score=96.80  Aligned_cols=46  Identities=17%  Similarity=0.340  Sum_probs=42.6

Q ss_pred             CccHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcCCCCC
Q 015628          170 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIPEQ  218 (403)
Q Consensus       170 g~~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~GIP~~  218 (403)
                      ...|+..|++|++||   | +|+.+++||+++++|++||||||++|||+.
T Consensus        26 e~~ye~qi~qL~eMG---F~dr~~~~~AL~~t~Gnve~Ave~L~~~~~~~   72 (74)
T 1vej_A           26 EGRYQQELEELKALG---FANRDANLQALVATDGDIHAAIEMLLGASGPS   72 (74)
T ss_dssp             TTTSHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHTCCCCC
T ss_pred             hHHHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHhCCCCC
Confidence            356899999999999   9 899999999999999999999999998863

>1vg5_A RSGI RUH-014, rhomboid family protein; UBA domain, cDNA, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=99.25  E-value=7.2e-12  Score=97.68  Aligned_cols=43  Identities=37%  Similarity=0.424  Sum_probs=40.2

Q ss_pred             ccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCC
Q 015628          171 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  216 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP  216 (403)
                      +.+++.|++||+||   |+|++|++|||+++||++||||||++|+.
T Consensus        27 ~~~ee~I~~L~eMG---F~r~~a~~AL~~~~~nve~Ave~Ll~~~~   69 (73)
T 1vg5_A           27 AASEEQIQKLVAMG---FDRTQVEVALAAADDDLTVAVEILMSQSG   69 (73)
T ss_dssp             CCCHHHHHHHHTTT---CCHHHHHHHHHHHTSCHHHHHHHHHTCSC
T ss_pred             cccHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHHCCC
Confidence            45789999999999   99999999999999999999999999854

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1

Probab=99.24  E-value=1.7e-11  Score=104.69  Aligned_cols=74  Identities=14%  Similarity=0.130  Sum_probs=64.2

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCC---ee----cCCCCcccccccCCCcEEEE
Q 015628            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g~-~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~G---ki----L~D~~tLsd~gI~~~s~I~v   72 (403)
                      |+|+|+...+. .++++|++++||.+||.+|+..+|   +|+++|||+|.|   +.    ++|+++|.+|||++|++|||
T Consensus         7 v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~G---ip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihv   83 (122)
T 1t0y_A            7 YDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVG---TTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHA   83 (122)
T ss_dssp             EEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHC---CCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEE
T ss_pred             EEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhC---CCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEE
Confidence            46778876553 688999999999999999999999   999999999977   43    48899999999999999999


Q ss_pred             EEecC
Q 015628           73 MLTKS   77 (403)
Q Consensus        73 ~v~k~   77 (403)
                      +...+
T Consensus        84 vd~~p   88 (122)
T 1t0y_A           84 VDVTG   88 (122)
T ss_dssp             EECTT
T ss_pred             EeCCC
Confidence            97543

>4ae4_A Ubiquitin-associated protein 1; protein transport, endosomal sorting, tetherin, VPU, HIV-1, monoubiquitin; HET: NHE; 1.65A {Homo sapiens} PDB: 4ae4_B*

Probab=99.23  E-value=4.4e-11  Score=101.77  Aligned_cols=40  Identities=23%  Similarity=0.374  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          358 EEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       358 ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      +....|.+|++|||++.+|.+|+..|+.|.+.|+.|||..
T Consensus        75 ~~~~~v~~L~eMGF~~~~a~~AL~~~~nd~erAlewL~~~  114 (118)
T 4ae4_A           75 EFLQLMSKFKEMGFELKDIKEVLLLHNNDQDNALEDLMAR  114 (118)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence            4557899999999999999999999999999999999975

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=99.22  E-value=4.1e-11  Score=93.01  Aligned_cols=71  Identities=15%  Similarity=0.227  Sum_probs=68.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+||+.+|+.+.+.|.+++++..|+++++++.|   +++..+||+|.|+.|.++.|.++|++.+|++|+|++
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~g---i~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~~   72 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG---LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQ   72 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHT---CCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC---CCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEC
Confidence            68999999999999999999999999999999999   999999999999999999999999999999999874

>2bwb_A Ubiquitin-like protein DSK2; UBA, signaling protein; 2.3A {Saccharomyces cerevisiae} SCOP: a.5.2.1 PDB: 2bwe_A

Probab=99.21  E-value=1.6e-11  Score=87.42  Aligned_cols=41  Identities=29%  Similarity=0.464  Sum_probs=38.1

Q ss_pred             ccHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          171 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      ..++..|++|++||   | +|+.+++||+++++|++||||||++|
T Consensus         5 ~~~~~~i~~L~~MG---F~d~~~~~~AL~~~~gnv~~Ave~L~~~   46 (46)
T 2bwb_A            5 ERYEHQLRQLNDMG---FFDFDRNVAALRRSGGSVQGALDSLLNG   46 (46)
T ss_dssp             HHTHHHHHHHHHTT---CCCHHHHHHHHHHHTTCHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHcc
Confidence            34789999999999   9 79999999999999999999999986

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1

Probab=99.20  E-value=5.8e-11  Score=96.56  Aligned_cols=75  Identities=15%  Similarity=0.224  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+.+|+.+.+.|.+++++..||+.++++.|   +++..+||+|.|+.|.++.|.++|++.++++|.|++...+
T Consensus         6 i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~g---i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~g   80 (91)
T 2io0_B            6 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG---LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTG   80 (91)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTT---CCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC---CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            57899999999999999999999999999999999   9999999999999999999999999999999999987655

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.16  E-value=1.2e-10  Score=92.01  Aligned_cols=70  Identities=13%  Similarity=0.236  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~-~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      |+|+|++.+|+ .+.+.|..++++..||+.++++.|   ++++.+||+|.|+.|.++.|.++|++.++++|+|+
T Consensus         8 i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~g---i~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A            8 LRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMG---LSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             EEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHT---CTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             EEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhC---CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            67999999996 899999999999999999999999   99999999999999999999999999999999987

>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.16  E-value=3.1e-11  Score=84.64  Aligned_cols=38  Identities=37%  Similarity=0.541  Sum_probs=36.4

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          360 REAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       360 ~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      .++|++|++|||+|++|++||.+|++|++.|++|||++
T Consensus         5 e~~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~L~~~   42 (43)
T 2g3q_A            5 SLAVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDS   42 (43)
T ss_dssp             HHHHHHHHTTTSCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCcCHHHHHHHHHcC
Confidence            47899999999999999999999999999999999986

>2knz_A Ubiquilin-4; cytoplasm, endoplasmic reticulum, nucleus, phosphoprotein, protein binding; NMR {Mus musculus}

Probab=99.16  E-value=3.3e-11  Score=88.39  Aligned_cols=43  Identities=26%  Similarity=0.375  Sum_probs=40.6

Q ss_pred             ccHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcCCC
Q 015628          171 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIP  216 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~GIP  216 (403)
                      ..|+..|++|++||   | +|+.+++||++++||.+||||||++|++
T Consensus         9 ~~~~~~l~~L~~MG---F~~~~~~~~AL~~t~gnve~Ave~L~~~~~   52 (53)
T 2knz_A            9 VRFQQQLEQLNSMG---FINREANLQALIATGGDINAAIERLLGSQL   52 (53)
T ss_dssp             HHHHHHHHHHHTTT---CCCHHHHHHHHHHHTSCHHHHHHHHHHCCC
T ss_pred             hHHHHHHHHHHHcC---CCCHHHHHHHHHHhCCCHHHHHHHHHHcCC
Confidence            45889999999999   9 9999999999999999999999999865

>1veg_A NEDD8 ultimate buster-1; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.16  E-value=3.9e-11  Score=95.59  Aligned_cols=44  Identities=27%  Similarity=0.381  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc--C-CCCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS--G-IPEQT  219 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~--G-IP~~~  219 (403)
                      .+..|++||+||   |+|++|++|||+++||++||+|||++  | ||+.+
T Consensus        29 ~ee~I~~Lv~MG---F~~~~A~~AL~~t~gdve~A~e~L~sh~~~ip~~~   75 (83)
T 1veg_A           29 SQESINQLVYMG---FDTVVAEAALRVFGGNVQLAAQTLAHHGGSLPPDL   75 (83)
T ss_dssp             CHHHHHHHHHHS---CCHHHHHHHHHHTTTCHHHHHHHHHHHTSSCCTTS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCCCchhh
Confidence            478999999999   99999999999999999999999999  7 77654

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=99.14  E-value=1.2e-10  Score=95.07  Aligned_cols=74  Identities=15%  Similarity=0.231  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+|++.+|+.+.+.|..++++..|+..++++.|   ++++.+||+|.|+.|.++.|+.+|++.++++|+|++...
T Consensus        18 i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~g---i~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q~   91 (93)
T 2d07_B           18 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG---LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT   91 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC-
T ss_pred             EEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhC---CCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeecc
Confidence            57889999999999999999999999999999999   899999999999999999999999999999999998754

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.14  E-value=1.2e-10  Score=97.07  Aligned_cols=76  Identities=14%  Similarity=0.211  Sum_probs=71.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+|++.+|+.+.+.|..++++..||..++++.|   +++..+||+|.|+.|.++.|+.+|++.++++|+|++.....
T Consensus        25 I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~g---i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~GG  100 (104)
T 1wz0_A           25 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG---LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTSG  100 (104)
T ss_dssp             EEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHT---CCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCCCC
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhC---CCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            57899999999999999999999999999999999   99999999999999999999999999999999999876553

>2jy5_A Ubiquilin-1; UBA, alternative splicing, cytoplasm, nucleus, phosphoprotein, proteasome, signaling protein; NMR {Homo sapiens} PDB: 2jy6_B

Probab=99.12  E-value=9.2e-11  Score=85.68  Aligned_cols=41  Identities=27%  Similarity=0.428  Sum_probs=38.9

Q ss_pred             ccHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          171 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      ..++..|++|++||   | +|+.+++||++++||++||||||++|
T Consensus        10 ~~~~~~l~~L~~MG---F~~~~~~~~AL~~t~gn~e~A~e~L~~~   51 (52)
T 2jy5_A           10 VRFQQQLEQLSAMG---FLNREANLQALIATGGDINAAIERLLGS   51 (52)
T ss_dssp             TTTHHHHHHHHHTT---CCCHHHHHHHHHHHTTCHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHHcC---CCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            45889999999999   9 99999999999999999999999876

>1wji_A Tudor domain containing protein 3; UBA domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.10  E-value=8.8e-11  Score=89.14  Aligned_cols=42  Identities=29%  Similarity=0.369  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  217 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~  217 (403)
                      .++.|++|++||   |+|++|++|||+++||++||+|||+++..+
T Consensus         9 ~~~~I~~L~~MG---F~~~~a~~AL~~~~~nve~A~e~L~~~~~~   50 (63)
T 1wji_A            9 DEKALKHITEMG---FSKEASRQALMDNGNNLEAALNVLLTSNKQ   50 (63)
T ss_dssp             CHHHHHHHHTTT---CCHHHHHHHHHHTTSCHHHHHHHHHHHSSC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHHCCCC
Confidence            478999999999   999999999999999999999999998543

>1wr1_B Ubiquitin-like protein DSK2; UBA domain, UBA-ubiquitin complex, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.06  E-value=1.3e-10  Score=86.78  Aligned_cols=41  Identities=29%  Similarity=0.464  Sum_probs=38.9

Q ss_pred             ccHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          171 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      ..++..|++|++||   | +|+.+++||+++++|++||||||++|
T Consensus        15 ~~~~~qi~~L~~MG---F~d~~~~~~AL~~~~gnve~Ave~L~~~   56 (58)
T 1wr1_B           15 ERYEHQLRQLNDMG---FFDFDRNVAALRRSGGSVQGALDSLLNG   56 (58)
T ss_dssp             HHTHHHHHHHHHHT---CCCHHHHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            56889999999999   9 79999999999999999999999988

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.06  E-value=2.3e-10  Score=96.26  Aligned_cols=75  Identities=15%  Similarity=0.248  Sum_probs=70.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+|++.+|+.+.+.|..++++..||+.++++.|   +++..+||+|.|+.|.++.|..+|++.++++|.|++....
T Consensus        27 I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~g---i~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q~G  101 (110)
T 2k8h_A           27 VAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQG---ISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQTG  101 (110)
T ss_dssp             EEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHT---CCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC---CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcccC
Confidence            57999999999999999999999999999999999   9999999999999999999999999999999999987543

>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.06  E-value=1.6e-10  Score=88.40  Aligned_cols=45  Identities=18%  Similarity=0.198  Sum_probs=41.2

Q ss_pred             ccHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcCCCCC
Q 015628          171 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIPEQ  218 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~GIP~~  218 (403)
                      ..|+..|++|++||   | +|+.+++|||++++|++||||||++++++.
T Consensus        17 ~~y~~ql~qL~~MG---F~d~~an~~AL~at~Gnve~Ave~L~~~~~~~   62 (67)
T 2dna_A           17 VRFSKEMECLQAMG---FVNYNANLQALIATDGDTNAAIYKLKSSQGFS   62 (67)
T ss_dssp             HHTHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHHCCSSS
T ss_pred             HHHHHHHHHHHHcC---CCcHHHHHHHHHHcCCCHHHHHHHHHhCCCcc
Confidence            45788999999999   9 788889999999999999999999998863

>1wji_A Tudor domain containing protein 3; UBA domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.05  E-value=1.4e-10  Score=88.01  Aligned_cols=43  Identities=23%  Similarity=0.366  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEF  401 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~  401 (403)
                      +.++|++|++|||+|++|++||.+|++|.+.|++|||++..+.
T Consensus         9 ~~~~I~~L~~MGF~~~~a~~AL~~~~~nve~A~e~L~~~~~~~   51 (63)
T 1wji_A            9 DEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQK   51 (63)
T ss_dssp             CHHHHHHHHTTTCCHHHHHHHHHHTTSCHHHHHHHHHHHSSCC
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHCCCCc
Confidence            4578999999999999999999999999999999999986553

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1

Probab=99.04  E-value=4e-10  Score=94.12  Aligned_cols=73  Identities=11%  Similarity=0.157  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+|++ +|+.+.+.|..++++..||+.++++.|   +++..+||+|.|+.|.++.|..+|++.++++|.|+++..
T Consensus        32 I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~g---i~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q~  104 (106)
T 2eke_C           32 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQI  104 (106)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC-
T ss_pred             EEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhC---CCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeecc
Confidence            5788999 999999999999999999999999999   899999999999999999999999999999999998754

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.04  E-value=1.1e-10  Score=88.56  Aligned_cols=43  Identities=40%  Similarity=0.677  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  218 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~~  218 (403)
                      .++.|++|++||   |+|++|++|||+++||++||+|||+.++++.
T Consensus         9 ~~~~v~~L~~MG---F~~~~a~~AL~~t~~nve~A~e~L~~~~~d~   51 (63)
T 2dak_A            9 PEDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSHIDDL   51 (63)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTSCSHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCCc
Confidence            578999999999   9999999999999999999999999997753

>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=99.01  E-value=3.5e-10  Score=88.30  Aligned_cols=40  Identities=20%  Similarity=0.479  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  215 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GI  215 (403)
                      .++.|++|++||   |+|++|++|||+++||++||||||+++.
T Consensus        29 ~~~~v~~L~~MG---F~~~~a~~AL~~t~~nve~Ave~L~~~~   68 (73)
T 1wiv_A           29 DQSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFNNS   68 (73)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence            478999999999   9999999999999999999999999884

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.99  E-value=1e-09  Score=89.66  Aligned_cols=72  Identities=18%  Similarity=0.238  Sum_probs=61.9

Q ss_pred             EEEEEe---CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCC------ee-c-CCCCcccccccCCCcEE
Q 015628            2 KVFVKT---LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG------KV-L-KDVTTLEENKVAENSFV   70 (403)
Q Consensus         2 kI~VKt---l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~G------ki-L-~D~~tLsd~gI~~~s~I   70 (403)
                      +|+|+.   .+|+.+++.+..++||.+||.+|+..+|   +|+..|||+|.+      .+ | +|..+|.+|+|.+|++|
T Consensus        11 ~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~g---ip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I   87 (97)
T 1wjn_A           11 TLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLK---VPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCL   87 (97)
T ss_dssp             EEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTT---CCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEE
T ss_pred             EEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHC---CChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEE
Confidence            566765   4678899999999999999999999999   999999999863      22 5 66789999999999999


Q ss_pred             EEEEec
Q 015628           71 VVMLTK   76 (403)
Q Consensus        71 ~v~v~k   76 (403)
                      ||....
T Consensus        88 ~V~d~~   93 (97)
T 1wjn_A           88 LVRWSG   93 (97)
T ss_dssp             EEECCS
T ss_pred             EEEecC
Confidence            998754

>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} SCOP: a.5.2.1

Probab=98.99  E-value=4.7e-10  Score=77.02  Aligned_cols=39  Identities=28%  Similarity=0.480  Sum_probs=36.2

Q ss_pred             ccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHH
Q 015628          171 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  212 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~  212 (403)
                      +++++.|++|++||   |+|+++++||+++.+|+++|++||+
T Consensus         2 ~~~~~~i~~L~~mG---f~~~~a~~AL~~~~~n~e~A~~~L~   40 (40)
T 1z96_A            2 PGLNSKIAQLVSMG---FDPLEAAQALDAANGDLDVAASFLL   40 (40)
T ss_dssp             -CHHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             chHHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHC
Confidence            35788999999999   9999999999999999999999994

>2crn_A Ubash3A protein; compact three-helix bundle, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.98  E-value=2.8e-10  Score=86.65  Aligned_cols=43  Identities=23%  Similarity=0.365  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHcCCCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  218 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~GIP~~  218 (403)
                      .+..|++|++||   |+|+.|++||++++| |+++|++||+.++++.
T Consensus         9 ~e~~v~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~wL~~h~~d~   52 (64)
T 2crn_A            9 SPSLLEPLLAMG---FPVHTALKALAATGRKTAEEALAWLHDHCNDP   52 (64)
T ss_dssp             SCSSHHHHHHTS---CCHHHHHHHHHHHTSCCHHHHHHHHHHHSSST
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCCHHHHHHHHHhCCCCc
Confidence            456899999999   999999999999999 9999999999998753

>1vg5_A RSGI RUH-014, rhomboid family protein; UBA domain, cDNA, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=98.98  E-value=4e-10  Score=87.79  Aligned_cols=48  Identities=27%  Similarity=0.362  Sum_probs=43.5

Q ss_pred             ccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          353 VTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       353 ~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      .+.+++..++|++|++|||+|++|++||.+|++|.+.|++|||++...
T Consensus        23 ~~~~~~~ee~I~~L~eMGF~r~~a~~AL~~~~~nve~Ave~Ll~~~~p   70 (73)
T 1vg5_A           23 QGRVAASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQSGP   70 (73)
T ss_dssp             CCCSCCCHHHHHHHHTTTCCHHHHHHHHHHHTSCHHHHHHHHHTCSCS
T ss_pred             ccCCcccHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHCCCC
Confidence            467777788999999999999999999999999999999999987543

>2dkl_A Trinucleotide repeat containing 6C protein; TNRC6C, KIAA1582 protein, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.97  E-value=6.5e-10  Score=89.19  Aligned_cols=44  Identities=27%  Similarity=0.336  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~~  402 (403)
                      +.++|++|++|||+|+.|++||.+|++|++.|++|||+|.+|.|
T Consensus        21 n~~~I~qL~~MGF~~~~a~~AL~~~n~n~e~A~ewL~~h~~D~D   64 (85)
T 2dkl_A           21 MSRLIKQLTDMGFPREPAEEALKSNNMNLDQAMSALLEKKVDVD   64 (85)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHTTSCCSS
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHCcCCcc
Confidence            35679999999999999999999999999999999999988866

>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.97  E-value=5.5e-10  Score=83.06  Aligned_cols=49  Identities=27%  Similarity=0.421  Sum_probs=45.9

Q ss_pred             cccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          352 AVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       352 ~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      ...|++.|.++|+.|+.|||++++|+.|+-+|+.|.|.|++|||+|+.-
T Consensus        12 l~~ls~se~e~V~~LvsMGFs~~qA~kALKat~~NvErAaDWLFSH~D~   60 (63)
T 1wgn_A           12 LQMLSPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHSGP   60 (63)
T ss_dssp             HHTCCHHHHHHHHHHHHHHCCHHHHHHHHHHHCSCHHHHHHHHHHHSCC
T ss_pred             HHhhCcchHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence            4579999999999999999999999999999999999999999998653

>2cpw_A CBL-interacting protein STS-1 variant; ubiquitin associated domain, UBA, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.97  E-value=5.8e-10  Score=84.87  Aligned_cols=42  Identities=24%  Similarity=0.359  Sum_probs=39.2

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHhccCCCCC
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNK-NEELAANYLLDHMHEFE  402 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~-ne~~a~~~L~~~~~d~~  402 (403)
                      +.|++|++|||+++.|++||.+|++ |++.|++|||++..|.|
T Consensus        21 ~~i~~L~~MGF~~~~a~~AL~~t~~~nve~A~ewL~~~~~d~d   63 (64)
T 2cpw_A           21 SALDVLLSMGFPRARAQKALASTGGRSVQTACDWLFSHSGPSS   63 (64)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHTTTSCHHHHHHHHHSCCSCCC
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCCCC
Confidence            5799999999999999999999997 99999999999987755

>2dag_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5 (USP 5), UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.96  E-value=6.7e-10  Score=86.89  Aligned_cols=43  Identities=21%  Similarity=0.370  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHcCCCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  218 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~GIP~~  218 (403)
                      .+..|++|++||   |+|++|++|||+++| |.++|+|||+.++++.
T Consensus         9 ~e~~v~~L~~MG---F~~~~a~~AL~~t~n~~ve~A~ewL~~~~~d~   52 (74)
T 2dag_A            9 DESVIIQLVEMG---FPMDACRKAVYYTGNSGAEAAMNWVMSHMDDP   52 (74)
T ss_dssp             CHHHHHHHHHHS---CCHHHHHHHHHHHTSCCHHHHHHHHHHHTTST
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCCHHHHHHHHHhCCCCc
Confidence            478999999999   999999999999997 7999999999998754

>1whc_A RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain, structural genomics, riken structural genomics/proteomics initiative, unknown function; NMR {Mus musculus} SCOP: a.5.2.1

Probab=98.96  E-value=4.2e-10  Score=85.66  Aligned_cols=42  Identities=19%  Similarity=0.344  Sum_probs=38.4

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhh-CChHHHHHHHHcCCCCC
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAY-NNPERAVEYLYSGIPEQ  218 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAaf-nNPdRAvEyL~~GIP~~  218 (403)
                      +..|++|++||   |+|++|++|||+++ +|+++|++||+.++++.
T Consensus        10 ~~~v~~L~~MG---F~~~~a~~AL~~t~~~nve~A~ewLl~~~~d~   52 (64)
T 1whc_A           10 LTALESLIEMG---FPRGRAEKALALTGNQGIEAAMDWLMEHEDDP   52 (64)
T ss_dssp             CCHHHHHHTTT---CCHHHHHHHHHHHTSCCHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhcCCCHHHHHHHHHhCCCCc
Confidence            35899999999   99999999999995 89999999999997754

>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} SCOP: a.5.2.1

Probab=98.95  E-value=7.2e-10  Score=76.07  Aligned_cols=39  Identities=33%  Similarity=0.488  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHh
Q 015628          357 PEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLL  395 (403)
Q Consensus       357 ~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~  395 (403)
                      ++..++|++|++|||++++|++||.+|++|.+.|++|||
T Consensus         2 ~~~~~~i~~L~~mGf~~~~a~~AL~~~~~n~e~A~~~L~   40 (40)
T 1z96_A            2 PGLNSKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL   40 (40)
T ss_dssp             -CHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             chHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHC
Confidence            345678999999999999999999999999999999997

>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.94  E-value=8.4e-10  Score=79.56  Aligned_cols=41  Identities=27%  Similarity=0.427  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          357 PEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       357 ~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      ++..+.|++|++|||+|++|+.||.+|++|.+.|++|||++
T Consensus         6 ~~~~~~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~e~L~~g   46 (49)
T 1ify_A            6 SEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTG   46 (49)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHTTTSCSHHHHHHHHHC
T ss_pred             ccCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            45667899999999999999999999999999999999986

>2cpw_A CBL-interacting protein STS-1 variant; ubiquitin associated domain, UBA, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.94  E-value=5.5e-10  Score=85.02  Aligned_cols=40  Identities=23%  Similarity=0.408  Sum_probs=37.4

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHcCCC
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIP  216 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~GIP  216 (403)
                      +..|++|++||   |+|++|++|||++.| |+++|+|||++++-
T Consensus        20 e~~i~~L~~MG---F~~~~a~~AL~~t~~~nve~A~ewL~~~~~   60 (64)
T 2cpw_A           20 GSALDVLLSMG---FPRARAQKALASTGGRSVQTACDWLFSHSG   60 (64)
T ss_dssp             CCHHHHHHHHT---CCHHHHHHHHHHTTTSCHHHHHHHHHSCCS
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHcCCCCHHHHHHHHHhCCC
Confidence            46899999999   999999999999998 99999999998854

>2dag_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5 (USP 5), UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.93  E-value=7.8e-10  Score=86.53  Aligned_cols=44  Identities=23%  Similarity=0.417  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHhccCCCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNK-NEELAANYLLDHMHEFE  402 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~-ne~~a~~~L~~~~~d~~  402 (403)
                      +.++|++|++|||+|..|++||++|++ |++.|++|||++..|.+
T Consensus         9 ~e~~v~~L~~MGF~~~~a~~AL~~t~n~~ve~A~ewL~~~~~d~d   53 (74)
T 2dag_A            9 DESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDPD   53 (74)
T ss_dssp             CHHHHHHHHHHSCCHHHHHHHHHHHTSCCHHHHHHHHHHHTTSTT
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHhCCCCcc
Confidence            456799999999999999999999995 89999999999987654

>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.92  E-value=7.9e-10  Score=88.33  Aligned_cols=44  Identities=18%  Similarity=0.328  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~~  402 (403)
                      +.++|++|++|||+++.|++||.+|++|++.|++|||+|..|.+
T Consensus        29 ~e~~i~~L~~MGF~~~~a~~AL~~t~~nve~A~ewL~~~~~d~d   72 (83)
T 2dai_A           29 DEAALRQLTEMGFPENRATKALQLNHMSVPQAMEWLIEHAEDPT   72 (83)
T ss_dssp             CHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHHGGGCST
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHCCCCcc
Confidence            45679999999999999999999999999999999999876643

>2ekk_A UBA domain from E3 ubiquitin-protein ligase HUWE1; ubiquitin associated domain, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.92  E-value=7.8e-10  Score=78.97  Aligned_cols=38  Identities=37%  Similarity=0.597  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .++.|++|++||   |+|+++++|||++ ||+++|+|||++.
T Consensus         9 ~~~~v~~L~~MG---F~~~~a~~AL~~~-~n~e~A~~~L~~h   46 (47)
T 2ekk_A            9 NQQQLQQLMDMG---FTREHAMEALLNT-STMEQATEYLLTH   46 (47)
T ss_dssp             CHHHHHHHHHHH---CCHHHHHHHHHHS-CSHHHHHHHHHTC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHc-CCHHHHHHHHHcC
Confidence            478999999999   9999999999999 7999999999864

>1whc_A RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain, structural genomics, riken structural genomics/proteomics initiative, unknown function; NMR {Mus musculus} SCOP: a.5.2.1

Probab=98.91  E-value=1.1e-09  Score=83.24  Aligned_cols=42  Identities=29%  Similarity=0.442  Sum_probs=38.6

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHHhccCCCCC
Q 015628          361 EAIERLEAMGFDRALVLEVFFAC-NKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac-~~ne~~a~~~L~~~~~d~~  402 (403)
                      +.|++|++|||+|..|++||.+| ++|++.|++|||++..|.+
T Consensus        11 ~~v~~L~~MGF~~~~a~~AL~~t~~~nve~A~ewLl~~~~d~d   53 (64)
T 1whc_A           11 TALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDDPD   53 (64)
T ss_dssp             CHHHHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhcCCCHHHHHHHHHhCCCCcc
Confidence            46999999999999999999999 7999999999999877654

>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=98.89  E-value=1.3e-09  Score=85.06  Aligned_cols=46  Identities=13%  Similarity=0.287  Sum_probs=41.6

Q ss_pred             CHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015628          356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEF  401 (403)
Q Consensus       356 t~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~  401 (403)
                      ++.+.++|++|++|||+|++|++||.+|++|.+.|++|||++..|.
T Consensus        26 ~~~~~~~v~~L~~MGF~~~~a~~AL~~t~~nve~Ave~L~~~~~d~   71 (73)
T 1wiv_A           26 SDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNSGPS   71 (73)
T ss_dssp             CSSCHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHHSCCSS
T ss_pred             CCCCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHhCCCCC
Confidence            4456678999999999999999999999999999999999987764

>2jy5_A Ubiquilin-1; UBA, alternative splicing, cytoplasm, nucleus, phosphoprotein, proteasome, signaling protein; NMR {Homo sapiens} PDB: 2jy6_B

Probab=98.89  E-value=1.5e-09  Score=79.22  Aligned_cols=38  Identities=32%  Similarity=0.473  Sum_probs=36.1

Q ss_pred             HHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          361 EAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       361 ~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      +.|++|++||| +|+.|++||.+|++|.+.|++|||+++
T Consensus        14 ~~l~~L~~MGF~~~~~~~~AL~~t~gn~e~A~e~L~~~~   52 (52)
T 2jy5_A           14 QQLEQLSAMGFLNREANLQALIATGGDINAAIERLLGSS   52 (52)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHTTCC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhCc
Confidence            67999999999 999999999999999999999999863

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.87  E-value=6.7e-10  Score=84.23  Aligned_cols=43  Identities=23%  Similarity=0.520  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEF  401 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~  401 (403)
                      +.+.|++|++|||+|+.|++||.+|++|.+.|++|||++..|.
T Consensus         9 ~~~~v~~L~~MGF~~~~a~~AL~~t~~nve~A~e~L~~~~~d~   51 (63)
T 2dak_A            9 PEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDL   51 (63)
T ss_dssp             CHHHHHHHHHHTCCHHHHHHHHHHTTSCSHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCCc
Confidence            3467999999999999999999999999999999999986553

>2ooa_A E3 ubiquitin-protein ligase CBL-B; alpha-helical domain; 1.56A {Homo sapiens} PDB: 2oob_A 2jnh_A 2do6_A

Probab=98.86  E-value=2.5e-09  Score=76.95  Aligned_cols=37  Identities=22%  Similarity=0.245  Sum_probs=35.5

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      +.|++|++|||+|++||+|+..|++|.++|+|+|++-
T Consensus        13 ~~Ia~Lm~mGFsr~~ai~AL~~a~nnve~AaniLlef   49 (52)
T 2ooa_A           13 AKIAKLMGEGYAFEEVKRALEIAQNNVEVARSILREF   49 (52)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHh
Confidence            6799999999999999999999999999999999984

>2crn_A Ubash3A protein; compact three-helix bundle, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.86  E-value=2.2e-09  Score=81.65  Aligned_cols=42  Identities=31%  Similarity=0.396  Sum_probs=38.0

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHhccCCCCC
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNK-NEELAANYLLDHMHEFE  402 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~-ne~~a~~~L~~~~~d~~  402 (403)
                      +.|++|++|||+|+.|++|+++|++ |++.|.||||+|..|.+
T Consensus        11 ~~v~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~wL~~h~~d~d   53 (64)
T 2crn_A           11 SLLEPLLAMGFPVHTALKALAATGRKTAEEALAWLHDHCNDPS   53 (64)
T ss_dssp             SSHHHHHHTSCCHHHHHHHHHHHTSCCHHHHHHHHHHHSSSTT
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHhCCCCcc
Confidence            3599999999999999999999976 99999999999987643

>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.84  E-value=3e-09  Score=84.96  Aligned_cols=43  Identities=23%  Similarity=0.366  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  218 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~~  218 (403)
                      .+..|++|++||   |+|++|++|||+++||.++|+|||+.++.+.
T Consensus        29 ~e~~i~~L~~MG---F~~~~a~~AL~~t~~nve~A~ewL~~~~~d~   71 (83)
T 2dai_A           29 DEAALRQLTEMG---FPENRATKALQLNHMSVPQAMEWLIEHAEDP   71 (83)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHHGGGCS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHHCCCCc
Confidence            578999999999   9999999999999999999999999986643

>1vek_A UBP14, ubiquitin-specific protease 14, putative; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=98.83  E-value=2.6e-09  Score=85.52  Aligned_cols=43  Identities=26%  Similarity=0.365  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHcCCCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  218 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~GIP~~  218 (403)
                      .+..|++|++||   |+|++|++|||+++| |.++|++||+.++++.
T Consensus        29 ~e~~v~~L~~MG---F~~~~a~~AL~~t~n~n~e~A~ewL~~h~~d~   72 (84)
T 1vek_A           29 NEEIVAQLVSMG---FSQLHCQKAAINTSNAGVEEAMNWLLSHMDDP   72 (84)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTTCCHHHHHHHHHHHTTCS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHHcCCCHHHHHHHHHhCCCcc
Confidence            478999999999   999999999999985 9999999999997753

>2ekk_A UBA domain from E3 ubiquitin-protein ligase HUWE1; ubiquitin associated domain, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.82  E-value=2.5e-09  Score=76.34  Aligned_cols=38  Identities=32%  Similarity=0.579  Sum_probs=35.3

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          360 REAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       360 ~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      .+.|++|++|||+++.|++||.+|+ |.+.|++|||+|+
T Consensus        10 ~~~v~~L~~MGF~~~~a~~AL~~~~-n~e~A~~~L~~h~   47 (47)
T 2ekk_A           10 QQQLQQLMDMGFTREHAMEALLNTS-TMEQATEYLLTHP   47 (47)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHSC-SHHHHHHHHHTCC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHcC-CHHHHHHHHHcCC
Confidence            4579999999999999999999996 9999999999874

>2knz_A Ubiquilin-4; cytoplasm, endoplasmic reticulum, nucleus, phosphoprotein, protein binding; NMR {Mus musculus}

Probab=98.82  E-value=5e-09  Score=76.72  Aligned_cols=38  Identities=29%  Similarity=0.471  Sum_probs=35.9

Q ss_pred             HHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          361 EAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       361 ~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      +.|++|++||| +|+.|++||.+|++|.+.|++|||++.
T Consensus        13 ~~l~~L~~MGF~~~~~~~~AL~~t~gnve~Ave~L~~~~   51 (53)
T 2knz_A           13 QQLEQLNSMGFINREANLQALIATGGDINAAIERLLGSQ   51 (53)
T ss_dssp             HHHHHHHTTTCCCHHHHHHHHHHHTSCHHHHHHHHHHCC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHcC
Confidence            45999999999 999999999999999999999999875

>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.81  E-value=3.8e-09  Score=78.57  Aligned_cols=39  Identities=28%  Similarity=0.577  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      -++.|..|++||   |.++|+++||++.-||.|||+|||.+-
T Consensus        19 e~e~V~~LvsMG---Fs~~qA~kALKat~~NvErAaDWLFSH   57 (63)
T 1wgn_A           19 ERQCVETVVNMG---YSYECVLRAMKKKGENIEQILDYLFAH   57 (63)
T ss_dssp             HHHHHHHHHHHH---CCHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            477899999999   999999999999999999999999874

>2d9s_A CBL E3 ubiquitin protein ligase; UBA domain, dimer, protein binding, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.78  E-value=5.7e-09  Score=75.41  Aligned_cols=38  Identities=26%  Similarity=0.378  Sum_probs=35.4

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      +.|++|++|||+|++||+|+..|++|+|+|+|+|++..
T Consensus        11 ~~I~~L~~lGF~r~~ai~AL~~a~nnve~Aa~iL~ef~   48 (53)
T 2d9s_A           11 SEIERLMSQGYSYQDIQKALVIAHNNIEMAKNILREFS   48 (53)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHTTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhcCCHHHHHHHHHHhc
Confidence            34999999999999999999999999999999999753

>1vek_A UBP14, ubiquitin-specific protease 14, putative; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=98.77  E-value=5.6e-09  Score=83.60  Aligned_cols=44  Identities=30%  Similarity=0.451  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHHhccCCCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFAC-NKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac-~~ne~~a~~~L~~~~~d~~  402 (403)
                      +.++|++|++|||+|..|++||++| ++|++.|++|||+|..|.+
T Consensus        29 ~e~~v~~L~~MGF~~~~a~~AL~~t~n~n~e~A~ewL~~h~~d~d   73 (84)
T 1vek_A           29 NEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPD   73 (84)
T ss_dssp             CHHHHHHHHHHTCCHHHHHHHHHHTTTCCHHHHHHHHHHHTTCST
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHHhCCCccc
Confidence            5578999999999999999997777 5899999999999877643

>1veg_A NEDD8 ultimate buster-1; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1

Probab=98.76  E-value=8.3e-09  Score=82.15  Aligned_cols=42  Identities=31%  Similarity=0.378  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      ..+.|++|++|||+|++|++||.+|++|.+.|++|||+|..+
T Consensus        29 ~ee~I~~Lv~MGF~~~~A~~AL~~t~gdve~A~e~L~sh~~~   70 (83)
T 1veg_A           29 SQESINQLVYMGFDTVVAEAALRVFGGNVQLAAQTLAHHGGS   70 (83)
T ss_dssp             CHHHHHHHHHHSCCHHHHHHHHHHTTTCHHHHHHHHHHHTSS
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence            346799999999999999999999999999999999998664

>2lbc_A Ubiquitin carboxyl-terminal hydrolase 13; tandem UBA of USP13; NMR {Homo sapiens}

Probab=98.75  E-value=8.8e-09  Score=88.35  Aligned_cols=41  Identities=41%  Similarity=0.608  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  216 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP  216 (403)
                      .+..|++|++||   |+|++|++|||+++||++||+|||+++++
T Consensus        78 ~e~~v~~L~~MG---F~~~~a~~AL~~~~~~~e~A~e~L~~~~~  118 (126)
T 2lbc_A           78 PEEIVAIITSMG---FQRNQAIQALRATNNNLERALDWIFSHPE  118 (126)
T ss_dssp             CHHHHHHHHHHT---SCHHHHHHHHHHHTSCHHHHHHHHHTCCS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            478999999999   99999999999999999999999999987

>2dah_A Ubiquilin-3; UBA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.72  E-value=1.3e-08  Score=74.82  Aligned_cols=41  Identities=29%  Similarity=0.442  Sum_probs=37.0

Q ss_pred             cHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcCC
Q 015628          172 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGI  215 (403)
Q Consensus       172 ~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~GI  215 (403)
                      .|+..|++|++||   | +|+.+++||+++.+|.+||||||+++.
T Consensus         8 ~~~~~l~~L~~MG---F~d~~~n~~AL~~~~Gdv~~Ave~L~~~~   49 (54)
T 2dah_A            8 HFQVQLEQLRSMG---FLNREANLQALIATGGDVDAAVEKLRQSS   49 (54)
T ss_dssp             SSHHHHHHHHHHT---CCCHHHHHHHHHHHTSCHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHcC---CCcHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence            4788999999999   9 566689999999999999999999873

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=98.71  E-value=5.1e-08  Score=82.35  Aligned_cols=73  Identities=19%  Similarity=0.273  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+|++.+|+.+.+.|..++++..|++..+++.|   ++...+||+|.|+.|.++.|..++++.++++|.|++..
T Consensus        41 I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~G---l~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~Q  113 (115)
T 3kyd_D           41 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ  113 (115)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHT---CCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhC---CChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEeec
Confidence            46788888899999999999999999999999999   99999999999999999999999999999999999753

>2cwb_A Chimera of immunoglobulin G binding protein G and ubiquitin-like protein SB132; helical bundle, protein binding; NMR {Streptococcus SP} PDB: 2den_A

Probab=98.71  E-value=1.4e-08  Score=84.81  Aligned_cols=42  Identities=33%  Similarity=0.509  Sum_probs=39.0

Q ss_pred             cHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcCCC
Q 015628          172 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIP  216 (403)
Q Consensus       172 ~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~GIP  216 (403)
                      .++..|++|.+||   | +|+.+++||+++++|++||||||++|.+
T Consensus        65 ~~~~qL~qL~eMG---F~d~~~ni~AL~~t~Gdve~AVe~L~~~~~  107 (108)
T 2cwb_A           65 QWQPQLQQLRDMG---IQDDELSLRALQATGGDIQAALELIFAGGA  107 (108)
T ss_dssp             TTHHHHHHHHTTT---CCCHHHHHHHHHHHTSCHHHHHHHHHHTSC
T ss_pred             chHHHHHHHHHcC---CCCHHHHHHHHHHhCCCHHHHHHHHHhcCC
Confidence            4788999999999   9 8899999999999999999999999844

>2bwb_A Ubiquitin-like protein DSK2; UBA, signaling protein; 2.3A {Saccharomyces cerevisiae} SCOP: a.5.2.1 PDB: 2bwe_A

Probab=98.68  E-value=2.3e-08  Score=71.08  Aligned_cols=37  Identities=22%  Similarity=0.275  Sum_probs=34.1

Q ss_pred             HHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          361 EAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       361 ~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      +.|++|++||| +|+.+++|+.+|++|.+.|++|||++
T Consensus         9 ~~i~~L~~MGF~d~~~~~~AL~~~~gnv~~Ave~L~~~   46 (46)
T 2bwb_A            9 HQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG   46 (46)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHHCC
T ss_pred             HHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHcc
Confidence            45999999999 68889999999999999999999974

>2dkl_A Trinucleotide repeat containing 6C protein; TNRC6C, KIAA1582 protein, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.65  E-value=2.5e-08  Score=79.99  Aligned_cols=38  Identities=29%  Similarity=0.430  Sum_probs=36.8

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      +..|++|++||   |+|++|++||++.++|+++|+|||+..
T Consensus        22 ~~~I~qL~~MG---F~~~~a~~AL~~~n~n~e~A~ewL~~h   59 (85)
T 2dkl_A           22 SRLIKQLTDMG---FPREPAEEALKSNNMNLDQAMSALLEK   59 (85)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHTT
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHHC
Confidence            78999999999   999999999999999999999999986

>1vej_A Riken cDNA 4931431F19; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1

Probab=98.62  E-value=4.2e-08  Score=76.51  Aligned_cols=42  Identities=26%  Similarity=0.400  Sum_probs=37.5

Q ss_pred             HHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015628          360 REAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHMHEF  401 (403)
Q Consensus       360 ~~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~  401 (403)
                      .+.|++|++||| +|+.+++||.+|++|++.|++|||++...+
T Consensus        30 e~qi~qL~eMGF~dr~~~~~AL~~t~Gnve~Ave~L~~~~~~~   72 (74)
T 1vej_A           30 QQELEELKALGFANRDANLQALVATDGDIHAAIEMLLGASGPS   72 (74)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHTCCCCC
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHhCCCCC
Confidence            346999999999 799999999999999999999999975543

>2dah_A Ubiquilin-3; UBA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.61  E-value=4.6e-08  Score=71.84  Aligned_cols=41  Identities=24%  Similarity=0.379  Sum_probs=35.8

Q ss_pred             HHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          360 REAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       360 ~~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      .+.|++|++||| +++.+++||.+|++|.+.|++|||+++..
T Consensus        10 ~~~l~~L~~MGF~d~~~n~~AL~~~~Gdv~~Ave~L~~~~~~   51 (54)
T 2dah_A           10 QVQLEQLRSMGFLNREANLQALIATGGDVDAAVEKLRQSSGP   51 (54)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHHHSCS
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            356999999999 55668999999999999999999987643

>1wr1_B Ubiquitin-like protein DSK2; UBA domain, UBA-ubiquitin complex, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=98.61  E-value=4.1e-08  Score=73.14  Aligned_cols=38  Identities=21%  Similarity=0.241  Sum_probs=35.2

Q ss_pred             HHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          361 EAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       361 ~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      +.|++|++||| +|+.+++||.+|++|.+.|++|||+++
T Consensus        19 ~qi~~L~~MGF~d~~~~~~AL~~~~gnve~Ave~L~~~~   57 (58)
T 1wr1_B           19 HQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNGD   57 (58)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHHTC
T ss_pred             HHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence            45999999999 699999999999999999999999874

>2juj_A E3 ubiquitin-protein ligase CBL; alpha helix, UBA domain, calcium, cytoplasm, metal- binding, phosphorylation, proto-oncogene, SH2 domain; NMR {Homo sapiens}

Probab=98.55  E-value=7.4e-08  Score=69.76  Aligned_cols=38  Identities=24%  Similarity=0.346  Sum_probs=35.7

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          360 REAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       360 ~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      .+.|.+|++|||+|+.|++|+..|+.|.|+|.|+|++-
T Consensus         8 e~~Ia~L~smGfsr~da~~AL~ia~Ndv~~AtNiLlEf   45 (56)
T 2juj_A            8 SSEIENLMSQGYSYQDIQKALVIAQNNIEMAKNILREF   45 (56)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHTTTCSHHHHHHHHHS
T ss_pred             hHHHHHHHHcCCCHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            45799999999999999999999999999999999974

>1dv0_A DNA repair protein HHR23A; helical bundle, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.5.2.1 PDB: 1f4i_A

Probab=98.52  E-value=1.9e-08  Score=71.78  Aligned_cols=41  Identities=22%  Similarity=0.327  Sum_probs=38.2

Q ss_pred             cHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCC
Q 015628          172 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  215 (403)
Q Consensus       172 ~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GI  215 (403)
                      +-+.+|++|++||   |+|.+|++||.+.-+|.++|++||+++.
T Consensus         3 ~e~eaI~rL~~mG---F~~~~a~~Al~a~~~n~e~A~~~Lf~~~   43 (47)
T 1dv0_A            3 QEKEAIERLKALG---FPESLVIQAYFACEKNENLAANFLLSQN   43 (47)
T ss_dssp             CCHHHHTTTTTTT---CCHHHHHHHHTTTTSCHHHHHHHTTSCC
T ss_pred             chHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCc
Confidence            4578999999999   9999999999999999999999999874

>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=98.48  E-value=1.7e-07  Score=71.57  Aligned_cols=47  Identities=26%  Similarity=0.291  Sum_probs=39.3

Q ss_pred             CCHHH--HHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015628          355 VTPEE--REAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHMHEF  401 (403)
Q Consensus       355 lt~ee--~~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~  401 (403)
                      ..+|+  ...|++|++||| +|+.+++|+.+|++|.+.|++|||++..|.
T Consensus        13 ~~pe~~y~~ql~qL~~MGF~d~~an~~AL~at~Gnve~Ave~L~~~~~~~   62 (67)
T 2dna_A           13 QAPEVRFSKEMECLQAMGFVNYNANLQALIATDGDTNAAIYKLKSSQGFS   62 (67)
T ss_dssp             CCHHHHTHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHHCCSSS
T ss_pred             CChHHHHHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhCCCcc
Confidence            34555  345999999998 677789999999999999999999986653

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.46  E-value=4.7e-07  Score=83.47  Aligned_cols=76  Identities=11%  Similarity=0.116  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~~   80 (403)
                      ++|+|+ .+|+.+.+.|..++++..||+..+++.|   ++..++||+|.|+.|.++.|..++++.+|++|.|++...+..
T Consensus        30 I~LkV~-~~g~~v~fkIk~~t~l~kL~~ay~er~G---i~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q~gg~  105 (200)
T 3pge_A           30 INLKVS-DGSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGG  105 (200)
T ss_dssp             EEEEEE-CSSCEEEEEECTTSCTHHHHHHHHHHHS---SCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCSCCC
T ss_pred             EEEEEe-cCCCEEEEEEecCCHHHHHHHHHHHHhC---CChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCcCc
Confidence            467787 4889999999999999999999999999   999999999999999999999999999999999999876644

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=98.46  E-value=1e-07  Score=75.47  Aligned_cols=69  Identities=10%  Similarity=0.181  Sum_probs=57.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCee---c--CCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV---L--KDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~Gki---L--~D~~tLsd~gI~~~s~I~v~   73 (403)
                      |.|.||+.+| .+.|+|++++||.+||++|.+.++   ++++.|.|.++-..   |  .++.+|+++||+.|+.|+|.
T Consensus         5 m~lRvrs~~G-~~Ri~v~~~~t~~~L~~~I~~~~~---i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A            5 IIIRVQSPDG-VKRITATKRETAATFLKKVAKEFG---FQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCEEECSSE-EEECCCCSSCCHHHHHHHHHHHTC---CCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             EEEEEECCCC-CEEEEcCCcChHHHHHHHHHHHcC---CCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            6789998887 678999999999999999999999   88888777654433   3  46789999999999999874

>2oo9_A E3 ubiquitin-protein ligase CBL; alpha-helical domain, homodimer; 2.10A {Homo sapiens}

Probab=98.43  E-value=2.5e-07  Score=64.64  Aligned_cols=37  Identities=24%  Similarity=0.357  Sum_probs=35.3

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      .+|.+|+.|||+++.|++|+..|+.|.|+|.|.|++.
T Consensus         6 ~~I~~L~s~Gf~~~~~~rAL~ia~Nnie~A~nIL~ef   42 (46)
T 2oo9_A            6 SEIENLMSQGYSYQDIQKALVIAQNNIEMAKNILREF   42 (46)
T ss_dssp             HHHHHHHHTTBCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhhccHHHHHHHHHHh
Confidence            5699999999999999999999999999999999875

>3k9o_A Ubiquitin-conjugating enzyme E2 K; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 3k9p_A 1yla_A 2o25_A

Probab=98.42  E-value=1.9e-07  Score=86.19  Aligned_cols=75  Identities=27%  Similarity=0.282  Sum_probs=56.2

Q ss_pred             hCHHHHHHHHHcHHHHHHHhcCCCCCCCCcccccccccCCccccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHH
Q 015628          311 QNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELA  390 (403)
Q Consensus       311 ~nP~l~~lI~~n~e~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a  390 (403)
                      -|++.+++...|++.|.+...+-...        ...    .-...++-.+.|++|++|||+|++|++|+..|+||++.|
T Consensus       127 ~n~~aa~~~~~~~~~f~~~a~~~~~~--------~a~----~~~~~~~~eekV~~l~~MGf~~~~a~~AL~~~~wd~~~A  194 (201)
T 3k9o_A          127 QDAVVANQYKQNPEMFKQTARLWAHV--------YAG----APVSSPEYTKKIENLCAMGFDRNAVIVALSSKSWDVETA  194 (201)
T ss_dssp             SCHHHHHHHHHCHHHHHHHHHHHHHH--------HHC----CCCCCHHHHHHHHHHHTTTCCHHHHHHHHHHTTTCHHHH
T ss_pred             ccHHHHHHHHHCHHHHHHHHHHHHHH--------hcc----cccccchhHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHH
Confidence            36788888888999988875432100        000    001233446789999999999999999999999999999


Q ss_pred             HHHHhcc
Q 015628          391 ANYLLDH  397 (403)
Q Consensus       391 ~~~L~~~  397 (403)
                      +++||++
T Consensus       195 ~e~L~~~  201 (201)
T 3k9o_A          195 TELLLSN  201 (201)
T ss_dssp             HHHHHHC
T ss_pred             HHHHhcC
Confidence            9999985

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=98.41  E-value=3.3e-07  Score=83.60  Aligned_cols=75  Identities=11%  Similarity=0.121  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+|+ .+|+.+.+.|..++++..|++..+++.|   +++..+||+|.|+.|.++.|..++++.++|+|.|++...+.
T Consensus        58 InLKVk-~dG~eV~FKIKrtTpL~KLmeAYcERqG---L~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~GG  132 (207)
T 3tix_A           58 INLKVS-DGSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGG  132 (207)
T ss_dssp             EEEEEE-CSSCEEEEEEETTSCTHHHHHHHHHHTT---CCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCTT
T ss_pred             EEEEEe-cCCCEEEEEEccCChHHHHHHHHHHHhC---CCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            356776 4889999999999999999999999999   99999999999999999999999999999999999876553

>2ooa_A E3 ubiquitin-protein ligase CBL-B; alpha-helical domain; 1.56A {Homo sapiens} PDB: 2oob_A 2jnh_A 2do6_A

Probab=98.41  E-value=3e-07  Score=66.13  Aligned_cols=38  Identities=34%  Similarity=0.424  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      .+..|+.||+||   |+|++|++||+.+-||.|-|..+|+.
T Consensus        11 ~~~~Ia~Lm~mG---Fsr~~ai~AL~~a~nnve~AaniLle   48 (52)
T 2ooa_A           11 VDAKIAKLMGEG---YAFEEVKRALEIAQNNVEVARSILRE   48 (52)
T ss_dssp             CHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            357999999999   99999999999999999999999974

>2d9s_A CBL E3 ubiquitin protein ligase; UBA domain, dimer, protein binding, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.35  E-value=5.2e-07  Score=65.19  Aligned_cols=38  Identities=26%  Similarity=0.401  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      .+..|..||+||   |+|++|++||+.+-||.|-|..+|+.
T Consensus         9 ~e~~I~~L~~lG---F~r~~ai~AL~~a~nnve~Aa~iL~e   46 (53)
T 2d9s_A            9 LSSEIERLMSQG---YSYQDIQKALVIAHNNIEMAKNILRE   46 (53)
T ss_dssp             SHHHHHHHHHHT---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHcC---CCHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            356799999999   99999999999999999999999985

>4ae4_A Ubiquitin-associated protein 1; protein transport, endosomal sorting, tetherin, VPU, HIV-1, monoubiquitin; HET: NHE; 1.65A {Homo sapiens} PDB: 4ae4_B*

Probab=98.34  E-value=5.4e-07  Score=76.49  Aligned_cols=45  Identities=31%  Similarity=0.510  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          354 TVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       354 ~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      .|+++|++.|.+|.+|||++..|++|+.+|+.|.+.|.||||.++
T Consensus         3 ~l~~~e~~~v~~l~~MGFp~~~~~kAl~~~g~~~e~amewL~~h~   47 (118)
T 4ae4_A            3 HMSPSERQCVETVVNMGYSYECVLRAMKAAGANIEQILDYLFAHG   47 (118)
T ss_dssp             CSCHHHHHHHHHHHHTTCCHHHHHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHCcCHHHHHHHHHHhc
Confidence            589999999999999999999999999999999999999999874

>2oo9_A E3 ubiquitin-protein ligase CBL; alpha-helical domain, homodimer; 2.10A {Homo sapiens}

Probab=98.26  E-value=1.4e-06  Score=60.77  Aligned_cols=41  Identities=29%  Similarity=0.447  Sum_probs=38.5

Q ss_pred             CccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          170 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       170 g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      |+.+|..|..||+||   |+|+.|++||-.+-||.+-|-+.|+.
T Consensus         1 ~~~~e~~I~~L~s~G---f~~~~~~rAL~ia~Nnie~A~nIL~e   41 (46)
T 2oo9_A            1 GSQLSSEIENLMSQG---YSYQDIQKALVIAQNNIEMAKNILRE   41 (46)
T ss_dssp             CCHHHHHHHHHHHTT---BCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHcC---CCHHHHHHHHHHhhccHHHHHHHHHH
Confidence            567899999999999   99999999999999999999999974

>2cwb_A Chimera of immunoglobulin G binding protein G and ubiquitin-like protein SB132; helical bundle, protein binding; NMR {Streptococcus SP} PDB: 2den_A

Probab=98.25  E-value=9.2e-07  Score=73.75  Aligned_cols=40  Identities=20%  Similarity=0.303  Sum_probs=36.4

Q ss_pred             HHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015628          360 REAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHMH  399 (403)
Q Consensus       360 ~~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~~  399 (403)
                      .+.|++|++||| +|+.+++||.+|++|++.|++|||+++.
T Consensus        67 ~~qL~qL~eMGF~d~~~ni~AL~~t~Gdve~AVe~L~~~~~  107 (108)
T 2cwb_A           67 QPQLQQLRDMGIQDDELSLRALQATGGDIQAALELIFAGGA  107 (108)
T ss_dssp             HHHHHHHHTTTCCCHHHHHHHHHHHTSCHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhcCC
Confidence            457999999999 7799999999999999999999998753

>3goe_A DNA repair protein RAD60; SUMO-like domain, sumoylation, SUMO, genome stability, DNA damage, DNA recombination, nucleus; HET: DNA; 0.97A {Schizosaccharomyces pombe} PDB: 3rcz_A*

Probab=98.23  E-value=6.5e-06  Score=64.40  Aligned_cols=70  Identities=16%  Similarity=0.224  Sum_probs=65.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~-~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      .+.+|+.+...+.+.|.++.+|.+|-+.-+.+.|   ++.+ .++|.|.|..|+.+.++.+|++.+++.|-||+
T Consensus        11 ~~~~~~~~~~dl~f~I~~~t~v~kLi~ayc~~~~---I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           11 TLLLRSSKSEDLRLSIPVDFTVKDLIKRYCTEVK---ISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             EEEEEESSSCCEEEEEETTSBHHHHHHHHHHHHT---CCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HHhhhccCCCCeEEEecCCCCHHHHHHHHHHHcC---CCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            4567777778899999999999999999999999   9999 99999999999999999999999999999986

>3e46_A Ubiquitin-conjugating enzyme E2-25 kDa; huntington interacting, ligase, alternative splicing, cytoplasm, UBL conjugation, UBL conjugation pathway; 1.86A {Homo sapiens} SCOP: a.5.2.1 d.20.1.1 PDB: 3f92_A*

Probab=98.21  E-value=1.2e-06  Score=83.68  Aligned_cols=75  Identities=25%  Similarity=0.259  Sum_probs=57.9

Q ss_pred             hCHHHHHHHHHcHHHHHHHhcCCCCCCCCcccccccccCCccccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHH
Q 015628          311 QNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELA  390 (403)
Q Consensus       311 ~nP~l~~lI~~n~e~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a  390 (403)
                      -|++.+++...|++.|.+...+-...        ...    .....++-.+.|++|++|||+|+.|++|+..|+||++.|
T Consensus       179 ln~eaa~l~~~d~~~f~~~ar~~t~~--------yA~----~~~~~~~~~~~v~~l~~mgf~~~~~~~al~~~nWd~~~A  246 (253)
T 3e46_A          179 QDAVVANQYKQNPEMFKQTARLWAHV--------YAG----APVSSPEYTKKIENLCAAGFDRNAVIVALSSKSWDVETA  246 (253)
T ss_dssp             SCHHHHHHHHHCHHHHHHHHHHHHHH--------HHC----CSCCCHHHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHH
T ss_pred             hhHHHHHHHHHCHHHHHHHHHHHHHH--------hcc----cccCcchHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHH
Confidence            47889999999999998886432110        000    011234556789999999999999999999999999999


Q ss_pred             HHHHhcc
Q 015628          391 ANYLLDH  397 (403)
Q Consensus       391 ~~~L~~~  397 (403)
                      .++||++
T Consensus       247 ~e~L~~~  253 (253)
T 3e46_A          247 TELLLSN  253 (253)
T ss_dssp             HHHHHHC
T ss_pred             HHHHhcC
Confidence            9999974

>1wj7_A Hypothetical protein (RSGI RUH-015); UBA domain, ubiquitin associated domain, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: a.5.2.1

Probab=98.18  E-value=2.5e-06  Score=70.36  Aligned_cols=42  Identities=21%  Similarity=0.318  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          359 EREAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       359 e~~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      -.+.|++|++| ||++++|+.||..|++|++.|+++||+...|
T Consensus        39 ~eekVk~L~EmtG~seeeAr~AL~~~ngDl~~AI~~Lleg~~~   81 (104)
T 1wj7_A           39 FEEKVKQLIDITGKNQDECVIALHDCNGDVNRAINVLLEGNPD   81 (104)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHTCSSS
T ss_pred             HHHHHHHHHHhhCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            34669999999 9999999999999999999999999987643

>2juj_A E3 ubiquitin-protein ligase CBL; alpha helix, UBA domain, calcium, cytoplasm, metal- binding, phosphorylation, proto-oncogene, SH2 domain; NMR {Homo sapiens}

Probab=98.17  E-value=1.9e-06  Score=62.44  Aligned_cols=38  Identities=26%  Similarity=0.399  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      .|..|..||+||   |+|+.|++||+.+-||.+-|-..|+.
T Consensus         7 ~e~~Ia~L~smG---fsr~da~~AL~ia~Ndv~~AtNiLlE   44 (56)
T 2juj_A            7 LSSEIENLMSQG---YSYQDIQKALVIAQNNIEMAKNILRE   44 (56)
T ss_dssp             HHHHHHHHHTTT---CCHHHHHHHHHHTTTCSHHHHHHHHH
T ss_pred             ChHHHHHHHHcC---CCHHHHHHHHHHhcccHHHHHHHHHH
Confidence            578999999999   99999999999999999999999986

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=98.11  E-value=3.7e-07  Score=84.35  Aligned_cols=75  Identities=11%  Similarity=0.122  Sum_probs=0.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+| +.+|+.+.+.|..++++..||+..+++.|   +++..+||+|.|+.|.++.|..++++.+||+|.|+....+.
T Consensus        22 InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqG---Ls~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~GG   96 (227)
T 3v7o_A           22 INLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG   96 (227)
T ss_dssp             ------------------------------------------------------------------------------C
T ss_pred             EEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhC---CCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccCC
Confidence            56777 67888899999999999999999999999   99999999999999999999999999999999999876543

>3k9o_A Ubiquitin-conjugating enzyme E2 K; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 3k9p_A 1yla_A 2o25_A

Probab=98.09  E-value=2.4e-06  Score=78.73  Aligned_cols=43  Identities=33%  Similarity=0.470  Sum_probs=40.1

Q ss_pred             cCCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          168 VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       168 ~~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      ..++.+++.|++|++||   |+|++|+.||+...+|.++|+|||++
T Consensus       158 ~~~~~~eekV~~l~~MG---f~~~~a~~AL~~~~wd~~~A~e~L~~  200 (201)
T 3k9o_A          158 VSSPEYTKKIENLCAMG---FDRNAVIVALSSKSWDVETATELLLS  200 (201)
T ss_dssp             CCCHHHHHHHHHHHTTT---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             cccchhHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            34667899999999999   99999999999999999999999985

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=98.07  E-value=1.5e-05  Score=65.32  Aligned_cols=70  Identities=10%  Similarity=0.202  Sum_probs=63.7

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~-~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      ++|+|+..+|+ .+.+.|..+.++..|....+++.|   +++...||+|.|..|..+.|..++++.++++|.|+
T Consensus        26 I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g---~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           26 LQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMG---LSGRKLSFFFDGTKLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             EEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTT---CSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHC---CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            35677777784 788999999999999999999999   88999999999999999999999999999999886

>2cp8_A NEXT to BRCA1 gene 1 protein; UBA domain, structural genomics, human, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.03  E-value=3.2e-06  Score=61.69  Aligned_cols=46  Identities=28%  Similarity=0.256  Sum_probs=39.6

Q ss_pred             CHHHHHH--HHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015628          356 TPEEREA--IERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHMHEF  401 (403)
Q Consensus       356 t~ee~~a--i~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~  401 (403)
                      .+||+.+  +++|.+||| |++..++++..|++|.+.|++.|+.....|
T Consensus         4 ~~ee~~a~~L~~L~eMGF~D~~~N~~aL~~~~gnv~~aI~~Ll~~~~~~   52 (54)
T 2cp8_A            4 GSSGQTAALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELLQLSGPS   52 (54)
T ss_dssp             SSCTTHHHHHHHHHHHTCCCHHHHHHHHTTTTTCHHHHHHHHHHHSSSC
T ss_pred             CHHHhhHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhccCCC
Confidence            3455555  889999999 999999999999999999999999865544

>1wj7_A Hypothetical protein (RSGI RUH-015); UBA domain, ubiquitin associated domain, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: a.5.2.1

Probab=97.96  E-value=1.1e-05  Score=66.52  Aligned_cols=44  Identities=27%  Similarity=0.571  Sum_probs=41.4

Q ss_pred             ccHHHHHHHHHHc-CCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCC
Q 015628          171 SNLEATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  217 (403)
Q Consensus       171 ~~~e~~v~~i~~M-G~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~  217 (403)
                      ++++..|+.|++| |   |++++++.||..+.++.++|++||+.|.|+
T Consensus        37 ~d~eekVk~L~EmtG---~seeeAr~AL~~~ngDl~~AI~~Lleg~~~   81 (104)
T 1wj7_A           37 ADFEEKVKQLIDITG---KNQDECVIALHDCNGDVNRAINVLLEGNPD   81 (104)
T ss_dssp             HHHHHHHHHHHHHTC---CCHHHHHHHHHHHTSCHHHHHHHHHTCSSS
T ss_pred             ccHHHHHHHHHHhhC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            4578999999999 9   999999999999999999999999999874

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A

Probab=97.92  E-value=4.8e-06  Score=83.52  Aligned_cols=42  Identities=24%  Similarity=0.390  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      ..++|.+|++|||+|++|++|+.+|++|.+.|++|||++..|
T Consensus       168 ~~~~i~~l~~MGf~~~~~~~AL~a~~nn~~~A~e~L~~gip~  209 (368)
T 1oqy_A          168 YETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPG  209 (368)
T ss_dssp             HHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTTTTSSTT
T ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            456799999999999999999999999999999999987654

>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase; ssgcid, seattle structural genomics center for in disease; HET: FK5; 1.50A {Burkholderia pseudomallei} PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A* 4giv_A* 1euv_B 3v60_A 3v61_A 3v62_A*

Probab=97.75  E-value=5.3e-05  Score=70.15  Aligned_cols=73  Identities=11%  Similarity=0.141  Sum_probs=67.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      +|+|++ +|+.+.+.|..++++..||+..+++.|   ++..++||+|.|+.+.++.+..++.+.++++|.++.....
T Consensus        23 ~ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g---~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~eq~G   95 (209)
T 3uf8_A           23 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (209)
T ss_dssp             EEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECSCTT
T ss_pred             EEEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhC---CChheEEEEECCEeccCCCChHHhhhcccccchhhccccc
Confidence            567776 677888999999999999999999999   9999999999999999999999999999999999987655

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=97.75  E-value=0.00011  Score=59.70  Aligned_cols=72  Identities=11%  Similarity=0.197  Sum_probs=66.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      +.|.|+ .+|..+.+.|..++....|.+..+.+.|   +.+...+++|.|..+.++.|-.++++.++++|-+++.+
T Consensus        22 IniKV~-~~g~ev~FkIK~tt~l~KL~~aYc~r~g---v~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~~~   93 (95)
T 2l76_A           22 FPLKIR-CRADLVRLPLRMSEPLQSVVDHMATHLG---VSPSRILLLFGETELSPTATPRTLKLGVADIIDCVVLT   93 (95)
T ss_dssp             EEEEEE-CSSSEEEEEECSSSCTHHHHHHHHHHHT---SCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEECC
T ss_pred             EEEEEE-cCCcEEEEEEecCChHHHHHHHHHhhcC---CChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEEec
Confidence            357788 4788899999999999999999999999   89999999999999999999999999999999999864

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=97.72  E-value=0.0001  Score=59.91  Aligned_cols=63  Identities=16%  Similarity=0.093  Sum_probs=49.2

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecC--CCCccccccc-CCCcEEEEEE
Q 015628            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK--DVTTLEENKV-AENSFVVVML   74 (403)
Q Consensus         9 ~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~--D~~tLsd~gI-~~~s~I~v~v   74 (403)
                      .++.+.|.|.+++||..||++|++++|   +++.+|+|||.||.|.  ..+.-..|-- ...+-|+|+-
T Consensus        22 ~a~~h~v~I~~~etv~~~ke~V~eqTg---Ip~~~Q~LL~eg~~l~l~p~~~a~~~p~Tt~~~Pl~L~s   87 (94)
T 4efo_A           22 QMTAHKIYIHSYNTATIFHELVYKQTK---IISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVS   87 (94)
T ss_dssp             TTEEEEEEEETTCBHHHHHHHHHHHHC---CCGGGEEEEETTEEECCCTTCBGGGSCCCBTTBCEEEEE
T ss_pred             cceEEEEEeccchHHHHHHHHHHHHhC---CCHHHHHHHhCCCccccCCCCccccCCCCCCCCCEEEEe
Confidence            467788999999999999999999999   9999999999998764  4445555533 3344555553

>2cp8_A NEXT to BRCA1 gene 1 protein; UBA domain, structural genomics, human, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=97.68  E-value=3.8e-05  Score=56.01  Aligned_cols=42  Identities=24%  Similarity=0.342  Sum_probs=38.6

Q ss_pred             CccHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          170 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       170 g~~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      -+.|...+.+|.+||   | +++..++|||...+|.++||++|+.+
T Consensus         6 ee~~a~~L~~L~eMG---F~D~~~N~~aL~~~~gnv~~aI~~Ll~~   48 (54)
T 2cp8_A            6 SGQTAALMAHLFEMG---FCDRQLNLRLLKKHNYNILQVVTELLQL   48 (54)
T ss_dssp             CTTHHHHHHHHHHHT---CCCHHHHHHHHTTTTTCHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHcC---CCcHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            355778999999999   9 99999999999999999999999975

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=97.60  E-value=8.7e-05  Score=58.76  Aligned_cols=70  Identities=13%  Similarity=0.226  Sum_probs=58.9

Q ss_pred             EEEEEe--CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC---CCcEEEeCCeecCCCCcccccccCCCcEEEE
Q 015628            2 KVFVKT--LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA---SQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         2 kI~VKt--l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~---~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      +|+|..  ..++.|.+.+....||..|+..|.+.++-+ .+.   ...|+.-++.+|.++..|.+|+|.+||.|.+
T Consensus         6 ~ITidl~~y~~~~~DLRIP~~~tvK~Li~~l~ea~~l~-~~~~~~~~irv~NK~~~L~~~~~L~d~~ItnGD~Lei   80 (81)
T 2bps_A            6 DITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVS-MPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEI   80 (81)
T ss_dssp             EEEEECTTTTCCEEEEEEETTSBTTHHHHHHHHHSCCC-SCCCTTCEEEEGGGTEEEETTSBTGGGTCCTTCEEEE
T ss_pred             EEEEEeeccCCceEEEECCCchhHHHHHHHHHHHhCCC-cCCCCCCEEEEecCCEEEcCCCEEeeCCcCCCCEEEE
Confidence            566664  578999999999999999999999999843 221   2457788999999999999999999999876

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=97.54  E-value=0.00013  Score=62.58  Aligned_cols=69  Identities=25%  Similarity=0.243  Sum_probs=56.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-------------------------------------Cc
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-------------------------------------QQ   44 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~-------------------------------------~Q   44 (403)
                      .|+|+.++|+..++.|+.+.+|.+++..|+.+.|   ++..                                     ++
T Consensus        13 ~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kig---I~n~~ey~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~   89 (128)
T 2kc2_A           13 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIG---ITNHDEYSLVRELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQ   89 (128)
T ss_dssp             EEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHT---CCCCSSEEEEEECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCC
T ss_pred             cEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhC---CCCcccccccccccccccccCchhhccccccccchhHHHHHHH
Confidence            3899999999999999999999999999999999   5533                                     44


Q ss_pred             EEEe--CCeecCCCCcccccccCCCcEEEEE
Q 015628           45 MLIH--QGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus        45 kLiy--~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      ||-.  .+..|+++++|.++||.++++|.|-
T Consensus        90 kL~~dd~~~WLD~srtL~EQGI~e~~tllLR  120 (128)
T 2kc2_A           90 KLHTDDELNWLDHGRTLREQGVEEHETLLLR  120 (128)
T ss_dssp             SCCCSSSEEEECSSSCHHHHTCCTTSEEEEE
T ss_pred             HhcccCCCCcccCCCcHHHcCCCCCCEEEEE
Confidence            4422  2366788999999999999996543

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=97.52  E-value=1.3e-05  Score=79.88  Aligned_cols=74  Identities=11%  Similarity=0.150  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      ++|+|++ +|+.+.+.|..++++..|++..+++.|   ++...+|++|.|+.|.++.|.+++++++|++|.|+....+
T Consensus        22 I~LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G---~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q~g   95 (360)
T 3ix6_A           22 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (360)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             EEEEEec-CCcEEEEEEecCChHHHHHHHHHHHhC---CCcceEEEEECCeECCCCCChHHcCCCccchhhhhhccCc
Confidence            3566776 677788899999999999999999999   8999999999999999999999999999999999987544

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=97.39  E-value=0.00054  Score=55.11  Aligned_cols=73  Identities=18%  Similarity=0.152  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |.|+|-..+++.+.|.|.++.++.++-+...+++|   +.+++-.|.|++|.|+-+..+.-.||-+|..|.++.+.
T Consensus        10 m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~g---l~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~s   82 (90)
T 2al3_A           10 SAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQD---FNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVS   82 (90)
T ss_dssp             CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTT---CCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSS
T ss_pred             cEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhC---CChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEcc
Confidence            67899999999999999999999999999999999   88888899999999988999999999999999988653

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=97.27  E-value=3.9e-05  Score=77.08  Aligned_cols=74  Identities=9%  Similarity=0.116  Sum_probs=0.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      .|+|+. +|+.+.+.|..++++..||+..+++.|   ++..+++|+|.|+.|.++.|.+++++.++++|.+++.....
T Consensus        32 ~lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g---~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~gg  105 (389)
T 4da1_A           32 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIGG  105 (389)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             EEEEec-CCcEEEEEECCCChHHHHHHHHHHHhC---CCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeeccccc
Confidence            456665 667778999999999999999999999   99999999999999999999999999999999999876543

>3qx1_A FAS-associated factor 1; UBX, protein binding, P97 binding; 1.60A {Homo sapiens} PDB: 3qwz_B* 3qc8_B 3qca_A 3qq8_B 3r3m_B 1h8c_A

Probab=97.20  E-value=0.0012  Score=52.05  Aligned_cols=68  Identities=18%  Similarity=0.244  Sum_probs=58.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecC---CCCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~---D~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.||..+|+.+.-.+..++||.+|...|.. .+   ++....+|+  |-.|.|.   .+++|.++|+.+..+|+|-
T Consensus         9 ~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~-~~---~~~~~f~L~t~fPrk~l~~~d~~~TL~e~gL~p~a~L~ve   81 (84)
T 3qx1_A            9 KLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KG---FPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   81 (84)
T ss_dssp             EEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TT---CCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cC---CCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEEE
Confidence            6889999999888889999999999999987 56   667888887  6678884   4689999999998888775

>2dzk_A UBX domain-containing protein 2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} PDB: 2kxj_A

Probab=97.19  E-value=0.0032  Score=52.26  Aligned_cols=71  Identities=13%  Similarity=0.209  Sum_probs=60.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecC--C-CCcccccccCCCcEEEEEEe
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--D-VTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~--D-~~tLsd~gI~~~s~I~v~v~   75 (403)
                      +|.||..+|+.+.-.+..++||.+|...|....+   .+....+|+  |-.|.|.  | +++|.++|+.+..+|+|...
T Consensus        15 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~---~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~~   90 (109)
T 2dzk_A           15 RIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVG---NTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLPA   90 (109)
T ss_dssp             EEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHT---TSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEECC
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccC---CCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEEC
Confidence            6899999999999999999999999999999877   556677886  6788886  3 68999999998877766543

>2cos_A Serine/threonine protein kinase LATS2; UBA domain, structure genomics, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=97.18  E-value=0.00046  Score=49.96  Aligned_cols=42  Identities=29%  Similarity=0.414  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHc-CCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYS-GIPE  217 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~-GIP~  217 (403)
                      .-++++.|++||   |+++-|++||+..-| ..+-|+|||.- +.|+
T Consensus         9 n~qmlq~L~eMG---Fd~erae~Alk~Tg~~Gle~AmewL~k~~~~~   52 (54)
T 2cos_A            9 NRQMLQELVNAG---CDQEMAGRALKQTGSRSIEAALEYISKMSGPS   52 (54)
T ss_dssp             CHHHHHHHHHHH---CCHHHHHHHHHHHTSCCHHHHHHHHHHHSCSC
T ss_pred             HHHHHHHHHHcC---CCHHHHHHHHHHhCcccHHHHHHHHHHhcCCC
Confidence            457899999999   999999999999877 79999999975 4443

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens}

Probab=97.00  E-value=0.0008  Score=74.29  Aligned_cols=40  Identities=25%  Similarity=0.543  Sum_probs=36.5

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      +.|..|.+|||++.++++|+.+|++|.+.|++|||++..|
T Consensus       722 e~i~~l~~mGf~~~~a~~aL~~t~~~~eraidwlfs~~d~  761 (854)
T 3ihp_A          722 DCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDD  761 (854)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHhhcCcHHHHHHhhhcCccc
Confidence            4488899999999999999999999999999999997654

>2pwq_A Ubiquitin conjugating enzyme; structural genomics consortium, SGC, ligase; 1.90A {Plasmodium yoelii}

Probab=96.92  E-value=0.00014  Score=67.67  Aligned_cols=73  Identities=21%  Similarity=0.313  Sum_probs=16.5

Q ss_pred             CHHHHHHHHHcHHHHHHHhcCCCCCCCCcccccccccCCccccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHH
Q 015628          312 NPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAA  391 (403)
Q Consensus       312 nP~l~~lI~~n~e~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~  391 (403)
                      |++.+++...|++.|.+...+-...-        ...  ..   ..+-.+.|+||++|||+++.++.|+..|+||++.|+
T Consensus       143 n~eaa~~~~~d~~~f~~~ar~~t~~y--------a~~--~~---~~~~~~~v~~~~~mgf~~~~~~~al~~~~~~~~~~~  209 (216)
T 2pwq_A          143 DAEVAKMYKENHALFVKTASVWTKTF--------ATG--PK---EEPREVIIKKITEMGFSEDQAKNALIKANWNETLAL  209 (216)
T ss_dssp             CHHHHHHHHHCHHHHHHHHHHHHHHH--------SCC--C----------------------------------------
T ss_pred             cHHHHHHHHHCHHHHHHHHHHHHHHh--------cCC--Cc---ccchhhHHHHHHHcCCCHHHHHHHHHHcCCchHHHH
Confidence            67777888888888887753321000        000  00   012246799999999999999999999999999999


Q ss_pred             HHHhcc
Q 015628          392 NYLLDH  397 (403)
Q Consensus       392 ~~L~~~  397 (403)
                      +.||+.
T Consensus       210 ~~l~~~  215 (216)
T 2pwq_A          210 NTLLEN  215 (216)
T ss_dssp             ------
T ss_pred             HHHhcC
Confidence            999974

>3e46_A Ubiquitin-conjugating enzyme E2-25 kDa; huntington interacting, ligase, alternative splicing, cytoplasm, UBL conjugation, UBL conjugation pathway; 1.86A {Homo sapiens} SCOP: a.5.2.1 d.20.1.1 PDB: 3f92_A*

Probab=96.91  E-value=0.00087  Score=63.82  Aligned_cols=43  Identities=30%  Similarity=0.431  Sum_probs=40.1

Q ss_pred             cCCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          168 VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       168 ~~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      +.++++++.|++|++||   |+|++|+.||+..-.|-++|+|||+.
T Consensus       210 ~~~~~~~~~v~~l~~mg---f~~~~~~~al~~~nWd~~~A~e~L~~  252 (253)
T 3e46_A          210 VSSPEYTKKIENLCAAG---FDRNAVIVALSSKSWDVETATELLLS  252 (253)
T ss_dssp             CCCHHHHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             cCcchHHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            34678999999999999   99999999999999999999999985

>1wj4_A KIAA0794 protein; UBX domain, beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.2

Probab=96.54  E-value=0.0053  Score=52.16  Aligned_cols=69  Identities=22%  Similarity=0.344  Sum_probs=58.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeec--CC-CCcccccccCCCcEEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVL--KD-VTTLEENKVAENSFVVVML   74 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL--~D-~~tLsd~gI~~~s~I~v~v   74 (403)
                      +|.||..+|+.+.-.+..++||.+|...|... +   ++....+|+  |-.|.|  .| +++|.++|+.+...|+|..
T Consensus        45 ~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~---~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~~  118 (124)
T 1wj4_A           45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-G---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE  118 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-H---CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C---CCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEEE
Confidence            68899999999988999999999999999876 6   666778887  678988  34 7899999999988777653

>1wgl_A TOLL-interacting protein; CUE domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, immune system; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=96.25  E-value=0.0056  Score=45.40  Aligned_cols=41  Identities=27%  Similarity=0.337  Sum_probs=35.3

Q ss_pred             HHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015628          361 EAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDHMHEF  401 (403)
Q Consensus       361 ~ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~  401 (403)
                      ++|+.|.+|  ++++..+..+|.+|++|.+.|.+.||+-.++.
T Consensus        11 e~l~~L~emFP~ld~~~I~~vL~a~~gdvd~aI~~LL~m~~~~   53 (59)
T 1wgl_A           11 EDLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQMGEEP   53 (59)
T ss_dssp             HHHHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHSSCCC
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcCcCCC
Confidence            458889999  56899999999999999999999999865543

>2cr5_A Reproduction 8; UBX domain, D0H8S2298E protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.2

Probab=96.15  E-value=0.028  Score=46.44  Aligned_cols=69  Identities=16%  Similarity=0.130  Sum_probs=56.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecC--CCCcccccccCCCcEEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--DVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~--D~~tLsd~gI~~~s~I~v~v   74 (403)
                      +|.||..+|+.+.-.+..++||.+|...|... +   +.....+|+  |-.|.|.  .+++|.++||.+..+|+|..
T Consensus        25 ~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~---~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve~   97 (109)
T 2cr5_A           25 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-G---YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEE   97 (109)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-T---CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C---CCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEEe
Confidence            68899999998888899999999999999865 4   456678886  6688886  36899999999988776643

>1tte_A Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiquitin-dependent degradation, ligase; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1 d.20.1.1

Probab=96.05  E-value=0.0045  Score=57.46  Aligned_cols=77  Identities=13%  Similarity=0.140  Sum_probs=48.5

Q ss_pred             hCHHHHHHHHHcHHHHHHHhcCCCCCC-CCcccccccccCCccccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHH
Q 015628          311 QNPHLMRLIQEHQTDFLRLINEPVEGG-EGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEEL  389 (403)
Q Consensus       311 ~nP~l~~lI~~n~e~Fl~~l~~~~~~~-~g~~~~~~~~~~~~~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~  389 (403)
                      .|++..++...|++.|.+...+-...- .....+..+..  ....+-..+.+.|+||++|||+++.|++||..|++|+..
T Consensus       122 ln~eaa~~~~~d~~~f~~~ar~~t~~yA~~~~~~~~~~~--~~~~~~g~~~~~v~~~~~mg~~~~~~~~al~~~~~~~~~  199 (215)
T 1tte_A          122 QDAEVAQHYLRDRESFNKTAALWTRLYASETSNGQKGNV--EESDLYGIDHDLIDEFESQGFEKDKIVEVLRRLGVKSLD  199 (215)
T ss_dssp             SCHHHHHHHHHCHHHHHHHHHHHHHHSSCCCSCCSSCCC--SCSSCCCCSHHHHHHHHHHTCCHHHHHHHHHHSCCSSCC
T ss_pred             cCHHHHHHHHHCHHHHHHHHHHHHHHhccCCCcccccch--hhhhhccccHHHHHHHHHcCCCHHHHHHHHHHcCCCccc
Confidence            467777788888888877643211000 00000000000  123345566789999999999999999999999999843

>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain, protein binding; HET: ADP; 2.90A {Rattus norvegicus} SCOP: d.15.1.2 PDB: 1i42_A 1jru_A

Probab=95.96  E-value=0.021  Score=48.62  Aligned_cols=66  Identities=18%  Similarity=0.293  Sum_probs=54.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecCC-CCcccccccCCCcE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENSF   69 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~D-~~tLsd~gI~~~s~   69 (403)
                      +|.||..+|+.+.-.+..++||.+|...|......  +......|+  |-.|.|.| +++|.++|+.+...
T Consensus        54 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~--~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psav  122 (127)
T 1s3s_G           54 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPA--MAATSFVLMTTFPNKELADENQTLKEANLLNAVI  122 (127)
T ss_dssp             CEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSG--GGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcC--CCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceE
Confidence            58999999999999999999999999999886321  445677786  67899976 68999999998433

>2dam_A ETEA protein; KIAA0887, UBA-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.41  E-value=0.035  Score=42.07  Aligned_cols=47  Identities=19%  Similarity=0.145  Sum_probs=42.6

Q ss_pred             cccCCHHHHHHHHHHHHc-C-CChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          352 AVTVTPEEREAIERLEAM-G-FDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       352 ~~~lt~ee~~ai~rL~~l-G-F~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      ...||.+..+.|.+.+++ | -+...|++.+.+|+||.+.|++..|++.
T Consensus        11 ~~~Ls~~~~e~i~qF~~ITg~~d~~~A~~~Le~~~WnLe~Av~~ff~~~   59 (67)
T 2dam_A           11 ERDLTQEQTEKLLQFQDLTGIESMDQCRHTLEQHNWNIEAAVQDRLNEQ   59 (67)
T ss_dssp             CCCCCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHTSCHHHHHHHHHHSS
T ss_pred             hhhcChhHHHHHHHHHHHhCCCCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence            347899999999999998 8 6899999999999999999999999863

>2dal_A Protein KIAA0794; FAS associted factor 1, UBA-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.17  E-value=0.041  Score=40.98  Aligned_cols=47  Identities=21%  Similarity=0.352  Sum_probs=42.5

Q ss_pred             cccCCHHHHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          352 AVTVTPEEREAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       352 ~~~lt~ee~~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      ...|++...+.|.+.+++ |-++..|++.+.+|+||.+.|++..|++.
T Consensus         8 ~~~~s~~~~e~i~qF~~iTg~~~~~A~~~Le~~~WnLe~Av~~ff~~~   55 (62)
T 2dal_A            8 GSAASSALKGLIQQFTTITGASESVGKHMLEACNNNLEMAVTMFLDGG   55 (62)
T ss_dssp             CCSSCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTSCHHHHHHHHHHSC
T ss_pred             hhhcCccHHHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence            457888888899999997 89999999999999999999999999864

>2cos_A Serine/threonine protein kinase LATS2; UBA domain, structure genomics, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=94.95  E-value=0.021  Score=41.26  Aligned_cols=43  Identities=16%  Similarity=0.205  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHhccCC
Q 015628          357 PEEREAIERLEAMGFDRALVLEVFFACNK-NEELAANYLLDHMH  399 (403)
Q Consensus       357 ~ee~~ai~rL~~lGF~~~~~~~a~~ac~~-ne~~a~~~L~~~~~  399 (403)
                      ++-+.-++.|.+||||++.|..|+-..+. ..+.|..||+.-.+
T Consensus         7 ~vn~qmlq~L~eMGFd~erae~Alk~Tg~~Gle~AmewL~k~~~   50 (54)
T 2cos_A            7 GVNRQMLQELVNAGCDQEMAGRALKQTGSRSIEAALEYISKMSG   50 (54)
T ss_dssp             SCCHHHHHHHHHHHCCHHHHHHHHHHHTSCCHHHHHHHHHHHSC
T ss_pred             hhHHHHHHHHHHcCCCHHHHHHHHHHhCcccHHHHHHHHHHhcC
Confidence            33445599999999999999999988764 89999999986433

>1wgl_A TOLL-interacting protein; CUE domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, immune system; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=94.95  E-value=0.023  Score=42.05  Aligned_cols=39  Identities=28%  Similarity=0.356  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHc--CCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          173 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       173 ~e~~v~~i~~M--G~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .|+.|..|.+|  .   ++++.|+..|++.-+|.|+|++.|+.-
T Consensus         9 ~ee~l~~L~emFP~---ld~~~I~~vL~a~~gdvd~aI~~LL~m   49 (59)
T 1wgl_A            9 SEEDLKAIQDMFPN---MDQEVIRSVLEAQRGNKDAAINSLLQM   49 (59)
T ss_dssp             CHHHHHHHHHHCSS---SCHHHHHHHHTTTTTCHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            58899999999  5   899999999999999999999999975

>1v92_A NSFL1 cofactor P47; 3-helix bundle, recombination; NMR {Rattus norvegicus} SCOP: a.5.2.3

Probab=94.69  E-value=0.052  Score=37.52  Aligned_cols=40  Identities=10%  Similarity=0.125  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          359 EREAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       359 e~~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      ..+.|...+++ |-++..+++-+.+|+||.+.|++..|+++
T Consensus         5 ~~~~i~~F~~iTg~~~~~A~~~L~~~~wdle~Ai~~ff~~~   45 (46)
T 1v92_A            5 RQDALREFVAVTGAEEDRARFFLESAGWDLQIALASFYEDG   45 (46)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHTTSCSHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence            45679999887 89999999999999999999999999864

>2pwq_A Ubiquitin conjugating enzyme; structural genomics consortium, SGC, ligase; 1.90A {Plasmodium yoelii}

Probab=94.60  E-value=0.006  Score=56.69  Aligned_cols=41  Identities=24%  Similarity=0.293  Sum_probs=0.0

Q ss_pred             cHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCC
Q 015628          172 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  215 (403)
Q Consensus       172 ~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GI  215 (403)
                      .++..|+++++||   |+|+++++||+..--+-++|+|.|+.|+
T Consensus       176 ~~~~~v~~~~~mg---f~~~~~~~al~~~~~~~~~~~~~l~~~~  216 (216)
T 2pwq_A          176 PREVIIKKITEMG---FSEDQAKNALIKANWNETLALNTLLENS  216 (216)
T ss_dssp             --------------------------------------------
T ss_pred             chhhHHHHHHHcC---CCHHHHHHHHHHcCCchHHHHHHHhcCC
Confidence            3578999999999   9999999999999999999999999884

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=94.60  E-value=0.095  Score=40.30  Aligned_cols=60  Identities=17%  Similarity=0.246  Sum_probs=46.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      |+|+||........+++....||.+|-++    .|   +++...-+..+|+++..+.      +.+||.|.++
T Consensus         1 M~v~Vkl~g~~~~~~ev~~g~Tv~dLL~~----Lg---l~~~~VvV~vNG~~v~~d~------~l~GD~VeIv   60 (74)
T 2l32_A            1 MNVTVEVVGEETSEVAVDDDGTYADLVRA----VD---LSPHEVTVLVDGRPVPEDQ------SVEVDRVKVL   60 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHHT----TC---CCSSCCCEECCCCCCCTTS------SSCCCCEEEC
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHHH----cC---CCcceEEEEECCEECCHHH------CCCCCEEEEE
Confidence            99999977445556899999999998765    67   8888887788999987665      2348888766

>2daj_A KIAA0977 protein, COBL-like 1; ubiquitin-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.43  E-value=0.17  Score=40.14  Aligned_cols=70  Identities=14%  Similarity=0.208  Sum_probs=58.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEe---CCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy---~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      ++.|....-+++.+.|+|..++.+|--.|.++..   +.++.-.|..   .+..|+-+++|.||||++   ++.+=.++
T Consensus        12 RLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kce---fdp~~~~Ll~d~~~~e~LdLskSLndlgirE---Lya~d~~~   84 (91)
T 2daj_A           12 RVVINFKKTQKTIVRVSPHASLQELAPIICSKCE---FDPLHTLLLKDYQSQEPLDLTKSLNDLGLRE---LYAMDVNR   84 (91)
T ss_dssp             EEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTT---CCTTSEEEESCSSCCCBCCTTSCHHHHTCSE---EEEEECCC
T ss_pred             EEEEeecCcceeEEEeCCCCcHHHHHHHHhhccc---CChhhEEEecCCCCCcccchhcchhhhhhhh---hheecccc
Confidence            5777777888899999999999999999999977   7788887764   466788899999999997   66665444

>4fp9_B Mterf domain-containing protein 2; modification enzyme, transferase; HET: SAM; 2.90A {Homo sapiens}

Probab=94.24  E-value=0.34  Score=47.71  Aligned_cols=93  Identities=16%  Similarity=0.296  Sum_probs=52.5

Q ss_pred             HHHHHHHhCccchHHHHHHHHhhCHHHHHHHHHcHHHHHHHhcCCCCCCCCcccccccccCCccccCCHHHHHH-HHHH-
Q 015628          289 ALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREA-IERL-  366 (403)
Q Consensus       289 ~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI~~n~e~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~ee~~a-i~rL-  366 (403)
                      .+..+|..+|.+|..=+..           |..+= +|++-|+.....     ....-...|..+.++.+.... +.-| 
T Consensus        94 ~V~kiL~k~P~lL~~s~e~-----------L~~~l-~fL~~lGl~~~~-----i~~ll~~~P~lL~~s~e~i~~~v~~L~  156 (335)
T 4fp9_B           94 PVCVVLKKSPQLLKLPIMQ-----------MRKRS-SYLQKLGLGEGK-----LKRVLYCCPEIFTMRQQDINDTVRLLK  156 (335)
T ss_dssp             HHHHHHHHCGGGGGSCHHH-----------HHHHH-HHHHHTTCTTTT-----HHHHHHHCGGGGTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHhChhhccCCHHH-----------HHHHH-HHHHHcCCCHHH-----HHHHHHhCchhhccChHHHHHHHHHHH
Confidence            4567888899887622222           32332 455555443211     111111123467778877555 4545 


Q ss_pred             HHcCCChHHHHHHHHHhC-------CCHHHHHHHHhccC
Q 015628          367 EAMGFDRALVLEVFFACN-------KNEELAANYLLDHM  398 (403)
Q Consensus       367 ~~lGF~~~~~~~a~~ac~-------~ne~~a~~~L~~~~  398 (403)
                      ..|||+++++..++..|=       .+..--.+||...+
T Consensus       157 ~~lGfS~~ev~~mv~r~P~lL~~S~e~L~~K~efLv~~M  195 (335)
T 4fp9_B          157 EKCLFTVQQVTKILHSCPSVLREDLGQLEYKFQYAYFRM  195 (335)
T ss_dssp             HTSCCCHHHHHHHHHHCGGGGTSCHHHHHHHHHHHHTTT
T ss_pred             HHcCCCHHHHHHHHHhCChhhhCCHHHHHHHHHHHHHHh
Confidence            478999999999998883       23444455565543

>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.02  E-value=0.074  Score=40.33  Aligned_cols=38  Identities=18%  Similarity=0.281  Sum_probs=33.2

Q ss_pred             HHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          360 REAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       360 ~~ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      .++++.|++|  .+++..+..+|.+|++|.+.|++.||+-
T Consensus        19 ~~~v~~L~~MFP~lD~~vI~~vL~a~~G~vd~aId~LL~m   58 (67)
T 2dhy_A           19 NQAMDDFKTMFPNMDYDIIECVLRANSGAVDATIDQLLQM   58 (67)
T ss_dssp             HHHHHHHHHHCSSSCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            4569999999  3479999999999999999999999963

>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.92  E-value=0.11  Score=39.44  Aligned_cols=45  Identities=13%  Similarity=0.137  Sum_probs=38.8

Q ss_pred             CCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          169 AGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       169 ~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .+.+++..|..|.+|= =.++++-|+..|++.-+|.|+||+-|+.-
T Consensus        14 ~~~~~~~~v~~L~~MF-P~lD~~vI~~vL~a~~G~vd~aId~LL~m   58 (67)
T 2dhy_A           14 RRLEFNQAMDDFKTMF-PNMDYDIIECVLRANSGAVDATIDQLLQM   58 (67)
T ss_dssp             CCCCSHHHHHHHHHHC-SSSCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHC-CCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            4566899999999992 12799999999999999999999999863

>2di0_A Activating signal cointegrator 1 complex subunit 2; ASCC2, CUE domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=93.88  E-value=0.19  Score=38.53  Aligned_cols=50  Identities=14%  Similarity=0.341  Sum_probs=43.2

Q ss_pred             cCCccHHHHHHHHHHc--CCCCCCHHHHHHHHHHhhCChHHHHHHHHcC-CCCCCC
Q 015628          168 VAGSNLEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG-IPEQTA  220 (403)
Q Consensus       168 ~~g~~~e~~v~~i~~M--G~~~f~R~qv~~ALrAafnNPdRAvEyL~~G-IP~~~~  220 (403)
                      +.+.+.+..|.+|.++  -   |....|.++|..--+|+|+.|.+|+.| +|.++.
T Consensus         8 ~~~~~l~s~I~qV~DLfPd---LG~gfi~~~L~~y~~nvE~vin~LLE~~LPp~L~   60 (71)
T 2di0_A            8 MCGVELDSLISQVKDLLPD---LGEGFILACLEYYHYDPEQVINNILEERLAPTLS   60 (71)
T ss_dssp             CSSHHHHHHHHHHHHHCCS---SCHHHHHHHHHHTTTCHHHHHHHHHTTCCCTTTT
T ss_pred             CcHHHHHHHHHHHHHHccc---CCHHHHHHHHHHhCCCHHHHHHHHHccCCCHHHH
Confidence            4677899999999997  4   679999999999778999999999998 777653

>1otr_A Protein CUE2; protein-protein complex, cell cycle; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.4

Probab=93.79  E-value=0.086  Score=37.53  Aligned_cols=39  Identities=15%  Similarity=0.236  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHc--CCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          173 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       173 ~e~~v~~i~~M--G~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .+..|+.|.+|  .   -++++|+++|+++-+|-|||+..|+++
T Consensus         4 ~e~~v~~L~EMFP~---~~~~~ik~~L~~~~Gd~d~Ai~~LL~~   44 (49)
T 1otr_A            4 HESKLSILMDMFPA---ISKSKLQVHLLENNNDLDLTIGLLLKE   44 (49)
T ss_dssp             HHHHHHHHHHHCSS---SCHHHHHHHHHHTTTCSHHHHHHHHHH
T ss_pred             hHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            46789999999  4   589999999999999999999999987

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=93.78  E-value=0.29  Score=40.66  Aligned_cols=64  Identities=20%  Similarity=0.252  Sum_probs=45.7

Q ss_pred             CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCcEEEe----CCeecCCC-------------CcccccccCC
Q 015628           10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGKVLKDV-------------TTLEENKVAE   66 (403)
Q Consensus        10 g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~------~~QkLiy----~GkiL~D~-------------~tLsd~gI~~   66 (403)
                      +..+.+.|-..+||.++|+||-...-+. +|.      +.+.|-|    .|++|.|.             .||..|+|.+
T Consensus        23 ~~~i~vkVLdCDTItQvKeKiLd~vyk~-~pyS~rP~~~~~dLEwr~g~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~d  101 (111)
T 4e71_A           23 VDAIPVKVLNCDTISQVKEKIIDQVYRG-QPCSCWPRPDSVVLEWRPGSTAQILSDLDLTSQREGRWKRVNTLMHYNVRD  101 (111)
T ss_dssp             CCCEEEEEETTCBHHHHHHHHHHHHTC----------CCSEEEEEC--CCCEECCSSCTTSCC---CCCCCBHHHHTCCT
T ss_pred             CCceeeeeeccCcHHHHHHHHHHHHHcC-CccccCCCCCceeeEEecCCCCccccccCccceecCcceEecchhhcCCCC
Confidence            4557788889999999999999776432 443      4555654    35778762             3688999999


Q ss_pred             CcEEEEEE
Q 015628           67 NSFVVVML   74 (403)
Q Consensus        67 ~s~I~v~v   74 (403)
                      |.+|.++-
T Consensus       102 gatl~l~~  109 (111)
T 4e71_A          102 GATLILSK  109 (111)
T ss_dssp             TCEEEEEE
T ss_pred             CCEEEEEe
Confidence            99998764

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=93.67  E-value=0.36  Score=36.28  Aligned_cols=61  Identities=18%  Similarity=0.270  Sum_probs=44.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+|.... ....+++....||.+|.+++    +   ++.....+..+|+++..+.     -+++||.|.++-
T Consensus         5 m~i~vNg~~-~~~~~~~~~~~tv~~Ll~~l----~---~~~~~v~vavN~~~v~~~~-----~L~~gD~V~ii~   65 (70)
T 1ryj_A            5 MKFTVITDD-GKKILESGAPRRIKDVLGEL----E---IPIETVVVKKNGQIVIDEE-----EIFDGDIIEVIR   65 (70)
T ss_dssp             EEEEEEETT-EEEEEEESSCCBHHHHHHHT----T---CCTTTEEEEETTEECCTTS-----BCCTTCEEEEEE
T ss_pred             EEEEEeCcc-CceeEECCCCCcHHHHHHHh----C---CCCCCEEEEECCEECCCcc-----cCCCCCEEEEEe
Confidence            567776432 23456777778999999875    4   5566777889999997665     578899998873

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens}

Probab=92.80  E-value=0.079  Score=58.41  Aligned_cols=40  Identities=40%  Similarity=0.684  Sum_probs=37.5

Q ss_pred             cHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          172 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       172 ~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      ..++.|..|++||   |++++.++||++.-||.+|||+||.+.
T Consensus       719 ~~~e~i~~l~~mG---f~~~~a~~aL~~t~~~~eraidwlfs~  758 (854)
T 3ihp_A          719 PPEDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSH  758 (854)
T ss_dssp             CCHHHHHHHHTTT---CCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHcC---CCHHHHHHHHHhhcCcHHHHHHhhhcC
Confidence            3578899999999   999999999999999999999999985

>2r2o_A Plexin-B1; effector domain, structural genomics, structural GEN consortium, SGC, glycoprotein, membrane, phosphorylation, R secreted, transmembrane; 2.00A {Homo sapiens} PDB: 2rex_A* 2jph_A

Probab=92.77  E-value=0.32  Score=41.86  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=47.3

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCcEEEe----CCe-ecCCC-------------CcccccccCC
Q 015628           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGK-VLKDV-------------TTLEENKVAE   66 (403)
Q Consensus        11 ~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~------~~QkLiy----~Gk-iL~D~-------------~tLsd~gI~~   66 (403)
                      ..+.+.|-..+||.++|+||-...-++ +|.      ++.-|-+    .|+ +|.|.             .||..|+|.+
T Consensus        41 ~~i~VkVLdCDTItQvKeKiLDavYk~-~PySqRP~~~d~dLEwr~g~~g~liL~D~D~tS~~~~~wkrLNTL~HY~V~D  119 (138)
T 2r2o_A           41 QGVPVKVLDCDTISQAKEKMLDQLYKG-VPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPD  119 (138)
T ss_dssp             CCEEEEEETTCBHHHHHHHHHHHHTTT-SCGGGCCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBHHHHTCCT
T ss_pred             CceeEEEeccccHHHHHHHHHHHHHcC-CccccCCCccceeEEEecCCcCceEeeccCCcccccCCceeecchhccCCCC
Confidence            457888889999999999999887654 543      2344544    344 47663             2799999999


Q ss_pred             CcEEEEEEec
Q 015628           67 NSFVVVMLTK   76 (403)
Q Consensus        67 ~s~I~v~v~k   76 (403)
                      |.+|.++-+.
T Consensus       120 ga~l~l~~~~  129 (138)
T 2r2o_A          120 GATVALVPCL  129 (138)
T ss_dssp             TCEEEEEEC-
T ss_pred             CCEEEEEECC
Confidence            9999887654

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=92.75  E-value=0.43  Score=43.91  Aligned_cols=61  Identities=13%  Similarity=0.255  Sum_probs=50.4

Q ss_pred             EEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CcEEE--e-CC--eecCC-CCcccccccCCCcEEEEEEec
Q 015628           13 FEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLI--H-QG--KVLKD-VTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus        13 ~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~-~QkLi--y-~G--kiL~D-~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      +.+.++..+||.+|++++...++   ++.+ ..||-  | .+  ..|.| +++|.+++|.++..|+|=++.
T Consensus       142 ~~~~~Sk~~ti~~l~~~~~~~~~---i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~r~  209 (217)
T 4a3p_A          142 VTRRFSKADTIDTIEKEIRKIFS---IPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKN  209 (217)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTT---CCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEECC
T ss_pred             eEEEEcccchHHHHHHHHHHHhC---CCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEEec
Confidence            56788999999999999999999   8886 68883  4 22  45666 579999999999999888764

>1otr_A Protein CUE2; protein-protein complex, cell cycle; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.4

Probab=92.56  E-value=0.17  Score=35.95  Aligned_cols=40  Identities=15%  Similarity=0.227  Sum_probs=34.8

Q ss_pred             HHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015628          360 REAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDHMH  399 (403)
Q Consensus       360 ~~ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~~~~  399 (403)
                      .+.|+.|.+|  .-++.++..+|.+|++|.+.|.+.|++...
T Consensus         5 e~~v~~L~EMFP~~~~~~ik~~L~~~~Gd~d~Ai~~LL~~~~   46 (49)
T 1otr_A            5 ESKLSILMDMFPAISKSKLQVHLLENNNDLDLTIGLLLKEND   46 (49)
T ss_dssp             HHHHHHHHHHCSSSCHHHHHHHHHHTTTCSHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhccc
Confidence            3568999999  457999999999999999999999998643

>3jyu_A Ubiquitin carboxyl-terminal hydrolase; domain in ubiquitin-specific peptidases (DUSP), proto- oncogene, ubiquitin-fold, UBL, protease, thioesterase; HET: 1PS; 2.37A {Mus musculus}

Probab=92.43  E-value=0.63  Score=43.20  Aligned_cols=61  Identities=13%  Similarity=0.249  Sum_probs=50.4

Q ss_pred             EEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CcEEEe-C----CeecCC-CCcccccccCCCcEEEEEEec
Q 015628           13 FEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIH-Q----GKVLKD-VTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus        13 ~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~-~QkLiy-~----GkiL~D-~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      +++.++..+||.+|++++...++   ++.+ ..||-. .    ...|.| +.+|.+++|.++..|+|=++.
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~---i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE~r~  221 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFN---IPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQN  221 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTT---CCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEEECC
T ss_pred             EEEEecccCcHHHHHHHHHHHhC---CCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEEEec
Confidence            55678999999999999999999   8887 688842 2    346766 589999999999999888764

>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.2

Probab=92.35  E-value=0.19  Score=37.72  Aligned_cols=36  Identities=14%  Similarity=0.235  Sum_probs=32.2

Q ss_pred             HHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          362 AIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       362 ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      .|+.|.+. |....+|.+|+..||+|.+.|..||-+.
T Consensus        12 ~Vk~LRe~TGag~~dcKkAL~e~~GDi~~Ai~~Lr~k   48 (64)
T 2cp9_A           12 LLMKLRRKTGYSFVNCKKALETCGGDLKQAEIWLHKE   48 (64)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            38888876 9999999999999999999999999654

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1

Probab=91.88  E-value=0.91  Score=36.20  Aligned_cols=68  Identities=21%  Similarity=0.291  Sum_probs=47.3

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCC--CCC------CCCCcEEEeCCeecCCCCcccccccC
Q 015628            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGS--DVY------PASQQMLIHQGKVLKDVTTLEENKVA   65 (403)
Q Consensus         1 MkI~VKtl~------g-~~~~ieV~~~~TV~dLK~kI~~~~g~--~~i------p~~~QkLiy~GkiL~D~~tLsd~gI~   65 (403)
                      |+|+||...      | ....+++....||.+|.+.+......  ..+      ......+..+|+....     ++-|+
T Consensus        10 ~~v~V~~FA~lre~~g~~~~~~e~~~~~Tv~~Ll~~L~~~~p~l~~~l~~~~g~~~~~v~v~VNg~~v~~-----~~~L~   84 (98)
T 1vjk_A           10 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSW-----DEELK   84 (98)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCT-----TCBCC
T ss_pred             EEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHhHChhHHHHhhccccccCCcEEEEECCEECCC-----CCCCC
Confidence            678888653      3 46678887789999999999877421  000      0134567788887753     55688


Q ss_pred             CCcEEEEE
Q 015628           66 ENSFVVVM   73 (403)
Q Consensus        66 ~~s~I~v~   73 (403)
                      +||.|.++
T Consensus        85 dGDeV~i~   92 (98)
T 1vjk_A           85 DGDVVGVF   92 (98)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEE
Confidence            99998876

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=90.89  E-value=0.99  Score=38.27  Aligned_cols=65  Identities=20%  Similarity=0.277  Sum_probs=47.1

Q ss_pred             CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCcEEEe----CCe-ecCCC-------------CcccccccC
Q 015628           10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGK-VLKDV-------------TTLEENKVA   65 (403)
Q Consensus        10 g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~------~~QkLiy----~Gk-iL~D~-------------~tLsd~gI~   65 (403)
                      +..+.+.|-..+||.++|+||-...-+. +|.      +.+.|-|    .|+ +|.|.             .||..|+|.
T Consensus        16 ~~~i~VkVLdCDTItQvKeKiLd~vyk~-~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~~krLNTL~HY~V~   94 (127)
T 3h6n_A           16 MDSLSVRAMDTDTLTQVKEKILEAFCKN-VPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDGRKKLNTLAHYKIP   94 (127)
T ss_dssp             CCCEEEEEETTSBHHHHHHHHHHHHSTT-SCGGGSCCGGGEEEEEECSSSCEEECCSSSTTSCEETTEECCCBTTTTTCC
T ss_pred             CCceeeeeeccCchhhhhHHHHHHHhcc-CCcccCCCCcccceEEecCCCCceEeecCCCcceecCceeEeccccccCCC
Confidence            4557788889999999999999876433 443      4556654    234 46652             368899999


Q ss_pred             CCcEEEEEEe
Q 015628           66 ENSFVVVMLT   75 (403)
Q Consensus        66 ~~s~I~v~v~   75 (403)
                      +|.+|.+..+
T Consensus        95 dgatv~l~~~  104 (127)
T 3h6n_A           95 EGASLAMSLI  104 (127)
T ss_dssp             TTCEEEEEEC
T ss_pred             CCCEEEEEEc
Confidence            9999988754

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A

Probab=90.76  E-value=0.95  Score=42.41  Aligned_cols=41  Identities=20%  Similarity=0.393  Sum_probs=31.5

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHH-------hh-CChHHHHHHHHc-CCCC
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRA-------AY-NNPERAVEYLYS-GIPE  217 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrA-------af-nNPdRAvEyL~~-GIP~  217 (403)
                      ..+|+.|.+||   ++..++++..+.       .. .|...-++||.. |++.
T Consensus         6 s~~l~~L~~lG---v~~~~i~k~p~~~p~lL~~~~~~~l~~~l~fL~~lG~~~   55 (270)
T 3m66_A            6 SETLQKLVLLG---VDLSKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIED   55 (270)
T ss_dssp             HHHHHHHHHTT---CCHHHHTTSHHHHHHHHTCCHHHHTHHHHHHHHHHTCCG
T ss_pred             hHHHHHHHHcC---CCHHHHhhccchhhhhhccChhhhHHHHHHHHHHcCCCH
Confidence            46899999999   999999876555       32 256668899977 7664

>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.2

Probab=90.75  E-value=0.39  Score=35.99  Aligned_cols=36  Identities=14%  Similarity=0.167  Sum_probs=33.1

Q ss_pred             HHHHHHHHc-CCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          175 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       175 ~~v~~i~~M-G~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      ..|..|.++ |   +...+|..||..+-+|.+.|++||..
T Consensus        11 ~~Vk~LRe~TG---ag~~dcKkAL~e~~GDi~~Ai~~Lr~   47 (64)
T 2cp9_A           11 ELLMKLRRKTG---YSFVNCKKALETCGGDLKQAEIWLHK   47 (64)
T ss_dssp             HHHHHHHHHHC---CCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            579999996 8   89999999999999999999999963

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=90.70  E-value=0.64  Score=35.10  Aligned_cols=65  Identities=6%  Similarity=0.183  Sum_probs=44.3

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCC--CCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPA--SQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~-~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~--~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      |+|+||....- .-.+++ ...||.+|++.+....+   +..  ....+..+|+.+.+    .+.-+++||.|.++
T Consensus         1 M~v~V~~fa~l~~~~~e~-~~~tv~~ll~~L~~~~~---l~~~l~~~~vavN~~~v~~----~~~~l~~gDeV~i~   68 (74)
T 3rpf_C            1 MMVEVRFFGPIKEENFFI-KANDLKELRAILQEKEG---LKEWLGVCAIALNDHLIDN----LNTPLKDGDVISLL   68 (74)
T ss_dssp             CEEEEEECTTCCCCCEEE-ECSSHHHHHHHHHTCTT---TTTTTTTCEEEESSSEECC----TTCCCCTTCEEEEE
T ss_pred             CEEEEEEEeecceeEEee-CCCcHHHHHHHHHHCcC---HHHHhhccEEEECCEEcCC----CCcCCCCCCEEEEE
Confidence            88999976431 134666 56799999999986533   221  34566678887543    24568899999887

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=90.25  E-value=0.67  Score=38.84  Aligned_cols=65  Identities=25%  Similarity=0.360  Sum_probs=45.6

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC------CcEEEe-CC---e-ecCCC-------------CcccccccCC
Q 015628           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPAS------QQMLIH-QG---K-VLKDV-------------TTLEENKVAE   66 (403)
Q Consensus        11 ~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~------~QkLiy-~G---k-iL~D~-------------~tLsd~gI~~   66 (403)
                      ..+.+.|-..+||.++|+||-...-+. +|.+      .+.|-| .|   + +|.|.             .||..|+|.+
T Consensus        27 ~~i~VkVLdCDTItQvKeKiLd~vyk~-~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~d  105 (117)
T 4e74_A           27 PEVPVKILNCDTITQVKEKILDAIFKN-VPCSHRPKAADMDLEWRQGSGARMILQDEDITTKIENDWKRLNTLAHYQVPD  105 (117)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTT-SCGGGSCCGGGEEEEEECTTSCEEEECSSSTTCCC---CCCCCBHHHHTCCT
T ss_pred             CceEeeeecCCchHHHHHHHHHHHhcC-CCcccCCCCCceeEEEecCCCCceEeecCCCccEecCcceEeccccccCCCC
Confidence            347778888999999999999776432 4433      445544 23   3 46552             3689999999


Q ss_pred             CcEEEEEEec
Q 015628           67 NSFVVVMLTK   76 (403)
Q Consensus        67 ~s~I~v~v~k   76 (403)
                      |.+|.++.+.
T Consensus       106 gatl~l~~~~  115 (117)
T 4e74_A          106 GSVVALVSKQ  115 (117)
T ss_dssp             TCEEEEEECC
T ss_pred             CCEEEEEeCC
Confidence            9999887543

>1pve_A HHR23B, UV excision repair protein RAD23 homolog B; XPC binding domain, solution structure, nucleotide excision repair, chaps, DNA binding protein; NMR {Homo sapiens} SCOP: a.189.1.1

Probab=89.84  E-value=0.14  Score=39.37  Aligned_cols=39  Identities=23%  Similarity=0.474  Sum_probs=28.4

Q ss_pred             HHhhCcHHHH--HHHHHHHhCccchHHHHHHHHhhCH-HHHHHHHHc
Q 015628          279 DFLRNSQQFQ--ALRTMVQANPQILQPMLQELGKQNP-HLMRLIQEH  322 (403)
Q Consensus       279 ~~Lr~~pqf~--~lR~~vq~NP~lL~~~lq~i~~~nP-~l~~lI~~n  322 (403)
                      +.+++||++.  -|.++-++||++++     +.++|| +|+++|++-
T Consensus        20 ~~vqqNP~lL~~lLqqL~~~NPqL~q-----~I~~n~e~Fl~ll~e~   61 (72)
T 1pve_A           20 QIIQQNPSLLPALLQQIGRENPQLLQ-----QISQHQEHFIQMLNEP   61 (72)
T ss_dssp             HHHTTCGGGHHHHHHHHHTTCHHHHH-----HHHTTHHHHHHHHHSC
T ss_pred             HHHHHCHHHHHHHHHHHHhHCHHHHH-----HHHHCHHHHHHHHcCC
Confidence            5566688864  56778899999876     556775 588888653

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A

Probab=88.25  E-value=1.3  Score=43.41  Aligned_cols=71  Identities=13%  Similarity=0.057  Sum_probs=53.3

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCC-CCCCCCcEEEe------CCeecCCCCcccccccCCCcEEEEEE
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSD-VYPASQQMLIH------QGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~-~ip~~~QkLiy------~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      +.|... +.+.++.++++.||.++..+|.++.... ..+.++--|..      +|+=|++.++|..|++.+++.|....
T Consensus         6 ~~~~~~-~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~~   83 (371)
T 3ivf_A            6 LKISIG-NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYRK   83 (371)
T ss_dssp             EEEEET-TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEEE
T ss_pred             EEEEec-ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeeccC
Confidence            445543 6778899999999999999998886520 12345556655      45668889999999999999887664

>2qho_B E3 ubiquitin-protein ligase EDD1; protein-protein complex, protein binding/ligase complex; 1.85A {Homo sapiens}

Probab=87.84  E-value=0.57  Score=33.07  Aligned_cols=35  Identities=26%  Similarity=0.385  Sum_probs=29.8

Q ss_pred             HHHHHH--cCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          363 IERLEA--MGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       363 i~rL~~--lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      |.+-..  -|=+|+..|+-+...+-|.++|+|-|++.
T Consensus        13 i~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsR   49 (53)
T 2qho_B           13 ISQAQVVLQGKSRSVIIRELQRTNLDVNLAVNNLLSR   49 (53)
T ss_dssp             HHHHHHHSTTCCHHHHHHHHHHTTTCHHHHHHHHHC-
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHhCccHHHHHHHHhcc
Confidence            555444  38999999999999999999999999987

>2f4m_B UV excision repair protein RAD23 homolog B; glycoproteins, ubiquitin-dependent protein degradation, NUCL excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: a.189.1.1 PDB: 2f4o_B*

Probab=87.80  E-value=0.22  Score=37.01  Aligned_cols=36  Identities=22%  Similarity=0.454  Sum_probs=25.2

Q ss_pred             hhCcHHHH--HHHHHHHhCccchHHHHHHHHhhCHH-HHHHHHH
Q 015628          281 LRNSQQFQ--ALRTMVQANPQILQPMLQELGKQNPH-LMRLIQE  321 (403)
Q Consensus       281 Lr~~pqf~--~lR~~vq~NP~lL~~~lq~i~~~nP~-l~~lI~~  321 (403)
                      +++||+..  -|.++-++||++++     +.++||+ |+++|++
T Consensus        20 vq~NP~~L~~lLqql~~~nP~l~~-----~I~~n~e~Fl~ll~e   58 (61)
T 2f4m_B           20 IQQNPSLLPALLQQIGRENPQLLQ-----QISQHQEHFIQMLNE   58 (61)
T ss_dssp             HHHCGGGHHHHHHHHHHHCHHHHH-----HHHHSHHHHHHHHTS
T ss_pred             HHHCHHHHHHHHHHHHhHCHHHHH-----HHHHCHHHHHHHHcc
Confidence            34478764  56778899999876     5567754 7887753

>2dzl_A Protein FAM100B; UBA-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.73  E-value=0.96  Score=33.95  Aligned_cols=41  Identities=12%  Similarity=0.106  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          358 EEREAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       358 ee~~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      .+.+.|...+++ |=++..+++.+.+|+||-+.|++.+|++.
T Consensus        16 ~~q~~i~qF~~iTg~~~~~A~~~Le~~~WdLe~Al~~ff~~~   57 (66)
T 2dzl_A           16 RHQVMINQFVLAAGCAADQAKQLLQAAHWQFETALSTFFQET   57 (66)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHTTTTCHHHHHHHHHTCS
T ss_pred             ccHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence            333579999887 89999999999999999999999999864

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A*

Probab=86.80  E-value=1.3  Score=43.07  Aligned_cols=38  Identities=21%  Similarity=0.273  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHH----HHhhCChHHHHHHHHc
Q 015628          173 LEATVQQILDMGGGSWDRETVIRAL----RAAYNNPERAVEYLYS  213 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~AL----rAafnNPdRAvEyL~~  213 (403)
                      .+.+|+.|.++|   +++++++++-    ..+-.|||.-++||..
T Consensus        19 ~~~~v~~L~s~G---l~~~~~~~~~p~l~~~s~~~~~~vl~fL~~   60 (343)
T 3mva_O           19 NEDLLKNLLTMG---VDIDMARKRQPGVFHRMITNEQDLKMFLLS   60 (343)
T ss_dssp             -CCHHHHHHHHT---CCHHHHHHHCGGGGGCSCCCHHHHHHHHHH
T ss_pred             cHHHHHHHHHcC---CCHHHHHHhCchhhccCcccHHHHHHHHHH
Confidence            456899999999   9999886652    1234589999999974

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=86.68  E-value=4.3  Score=31.33  Aligned_cols=56  Identities=9%  Similarity=0.165  Sum_probs=41.0

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCC-----C-----CCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYP-----A-----SQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus        11 ~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip-----~-----~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      ....+++....||.+|++.+...+..  +.     .     ....+..+|+....     ++-|++||.|.++
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~--~~~~~l~~~g~l~~~~~v~VN~~~v~~-----~~~l~~gDeV~i~   83 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPA--LESRVFGDDGELYDHINVLRNGEAAAL-----GEATAAGDELALF   83 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGG--GHHHHBCTTSCBCTTSEEEETTEECCT-----TSBCCTTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcH--HHHHHhccCCcccccEEEEECCEECCC-----CcccCCCCEEEEE
Confidence            56788888788999999999887531  10     0     12567778888765     4568889999887

>1ip9_A BEM1 protein; ubiquitin alpha/beta roll, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 1ipg_A 2kfk_A

Probab=85.93  E-value=0.98  Score=35.64  Aligned_cols=43  Identities=14%  Similarity=0.116  Sum_probs=32.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE-eCC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-HQG   50 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi-y~G   50 (403)
                      ||.|- .++-.|-|.|..+.+..+||.||..+..   +  +...|+ |++
T Consensus        14 KVK~y-y~DDIiAIrvP~di~~~~L~dKi~~RLk---~--~~~~l~~ykd   57 (85)
T 1ip9_A           14 KIKFY-YKDDIFALMLKGDTTYKELRSKIAPRID---T--DNFKLQTKLF   57 (85)
T ss_dssp             EEEEC-BTTCCEEEEECSCCCHHHHHHHHHHHHT---S--SCEEEEECCS
T ss_pred             EEEEE-ecCcEEEEECCCCCCHHHHHHHHHHHhc---c--cceEEEEecC
Confidence            44444 3466899999999999999999999987   4  566654 443

>1ufz_A Hypothetical protein BAB28515; HBS1-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, translatio; NMR {Mus musculus} SCOP: a.5.9.1

Probab=85.92  E-value=1.5  Score=34.45  Aligned_cols=45  Identities=9%  Similarity=0.265  Sum_probs=37.6

Q ss_pred             ccCCHHHHHH----HHHHHH-cC--CChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          353 VTVTPEEREA----IERLEA-MG--FDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       353 ~~lt~ee~~a----i~rL~~-lG--F~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      -+|++.|++.    ++.+.+ ||  .++.+.++|.++|+-|.+.|.+++|+.
T Consensus        24 ~~Ls~~d~arL~SCLd~iR~VlGdsV~e~~Lv~ailk~dfD~ekALd~vL~~   75 (83)
T 1ufz_A           24 HQLSEIDQARLYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQ   75 (83)
T ss_dssp             HHCCHHHHHHHHHHHHHHHHHTTTTSCHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHcccCCHHHHHHHHHHhcCCHHHHHHHHHhc
Confidence            3588888876    455555 47  899999999999999999999999964

>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.3.3 PDB: 1xo3_A

Probab=85.56  E-value=0.95  Score=37.55  Aligned_cols=69  Identities=12%  Similarity=0.078  Sum_probs=42.6

Q ss_pred             CEEEEEeCC------C--cEEEEEeCC---CCcHHHHHHHHHHHhCCCCCCCCCcEEEeC-Ce------ecCCCCc---c
Q 015628            1 MKVFVKTLK------G--THFEIEVKP---EDKVSDVKKNIETVQGSDVYPASQQMLIHQ-GK------VLKDVTT---L   59 (403)
Q Consensus         1 MkI~VKtl~------g--~~~~ieV~~---~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~-Gk------iL~D~~t---L   59 (403)
                      |+|+|+...      |  +.++|++..   ..||.+|...|.+.+.     ..+.+|+.. |+      +|-++..   |
T Consensus        12 M~v~V~~~~~Lr~~~g~~~~~~vel~~~~~~~TV~~Ll~~L~~~~~-----~~~~~lf~~~g~lr~~i~VlVN~~di~~l   86 (114)
T 1wgk_A           12 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLL-----KERPELFIQGDSVRPGILVLINDADWELL   86 (114)
T ss_dssp             EEEEEEECTTTGGGTTTCSEEEEEECCCSSCCBHHHHHHHHTTTTC-----CSCHHHHCCSSSCCSSEEEEESSSBHHHH
T ss_pred             cEEEEEEchHHHHHhCCceEEEEEeCCCCCCCCHHHHHHHHHHHcc-----chhHhhCccCCcccCCeEEEECCeeeecc
Confidence            678888543      3  356788873   3699999999987752     233343322 22      2323332   2


Q ss_pred             --cccccCCCcEEEEEE
Q 015628           60 --EENKVAENSFVVVML   74 (403)
Q Consensus        60 --sd~gI~~~s~I~v~v   74 (403)
                        .++-+++||.|.++-
T Consensus        87 ~gldt~L~dGDeV~iip  103 (114)
T 1wgk_A           87 GELDYQLQDQDSILFIS  103 (114)
T ss_dssp             CTTTCBCCSSEEEEEEE
T ss_pred             CCcCcCCCCCCEEEEeC
Confidence              357799999987764

>4dbg_B Ring finger protein 31; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens}

Probab=85.30  E-value=0.91  Score=39.90  Aligned_cols=38  Identities=18%  Similarity=0.252  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHcC-CChHHHHHHHHHhCCCHHHHHHHH
Q 015628          357 PEEREAIERLEAMG-FDRALVLEVFFACNKNEELAANYL  394 (403)
Q Consensus       357 ~ee~~ai~rL~~lG-F~~~~~~~a~~ac~~ne~~a~~~L  394 (403)
                      ..-+.+++.|..+| |++++|++|+...++|++.|...|
T Consensus       100 ~~R~~K~~eL~s~G~~~~~~~~~aL~~~~Gdv~~Al~eL  138 (162)
T 4dbg_B          100 RTRRRKVQELQSLGFGPEEGSLQALFQHGGDVSRALTEL  138 (162)
T ss_dssp             HHHHHHHHHHHHTTCCGGGTHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCchHHHHHHHHHHcCCcHHHHHHHH
Confidence            34456799999999 599999999999999999998876

>1oey_A P67-PHOX, neutrophil cytosol factor 2; immune system, PB1 heterodimer/complex, NADPH oxidase, PB1 D heterodimerization; 2.0A {Homo sapiens} SCOP: d.15.2.2

Probab=85.02  E-value=1.5  Score=34.54  Aligned_cols=44  Identities=11%  Similarity=0.052  Sum_probs=37.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~G   50 (403)
                      +|+|..  .-++.|.|..+.+..+|+.+|.++.+   ++.+..+|.|+.
T Consensus         7 ~VKV~~--~~tvairvp~~~~y~~L~~~l~~kL~---l~~~~~~LsYk~   50 (83)
T 1oey_A            7 TLKVHY--KYTVVMKTQPGLPYSQVRDMVSKKLE---LRLEHTKLSYRP   50 (83)
T ss_dssp             EEEEES--SSEEEEEECTTCCHHHHHHHHHHHTT---CCGGGCCEEECC
T ss_pred             EEEEEE--EEEEEEECCCCCCHHHHHHHHHHHhC---CCcceeEEEeeC
Confidence            455553  36889999999999999999999999   888899999965

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=84.72  E-value=1.7  Score=34.40  Aligned_cols=57  Identities=9%  Similarity=0.239  Sum_probs=40.7

Q ss_pred             CCCcEEEEEeCCC-CcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            8 LKGTHFEIEVKPE-DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         8 l~g~~~~ieV~~~-~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      ++|+.  +++... .||.+|.+.+    +   ++.....+..+|+++..+ ...+.-|++||.|.++-
T Consensus        25 vNGe~--~el~~~~~Tv~dLL~~L----~---~~~~~vaVavNg~iV~~~-~~~~~~L~dGD~Vei~~   82 (87)
T 1tyg_B           25 LNGKD--VKWKKDTGTIQDLLASY----Q---LENKIVIVERNKEIIGKE-RYHEVELCDRDVIEIVH   82 (87)
T ss_dssp             ETTEE--ECCSSSCCBHHHHHHHT----T---CTTSCCEEEETTEEECGG-GTTTSBCCSSSEEEEEE
T ss_pred             ECCEE--EECCCCCCcHHHHHHHh----C---CCCCCEEEEECCEECChh-hcCCcCCCCCCEEEEEc
Confidence            45664  445665 8999999875    5   566777788999988543 33445689999998874

>1p3q_Q VPS9P, vacuolar protein sorting-associated protein VPS9; trafficking, post translational modification, mono- ubiquitination; 1.70A {Saccharomyces cerevisiae} SCOP: a.5.2.4 PDB: 1mn3_A

Probab=84.70  E-value=0.42  Score=34.65  Aligned_cols=39  Identities=23%  Similarity=0.400  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhc
Q 015628          358 EEREAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLD  396 (403)
Q Consensus       358 ee~~ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~  396 (403)
                      |-.++|+.|++|  .+|++.+.-+++++++|.+.|++.||+
T Consensus        11 e~~~~~~~L~~MFP~lD~evI~~Vl~a~~G~~~~~IdaLLq   51 (54)
T 1p3q_Q           11 ERKDTLNTLQNMFPDMDPSLIEDVCIAAASRIGPCVDALLS   51 (54)
T ss_dssp             HHHHHHHHHHHHSTTSCHHHHHHHHHHSCC--CGGGC----
T ss_pred             HHHHHHHHHHHHcccCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            445679999999  689999999999999999999999986

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=83.92  E-value=2.9  Score=32.90  Aligned_cols=60  Identities=13%  Similarity=0.128  Sum_probs=51.4

Q ss_pred             EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628           14 EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus        14 ~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      ...++-..++..||+.++.+.|   +.-+.-.+...+..|+++++|.+-+|+-...|.+.+--
T Consensus         6 ~qhmDI~epL~~Lk~LLe~Rl~---i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqi   65 (89)
T 2juo_A            6 SQAIDINEPIGNLKKLLEPRLQ---CSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQV   65 (89)
T ss_dssp             EEEEESSSBGGGHHHHSHHHHC---SCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEE
T ss_pred             hhhccccCcHHHHHHHHHHHhc---CCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEE
Confidence            3455667789999999999999   78888888888888999999999999988888877653

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=82.50  E-value=3  Score=35.24  Aligned_cols=61  Identities=21%  Similarity=0.219  Sum_probs=41.1

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHh----CCCCCCCC----CcEEEe-C---CeecCC----------C----Cccccccc
Q 015628           11 THFEIEVKPEDKVSDVKKNIETVQ----GSDVYPAS----QQMLIH-Q---GKVLKD----------V----TTLEENKV   64 (403)
Q Consensus        11 ~~~~ieV~~~~TV~dLK~kI~~~~----g~~~ip~~----~QkLiy-~---GkiL~D----------~----~tLsd~gI   64 (403)
                      ..+.+.|-..+||.++|+||-...    +   +|..    .+.|-| .   |++|.|          .    .||..|+|
T Consensus        39 ~~v~VkVLdCDTItQVKEKILdavYk~k~---~pys~r~~d~dLEwr~g~~~~~L~D~D~tS~~~e~~wkrLNTL~HY~V  115 (126)
T 3kuz_A           39 RNISVNVLDCDTIGQAKEKIFQAFLSKNG---SPYGLQLNEIGLELQMGTRQKELLDIDSSSVILEDGITKLNTIGHYEI  115 (126)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHHHHHS---SCCSSCGGGEEEEEEETTEEEEECSSCTTCCBCTTSCBCCCBTGGGTC
T ss_pred             CceEeeeecCCcHHHHHHHHHHHHhccCC---CcCCCCccccceEEecCCCcceeeccCCcceEecCCeeEeccccccCC
Confidence            457888889999999999997553    4   5442    334433 1   234433          1    25788999


Q ss_pred             CCCcEEEEEE
Q 015628           65 AENSFVVVML   74 (403)
Q Consensus        65 ~~~s~I~v~v   74 (403)
                      .+|.+|.++.
T Consensus       116 ~Dgatlal~k  125 (126)
T 3kuz_A          116 SNGSTIKVFK  125 (126)
T ss_dssp             CTTCEEEEEE
T ss_pred             CCCCEEEEee
Confidence            9999997763

>2di0_A Activating signal cointegrator 1 complex subunit 2; ASCC2, CUE domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=82.25  E-value=2.3  Score=32.40  Aligned_cols=44  Identities=14%  Similarity=0.244  Sum_probs=36.2

Q ss_pred             CCHHHHH-HHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          355 VTPEERE-AIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       355 lt~ee~~-ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      ++..+++ .|.++++|  -+....+.+.+..+|.|.|.++|.|||+.
T Consensus         8 ~~~~~l~s~I~qV~DLfPdLG~gfi~~~L~~y~~nvE~vin~LLE~~   54 (71)
T 2di0_A            8 MCGVELDSLISQVKDLLPDLGEGFILACLEYYHYDPEQVINNILEER   54 (71)
T ss_dssp             CSSHHHHHHHHHHHHHCCSSCHHHHHHHHHHTTTCHHHHHHHHHTTC
T ss_pred             CcHHHHHHHHHHHHHHcccCCHHHHHHHHHHhCCCHHHHHHHHHccC
Confidence            3444444 48899988  46799999999999999999999999964

>3e21_A HFAF1, FAS-associated factor 1; UBA, alternative splicing, apoptosis, nucleus, phosphoprotein; 1.73A {Homo sapiens}

Probab=82.21  E-value=1.1  Score=31.16  Aligned_cols=36  Identities=14%  Similarity=0.151  Sum_probs=30.5

Q ss_pred             HHHHHHHHHc-CCCh-HHHHHHHHHhCCCHHHHHHHHh
Q 015628          360 REAIERLEAM-GFDR-ALVLEVFFACNKNEELAANYLL  395 (403)
Q Consensus       360 ~~ai~rL~~l-GF~~-~~~~~a~~ac~~ne~~a~~~L~  395 (403)
                      .+.|..++++ |-+. .+|++-+.+|+||-+.|++-.|
T Consensus         6 de~ia~F~~iTG~~d~~~A~~~Lea~nWDLe~Av~~f~   43 (45)
T 3e21_A            6 EMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVI   43 (45)
T ss_dssp             HHHHHHHHHHHCCCCHHHHHHHHHHTTTCHHHHHTTC-
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHcCCcHHHHHHHHc
Confidence            3568899998 9876 9999999999999999987543

>1q02_A Sequestosome 1; helical bundle, protein binding; NMR {Homo sapiens} SCOP: a.5.2.1 PDB: 2jy7_A 2jy8_A 2k0b_X 2knv_A 2rru_A 3b0f_A

Probab=81.90  E-value=1.4  Score=31.56  Aligned_cols=37  Identities=16%  Similarity=0.142  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHcCCChHHH--HHHHHHhCCCHHHHHHHHh
Q 015628          359 EREAIERLEAMGFDRALV--LEVFFACNKNEELAANYLL  395 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~--~~a~~ac~~ne~~a~~~L~  395 (403)
                      =.++|.++.+|||+-+--  -+.+.+++.|...|.+.|-
T Consensus        10 l~~al~qMl~MGF~negGWLt~LL~~k~gDI~~aLD~lq   48 (52)
T 1q02_A           10 LIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQ   48 (52)
T ss_dssp             HHHHHHHHHTTTCCCTTSHHHHHHHHTTTCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCccccHHHHHHHHccCCHHHHHHHhh
Confidence            357899999999976655  4899999999999998763

>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis} PDB: 3dwm_A

Probab=81.46  E-value=4.1  Score=31.77  Aligned_cols=72  Identities=14%  Similarity=0.128  Sum_probs=43.9

Q ss_pred             CEEEEEeCC------CcEEEEEeCCCCcHHHHHHHHHHHhCCC--CC-C-------CCCcEEEeCCeecCCCCccccccc
Q 015628            1 MKVFVKTLK------GTHFEIEVKPEDKVSDVKKNIETVQGSD--VY-P-------ASQQMLIHQGKVLKDVTTLEENKV   64 (403)
Q Consensus         1 MkI~VKtl~------g~~~~ieV~~~~TV~dLK~kI~~~~g~~--~i-p-------~~~QkLiy~GkiL~D~~tLsd~gI   64 (403)
                      |+|+||...      |+...++++ ..||.+|++.+..++..-  .+ .       .....+..+|+...+..-+ +.-|
T Consensus         1 M~v~V~~fa~lr~~~g~~~~~~~~-~~Tv~~ll~~L~~~~p~l~~~l~~~~~~g~~~~~~~v~VN~~~v~~~~~~-~~~L   78 (93)
T 3dwg_C            1 MNVTVSIPTILRPHTGGQKSVSAS-GDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVNIYVNDEDVRFSGGL-ATAI   78 (93)
T ss_dssp             -CEEEECCGGGGGGTTTCSEEEEC-CSBHHHHHHHHHHHSTTHHHHHBCSSSTTSBCTTEEEEETTEEGGGTTGG-GCBC
T ss_pred             CEEEEEEeHHHHHHhCCCeEEecC-CCCHHHHHHHHHHHChhHHHHHhccccCCcccCCEEEEECCEEccCcCCC-CcCC
Confidence            788888542      333346654 579999999998875310  00 0       0134566788776542222 4568


Q ss_pred             CCCcEEEEEE
Q 015628           65 AENSFVVVML   74 (403)
Q Consensus        65 ~~~s~I~v~v   74 (403)
                      ++||.|.++-
T Consensus        79 ~~gDeV~i~P   88 (93)
T 3dwg_C           79 ADGDSVTILP   88 (93)
T ss_dssp             CTTCEEEEEE
T ss_pred             CCCCEEEEEC
Confidence            9999998873

>1vd2_A Protein kinase C, IOTA type; PB1 domain, OPCA motif, APKC, ZIP/P62, MEK5, molecular recognition, transferase; NMR {Homo sapiens} SCOP: d.15.2.2 PDB: 1wmh_A

Probab=81.21  E-value=4.3  Score=32.21  Aligned_cols=68  Identities=9%  Similarity=0.133  Sum_probs=45.3

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CcEEEeCCeecCCCCc----------ccccccCCCcEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIHQGKVLKDVTT----------LEENKVAENSFV   70 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~-~QkLiy~GkiL~D~~t----------Lsd~gI~~~s~I   70 (403)
                      +|++. .+|..+.+.|+++.+..+|.++|...++   +... ...|-|.... .|-.+          |.-|.+..++.|
T Consensus         8 kvK~~-~~gdi~~~~v~~~i~~~~L~~kv~~~~~---~~~~~~f~lky~DEe-GD~itisSd~EL~eAl~l~~~n~~~~l   82 (89)
T 1vd2_A            8 RVKAY-YRGDIMITHFEPSISFEGLCNEVRDMCS---FDNEQLFTMKWIDEE-GDPCTVSSQLELEEAFRLYELNKDSEL   82 (89)
T ss_dssp             EEEEE-SSSCEEEEEECTTCCHHHHHHHHHHHTT---CCSSCCEEEEECCSS-SCCEECCSHHHHHHHHHHHHHTSCCCE
T ss_pred             EEEEE-eCCeEEEEECCCCCCHHHHHHHHHHHhC---CCCCCeEEEEEECCC-CCcccccCHHHHHHHHHHHHccCCCCE
Confidence            34444 4678889999999999999999999988   6543 4677786542 22222          333455556655


Q ss_pred             EEEE
Q 015628           71 VVML   74 (403)
Q Consensus        71 ~v~v   74 (403)
                      +++|
T Consensus        83 ~ihv   86 (89)
T 1vd2_A           83 LIHV   86 (89)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            5554

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=80.72  E-value=2.2  Score=31.38  Aligned_cols=61  Identities=7%  Similarity=0.202  Sum_probs=41.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+|   +|+.+  ++....||.+|.+.+    +   ++.....+..+|+++..+ ...+.-+++||.|.++-
T Consensus         1 m~i~v---Ng~~~--~~~~~~tv~~ll~~l----~---~~~~~v~vavN~~~v~~~-~~~~~~L~~gD~v~i~~   61 (66)
T 1f0z_A            1 MQILF---NDQAM--QCAAGQTVHELLEQL----D---QRQAGAALAINQQIVPRE-QWAQHIVQDGDQILLFQ   61 (66)
T ss_dssp             CCEEE---SSCEE--CCCTTCCHHHHHHHH----T---CCCSSEEEEETTEEECHH-HHTTCCCCTTEEECEEE
T ss_pred             CEEEE---CCEEE--EcCCCCcHHHHHHHc----C---CCCCCEEEEECCEECCch-hcCCcCCCCCCEEEEEe
Confidence            55544   46654  556778999999876    4   556677778899988542 12234578899988773

>2llw_A Heat shock protein STI1; DP domain, alpha helix, chaperone; NMR {Saccharomyces cerevisiae}

Probab=80.64  E-value=1.6  Score=33.22  Aligned_cols=26  Identities=23%  Similarity=0.395  Sum_probs=12.7

Q ss_pred             hCccchHHHHHHHHhhCHHHHHHHHHcH
Q 015628          296 ANPQILQPMLQELGKQNPHLMRLIQEHQ  323 (403)
Q Consensus       296 ~NP~lL~~~lq~i~~~nP~l~~lI~~n~  323 (403)
                      +||++. .+|++|. +||..++-...||
T Consensus        27 ~DP~~~-~~lq~~~-~NP~~~~k~~~nP   52 (71)
T 2llw_A           27 QDPVMQ-SILQQAQ-QNPAALQEHMKNP   52 (71)
T ss_dssp             TCTHHH-HHHHHHH-HCHHHHHHHHHSH
T ss_pred             CCHHHH-HHHHHHH-HCHHHHHHHHhCH
Confidence            555433 3444433 3555555555555

>1ef1_A Moesin; membrane, FERM domain, tail domain, membrane protein; 1.90A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1sgh_A 1j19_A 2emt_A 2ems_A 2d10_A 2d11_A 2yvc_A 2d2q_A 2zpy_A 1gc7_A 1gc6_A 1ni2_A

Probab=80.07  E-value=6.3  Score=37.03  Aligned_cols=73  Identities=16%  Similarity=0.180  Sum_probs=53.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CcEEEe---CCe--ecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIH---QGK--VLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~-~QkLiy---~Gk--iL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |.|.|..++| ++.+.|+.+.|+.+|-+.|....|   +... -.=|.|   +|.  -|+.++.|.+.+++.+..+.+..
T Consensus         2 i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~---L~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l~f   77 (294)
T 1ef1_A            2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIG---LREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKF   77 (294)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHT---CCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEE
T ss_pred             EEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcC---CCCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEEEE
Confidence            4688898988 688999999999999999999999   5432 223433   342  36777888887766666666655


Q ss_pred             ecC
Q 015628           75 TKS   77 (403)
Q Consensus        75 ~k~   77 (403)
                      +++
T Consensus        78 r~k   80 (294)
T 1ef1_A           78 RAK   80 (294)
T ss_dssp             EES
T ss_pred             EEE
Confidence            543

---

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	403
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	2e-26
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	8e-23
d2f4mb1	58	a.189.1.1 (B:275-332) XPC-binding domain of Rad23	1e-22
d1oqya2	44	a.5.2.1 (A:317-360) DNA repair protein Hhr23a {Hum	2e-22
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	2e-19
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	8e-19
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	1e-18
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	7e-18
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	1e-17
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	3e-17
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	7e-17
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	6e-16
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	7e-16
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	7e-16
d1oqya1	41	a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Hum	7e-16
d1oqya1	41	a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Hum	7e-08
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	8e-16
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	1e-15
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	1e-15
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	1e-15
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	3e-15
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	1e-13
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	1e-13
d1wgna_	63	a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1	1e-13
d1wgna_	63	a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1	9e-08
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	4e-13
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	9e-13
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	1e-12
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	1e-12
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	2e-12
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	8e-12
d1vg5a_	73	a.5.2.1 (A:) Rhomboid family protein At3g58460 {Th	3e-11
d1vg5a_	73	a.5.2.1 (A:) Rhomboid family protein At3g58460 {Th	7e-08
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	9e-11
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	2e-10
d1wiva_	73	a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress	3e-10
d1wiva_	73	a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress	1e-08
d1wjia_	63	a.5.2.1 (A:) Tudor domain containing protein 3, TD	3e-10
d1wjia_	63	a.5.2.1 (A:) Tudor domain containing protein 3, TD	3e-09
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	4e-10
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	7e-10
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	7e-10
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	9e-09
d1veka_	84	a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress	3e-08
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	3e-08
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	5e-08
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	9e-08
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	1e-05
d2g3qa1	43	a.5.2.1 (A:1339-1381) Endocytic protein Ede1, YBL0	2e-05
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	2e-05
d1whca_	64	a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus	2e-05
d1whca_	64	a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus	1e-04
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	4e-05
d2crna1	51	a.5.2.1 (A:8-58) Suppressor of T-cell receptor sig	1e-04
d2cpwa1	51	a.5.2.1 (A:8-58) Cbl-interacting protein p70, STS1	0.002
d2gqba1	130	a.282.1.1 (A:1-130) Hypothetical protein RPA2825 {	0.003
d2bwba1	44	a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharom	0.003

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 98.8 bits (246), Expect = 2e-26
 Identities = 27/75 (36%), Positives = 49/75 (65%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +KTL+   F+I ++P++ V  +K+ IE  +G D +P + Q LI+ GK+L D   + 
Sbjct: 3  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 62

Query: 61 ENKVAENSFVVVMLT 75
          + ++ E +FVVVM+T
Sbjct: 63 DYRIDEKNFVVVMVT 77

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 89.7 bits (222), Expect = 8e-23
 Identities = 38/86 (44%), Positives = 58/86 (67%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M+V +KTL+   F+I++ PE+ V  +K+ IE+ +G D +P + Q LI+ GK+L D T L+
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 61 ENKVAENSFVVVMLTKSKVSSSGAST 86
          E K+ E +FVVVM+TK K  S+ A  
Sbjct: 61 EYKIDEKNFVVVMVTKPKAVSTPAPA 86

>d2f4mb1 a.189.1.1 (B:275-332) XPC-binding domain of Rad23 homolog B (Hhr23b) {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: XPC-binding domain
superfamily: XPC-binding domain
family: XPC-binding domain
domain: XPC-binding domain of Rad23 homolog B (Hhr23b)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 88.2 bits (219), Expect = 1e-22
 Identities = 27/57 (47%), Positives = 44/57 (77%)

Query: 278 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV 334
           L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV
Sbjct: 2   LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 58

>d1oqya2 a.5.2.1 (A:317-360) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]} Length = 44

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 87.0 bits (216), Expect = 2e-22
 Identities = 26/42 (61%), Positives = 35/42 (83%)

Query: 356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH 397
           TP+E+EAIERL+A+GF  +LV++ +FAC KNE LAAN+LL  
Sbjct: 1   TPQEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQ 42

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 79.9 bits (197), Expect = 2e-19
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P D +  +K+ +E  +G    P  QQ LI+ GK L D  T +
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEG---IPPVQQRLIYAGKQLADDKTAK 57

Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIEGGSVLHLVL 71

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.0 bits (192), Expect = 8e-19
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 78.0 bits (192), Expect = 1e-18
 Identities = 24/93 (25%), Positives = 36/93 (38%), Gaps = 7/93 (7%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVL-KDVTTL 59
          + V +K L  T      +PED V  +K      Q       SQ  LI+QG++L     TL
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQE------SQMKLIYQGRLLQDPARTL 61

Query: 60 EENKVAENSFVVVMLTKSKVSSSGASTVSAAPA 92
              +  N  +    +    + SG S  S   +
Sbjct: 62 SSLNITNNCVIHCHRSPPGAAVSGPSASSGPSS 94

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.7 bits (186), Expect = 7e-18
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++VFVK   G  +   + P   +  +K+ IE  QG    P  QQ L  QG+VL+D   L 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLG 64

Query: 61 ENKVAENSFVVVMLTKSKVSSSG 83
             + ++  +++   K    SSG
Sbjct: 65 IYGIQDSDTLILSKKKGSGPSSG 87

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.9 bits (184), Expect = 1e-17
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + V+  KG     EV+    V+ +K+ +    G +        L  +GK L+D   L 
Sbjct: 4  LSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPLG 60

Query: 61 ENKVAENSFVVVML 74
          E  +   S V + L
Sbjct: 61 EYGLKPLSTVFMNL 74

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 73.6 bits (181), Expect = 3e-17
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +K+ +   +E+ V PE  V   K+ I    G    P + Q LI+ GK+LKD  T+E
Sbjct: 2  LNIHIKSGQDK-WEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTVE 57

Query: 61 ENKVAENSFVVVMLTKSK 78
             + +     V L KS+
Sbjct: 58 SYHIQDGH--SVHLVKSQ 73

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.6 bits (178), Expect = 7e-17
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V VKTL        V  +  V + K++I         P+ +Q LI+QG+VL+D   L+
Sbjct: 1  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQ 57

Query: 61 ENKVAENSFVVVM 73
          E  V      +V 
Sbjct: 58 EYNVGGKVIHLVE 70

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.7 bits (173), Expect = 6e-16
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 1  MKVFVKTLKGTH--FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
          + + VK+    H   E+       V  +K ++  V          Q LI+ GK+L D   
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERP-RPEDQRLIYSGKLLLDHQC 66

Query: 59 LEENKVAENSFVVVMLTKS--KVSSSG 83
          L +    +    V+ L  +     SSG
Sbjct: 67 LRDLLPKQEKRHVLHLVCNVKSGPSSG 93

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 116

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.2 bits (174), Expect = 7e-16
 Identities = 19/90 (21%), Positives = 33/90 (36%), Gaps = 5/90 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNI-----ETVQGSDVYPASQQMLIHQGKVLKD 55
           + + +  + G   E    P D  SD+ K++        +   V   +   LI+QG+ L  
Sbjct: 17  INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHG 76

Query: 56  VTTLEENKVAENSFVVVMLTKSKVSSSGAS 85
             TL   K+      V+ L   +      S
Sbjct: 77  NVTLGALKLPFGKTTVMHLVARETLPEPNS 106

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.9 bits (171), Expect = 7e-16
 Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 1  MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
          M + V+T+ G  T    +V  +  + ++++ +  +          Q L ++GK L++  T
Sbjct: 1  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD---VRPECQRLFYRGKQLENGYT 57

Query: 59 LEENKVAENSFVVVML 74
          L +  V  N  + +++
Sbjct: 58 LFDYDVGLNDIIQLLV 73

>d1oqya1 a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]} Length = 41

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.8 bits (169), Expect = 7e-16
 Identities = 23/44 (52%), Positives = 31/44 (70%), Gaps = 3/44 (6%)

Query: 170 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 213
           GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +
Sbjct: 1   GSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLT 41

>d1oqya1 a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]} Length = 41

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (110), Expect = 7e-08
 Identities = 11/39 (28%), Positives = 17/39 (43%)

Query: 357 PEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLL 395
            E    +  + +MG++R  V+    A   N   A  YLL
Sbjct: 2   SEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLL 40

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.9 bits (171), Expect = 8e-16
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M VFV+      F +EV  +  +  +K+ +   QG    PA Q  +I  GK L +  T++
Sbjct: 3  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQG---VPADQLRVIFAGKELPNHLTVQ 59

Query: 61 ENKVAENSFVVVML 74
             + + S V ++ 
Sbjct: 60 NCDLEQQSIVHIVQ 73

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.6 bits (170), Expect = 1e-15
 Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVLKDVT 57
          + + VK     +    +  +D V D+K+ ++T+ G       +Q L+    +GK  ++  
Sbjct: 8  LPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTG---VLPERQKLLGLKVKGKPAENDV 64

Query: 58 TLEENKVAENSFVVVMLTKSKVSSSG 83
           L   K+  N+ +++M T+    SSG
Sbjct: 65 KLGALKLKPNTKIMMMGTRESGPSSG 90

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.2 bits (169), Expect = 1e-15
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 3  VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKDVTTLE 60
          + VK L G  F++ +     VS++K  I    G     A QQ L     G  L+D   L 
Sbjct: 3  LTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG---VHAFQQRLAVHPSGVALQDRVPLA 59

Query: 61 ENKVAENSFVVVMLTKS 77
             +   S V++++ KS
Sbjct: 60 SQGLGPGSTVLLVVDKS 76

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.2 bits (169), Expect = 1e-15
 Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 1  MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
          M + V+T+ G  TH    +    KV ++++ I+ +          Q L ++GK ++D  T
Sbjct: 1  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFH---VEPGLQRLFYRGKQMEDGHT 57

Query: 59 LEENKVAENSFVVVMLTKS 77
          L + +V  N  + +++ +S
Sbjct: 58 LFDYEVRLNDTIQLLVRQS 76

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.4 bits (167), Expect = 3e-15
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           ++ ++   G   ++ V+  D V  +K+ +   +G        Q     G+ L D    E
Sbjct: 4  CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG---VEPGSQRWFFSGRPLTDKMKFE 60

Query: 61 ENKVAENSFVVVMLTKSK 78
          E K+ ++  V V++++  
Sbjct: 61 ELKIPKDYVVQVIVSQPV 78

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]} Length = 96

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.2 bits (156), Expect = 1e-13
 Identities = 18/101 (17%), Positives = 35/101 (34%), Gaps = 12/101 (11%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
             V VK  K     +E+  ++     K  +  + G       +Q ++ +G  LKD     
Sbjct: 8   YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPA---RQKVMVKGGTLKD-DDWG 63

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSA 101
             K+     V++M +   +           P+ +    SS 
Sbjct: 64  NIKMKNGMTVLMMGSADALPE--------EPSAKTSGPSSG 96

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 102

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.6 bits (157), Expect = 1e-13
 Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 8/97 (8%)

Query: 1   MKVFV----KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV 56
           M + V    + L    F ++V P+ ++S+ +   E   G    PA +  +++  ++L D 
Sbjct: 8   MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG---VPAEEAQIVYMEQLLTDD 64

Query: 57  T-TLEENKVAENSFVVVMLTKSKVSSSGASTVSAAPA 92
             +L    + +   VV++   +    +   T S   +
Sbjct: 65  HCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTPSGPSS 101

>d1wgna_ a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 1, UBAP1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.9 bits (153), Expect = 1e-13
 Identities = 14/54 (25%), Positives = 24/54 (44%)

Query: 346 ASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH 399
           + A  +   ++P ER+ +E +  MG+    VL       +N E   +YL  H  
Sbjct: 6   SGAYSELQMLSPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHSG 59

>d1wgna_ a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 1, UBAP1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (110), Expect = 9e-08
 Identities = 12/53 (22%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 161 GQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 213
           G  +   +   +    V+ +++MG   +  E V+RA++    N E+ ++YL++
Sbjct: 7   GAYSELQMLSPSERQCVETVVNMG---YSYECVLRAMKKKGENIEQILDYLFA 56

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.7 bits (152), Expect = 4e-13
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 5/86 (5%)

Query: 1   MKVFV--KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
           ++VF+  +  K     +E +      +++  I    G      +   ++   K L+   T
Sbjct: 18  IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG---LQENYIKIVINKKQLQLGKT 74

Query: 59  LEENKVAENSFVVVMLTKSKVSSSGA 84
           LEE  VA N   +V+  K     S  
Sbjct: 75  LEEQGVAHNVKAMVLELKQSSGPSSG 100

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.9 bits (150), Expect = 9e-13
 Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 3/70 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V      G    ++   +D + D+KK I    G      ++ +L     + KD  +L 
Sbjct: 29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRWNKIVLKKWYTIFKDHVSLG 85

Query: 61 ENKVAENSFV 70
          + ++ +   +
Sbjct: 86 DYEIHDGMNL 95

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 105

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.6 bits (149), Expect = 1e-12
 Identities = 19/102 (18%), Positives = 30/102 (29%), Gaps = 21/102 (20%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM--------------- 45
           M V V  + G    + V     V D+KK I+           ++                
Sbjct: 8   MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ---LKQEREGGVQHISWSYVWRTYH 64

Query: 46  LIHQGKVLKDVT-TLEENKVAENSFVVVMLTKSKVSSSGAST 86
           L   G+ L +    L +  +       V   K     SG S+
Sbjct: 65  LTSAGEKLTEDRKKLRDYGIRNRD--EVSFIKKLGQKSGPSS 104

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 83

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.8 bits (147), Expect = 1e-12
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 4/74 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V VKT +  H E  +     V   KK I          A + +LI  GK+L+D   L 
Sbjct: 11 IRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDILS 66

Query: 61 ENKVAENSFVVVML 74
          +  + + S V V++
Sbjct: 67 QRGILDGSTVHVVV 80

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.7 bits (147), Expect = 2e-12
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 8  LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAEN 67
          L G      +   D+VS +K  I    G    PA +Q L ++G  +KD  +L    +A  
Sbjct: 19 LNGQVLVFTLPLTDQVSVIKVKIHEATG---MPAGKQKLQYEGIFIKDSNSLAYYNMANG 75

Query: 68 SFVVVML 74
          + + + L
Sbjct: 76 AVIHLAL 82

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.5 bits (141), Expect = 8e-12
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V V    G    ++   ED V D KK +           ++ +L   G VLKD  +LE
Sbjct: 2  IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQI---GTQPNKIVLQKGGSVLKDHISLE 58

Query: 61 ENKVAENSFV 70
          + +V + + +
Sbjct: 59 DYEVHDQTNL 68

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Rhomboid family protein At3g58460
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 56.9 bits (137), Expect = 3e-11
 Identities = 16/55 (29%), Positives = 25/55 (45%)

Query: 344 QLASAMPQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHM 398
             A+ +PQ+        E I++L AMGFDR  V     A + +  +A   L+   
Sbjct: 14  ANAAVLPQSQGRVAASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQS 68

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Rhomboid family protein At3g58460
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 47.2 bits (112), Expect = 7e-08
 Identities = 21/82 (25%), Positives = 31/82 (37%), Gaps = 16/82 (19%)

Query: 133 AAPAPAPAPAPAPAPAPAPVSSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRET 192
           ++ +     AP    A  P S                    E  +Q+++ MG   +DR  
Sbjct: 2   SSGSSGSRQAPIANAAVLPQSQGRVAAS-------------EEQIQKLVAMG---FDRTQ 45

Query: 193 VIRALRAAYNNPERAVEYLYSG 214
           V  AL AA ++   AVE L S 
Sbjct: 46  VEVALAAADDDLTVAVEILMSQ 67

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.0 bits (135), Expect = 9e-11
 Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 3  VFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
          VF+   +  T    + K    V ++K+ +E +      P  +Q L    ++L D  TL E
Sbjct: 2  VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK---RPPDEQRLYKDDQLLDDGKTLGE 58

Query: 62 NKVAENS 68
                +
Sbjct: 59 CGFTSQT 65

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.5 bits (131), Expect = 2e-10
 Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 1  MKVFVKTLKGTHFEIEVKP-----EDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK- 54
          + V V        ++ V       E  V D+ + +E V G    P S Q LI +GK LK 
Sbjct: 2  LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIG---VPQSFQKLIFKGKSLKE 57

Query: 55 DVTTLEENKVAENSFVVVMLTKS 77
            T L    + +   V+++  K+
Sbjct: 58 METPLSALGIQDGCRVMLIGKKN 80

>d1wiva_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 54.1 bits (130), Expect = 3e-10
 Identities = 7/51 (13%), Positives = 23/51 (45%)

Query: 350 PQAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE 400
           P +   +  ++ +++ L + GF   +  +   A   + E A +++ ++   
Sbjct: 20  PISHQTSDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNSGP 70

>d1wiva_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 49.1 bits (117), Expect = 1e-08
 Identities = 8/41 (19%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG 214
           +++V  +L  G   +  +   +AL+A+  + E+A +++++ 
Sbjct: 30  QSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFNN 67

>d1wjia_ a.5.2.1 (A:) Tudor domain containing protein 3, TDRD3 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Tudor domain containing protein 3, TDRD3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.6 bits (129), Expect = 3e-10
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAG 230
           E  ++ I +MG   + +E   +AL    NN E A+  L +   ++  + P +  S+G
Sbjct: 10  EKALKHITEMG---FSKEASRQALMDNGNNLEAALNVLLTSNKQKPVMGPPSGPSSG 63

>d1wjia_ a.5.2.1 (A:) Tudor domain containing protein 3, TDRD3 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Tudor domain containing protein 3, TDRD3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (121), Expect = 3e-09
 Identities = 10/45 (22%), Positives = 19/45 (42%)

Query: 356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE 400
           +  + +A++ +  MGF +    +       N E A N LL    +
Sbjct: 6   SGVDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQ 50

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.2 bits (130), Expect = 4e-10
 Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           +KV VKT K    E  V     V   K+ I            Q +LI  GK+LKD  TL 
Sbjct: 33  IKVTVKTPKEKE-EFAVPENSSVQQFKEAISKRFK---SQTDQLVLIFAGKILKDQDTLI 88

Query: 61  ENKVAENSFVVVML 74
           ++ + +   V +++
Sbjct: 89  QHGIHDGLTVHLVI 102

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 7e-10
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +KV VKT K    +  V     +  +K+ I            Q +LI  GK+LKD  +L 
Sbjct: 8  IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLA 63

Query: 61 ENKVAENSFVVVMLTKSK 78
          +  V +   V +++ +  
Sbjct: 64 QCGVRDGLTVHLVIKRQH 81

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.4 bits (128), Expect = 7e-10
 Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +     T  +++V  +   S++K+ I ++ G    P + Q +++   ++ +  TL 
Sbjct: 18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMY-KGLVPEDKTLR 72

Query: 61 ENKVAENSFVVVMLTKSKVSSSG 83
          E KV   + ++V+ +     SSG
Sbjct: 73 EIKVTSGAKIMVVGSTISGPSSG 95

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 50.7 bits (121), Expect = 9e-09
 Identities = 12/80 (15%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 1  MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGSD----VYPASQQMLIHQGKVLKD 55
          +++  +   G+            VS +K+ + +    +         +  LI  GKVL++
Sbjct: 8  LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLEN 67

Query: 56 VTTLEENKVAENSFVVVMLT 75
            T+++ +   ++    + T
Sbjct: 68 SKTVKDYRSPVSNLAGAVTT 87

>d1veka_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 84

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 335 EGGEGNVLGQLASAMPQAVTVTPEEREAIERLEAMGFDRALVLE-VFFACNKNEELAANY 393
            GGE  +   +   + ++      E E + +L +MGF +    +      N   E A N+
Sbjct: 6   SGGEELLPDGVPEEVMESAQPVANE-EIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNW 64

Query: 394 LLDHMHE 400
           LL HM +
Sbjct: 65  LLSHMDD 71

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 2  KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
          K  ++ L  T           +S +K+ I       V       LI+ G+ LKD  TL+ 
Sbjct: 20 KSILQ-LPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDF 78

Query: 62 NKVAENSFVVVML 74
            +   S V V+ 
Sbjct: 79 YGIQPGSTVHVLR 91

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (114), Expect = 5e-08
 Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +K+ V     +    +VK    +  +K++    QG    P +    + +G+ + D  T +
Sbjct: 3  IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPK 59

Query: 61 ENKVAENSFVVVML 74
          E  + E   + V  
Sbjct: 60 ELGMEEEDVIEVYQ 73

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]} Length = 79

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

 Score = 47.1 bits (112), Expect = 9e-08
 Identities = 8/74 (10%), Positives = 24/74 (32%), Gaps = 4/74 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + V     +    ++K    +  + +     QG           ++ G  ++   T E
Sbjct: 5  INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPE 60

Query: 61 ENKVAENSFVVVML 74
          +  + +N  +    
Sbjct: 61 DLDMEDNDIIEAHR 74

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 11/79 (13%), Positives = 26/79 (32%), Gaps = 11/79 (13%)

Query: 6  KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK--------DVT 57
             +    E ++     V  VK  +  +      P S+ +L ++   +         D+ 
Sbjct: 18 NQPERQILEKQLPDSMTVQKVKGLLSRLLK---VPVSELLLSYESSKMPGREIELENDLQ 74

Query: 58 TLEENKVAENSFVVVMLTK 76
           L+   V     ++V  + 
Sbjct: 75 PLQFYSVENGDCLLVRWSG 93

>d2g3qa1 a.5.2.1 (A:1339-1381) Endocytic protein Ede1, YBL047C {Saccharomyces cerevisiae [TaxId: 4932]} Length = 43

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Endocytic protein Ede1, YBL047C
species: Saccharomyces cerevisiae [TaxId: 4932]

 Score = 39.5 bits (92), Expect = 2e-05
 Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH 397
           TP+   A+E L  MGF           CN + E A N+LLD 
Sbjct: 2   TPKSL-AVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDS 42

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 111

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 1   MKVFVKTL-KGTHFEIEVKPE-DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
           ++V       G   EI V+   + V  +K+ I         PA++Q L  +   LKD  +
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMS 86

Query: 59  LEENKVAENSFVVVMLTKSKVSSSG 83
           L    V     + + L +    SSG
Sbjct: 87  LAHYNVGAGEILTLSLRERSGPSSG 111

>d1whca_ a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 64

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA/UBX 33.3 kDa protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 355 VTPEEREAIERLEAMGFDRALVLEVFFAC-NKNEELAANYLLDHMHE 400
            +  E  A+E L  MGF R    +      N+  E A ++L++H  +
Sbjct: 5   SSGAELTALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDD 51

>d1whca_ a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 64

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA/UBX 33.3 kDa protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 174 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQTAVPPVARASAG 230
              ++ +++MG   + R    +AL    N   E A+++L     +     P++  S+G
Sbjct: 10  LTALESLIEMG---FPRGRAEKALALTGNQGIEAAMDWLMEHEDDPDVDEPLSGPSSG 64

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

 Score = 39.9 bits (93), Expect = 4e-05
 Identities = 9/62 (14%), Positives = 19/62 (30%), Gaps = 4/62 (6%)

Query: 2  KVFVKT-LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           + + T       E +      ++D+KK +E V G          +       +    L 
Sbjct: 6  DLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVG---TTVDSMRIQLFDGDDQLKGELT 62

Query: 61 EN 62
          + 
Sbjct: 63 DG 64

>d2crna1 a.5.2.1 (A:8-58) Suppressor of T-cell receptor signaling 2 (STS-2) {Human (Homo sapiens) [TaxId: 9606]} Length = 51

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Suppressor of T-cell receptor signaling 2 (STS-2)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (87), Expect = 1e-04
 Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)

Query: 361 EAIERLEAMGFDRALVLEVFFAC-NKNEELAANYLLDHMHE 400
             +E L AMGF     L+   A   K  E A  +L DH ++
Sbjct: 4   SLLEPLLAMGFPVHTALKALAATGRKTAEEALAWLHDHCND 44

>d2cpwa1 a.5.2.1 (A:8-58) Cbl-interacting protein p70, STS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 51

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Cbl-interacting protein p70, STS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.0 bits (78), Expect = 0.002
 Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 361 EAIERLEAMGFDRALVLEVFFAC-NKNEELAANYLLDH 397
            A++ L +MGF RA   +   +   ++ + A ++L  H
Sbjct: 14  SALDVLLSMGFPRARAQKALASTGGRSVQTACDWLFSH 51

>d2bwba1 a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 44

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 33.0 bits (76), Expect = 0.003
 Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 2/38 (5%)

Query: 177 VQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG 214
           ++Q+ DMG   +D +  + ALR +  + + A++ L +G
Sbjct: 9   LRQLNDMG--FFDFDRNVAALRRSGGSVQGALDSLLNG 44

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	403
d2f4mb1	58	XPC-binding domain of Rad23 homolog B (Hhr23b) {Hu	99.86
d1oqya2	44	DNA repair protein Hhr23a {Human (Homo sapiens) [T	99.83
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.83
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.81
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.8
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.8
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.79
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.78
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.78
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.77
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.77
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.76
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.75
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.75
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.74
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.73
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.73
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.72
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.7
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.69
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.69
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.68
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.67
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.66
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.66
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.65
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.64
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.63
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.6
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.59
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.59
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.58
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	99.55
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.5
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.42
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.29
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.28
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.24
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	99.24
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.19
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	99.16
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	99.16
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	99.15
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	99.12
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	99.12
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	99.11
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	99.11
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	99.1
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.07
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	99.0
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	98.79
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	98.76
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	98.73
d1x3zb1	57	Rad23 STI1 domain {Baker's yeast (Saccharomyces ce	98.69
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	98.64
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	98.62
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	98.54
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	98.47
d2bwba1	44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.44
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	98.35
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.33
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	98.32
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	98.31
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	98.31
d2bwba1	44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.29
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	98.21
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	98.01
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	98.0
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	97.96
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	97.95
d3e46a1	42	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal	97.7
d3e46a1	42	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal	97.33
d1z96a1	38	UBA-domain protein mud1 {Schizosaccharomyces pombe	97.16
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.01
d1oqya2	44	DNA repair protein Hhr23a {Human (Homo sapiens) [T	96.94
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	96.79
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.74
d1vega_	83	NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculu	96.66
d1z96a1	38	UBA-domain protein mud1 {Schizosaccharomyces pombe	96.59
d1wj7a1	91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	96.58
d1v92a_	46	NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {	96.49
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	96.28
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	96.19
d1wj7a1	91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	95.51
d2cosa1	41	Serine/threonine protein kinase LATS2 {Mouse (Mus	95.21
d1vega_	83	NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculu	95.17
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	95.07
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	94.3
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	93.82
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	93.63
d1ttea1	55	Ubiquitin-protein ligase ubc1 {Baker's yeast (Sacc	92.69
d2cp8a1	41	Migration-inducing protein 19 NBR1 {Human (Homo sa	92.63
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	92.52
d2cosa1	41	Serine/threonine protein kinase LATS2 {Mouse (Mus	92.43
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	91.96
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	91.92
d2dkla1	72	Trinucleotide repeat containing 6c protein, TNRC6C	91.0
d1ttea1	55	Ubiquitin-protein ligase ubc1 {Baker's yeast (Sacc	90.63
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	89.61
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	89.51
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	88.71
d2f4mb1	58	XPC-binding domain of Rad23 homolog B (Hhr23b) {Hu	87.39
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	87.29
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	87.24
d1ufza_	83	HBS1-like protein {Mouse (Mus musculus) [TaxId: 10	87.24
d2cp8a1	41	Migration-inducing protein 19 NBR1 {Human (Homo sa	82.77
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	82.35
d2dkla1	72	Trinucleotide repeat containing 6c protein, TNRC6C	82.31
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	80.21

>d2f4mb1 a.189.1.1 (B:275-332) XPC-binding domain of Rad23 homolog B (Hhr23b) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: XPC-binding domain
superfamily: XPC-binding domain
family: XPC-binding domain
domain: XPC-binding domain of Rad23 homolog B (Hhr23b)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.8e-22  Score=147.89  Aligned_cols=58  Identities=47%  Similarity=0.960  Sum_probs=56.2

Q ss_pred             chHHhhCcHHHHHHHHHHHhCccchHHHHHHHHhhCHHHHHHHHHcHHHHHHHhcCCC
Q 015628          277 TLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV  334 (403)
Q Consensus       277 ~l~~Lr~~pqf~~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI~~n~e~Fl~~l~~~~  334 (403)
                      +|++||++|+|++||++||+||++|+++||+|+++||+|+++|++|||+|++|||+++
T Consensus         1 pL~~Lr~~PqFq~lR~~vq~nP~~L~~lLqql~~~NP~L~q~I~~nqe~Fl~llnep~   58 (58)
T d2f4mb1           1 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV   58 (58)
T ss_dssp             GGGGGTTCHHHHHHHHHHHHCGGGHHHHHHHHHHHCHHHHHHHHHSHHHHHHHHTSCC
T ss_pred             CcHHHhcChHHHHHHHHHHHCHHHHHHHHHHHHhhCHHHHHHHHHCHHHHHHHHcCCC
Confidence            5899999999999999999999999999999999999999999999999999999873

>d1oqya2 a.5.2.1 (A:317-360) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.4e-22  Score=138.76  Aligned_cols=44  Identities=59%  Similarity=1.035  Sum_probs=42.1

Q ss_pred             CHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015628          356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH  399 (403)
Q Consensus       356 t~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~  399 (403)
                      |+||++||+||++|||+|+.|||||++|||||++|+||||++++
T Consensus         1 T~ee~~aIeRL~~LGF~r~~viqay~ACdKNEelAaN~L~~~~~   44 (44)
T d1oqya2           1 TPQEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQNF   44 (44)
T ss_dssp             CTTTHHHHHHHHHHTCCSHHHHHHTSSSSSCSSHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHhCcCHHHHHHHHHHccC
Confidence            78999999999999999999999999999999999999999753

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.6e-20  Score=152.22  Aligned_cols=79  Identities=46%  Similarity=0.740  Sum_probs=74.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+++.|.+.+|+++|||||+||+|+|+++|++|||+++++|+|++++++.
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~~   79 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKA   79 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCCC
Confidence            9999999999999999999999999999999998765589999999999999999999999999999999999986653

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.81  E-value=4.4e-20  Score=142.51  Aligned_cols=73  Identities=34%  Similarity=0.545  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+++|++|.++|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++|||+++++||+++|.
T Consensus         1 M~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~g---i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlrL   73 (73)
T d1bt0a_           1 MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEG---IPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLAL   73 (73)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhC---CChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEeeC
Confidence            99999999999999999999999999999999999   99999999999999999999999999999999999873

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=8.8e-20  Score=145.54  Aligned_cols=76  Identities=29%  Similarity=0.446  Sum_probs=73.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||||+||+|+|+++|++|+|+++++|||+++++..
T Consensus         8 mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~g   83 (87)
T d1wh3a_           8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSG   83 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTC---CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCC
T ss_pred             EEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHC---cChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCCC
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999887653

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.1e-19  Score=141.37  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|++|.++|++++||.+||++|+.+.|   +|++.|||+|+||.|+|+.+|++|||+++++|+|+++.++
T Consensus         1 MqI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~g---i~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~rlrg   75 (76)
T d1ogwa_           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECTTC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcC---CChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998764

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1e-19  Score=141.92  Aligned_cols=75  Identities=36%  Similarity=0.663  Sum_probs=71.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|...+|+++|||||+||+|+|+++|++|||+++++|+||++
T Consensus         3 ~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~vs   77 (77)
T d1oqya4           3 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT   77 (77)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEEC
Confidence            899999999999999999999999999999999886558999999999999999999999999999999999984

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=1.5e-19  Score=141.38  Aligned_cols=75  Identities=27%  Similarity=0.406  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+++.|   +|++.|||+|+||.|+|+.+|++|+|+++++||+++|.++
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~g---ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~rg   77 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQG---VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   77 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHT---CCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESSCC
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHC---cChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998764

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.4e-19  Score=140.84  Aligned_cols=75  Identities=20%  Similarity=0.376  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++|+|+++++|||+++++.
T Consensus         4 ~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~---ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~p~   78 (80)
T d1ttna1           4 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG---VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPV   78 (80)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTC---CCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSS
T ss_pred             EEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhC---CCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecCCC
Confidence            68999999999999999999999999999999999   9999999999999999999999999999999999998654

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.7e-19  Score=138.16  Aligned_cols=73  Identities=25%  Similarity=0.325  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+++|++|||++|++|++++|.
T Consensus         4 ~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~g---i~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lRL   76 (76)
T d1z2ma2           4 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhc---CChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            79999999999999999999999999999999999   99999999999999999999999999999999999873

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4.5e-19  Score=138.07  Aligned_cols=73  Identities=22%  Similarity=0.352  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCc-EEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGT-HFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~-~~~ie-V~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+++|+ ++.++ |++++||.+||.+|+.+.|   +|+++|||+|+||.|+|+.+|++|||+++++||+++|+
T Consensus         1 M~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1           1 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFH---VEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHC---cChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            89999999996 78885 9999999999999999999   99999999999999999999999999999999999986

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.9e-19  Score=138.99  Aligned_cols=73  Identities=29%  Similarity=0.400  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+||+++|++|.++|++++||.+||++|+.+.|   +|+++|||||+||.|+|+++|++|+| ++++|||+++.|
T Consensus         1 m~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~g---ip~~~qrLi~~Gk~L~d~~tL~dy~i-~~~ti~lv~r~P   73 (73)
T d1wx9a1           1 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAP   73 (73)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHC---CCTTTCCCEETTEECCSSSBHHHHTC-TTEEEBCCCSSC
T ss_pred             CEEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhC---CChHHEEEEECCeEccCCCCHHHhCC-CCCEEEEEecCC
Confidence            89999999999999999999999999999999999   99999999999999999999999999 578998887653

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2e-18  Score=134.32  Aligned_cols=72  Identities=21%  Similarity=0.327  Sum_probs=68.9

Q ss_pred             CEEEEEeCCC-cEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKG-THFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g-~~~~i-eV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+++| +++.+ +|++++||.+||.+|+.+.|   +|++.|||+|+||.|+|+.+|++|||+++++|||++|
T Consensus         1 M~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~g---ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~r   74 (76)
T d1wy8a1           1 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD---VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR   74 (76)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSC---CCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEEC
T ss_pred             CEEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHC---CCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEc
Confidence            8999999999 57877 59999999999999999999   9999999999999999999999999999999999986

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.1e-18  Score=134.16  Aligned_cols=73  Identities=29%  Similarity=0.383  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEe--CCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy--~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      .+|+||+++|+.|.|+|++++||.+||.+|+.+.|   +|+++|||+|  +||+|+|+.+|++|||++|++|+|++++
T Consensus         1 ~~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~g---ip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1           1 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG---VHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             CEEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHC---CCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhc---cCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            47999999999999999999999999999999999   9999999999  7999999999999999999999999976

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=5e-18  Score=137.59  Aligned_cols=75  Identities=25%  Similarity=0.272  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecC-CCCcccccccCCCcEEEEEEecCCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~-D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      |+|+||+++|+.|.|+|++++||.+||++|+   .   +++++|||||+||+|. |.++|++|+|.+|++|||++++++.
T Consensus         8 m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~---~---~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~~~~   81 (95)
T d1wiaa_           8 INVRLKFLNDTEELAVARPEDTVGTLKSKYF---P---GQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGA   81 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHS---S---STTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCC
T ss_pred             EEEEEEcCCCCEEEEEECCcCcHHHHHHHHh---c---CCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcCCCC
Confidence            8999999999999999999999999999984   3   5679999999999997 5579999999999999999987665


Q ss_pred             CC
Q 015628           80 SS   81 (403)
Q Consensus        80 ~~   81 (403)
                      ..
T Consensus        82 ~~   83 (95)
T d1wiaa_          82 AV   83 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=2.5e-18  Score=141.18  Aligned_cols=75  Identities=21%  Similarity=0.380  Sum_probs=68.9

Q ss_pred             CEEEE----EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecC-CCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFV----KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~V----Ktl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~-D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+|    |++++++|.|+|++++||.+||++|+.+.|   +|+++|||||+||.|. |.++|++|||++|++|+|+.+
T Consensus         8 m~itV~~~~~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~g---ip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~~r   84 (102)
T d1v5oa_           8 MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG---VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQK   84 (102)
T ss_dssp             EEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTC---CCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBC
T ss_pred             EEEEEEecccCCCCCEEEEEECCcccHHHHHHHHHHHhC---CCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEEEC
Confidence            88999    788899999999999999999999999999   9999999999999996 567999999999999988876


Q ss_pred             cCC
Q 015628           76 KSK   78 (403)
Q Consensus        76 k~k   78 (403)
                      +..
T Consensus        85 ~~~   87 (102)
T d1v5oa_          85 DNV   87 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.73  E-value=2.9e-18  Score=132.29  Aligned_cols=70  Identities=27%  Similarity=0.394  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      |+|+||++.|+++.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++|||++|++|+|.
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~---i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~   71 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIG---TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   71 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHC---CTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhc---ccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEE
Confidence            68999999999999999999999999999999999   99999999999999999999999999999999986

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.72  E-value=8.3e-18  Score=129.63  Aligned_cols=72  Identities=29%  Similarity=0.501  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+. +++|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+.+|++|||++|++|||+.++
T Consensus         2 i~I~Vk~~-~~~~~i~v~~~~tV~~lK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~~   73 (73)
T d2bwfa1           2 LNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ   73 (73)
T ss_dssp             EEEEEEET-TEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             EEEEEEeC-CeEEEEEECCCChHHHHHHHHHHHHC---cChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEeeC
Confidence            78999975 56799999999999999999999999   99999999999999999999999999999999999764

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=5e-18  Score=134.40  Aligned_cols=74  Identities=27%  Similarity=0.339  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||+.++ ++.|+|++++||.+||++|++++|   +++++|||+|+||.|+|+.+|++|||++|++|+|+++++.
T Consensus         8 i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~g---i~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~   81 (84)
T d1yqba1           8 IKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   81 (84)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCC
T ss_pred             EEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHC---cCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCC
Confidence            7899999765 689999999999999999999999   9999999999999999999999999999999999987654

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=1.1e-17  Score=135.80  Aligned_cols=74  Identities=20%  Similarity=0.204  Sum_probs=68.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+||..+++.+.|+|++++||.+||++|+..+|   +|+++|||||+||.|+|+ +|++|||++|++|+||.++..
T Consensus         8 ~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~g---vp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~t~~~   81 (96)
T d1wgga_           8 YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTG---VQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSADA   81 (96)
T ss_dssp             EEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTC---CCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCCC
T ss_pred             eEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcC---ccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEeeCCc
Confidence            68999998888889999999999999999999999   999999999999999986 799999999999999875443

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=3e-17  Score=134.67  Aligned_cols=71  Identities=31%  Similarity=0.356  Sum_probs=67.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|+||+.++ ++.|+|++++||.+||++|+.++|   +++++|||+|+||+|+|+.+|++|||++|++|||++|
T Consensus        33 i~V~Vk~~~~-~~~i~V~~~~tV~~LK~~I~~~~g---i~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~lvlr  103 (103)
T d1j8ca_          33 IKVTVKTPKE-KEEFAVPENSSVQQFKEAISKRFK---SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             EEEEEECSSC-EEEEEECTTCCHHHHHHHHHHHHC---SCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             EEEEEECCCc-cEEEEECCCChHHHHHHHHHHHHC---cCHHHeeeeeeeecccCCCcHHHcCCCCCCEEEEEEC
Confidence            7899998776 589999999999999999999999   9999999999999999999999999999999999985

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=4.5e-17  Score=136.50  Aligned_cols=76  Identities=24%  Similarity=0.256  Sum_probs=67.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHH--------HHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIE--------TVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~--------~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v   72 (403)
                      |+|+||+++|+++.|+|++++||.+||++|.        ++.+   +++++|||||.||+|+|+.+|++|+|.+|++++|
T Consensus        17 i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~---~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~l   93 (116)
T d1wgha_          17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQV---SSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVM   93 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCC---CCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEE
T ss_pred             EEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccC---CChHHeEEEECCEEecCCCCHHHcCCCCCCEEEE
Confidence            5799999999999999999999999999996        4455   8999999999999999999999999999998666


Q ss_pred             EEecCCC
Q 015628           73 MLTKSKV   79 (403)
Q Consensus        73 ~v~k~k~   79 (403)
                      ++..++.
T Consensus        94 hlv~r~~  100 (116)
T d1wgha_          94 HLVARET  100 (116)
T ss_dssp             EEEECSS
T ss_pred             EEEeCCC
Confidence            5544443

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=1.9e-17  Score=130.72  Aligned_cols=72  Identities=28%  Similarity=0.363  Sum_probs=67.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||+.++ .+.|+|++++||.+||++|++.++   +|+++|||+|+||+|+|+.+|++|||++|++|+|++|.
T Consensus        11 i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~---v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1          11 IRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             EEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTC---SCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             EEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhC---CChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEeC
Confidence            7899998765 578999999999999999999999   99999999999999999999999999999999999864

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=2.4e-17  Score=134.76  Aligned_cols=71  Identities=17%  Similarity=0.281  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+||+..|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||+|+|+.+|++|||++|++|+|+.
T Consensus        29 i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI~L~~   99 (100)
T d1uh6a_          29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHC---CCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHC---CCcceEEEEEEeecccCcCCHHHcCCCCCCEEEEEE
Confidence            47999999999999999999999999999999999   999999999999999999999999999999999975

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.1e-16  Score=127.28  Aligned_cols=68  Identities=26%  Similarity=0.387  Sum_probs=65.5

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         8 l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      ++|+++.|+|++++||.+||++|+.+.|   +|+++|+|+|+||.|+|+.+|++|||++|++|||++|+++
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~---ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~RG   86 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATG---MPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG   86 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTC---CCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhc---CChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            7899999999999999999999999999   9999999999999999999999999999999999998763

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=2.5e-17  Score=135.77  Aligned_cols=76  Identities=20%  Similarity=0.229  Sum_probs=70.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcE---------------EEeCCeecCCC-Cccccccc
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM---------------LIHQGKVLKDV-TTLEENKV   64 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~Qk---------------Liy~GkiL~D~-~tLsd~gI   64 (403)
                      |+|+||+++|++|.|+|+++.||.+||++|+...+   +|+++||               |+|+|+.|.|+ .+|.+|||
T Consensus         8 M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~---ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI   84 (105)
T d1v2ya_           8 MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ---LKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGI   84 (105)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHH---HHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTC
T ss_pred             EEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHC---cCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCC
Confidence            89999999999999999999999999999999999   9999997               99999999776 58999999


Q ss_pred             CCCcEEEEEEecCCC
Q 015628           65 AENSFVVVMLTKSKV   79 (403)
Q Consensus        65 ~~~s~I~v~v~k~k~   79 (403)
                      ++|++|||++++++.
T Consensus        85 ~~g~~l~lv~r~~~~   99 (105)
T d1v2ya_          85 RNRDEVSFIKKLGQK   99 (105)
T ss_dssp             CSSEEEEEEECSCSC
T ss_pred             CCCCEEEEEEecCCC
Confidence            999999999876543

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.65  E-value=2.9e-16  Score=128.11  Aligned_cols=78  Identities=17%  Similarity=0.264  Sum_probs=68.2

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCC--CCCC--CCCcEEEeCCeecCCCCcccccccCCCc------E
Q 015628            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGS--DVYP--ASQQMLIHQGKVLKDVTTLEENKVAENS------F   69 (403)
Q Consensus         1 MkI~VKtl~g~~~-~ieV~~~~TV~dLK~kI~~~~g~--~~ip--~~~QkLiy~GkiL~D~~tLsd~gI~~~s------~   69 (403)
                      |.|+||+++|+.+ .+.|++++||.+||++|+..+.+  ..+|  +++|||||+||+|+|+++|++|+|..|+      +
T Consensus         8 i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~~~~t   87 (101)
T d1se9a_           8 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTT   87 (101)
T ss_dssp             EEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEE
T ss_pred             EEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCCCceE
Confidence            6899999999987 69999999999999999987432  1276  7799999999999999999999999997      8


Q ss_pred             EEEEEecCC
Q 015628           70 VVVMLTKSK   78 (403)
Q Consensus        70 I~v~v~k~k   78 (403)
                      +||++|.+.
T Consensus        88 mHlVvrpp~   96 (101)
T d1se9a_          88 MHVIIQAPV   96 (101)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999987643

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=9.8e-17  Score=131.06  Aligned_cols=75  Identities=23%  Similarity=0.243  Sum_probs=68.0

Q ss_pred             CEEEE--EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            1 MKVFV--KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         1 MkI~V--Ktl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      |+|+|  |...|++|.|+|++++||.+||++|+.+.|   +++++|||||+||+|+|+++|++|||+++++|+||..+..
T Consensus        18 i~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~g---i~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~~~~   94 (100)
T d1wjua_          18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG---LQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELKQS   94 (100)
T ss_dssp             EEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTT---CCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECCCCC
T ss_pred             EEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHC---CCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEcCCC
Confidence            35555  556799999999999999999999999999   9999999999999999999999999999999998876543

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=6.5e-16  Score=124.45  Aligned_cols=75  Identities=20%  Similarity=0.232  Sum_probs=64.7

Q ss_pred             CEEEEEeCCCcE--EEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCc--EEEEEEec
Q 015628            1 MKVFVKTLKGTH--FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS--FVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~--~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s--~I~v~v~k   76 (403)
                      |+|+||+++++.  +.|+|++++||.+||++|++..+.. +|+++|||||+||+|+|+.+|++|+++.++  +|||+++.
T Consensus         8 i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~-~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~~~   86 (93)
T d1wgda_           8 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPER-PRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNV   86 (93)
T ss_dssp             CEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTC-CCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCC
T ss_pred             EEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCC-CChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEecC
Confidence            799999998754  8899999999999999999997533 899999999999999999999999776544  77777543

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=5.2e-16  Score=125.47  Aligned_cols=71  Identities=21%  Similarity=0.366  Sum_probs=66.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+|+ +++++|.|+|++++||.+||++|+..+|   +|+++|||+|+|+ |+|+.+|++|+|+++++|+||.+.
T Consensus        18 i~v~V~-~~~k~~~i~v~~~~TV~~LK~~I~~~tg---vp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~   88 (95)
T d1v86a_          18 VDLKII-WNKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             EEEEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHC---SCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSS
T ss_pred             EEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHhC---CChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecC
Confidence            578888 6899999999999999999999999999   9999999999997 999999999999999999998654

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=9.7e-16  Score=122.47  Aligned_cols=73  Identities=25%  Similarity=0.404  Sum_probs=66.8

Q ss_pred             CEEEEEeCCCcEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE---eCCeecCCCCcccccccCCCcEEEEEEec
Q 015628            1 MKVFVKTLKGTHFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (403)
Q Consensus         1 MkI~VKtl~g~~~~i-eV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi---y~GkiL~D~~tLsd~gI~~~s~I~v~v~k   76 (403)
                      |+|+||. .|+.|.+ +|++++||.+||++|+.+++   +|+++||||   |+||+|+|+.+|.+|+|++|++|+|+.++
T Consensus         8 ~~i~Vk~-~~~~~~i~~v~~~~tV~~LK~~i~~~t~---vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s~   83 (90)
T d1v5ta_           8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTG---VLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTR   83 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTC---CCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCC
T ss_pred             EEEEEEE-CCeEEEEEEeCCCCcHHHHHHHHHHHHc---CCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEeeC
Confidence            7899994 6777777 79999999999999999999   999999999   58999999999999999999999999764


Q ss_pred             C
Q 015628           77 S   77 (403)
Q Consensus        77 ~   77 (403)
                      .
T Consensus        84 ~   84 (90)
T d1v5ta_          84 E   84 (90)
T ss_dssp             S
T ss_pred             C
Confidence            3

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.59  E-value=5.9e-16  Score=128.66  Aligned_cols=76  Identities=24%  Similarity=0.318  Sum_probs=68.4

Q ss_pred             EEEEEeC-CCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCCC
Q 015628            2 KVFVKTL-KGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (403)
Q Consensus         2 kI~VKtl-~g~~~~ieV~~-~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k~   79 (403)
                      +|.|++. +|+++.|+|.+ ++||.+||.+|++++|   +|+++|||+|+||.|+|+.+|++|+|+++++|+|++|.+..
T Consensus        31 ~V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rGG  107 (111)
T d1we6a_          31 RVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG  107 (111)
T ss_dssp             EECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTT---CCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCS
T ss_pred             EEEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHC---CCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCCC
Confidence            3444443 58999999986 8999999999999999   99999999999999999999999999999999999998764


Q ss_pred             C
Q 015628           80 S   80 (403)
Q Consensus        80 ~   80 (403)
                      +
T Consensus       108 ~  108 (111)
T d1we6a_         108 P  108 (111)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=2.1e-15  Score=118.40  Aligned_cols=73  Identities=30%  Similarity=0.383  Sum_probs=65.8

Q ss_pred             CEEEEEeCCCcEEEEEe-----CCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecC-CCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEV-----KPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV-----~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~-D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|+|+ ..++.|.|+|     ++++||.+||++|+..+|   +|+++|||+|+|+.|. |+.+|++|||++|++|+||.
T Consensus         2 i~i~V~-~~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tg---vp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~   77 (81)
T d1wxva1           2 LTVTVT-HSNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIG---VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIG   77 (81)
T ss_dssp             EEEEEE-CSSSEEEEEECCCSSSSSCBHHHHHHHHHHHTC---CCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEES
T ss_pred             EEEEEE-ECCeeEEEEEecCCCCCccHHHHHHHHHHHHHC---cCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEE
Confidence            688997 5778888888     468899999999999999   9999999999999996 56899999999999999998


Q ss_pred             ecC
Q 015628           75 TKS   77 (403)
Q Consensus        75 ~k~   77 (403)
                      ++.
T Consensus        78 ~~~   80 (81)
T d1wxva1          78 KKN   80 (81)
T ss_dssp             CCS
T ss_pred             ecC
Confidence            764

>d1oqya1 a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=5.2e-16  Score=106.26  Aligned_cols=41  Identities=56%  Similarity=0.985  Sum_probs=39.6

Q ss_pred             CccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          170 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       170 g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      |+++|++|++|++||   |+|++|++|||+++||+|||+|||++
T Consensus         1 G~~~e~~i~~L~~MG---F~~~~a~~AL~~~~~N~e~A~~~LlS   41 (41)
T d1oqya1           1 GSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLT   41 (41)
T ss_dssp             TTTHHHHHHHHHTTT---CCSHHHHHHHHHSCSSTTHHHHTTTT
T ss_pred             ChhHHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            788999999999999   99999999999999999999999985

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=2.6e-14  Score=116.95  Aligned_cols=72  Identities=22%  Similarity=0.290  Sum_probs=61.7

Q ss_pred             EEEEeCCC-cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCc-------EEEEEE
Q 015628            3 VFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS-------FVVVML   74 (403)
Q Consensus         3 I~VKtl~g-~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s-------~I~v~v   74 (403)
                      |+|+...+ +++.++|++++||.+||++|+.+.|   +++++|||||+||.|+|+++|++|||.+++       ++++.+
T Consensus         2 ifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~~~~~~~~~~~l~~   78 (103)
T d2c9wb1           2 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK---RPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAF   78 (103)
T ss_dssp             EEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEE
T ss_pred             EEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhC---CCcccEEEEECCEEcCCCCCHHHcCCCcccccccCCcEEEEEE
Confidence            56665555 4688999999999999999999999   999999999999999999999999996544       666666


Q ss_pred             ecC
Q 015628           75 TKS   77 (403)
Q Consensus        75 ~k~   77 (403)
                      +..
T Consensus        79 ~~~   81 (103)
T d2c9wb1          79 RAD   81 (103)
T ss_dssp             EET
T ss_pred             ecC
Confidence            543

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=1.3e-13  Score=111.20  Aligned_cols=75  Identities=21%  Similarity=0.220  Sum_probs=67.4

Q ss_pred             CEEEEEe-CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCe-------ecCCCCcccccccCCCcEEEE
Q 015628            1 MKVFVKT-LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-------VLKDVTTLEENKVAENSFVVV   72 (403)
Q Consensus         1 MkI~VKt-l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~Gk-------iL~D~~tLsd~gI~~~s~I~v   72 (403)
                      |+|+|++ +++..++..+++++||.+||.+|+..+|   +|++.|||+|.|+       +++|+++|.+|+|.+|++|||
T Consensus         8 v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tG---ip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ihl   84 (95)
T d1v6ea_           8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVG---SPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHV   84 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTC---SCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEE
T ss_pred             EEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhC---cCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEEE
Confidence            5788987 4666788999999999999999999999   9999999999887       678999999999999999999


Q ss_pred             EEecCC
Q 015628           73 MLTKSK   78 (403)
Q Consensus        73 ~v~k~k   78 (403)
                      +.+.+.
T Consensus        85 vd~~p~   90 (95)
T d1v6ea_          85 IDHSGS   90 (95)
T ss_dssp             BCCSCC
T ss_pred             EeCCCC
Confidence            976643

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=2.4e-12  Score=103.89  Aligned_cols=74  Identities=18%  Similarity=0.207  Sum_probs=63.5

Q ss_pred             EEEEEe---CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCee-------c-CCCCcccccccCCCcEE
Q 015628            2 KVFVKT---LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV-------L-KDVTTLEENKVAENSFV   70 (403)
Q Consensus         2 kI~VKt---l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~Gki-------L-~D~~tLsd~gI~~~s~I   70 (403)
                      +|+|+.   .+++.+++.|+.++||.+||.+|+..+|   +|++.|+|+|.|+.       | +|+++|.+|||++|++|
T Consensus        11 ti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~g---ip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I   87 (97)
T d1wjna_          11 TLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLK---VPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCL   87 (97)
T ss_dssp             EEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTT---CCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEE
T ss_pred             EEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHC---cChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEE
Confidence            466664   4578899999999999999999999999   99999999998872       4 46789999999999999


Q ss_pred             EEEEecCC
Q 015628           71 VVMLTKSK   78 (403)
Q Consensus        71 ~v~v~k~k   78 (403)
                      +|....|+
T Consensus        88 ~V~~~~P~   95 (97)
T d1wjna_          88 LVRWSGPS   95 (97)
T ss_dssp             EEECCSSC
T ss_pred             EEEeCCCC
Confidence            99865543

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

Probab=99.28  E-value=3.7e-12  Score=98.85  Aligned_cols=73  Identities=11%  Similarity=0.141  Sum_probs=66.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecCC
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~k   78 (403)
                      +|+|++ +|+.+.+.|..++++..||+.++++.|   +++++++|+|+|+.|+++.|+++|+|+++++|+|+++..+
T Consensus         6 ~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~---i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~G   78 (79)
T d1euvb_           6 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   78 (79)
T ss_dssp             EEEEES-SSCEEEEEEETTSCTHHHHHHHHHHTT---CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCBC
T ss_pred             EEEECC-CCeEEEEEECCCCcHHHHHHHHHHHhC---CChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEeccC
Confidence            455554 678888999999999999999999999   9999999999999999999999999999999999998653

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.24  E-value=2.5e-12  Score=103.12  Aligned_cols=57  Identities=26%  Similarity=0.138  Sum_probs=50.3

Q ss_pred             CCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628           19 PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus        19 ~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      .+.||.+||++|+.+.......+++|||||+||.|+|+.+|++|||++|++|||+.|
T Consensus        36 ~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r   92 (94)
T d1x1ma1          36 GGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK   92 (94)
T ss_dssp             CCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEES
T ss_pred             CccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEe
Confidence            467999999999999764312468999999999999999999999999999999975

>d1wgna_ a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 1, UBAP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=2.5e-12  Score=95.82  Aligned_cols=48  Identities=27%  Similarity=0.433  Sum_probs=44.8

Q ss_pred             cccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015628          352 AVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH  399 (403)
Q Consensus       352 ~~~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~  399 (403)
                      ...+++.|.++|++|++|||+|++|++||++|++|.|.|++|||+|..
T Consensus        12 ~~~~~~~de~~v~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~Lls~~~   59 (63)
T d1wgna_          12 LQMLSPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHSG   59 (63)
T ss_dssp             HHTCCHHHHHHHHHHHHHHCCHHHHHHHHHHHCSCHHHHHHHHHHHSC
T ss_pred             cccCCchhHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            457899999999999999999999999999999999999999999753

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.8e-11  Score=94.42  Aligned_cols=74  Identities=19%  Similarity=0.276  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEecC
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~k~   77 (403)
                      |+|+|++.+|+.+.+.|..+.++..||..++++.|   +++..++|+|+|+.|.++.|+.+|+|++|++|.|+++..
T Consensus         3 I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~---~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q~   76 (77)
T d2uyzb1           3 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQT   76 (77)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC---CChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            57899999999999999999999999999999999   899999999999999999999999999999999998653

>d2g3qa1 a.5.2.1 (A:1339-1381) Endocytic protein Ede1, YBL047C {Saccharomyces cerevisiae [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Endocytic protein Ede1, YBL047C
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=99.16  E-value=1.8e-11  Score=82.24  Aligned_cols=41  Identities=39%  Similarity=0.597  Sum_probs=37.7

Q ss_pred             CHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       356 t~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      ||.+ .+|++|+.|||+++++++|+..|+||++.|.|||+++
T Consensus         2 tpk~-~ai~eL~~MGF~e~~A~~AL~k~~wnleaAtN~LLd~   42 (43)
T d2g3qa1           2 TPKS-LAVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDS   42 (43)
T ss_dssp             CHHH-HHHHHHHTTTSCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             CcHH-HHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            3444 7899999999999999999999999999999999986

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Rhomboid family protein At3g58460
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.16  E-value=4.4e-11  Score=91.48  Aligned_cols=40  Identities=40%  Similarity=0.474  Sum_probs=38.0

Q ss_pred             cHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          172 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       172 ~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      ..++.|++|++||   |+|++|++||+++.||.|||||||+..
T Consensus        28 ~~ee~i~~L~~MG---F~~~~a~~AL~~~~~n~e~A~~~Ll~~   67 (73)
T d1vg5a_          28 ASEEQIQKLVAMG---FDRTQVEVALAAADDDLTVAVEILMSQ   67 (73)
T ss_dssp             CCHHHHHHHHTTT---CCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             cCHHHHHHHHHhC---CCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            3588999999999   999999999999999999999999986

>d1wgna_ a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 1, UBAP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=1.1e-11  Score=92.15  Aligned_cols=43  Identities=28%  Similarity=0.557  Sum_probs=39.6

Q ss_pred             ccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC-CC
Q 015628          171 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG-IP  216 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G-IP  216 (403)
                      +..+++|++||+||   |+|++|++||+++.||++|||+||++. +|
T Consensus        17 ~~de~~v~~L~~MG---F~~~~a~~AL~~~~~n~e~A~~~Lls~~~p   60 (63)
T d1wgna_          17 PSERQCVETVVNMG---YSYECVLRAMKKKGENIEQILDYLFAHSGP   60 (63)
T ss_dssp             HHHHHHHHHHHHHH---CCHHHHHHHHHHHCSCHHHHHHHHHHHSCC
T ss_pred             chhHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence            45689999999999   999999999999999999999999985 44

>d1wiva_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.12  E-value=2.5e-11  Score=92.85  Aligned_cols=49  Identities=12%  Similarity=0.271  Sum_probs=43.7

Q ss_pred             cCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCCC
Q 015628          354 TVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       354 ~lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~~  402 (403)
                      ..++.+.++|++|++|||+|.+|++||++|++|.+.|++|||+|..+.|
T Consensus        24 ~~~~~d~~~i~~L~~MGF~~~~a~~AL~~~~~n~e~Av~~Lls~~~~~d   72 (73)
T d1wiva_          24 QTSDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNSGPSS   72 (73)
T ss_dssp             SSCSSCHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHHSCCSSC
T ss_pred             cCCCCCHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHHHcCCCCCC
Confidence            3445566789999999999999999999999999999999999987765

>d1wjia_ a.5.2.1 (A:) Tudor domain containing protein 3, TDRD3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Tudor domain containing protein 3, TDRD3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=3.8e-11  Score=89.37  Aligned_cols=43  Identities=28%  Similarity=0.372  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCCCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  218 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP~~  218 (403)
                      .++.|++||+||   |+|++|++||++..||+++||+||+++..+.
T Consensus         9 d~~~v~~L~~MG---F~~~~a~~AL~~~~~~~e~A~~wL~~~~~~~   51 (63)
T d1wjia_           9 DEKALKHITEMG---FSKEASRQALMDNGNNLEAALNVLLTSNKQK   51 (63)
T ss_dssp             CHHHHHHHHTTT---CCHHHHHHHHHHTTSCHHHHHHHHHHHSSCC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHHCCCCC
Confidence            378999999999   9999999999999999999999999996654

>d1oqya1 a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=1.4e-11  Score=83.93  Aligned_cols=39  Identities=28%  Similarity=0.457  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhc
Q 015628          358 EEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLD  396 (403)
Q Consensus       358 ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~  396 (403)
                      +..++|++|++|||+|++|++|+.+|++|.+.|++|||+
T Consensus         3 ~~e~~i~~L~~MGF~~~~a~~AL~~~~~N~e~A~~~LlS   41 (41)
T d1oqya1           3 EYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLT   41 (41)
T ss_dssp             THHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTTTT
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            456789999999999999999999999999999999995

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Rhomboid family protein At3g58460
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.11  E-value=2.8e-11  Score=92.64  Aligned_cols=45  Identities=29%  Similarity=0.409  Sum_probs=39.9

Q ss_pred             CCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015628          355 VTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH  399 (403)
Q Consensus       355 lt~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~  399 (403)
                      ....+.++|++|++|||+|++|++||.+|++|.|.|++|||++..
T Consensus        25 ~~~~~ee~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~Ll~~~~   69 (73)
T d1vg5a_          25 RVAASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQSG   69 (73)
T ss_dssp             CSCCCHHHHHHHHTTTCCHHHHHHHHHHHTSCHHHHHHHHHTCSC
T ss_pred             CcCcCHHHHHHHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHhCCC
Confidence            344456689999999999999999999999999999999999753

>d1wjia_ a.5.2.1 (A:) Tudor domain containing protein 3, TDRD3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Tudor domain containing protein 3, TDRD3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=3e-11  Score=89.91  Aligned_cols=46  Identities=22%  Similarity=0.314  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCCC
Q 015628          357 PEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       357 ~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~~  402 (403)
                      ..+.++|++|++|||+|..|++||++|++|.+.|++|||+|..|.+
T Consensus         7 ~~d~~~v~~L~~MGF~~~~a~~AL~~~~~~~e~A~~wL~~~~~~~~   52 (63)
T d1wjia_           7 GVDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQKP   52 (63)
T ss_dssp             SSCHHHHHHHHTTTCCHHHHHHHHHHTTSCHHHHHHHHHHHSSCCC
T ss_pred             ccCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHCCCCCC
Confidence            3456789999999999999999999999999999999999977654

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=99.07  E-value=1.9e-10  Score=91.35  Aligned_cols=72  Identities=14%  Similarity=0.127  Sum_probs=60.7

Q ss_pred             EEEEEe-CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCe-------ecCCCCcccccccCCCcEEEEE
Q 015628            2 KVFVKT-LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-------VLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKt-l~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~Gk-------iL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      .|.|.+ ..+..+++.++.++||.+||.+|+..+|   +|+..|||+|.|+       .++|+++|.+|||.+|..|||+
T Consensus         6 ~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~G---ip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvv   82 (90)
T d1t0ya_           6 DLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVG---TTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAV   82 (90)
T ss_dssp             EEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHC---CCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEE
T ss_pred             EEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHC---CChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEE
Confidence            355554 3344567889999999999999999999   9999999999886       4577899999999999999998


Q ss_pred             Eec
Q 015628           74 LTK   76 (403)
Q Consensus        74 v~k   76 (403)
                      -+.
T Consensus        83 d~~   85 (90)
T d1t0ya_          83 DVT   85 (90)
T ss_dssp             ECT
T ss_pred             eCC
Confidence            654

>d1wiva_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.00  E-value=1.6e-10  Score=88.32  Aligned_cols=39  Identities=21%  Similarity=0.507  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .++.|+.||+||   |+|++|++|||++.||.+|||+||++.
T Consensus        29 d~~~i~~L~~MG---F~~~~a~~AL~~~~~n~e~Av~~Lls~   67 (73)
T d1wiva_          29 DQSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFNN   67 (73)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHHS
T ss_pred             CHHHHHHHHhcC---CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            478999999999   999999999999999999999999986

>d1whca_ a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA/UBX 33.3 kDa protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.79  E-value=2.8e-09  Score=79.20  Aligned_cols=40  Identities=23%  Similarity=0.366  Sum_probs=37.1

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHcCCC
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIP  216 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~GIP  216 (403)
                      +++|++|++||   |+|+++++||++..| ++++|||||+...-
T Consensus        10 ~~~l~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~   50 (64)
T d1whca_          10 LTALESLIEMG---FPRGRAEKALALTGNQGIEAAMDWLMEHED   50 (64)
T ss_dssp             CCHHHHHHTTT---CCHHHHHHHHHHHTSCCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhCCCCHHHHHHHHHHCCC
Confidence            56999999999   999999999999998 79999999999743

>d1whca_ a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA/UBX 33.3 kDa protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.76  E-value=1.7e-09  Score=80.45  Aligned_cols=44  Identities=27%  Similarity=0.401  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHhccCCCCC
Q 015628          359 EREAIERLEAMGFDRALVLEVFFACNK-NEELAANYLLDHMHEFE  402 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac~~-ne~~a~~~L~~~~~d~~  402 (403)
                      |.++|++|++|||++..|.+|+++|+. |.|.|++|||+|+.|.+
T Consensus         9 d~~~l~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~d~d   53 (64)
T d1whca_           9 ELTALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDDPD   53 (64)
T ss_dssp             CCCHHHHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHHHHTTCSC
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHHCCCCCC
Confidence            446799999999999999999999965 89999999999987754

>d1veka_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.73  E-value=4.2e-09  Score=82.36  Aligned_cols=45  Identities=29%  Similarity=0.445  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHH-hCCCHHHHHHHHhccCCCCC
Q 015628          358 EEREAIERLEAMGFDRALVLEVFFA-CNKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       358 ee~~ai~rL~~lGF~~~~~~~a~~a-c~~ne~~a~~~L~~~~~d~~  402 (403)
                      .+.++|.+|++|||++..|++|++. |++|.+.|+||||+|..|.|
T Consensus        28 ~d~~~v~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~d~d   73 (84)
T d1veka_          28 ANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPD   73 (84)
T ss_dssp             CCHHHHHHHHHHTCCHHHHHHHHHHTTTCCHHHHHHHHHHHTTCST
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHHHcCCCCC
Confidence            3568899999999999999999877 78899999999999987764

>d1x3zb1 a.189.1.1 (B:253-309) Rad23 STI1 domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: XPC-binding domain
superfamily: XPC-binding domain
family: XPC-binding domain
domain: Rad23 STI1 domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.69  E-value=1.3e-08  Score=70.56  Aligned_cols=49  Identities=27%  Similarity=0.546  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHhCccchHHHHHHHHhhCHHHHHHHHHcHHHHHHHhcCC
Q 015628          285 QQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP  333 (403)
Q Consensus       285 pqf~~lR~~vq~NP~lL~~~lq~i~~~nP~l~~lI~~n~e~Fl~~l~~~  333 (403)
                      .++.+||++|.-||+.|.++|..|...+|+|++.|.+|||-|+.||.+.
T Consensus         8 edl~~lr~vvsg~peal~plle~ls~ryp~lre~im~npe~fismllea   56 (57)
T d1x3zb1           8 EDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEA   56 (57)
T ss_dssp             THHHHHHHHHHHCGGGHHHHHHHHHTTCHHHHHHHHTCHHHHHHHHHHC
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHhhHHHHHHHHhCHHHHHHHHHhh
Confidence            3567899999999999999999999999999999999999999999753

>d2cpwa1 a.5.2.1 (A:8-58) Cbl-interacting protein p70, STS1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Cbl-interacting protein p70, STS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.64  E-value=7.7e-09  Score=73.29  Aligned_cols=36  Identities=25%  Similarity=0.505  Sum_probs=34.0

Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHc
Q 015628          175 ATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYS  213 (403)
Q Consensus       175 ~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~  213 (403)
                      ..|+.|++||   |+++++++||++.-| |.++||+||+.
T Consensus        14 ~~l~~L~~MG---F~~~~a~~AL~~t~n~~ve~A~~WLl~   50 (51)
T d2cpwa1          14 SALDVLLSMG---FPRARAQKALASTGGRSVQTACDWLFS   50 (51)
T ss_dssp             CHHHHHHHHT---CCHHHHHHHHHHTTTSCHHHHHHHHHS
T ss_pred             HHHHHHHHcC---CCHHHHHHHHHHHCCCCHHHHHHHHHc
Confidence            4799999999   999999999999988 99999999985

>d2crna1 a.5.2.1 (A:8-58) Suppressor of T-cell receptor signaling 2 (STS-2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Suppressor of T-cell receptor signaling 2 (STS-2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=1.9e-08  Score=71.32  Aligned_cols=41  Identities=34%  Similarity=0.408  Sum_probs=36.9

Q ss_pred             HHHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHHhccCCCCC
Q 015628          362 AIERLEAMGFDRALVLEVFFAC-NKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       362 ai~rL~~lGF~~~~~~~a~~ac-~~ne~~a~~~L~~~~~d~~  402 (403)
                      .|++|++|||++..|.+|++.+ ++|.|.|.+|||+|..|.|
T Consensus         5 ~v~~L~~MGF~~~~a~~Al~~t~n~~ve~A~~Wl~~h~~d~d   46 (51)
T d2crna1           5 LLEPLLAMGFPVHTALKALAATGRKTAEEALAWLHDHCNDPS   46 (51)
T ss_dssp             SHHHHHHTSCCHHHHHHHHHHHTSCCHHHHHHHHHHHSSSTT
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHCCCCHHHHHHHHHHcCCCcC
Confidence            4899999999999999999998 4699999999999987653

>d2cpwa1 a.5.2.1 (A:8-58) Cbl-interacting protein p70, STS1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Cbl-interacting protein p70, STS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.54  E-value=3.6e-08  Score=69.74  Aligned_cols=37  Identities=27%  Similarity=0.460  Sum_probs=34.6

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHhcc
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNK-NEELAANYLLDH  397 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~-ne~~a~~~L~~~  397 (403)
                      .+|+.|++|||++..|.+|+++|+. |.|.|.+|||+|
T Consensus        14 ~~l~~L~~MGF~~~~a~~AL~~t~n~~ve~A~~WLl~H   51 (51)
T d2cpwa1          14 SALDVLLSMGFPRARAQKALASTGGRSVQTACDWLFSH   51 (51)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHTTTSCHHHHHHHHHSC
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHCCCCHHHHHHHHHcC
Confidence            4599999999999999999999987 999999999986

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.47  E-value=3.7e-07  Score=68.85  Aligned_cols=70  Identities=16%  Similarity=0.238  Sum_probs=65.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~   73 (403)
                      ++|+|+..+|+.+.+.|..+.++..|....+...+   +++...+|+|+|+.|..+.|.+++++++|+.|.|.
T Consensus         2 I~lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~~---~~~~~~~f~fdG~~i~~~~Tp~~l~med~D~Idv~   71 (72)
T d1wm3a_           2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG---LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHT---CCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhC---CCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            47888888999999999999999999999999999   88999999999999999999999999999999875

>d2bwba1 a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.44  E-value=1.2e-07  Score=64.76  Aligned_cols=40  Identities=30%  Similarity=0.404  Sum_probs=35.5

Q ss_pred             HHHHHH--HHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhc
Q 015628          357 PEEREA--IERLEAMGF-DRALVLEVFFACNKNEELAANYLLD  396 (403)
Q Consensus       357 ~ee~~a--i~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~  396 (403)
                      |||+-+  +++|.+||| +++..|+|+.+|++|.+.|+++||+
T Consensus         1 pe~ry~~QL~qL~~MGF~d~~~Ni~AL~~t~GdV~~Aie~Ll~   43 (44)
T d2bwba1           1 PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN   43 (44)
T ss_dssp             HHHHTHHHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHHC
T ss_pred             ChHHHHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHhC
Confidence            344444  899999998 9999999999999999999999996

>d2dnaa1 a.5.2.1 (A:12-61) Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquilin-like protein Ubqlnl
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.35  E-value=2.7e-07  Score=64.57  Aligned_cols=42  Identities=31%  Similarity=0.404  Sum_probs=37.1

Q ss_pred             HHHHHH--HHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          357 PEEREA--IERLEAMGF-DRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       357 ~ee~~a--i~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      +|++-+  +++|.+||| +++.+|+|+.+|++|.+.|+++|+++.
T Consensus         4 pe~ry~~QL~qL~~MGF~d~~~Ni~AL~~t~GdV~~Aie~Ll~~~   48 (50)
T d2dnaa1           4 PEVRFSKEMECLQAMGFVNYNANLQALIATDGDTNAAIYKLKSSQ   48 (50)
T ss_dssp             HHHHTHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHHCC
T ss_pred             hHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHHhcC
Confidence            445444  899999998 999999999999999999999999864

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NPL4-like protein 1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.33  E-value=4.8e-07  Score=70.86  Aligned_cols=70  Identities=20%  Similarity=0.176  Sum_probs=57.1

Q ss_pred             EEEEEeCCCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCcEEEeC--------------CeecCC-CCcccccccC
Q 015628            2 KVFVKTLKGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQ--------------GKVLKD-VTTLEENKVA   65 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~-~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~--------------GkiL~D-~~tLsd~gI~   65 (403)
                      -|.||+.+| +..|+|+. +.||.+||.+|++..+   +|+++|.|..+              -..|.| ..+|++|||.
T Consensus         2 iiRiRsrdG-~eRv~v~~~~~Tl~~LK~~Ie~~L~---VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~   77 (94)
T d1wf9a1           2 MLRVRSRDG-LERVSVDGPHITVSQLKTLIQDQLQ---IPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLA   77 (94)
T ss_dssp             EEEEECSSC-EEEEEECCTTSBHHHHHHHHHHHSC---CCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCC
T ss_pred             eEEEEecCC-ceEEEecCCCCcHHHHHHHHHHHhC---CCcccceeecChhhhccCCccccchhhhccCCccCHHHcCcc
Confidence            378898888 56788864 7899999999999999   99999999432              233555 4679999999


Q ss_pred             CCcEEEEEEe
Q 015628           66 ENSFVVVMLT   75 (403)
Q Consensus        66 ~~s~I~v~v~   75 (403)
                      +|++|++...
T Consensus        78 hGsivyL~y~   87 (94)
T d1wf9a1          78 HGSMVYLAYE   87 (94)
T ss_dssp             TTCEEECCCS
T ss_pred             CceEEEEEee
Confidence            9999998764

>d2g3qa1 a.5.2.1 (A:1339-1381) Endocytic protein Ede1, YBL047C {Saccharomyces cerevisiae [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Endocytic protein Ede1, YBL047C
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=98.32  E-value=4.3e-07  Score=60.69  Aligned_cols=39  Identities=23%  Similarity=0.342  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .+.+|++|++||   |+++++++||+.+..|-+-|+.||+-|
T Consensus         4 k~~ai~eL~~MG---F~e~~A~~AL~k~~wnleaAtN~LLd~   42 (43)
T d2g3qa1           4 KSLAVEELSGMG---FTEEEAHNALEKCNWDLEAATNFLLDS   42 (43)
T ss_dssp             HHHHHHHHHTTT---SCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             HHHHHHHHHhcC---CCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            367999999999   999999999999999999999999966

>d2crna1 a.5.2.1 (A:8-58) Suppressor of T-cell receptor signaling 2 (STS-2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Suppressor of T-cell receptor signaling 2 (STS-2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.31  E-value=3.2e-07  Score=64.81  Aligned_cols=37  Identities=27%  Similarity=0.442  Sum_probs=34.2

Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHcC
Q 015628          175 ATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSG  214 (403)
Q Consensus       175 ~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~G  214 (403)
                      +.|++|++||   |+|.++++||++.-| |.++||+||+..
T Consensus         4 ~~v~~L~~MG---F~~~~a~~Al~~t~n~~ve~A~~Wl~~h   41 (51)
T d2crna1           4 SLLEPLLAMG---FPVHTALKALAATGRKTAEEALAWLHDH   41 (51)
T ss_dssp             SSHHHHHHTS---CCHHHHHHHHHHHTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcC---CCHHHHHHHHHHHCCCCHHHHHHHHHHc
Confidence            3699999999   999999999999976 999999999975

>d1veka_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.31  E-value=2.9e-07  Score=71.69  Aligned_cols=40  Identities=28%  Similarity=0.377  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHHcCC
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGI  215 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~~GI  215 (403)
                      .+..|++|++||   |+|..+++||++..| |.++|++||+...
T Consensus        29 d~~~v~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~Wl~~h~   69 (84)
T d1veka_          29 NEEIVAQLVSMG---FSQLHCQKAAINTSNAGVEEAMNWLLSHM   69 (84)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTTCCHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHHcCCCHHHHHHHHHHcC
Confidence            378999999999   999999999999987 9999999999753

>d2bwba1 a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.29  E-value=5.7e-07  Score=61.32  Aligned_cols=40  Identities=30%  Similarity=0.473  Sum_probs=37.6

Q ss_pred             cHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          172 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       172 ~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .|..-+++|-+||   | +++..++||+++..|.++|||+|++|
T Consensus         4 ry~~QL~qL~~MG---F~d~~~Ni~AL~~t~GdV~~Aie~Ll~g   44 (44)
T d2bwba1           4 RYEHQLRQLNDMG---FFDFDRNVAALRRSGGSVQGALDSLLNG   44 (44)
T ss_dssp             HTHHHHHHHHHTT---CCCHHHHHHHHHHHTTCHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHcC---CCcHHHHHHHHHHcCCCHHHHHHHHhCc
Confidence            3677899999999   9 99999999999999999999999987

>d1veja1 a.5.2.1 (A:8-68) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.21  E-value=4e-07  Score=66.28  Aligned_cols=44  Identities=30%  Similarity=0.489  Sum_probs=38.2

Q ss_pred             ccCCHHHH--HHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhc
Q 015628          353 VTVTPEER--EAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLD  396 (403)
Q Consensus       353 ~~lt~ee~--~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~  396 (403)
                      ..+.+|++  .-+++|.+||| +++.+|+|+.+|++|.+.|+++||.
T Consensus        14 ~~~~~e~ry~~QL~qL~eMGF~d~~~Nl~AL~~t~Gdv~~Aie~Ll~   60 (61)
T d1veja1          14 TSLFTEGRYQQELEELKALGFANRDANLQALVATDGDIHAAIEMLLG   60 (61)
T ss_dssp             CGGGTTTTSHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            45666664  44999999999 7888899999999999999999985

>d2daha1 a.5.2.1 (A:8-48) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.01  E-value=3.2e-06  Score=56.72  Aligned_cols=36  Identities=28%  Similarity=0.466  Sum_probs=33.4

Q ss_pred             HHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          362 AIERLEAMGF-DRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       362 ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      .+++|.+||| +++..|+|+.+|++|.+.|+.+|+++
T Consensus         5 QL~~L~~MGF~d~~~Ni~AL~~t~Gdv~~Aie~Ll~~   41 (41)
T d2daha1           5 QLEQLRSMGFLNREANLQALIATGGDVDAAVEKLRQS   41 (41)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            4889999998 89999999999999999999999863

>d1veja1 a.5.2.1 (A:8-68) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.00  E-value=5.5e-06  Score=60.13  Aligned_cols=40  Identities=20%  Similarity=0.424  Sum_probs=36.9

Q ss_pred             ccHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          171 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       171 ~~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      ..|..-++.|.+||   | +++..++||+++.+|.++|||||+.
T Consensus        20 ~ry~~QL~qL~eMG---F~d~~~Nl~AL~~t~Gdv~~Aie~Ll~   60 (61)
T d1veja1          20 GRYQQELEELKALG---FANRDANLQALVATDGDIHAAIEMLLG   60 (61)
T ss_dssp             TTSHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcC---CCCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            45889999999999   9 7888899999999999999999973

>d2dnaa1 a.5.2.1 (A:12-61) Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquilin-like protein Ubqlnl
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.96  E-value=5.1e-06  Score=57.91  Aligned_cols=40  Identities=20%  Similarity=0.291  Sum_probs=37.6

Q ss_pred             cHHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHcC
Q 015628          172 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  214 (403)
Q Consensus       172 ~~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~G  214 (403)
                      .|..-++.|-+||   | +++..++||+++..|.++|||+|+.+
T Consensus         7 ry~~QL~qL~~MG---F~d~~~Ni~AL~~t~GdV~~Aie~Ll~~   47 (50)
T d2dnaa1           7 RFSKEMECLQAMG---FVNYNANLQALIATDGDTNAAIYKLKSS   47 (50)
T ss_dssp             HTHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcC---CCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            4778899999999   9 99999999999999999999999976

>d2daha1 a.5.2.1 (A:8-48) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.95  E-value=5.9e-06  Score=55.39  Aligned_cols=38  Identities=32%  Similarity=0.478  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          173 LEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      |+.-++.|-+||   | +++..++||+++..|.++|||+|+.
T Consensus         2 y~~QL~~L~~MG---F~d~~~Ni~AL~~t~Gdv~~Aie~Ll~   40 (41)
T d2daha1           2 FQVQLEQLRSMG---FLNREANLQALIATGGDVDAAVEKLRQ   40 (41)
T ss_dssp             SHHHHHHHHHHT---CCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHcC---CCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            567889999999   9 9999999999999999999999974

>d3e46a1 a.5.2.1 (A:157-198) Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.70  E-value=4.3e-05  Score=49.22  Aligned_cols=40  Identities=38%  Similarity=0.472  Sum_probs=36.5

Q ss_pred             CHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHh
Q 015628          356 TPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLL  395 (403)
Q Consensus       356 t~ee~~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~  395 (403)
                      ++|=-..|+.||+|||+++.||.|+..-.||.|-|...|+
T Consensus         3 speyt~kidklca~gf~knavi~alsskswdvetatelll   42 (42)
T d3e46a1           3 SPEYTKKIENLCAAGFDRNAVIVALSSKSWDVETATELLL   42 (42)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHccccccceeeeeccCccchhhHHHhhC
Confidence            4566678999999999999999999999999999999885

>d3e46a1 a.5.2.1 (A:157-198) Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.33  E-value=0.00021  Score=45.90  Aligned_cols=41  Identities=27%  Similarity=0.407  Sum_probs=37.9

Q ss_pred             CCccHHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHH
Q 015628          169 AGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  212 (403)
Q Consensus       169 ~g~~~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~  212 (403)
                      +.++|-..|.+|+.||   |+|.-|+.||.---.+.+.|-|.|+
T Consensus         2 sspeyt~kidklca~g---f~knavi~alsskswdvetatelll   42 (42)
T d3e46a1           2 SSPEYTKKIENLCAAG---FDRNAVIVALSSKSWDVETATELLL   42 (42)
T ss_dssp             CCHHHHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHcc---ccccceeeeeccCccchhhHHHhhC
Confidence            4577899999999999   9999999999999999999999885

>d1z96a1 a.5.2.1 (A:295-332) UBA-domain protein mud1 {Schizosaccharomyces pombe [TaxId: 4896]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA-domain protein mud1
species: Schizosaccharomyces pombe [TaxId: 4896]

Probab=97.16  E-value=0.00032  Score=43.84  Aligned_cols=35  Identities=34%  Similarity=0.503  Sum_probs=33.0

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHh
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLL  395 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~  395 (403)
                      ..|.+|+.|||+.-++.||+-+.++|-++|+.||+
T Consensus         4 skiaqlvsmgfdpleaaqaldaangdldvaasfll   38 (38)
T d1z96a1           4 SKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL   38 (38)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             hHHHHHHHcCCCHHHHHHHHhhhcCcHHHHHHhhC
Confidence            35899999999999999999999999999999986

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.01  E-value=0.0013  Score=49.78  Aligned_cols=68  Identities=18%  Similarity=0.229  Sum_probs=57.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecC---CCCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~---D~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.||..+|+.+.-.+..++||.+|...|... +   ......+|+  |-.|.|.   ++++|.++|+.+..+|+|-
T Consensus         7 ~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~-~---~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~vq   79 (82)
T d1h8ca_           7 KLRIRTPSGEFLERRFLASNKLQIVFDFVASK-G---FPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   79 (82)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-T---CCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCCCcHHHHHHHHHhc-C---CCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEEE
Confidence            68999999999999999999999999999874 5   566778886  6788884   4679999999988887753

>d1oqya2 a.5.2.1 (A:317-360) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.94  E-value=0.00012  Score=49.14  Aligned_cols=38  Identities=24%  Similarity=0.379  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      -..+|.+|++||   |+|++|+.|--|.-.|-+-|..||+.
T Consensus         4 e~~aIeRL~~LG---F~r~~viqay~ACdKNEelAaN~L~~   41 (44)
T d1oqya2           4 EKEAIERLKALG---FPESLVIQAYFACEKNENLAANFLLS   41 (44)
T ss_dssp             THHHHHHHHHHT---CCSHHHHHHTSSSSSCSSHHHHHHHH
T ss_pred             HHHHHHHHHHcC---CCHHHHHHHHHHhCcCHHHHHHHHHH
Confidence            367999999999   99999999999999999999999985

>d2al3a1 d.15.1.2 (A:10-85) Tether containing UBX domain for GLUT4 (Tug) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Tether containing UBX domain for GLUT4 (Tug)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.79  E-value=0.0026  Score=47.61  Aligned_cols=70  Identities=19%  Similarity=0.167  Sum_probs=65.5

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCCeecCCCCcccccccCCCcEEEEEEe
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~GkiL~D~~tLsd~gI~~~s~I~v~v~   75 (403)
                      |+|=..+|+..+|.|.|+.|+.++-+....++|   +.+++-.|.|.+|.|+-+..+.-.|+-+|..+-++-.
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~---~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~~   72 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQD---FNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPV   72 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTT---CCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECS
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhC---CChhHceeeeCCEEcCccceeeecCCCCCCEEEEEEc
Confidence            677888999999999999999999999999999   8899999999999999999999999999999998854

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.74  E-value=0.0022  Score=49.25  Aligned_cols=66  Identities=18%  Similarity=0.315  Sum_probs=53.6

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEEe--CCeecCC-CCcccccccCCCcEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKD-VTTLEENKVAENSFV   70 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy--~GkiL~D-~~tLsd~gI~~~s~I   70 (403)
                      +|.||..+|+.+...+..++||.+|...|......  .......|+.  --|.|.| +.+|.++|+.+ +.|
T Consensus        16 ~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~--~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~-s~v   84 (89)
T d1i42a_          16 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPA--MAATSFVLMTTFPNKELADENQTLKEANLLN-AVI   84 (89)
T ss_dssp             EEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTT--TSSCCEEEEETTTTEECCCCSSCSGGGTTCC-SEE
T ss_pred             EEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCcc--CCCCCEEEecCCCCcccCCCcCcHHHCCCcC-ceE
Confidence            68899999999999999999999999999876421  5566788874  4678855 78999999985 444

>d1vega_ a.5.2.1 (A:) NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: NEDD8 ultimate buster-1 (Nub1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.66  E-value=0.0011  Score=49.40  Aligned_cols=39  Identities=33%  Similarity=0.391  Sum_probs=36.2

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015628          361 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH  399 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~  399 (403)
                      +.|++|+=|||++..+..|+....+|+.+|+..|..|..
T Consensus        31 esidqLvYMGF~~~~Ae~ALRvfrGnVQlAaQtLahngG   69 (83)
T d1vega_          31 ESINQLVYMGFDTVVAEAALRVFGGNVQLAAQTLAHHGG   69 (83)
T ss_dssp             HHHHHHHHHSCCHHHHHHHHHHTTTCHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhcccHHHHHHHHHHhcccHHHHHHHHHHcCC
Confidence            569999999999999999999999999999999987753

>d1z96a1 a.5.2.1 (A:295-332) UBA-domain protein mud1 {Schizosaccharomyces pombe [TaxId: 4896]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA-domain protein mud1
species: Schizosaccharomyces pombe [TaxId: 4896]

Probab=96.59  E-value=0.0019  Score=40.20  Aligned_cols=37  Identities=30%  Similarity=0.499  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHH
Q 015628          173 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  212 (403)
Q Consensus       173 ~e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~  212 (403)
                      ++..|.+|++||   |+-=+...||.|+..+-|-|..||+
T Consensus         2 lnskiaqlvsmg---fdpleaaqaldaangdldvaasfll   38 (38)
T d1z96a1           2 LNSKIAQLVSMG---FDPLEAAQALDAANGDLDVAASFLL   38 (38)
T ss_dssp             HHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             cchHHHHHHHcC---CCHHHHHHHHhhhcCcHHHHHHhhC
Confidence            467899999999   9999999999999999999999984

>d1wj7a1 a.5.2.1 (A:8-98) Ubiquitin-associated protein 2-like Ubap2l {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 2-like Ubap2l
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.58  E-value=0.0017  Score=49.95  Aligned_cols=42  Identities=21%  Similarity=0.332  Sum_probs=37.3

Q ss_pred             HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015628          360 REAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDHMHEF  401 (403)
Q Consensus       360 ~~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~  401 (403)
                      .+.|+.|.+| |=++++|+-||.-||.|.+.|+||||+...|.
T Consensus        33 ~~kVkql~e~T~rsede~~~ALhDcn~D~~~AIn~lLEg~~~~   75 (91)
T d1wj7a1          33 EEKVKQLIDITGKNQDECVIALHDCNGDVNRAINVLLEGNPDT   75 (91)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHTCSSSC
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHhcCCccHHHHHHHHHhcCCCC
Confidence            3559999998 88999999999999999999999999976543

>d1v92a_ a.5.2.3 (A:) NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TAP-C domain-like
domain: NSFL1 (p97 ATPase) cofactor p47, UBA-like domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.49  E-value=0.002  Score=43.68  Aligned_cols=43  Identities=12%  Similarity=0.145  Sum_probs=39.3

Q ss_pred             CHHHHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhccC
Q 015628          356 TPEEREAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDHM  398 (403)
Q Consensus       356 t~ee~~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~~  398 (403)
                      ..++.+.|.+.+++ |-++..+.+-+.+|+||.+.|++..|+++
T Consensus         2 a~~~~~lI~qF~~iTg~~~~~A~~~Le~~~w~Le~Ai~~yfe~g   45 (46)
T d1v92a_           2 AEERQDALREFVAVTGAEEDRARFFLESAGWDLQIALASFYEDG   45 (46)
T ss_dssp             TTHHHHHHHHHHHHTCCCHHHHHHHHHHTTSCSHHHHHHHHHTC
T ss_pred             CccHHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHHhcC
Confidence            45677889999998 99999999999999999999999999875

>d1wj4a_ d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Hypothetical protein KIAA0794
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.28  E-value=0.0043  Score=50.55  Aligned_cols=68  Identities=21%  Similarity=0.337  Sum_probs=56.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecC---CCCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~---D~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.||..+|+.+...+..++||.+|...|... +   +.....+|+  |--|.|.   .+++|.++||.+..+|+|-
T Consensus        45 ~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~-~---~~~~~~~L~~~fPr~~l~~~d~~~TL~e~gL~P~~~L~ve  117 (124)
T d1wj4a_          45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-G---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-H---CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-c---cCCcceEEeecccccccccccccCcHHHcCCCCCCEEEEE
Confidence            68899999999999999999999999999775 3   445677776  5677774   3689999999998888654

>d2cr5a1 d.15.1.2 (A:8-103) UBX domain-containing protein 6 (Reproduction 8) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: UBX domain-containing protein 6 (Reproduction 8)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.19  E-value=0.0058  Score=47.25  Aligned_cols=68  Identities=15%  Similarity=0.121  Sum_probs=54.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCcEEE--eCCeecC-C-CCcccccccCCCcEEEEE
Q 015628            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK-D-VTTLEENKVAENSFVVVM   73 (403)
Q Consensus         2 kI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLi--y~GkiL~-D-~~tLsd~gI~~~s~I~v~   73 (403)
                      +|.||..+|+.+...+..++||.+|...|....    ......+|+  |-.+.|. | +++|.++||.+..+|+|-
T Consensus        18 ~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~~----~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v~   89 (96)
T d2cr5a1          18 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVG----YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVE   89 (96)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHHT----CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcccHHHHHHHHHHhc----cCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEEe
Confidence            689999999999999999999999999997653    345667776  4456664 3 689999999987776553

>d1wj7a1 a.5.2.1 (A:8-98) Ubiquitin-associated protein 2-like Ubap2l {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 2-like Ubap2l
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.51  E-value=0.011  Score=45.42  Aligned_cols=45  Identities=27%  Similarity=0.537  Sum_probs=41.1

Q ss_pred             CCccHHHHHHHHHHc-CCCCCCHHHHHHHHHHhhCChHHHHHHHHcCCC
Q 015628          169 AGSNLEATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  216 (403)
Q Consensus       169 ~g~~~e~~v~~i~~M-G~~~f~R~qv~~ALrAafnNPdRAvEyL~~GIP  216 (403)
                      ..+.++..|..||+| |   -..++|.-||-=+.|+.+|||+||+-|-+
T Consensus        28 ~D~~i~~kVkql~e~T~---rsede~~~ALhDcn~D~~~AIn~lLEg~~   73 (91)
T d1wj7a1          28 NDADFEEKVKQLIDITG---KNQDECVIALHDCNGDVNRAINVLLEGNP   73 (91)
T ss_dssp             CCHHHHHHHHHHHHHTC---CCHHHHHHHHHHHTSCHHHHHHHHHTCSS
T ss_pred             CcHHHHHHHHHHHHHhC---CCHHHHHHHHhcCCccHHHHHHHHHhcCC
Confidence            356789999999999 6   79999999999999999999999999855

>d2cosa1 a.5.2.1 (A:8-48) Serine/threonine protein kinase LATS2 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Serine/threonine protein kinase LATS2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.21  E-value=0.014  Score=37.24  Aligned_cols=36  Identities=31%  Similarity=0.475  Sum_probs=32.0

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhC-ChHHHHHHHH
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLY  212 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafn-NPdRAvEyL~  212 (403)
                      .++.+.|+.-|   |+.+-|+||||-..| |-+-|+||+.
T Consensus         3 RQMlqdl~~aG---~D~~m~iral~qt~~rsieaaie~is   39 (41)
T d2cosa1           3 RQMLQELVNAG---CDQEMAGRALKQTGSRSIEAALEYIS   39 (41)
T ss_dssp             HHHHHHHHHHH---CCHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhCcccHHHHHHHHh
Confidence            46899999999   999999999998865 7899999984

>d1vega_ a.5.2.1 (A:) NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: NEDD8 ultimate buster-1 (Nub1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.17  E-value=0.02  Score=42.40  Aligned_cols=45  Identities=27%  Similarity=0.387  Sum_probs=40.0

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc-C--CCCCCCC
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS-G--IPEQTAV  221 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~-G--IP~~~~~  221 (403)
                      .+.|.+|+-||   |+|+-++.|||.--.|..-|..-|.. |  +|..++-
T Consensus        30 QesidqLvYMG---F~~~~Ae~ALRvfrGnVQlAaQtLahngG~LP~dLq~   77 (83)
T d1vega_          30 QESINQLVYMG---FDTVVAEAALRVFGGNVQLAAQTLAHHGGSLPPDLQF   77 (83)
T ss_dssp             HHHHHHHHHHS---CCHHHHHHHHHHTTTCHHHHHHHHHHHTSSCCTTSSS
T ss_pred             HHHHHHHHHhc---ccHHHHHHHHHHhcccHHHHHHHHHHcCCcCCccccc
Confidence            57899999999   99999999999999999999998876 3  8877643

>d1wgla_ a.5.2.4 (A:) Toll-interacting protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Toll-interacting protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.07  E-value=0.015  Score=41.34  Aligned_cols=39  Identities=26%  Similarity=0.356  Sum_probs=34.6

Q ss_pred             HHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015628          362 AIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDHMHE  400 (403)
Q Consensus       362 ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d  400 (403)
                      .|+.|++|  .+|++.+.-+|.+|++|.+.|.|-||+-..+
T Consensus        12 ~i~~LkeMFP~~D~~vI~~VL~a~~G~vd~aid~LL~Msd~   52 (59)
T d1wgla_          12 DLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQMGEE   52 (59)
T ss_dssp             HHHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence            49999999  6899999999999999999999999985444

>d1vjka_ d.15.3.1 (A:) Molybdopterin synthase subunit MoaD {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.30  E-value=0.13  Score=38.25  Aligned_cols=68  Identities=21%  Similarity=0.224  Sum_probs=48.1

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCCC--------CCCCCCcEEEeCCeecCCCCcccccccC
Q 015628            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGSD--------VYPASQQMLIHQGKVLKDVTTLEENKVA   65 (403)
Q Consensus         1 MkI~VKtl~------g-~~~~ieV~~~~TV~dLK~kI~~~~g~~--------~ip~~~QkLiy~GkiL~D~~tLsd~gI~   65 (403)
                      |||+||...      | ....+++....||.+|++.+..+++.-        .......++..+|+...++     +-|+
T Consensus         2 mkI~v~~Fa~lre~~G~~~~~~~~~~~~Tv~~l~~~L~~~~~~~~~~l~~~~~~~~~~i~iavN~~~~~~d-----~~L~   76 (88)
T d1vjka_           2 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWD-----EELK   76 (88)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTT-----CBCC
T ss_pred             eEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHChHHHHHhhhccccccccEEEEEcceEcCCC-----cCcC
Confidence            899999764      3 467889998999999999999886410        0011234566677766543     4578


Q ss_pred             CCcEEEEE
Q 015628           66 ENSFVVVM   73 (403)
Q Consensus        66 ~~s~I~v~   73 (403)
                      +|+.|.++
T Consensus        77 ~gDevai~   84 (88)
T d1vjka_          77 DGDVVGVF   84 (88)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEe
Confidence            89999887

>d1mn3a_ a.5.2.4 (A:) Vacuolar protein sorting-associated protein vps9 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Vacuolar protein sorting-associated protein vps9
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.82  E-value=0.032  Score=38.81  Aligned_cols=40  Identities=25%  Similarity=0.401  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhc
Q 015628          357 PEEREAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLD  396 (403)
Q Consensus       357 ~ee~~ai~rL~~l--GF~~~~~~~a~~ac~~ne~~a~~~L~~  396 (403)
                      .|-.++++.|++|  ++|++.+.-+|.+|++|.+.|++-||+
T Consensus        10 ~e~~e~~~~Lk~MFP~~D~~VI~~VL~a~~G~vd~aidaLL~   51 (54)
T d1mn3a_          10 NERKDTLNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLS   51 (54)
T ss_dssp             HHHHHHHHHHHHHCTTSCHHHHHHHHSCSSCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            3445679999999  789999999999999999999999986

>d1aipc1 a.5.2.2 (C:2-53) Elongation factor Ts (EF-Ts), N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.63  E-value=0.058  Score=37.16  Aligned_cols=38  Identities=24%  Similarity=0.203  Sum_probs=33.8

Q ss_pred             HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          360 REAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       360 ~~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      ++-|..|.+. |++-.+|.+|+..|++|.+.|.+||=..
T Consensus         3 ~elvK~LR~~Tga~~~dcKkAL~e~~gD~ekA~e~Lr~~   41 (52)
T d1aipc1           3 MELIKKLREATGAGMMDVKRALEDAGWDEEKAVQLLRER   41 (52)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            5668888886 9999999999999999999999999643

>d1ttea1 a.5.2.1 (A:161-215) Ubiquitin-protein ligase ubc1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-protein ligase ubc1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.69  E-value=0.039  Score=38.24  Aligned_cols=25  Identities=24%  Similarity=0.571  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHh
Q 015628          359 EREAIERLEAMGFDRALVLEVFFAC  383 (403)
Q Consensus       359 e~~ai~rL~~lGF~~~~~~~a~~ac  383 (403)
                      |.+.|+..+.|||+|+.+|++|..-
T Consensus         9 d~~~V~~f~~mGF~rdKvI~VLrrl   33 (55)
T d1ttea1           9 DHDLIDEFESQGFEKDKIVEVLRRL   33 (55)
T ss_dssp             SHHHHHHHHHHTCCHHHHHHHHHHS
T ss_pred             CHHHHHHHHHcCCCchhHHHHHHHh
Confidence            4567999999999999999999864

>d2cp8a1 a.5.2.1 (A:8-48) Migration-inducing protein 19 NBR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Migration-inducing protein 19 NBR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.63  E-value=0.075  Score=34.33  Aligned_cols=37  Identities=32%  Similarity=0.351  Sum_probs=32.3

Q ss_pred             HHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHhc
Q 015628          360 REAIERLEAMGF-DRALVLEVFFACNKNEELAANYLLD  396 (403)
Q Consensus       360 ~~ai~rL~~lGF-~~~~~~~a~~ac~~ne~~a~~~L~~  396 (403)
                      ..-..+|++||| ||....+-+..-+.|...+++-|+.
T Consensus         3 ~~lM~~L~EMGF~DR~lNq~LL~KH~~nl~~vV~eLlq   40 (41)
T d2cp8a1           3 AALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELLQ   40 (41)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHTTTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcchhHHHHHHHHHccCcHHHHHHHHHc
Confidence            445789999999 8999999999999999999988764

>d1xb2b1 a.5.2.2 (B:56-111) Elongation factor Ts (EF-Ts), N-terminal domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=92.52  E-value=0.12  Score=35.94  Aligned_cols=39  Identities=15%  Similarity=0.303  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          359 EREAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       359 e~~ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      ..+.|..|.+. |.+-.+|.+|+..|++|.+.|..||-..
T Consensus         4 s~~lvk~LRe~Tga~~~dcKkAL~e~~gD~ekA~e~Lrkk   43 (56)
T d1xb2b1           4 SKELLMKLRRKTGYSFINCKKALETCGGDLKQAESWLHKQ   43 (56)
T ss_dssp             HHHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            34568888887 9999999999999999999999999653

>d2cosa1 a.5.2.1 (A:8-48) Serine/threonine protein kinase LATS2 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Serine/threonine protein kinase LATS2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.43  E-value=0.089  Score=33.39  Aligned_cols=34  Identities=18%  Similarity=0.324  Sum_probs=29.5

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHH
Q 015628          361 EAIERLEAMGFDRALVLEVFFAC-NKNEELAANYL  394 (403)
Q Consensus       361 ~ai~rL~~lGF~~~~~~~a~~ac-~~ne~~a~~~L  394 (403)
                      ..++.|..-|||++.||+|+... +|+.|.|..|+
T Consensus         4 QMlqdl~~aG~D~~m~iral~qt~~rsieaaie~i   38 (41)
T d2cosa1           4 QMLQELVNAGCDQEMAGRALKQTGSRSIEAALEYI   38 (41)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHHTSCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhCcccHHHHHHHH
Confidence            45777888899999999999876 58999999987

>d1efub3 a.5.2.2 (B:1-54) Elongation factor Ts (EF-Ts), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.96  E-value=0.13  Score=35.67  Aligned_cols=36  Identities=17%  Similarity=0.146  Sum_probs=32.1

Q ss_pred             HHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          362 AIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       362 ai~rL~~l-GF~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      .|..|.+. |++-.+|.+|+..|++|.+.|..||=..
T Consensus         7 ~iK~LR~~Tgag~~dCKkAL~e~~gD~ekA~e~Lr~k   43 (54)
T d1efub3           7 LVKELRERTGAGMMDCKKALTEANGDIELAIENMRKS   43 (54)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            47888876 9999999999999999999999999654

>d1wgla_ a.5.2.4 (A:) Toll-interacting protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Toll-interacting protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.92  E-value=0.087  Score=37.17  Aligned_cols=38  Identities=29%  Similarity=0.396  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHc--CCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          173 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       173 ~e~~v~~i~~M--G~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      .|+.|+.|.+|  .   ++++-|+.-|++.-+|.|+||+-||.
T Consensus         9 ~Ee~i~~LkeMFP~---~D~~vI~~VL~a~~G~vd~aid~LL~   48 (59)
T d1wgla_           9 SEEDLKAIQDMFPN---MDQEVIRSVLEAQRGNKDAAINSLLQ   48 (59)
T ss_dssp             CHHHHHHHHHHCSS---SCHHHHHHHHTTTTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            47789999999  5   89999999999999999999999984

>d2dkla1 a.5.2.1 (A:8-79) Trinucleotide repeat containing 6c protein, TNRC6C {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Trinucleotide repeat containing 6c protein, TNRC6C
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.00  E-value=0.19  Score=36.29  Aligned_cols=40  Identities=30%  Similarity=0.395  Sum_probs=37.0

Q ss_pred             HHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCCC
Q 015628          363 IERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEFE  402 (403)
Q Consensus       363 i~rL~~lGF~~~~~~~a~~ac~~ne~~a~~~L~~~~~d~~  402 (403)
                      |++|..|||+|+.+-+++-..+.|-+.|..-|++...|.|
T Consensus        18 ~KQfsnMGf~re~~e~~l~sN~m~L~~a~~~l~dKk~e~d   57 (72)
T d2dkla1          18 IKQLTDMGFPREPAEEALKSNNMNLDQAMSALLEKKVDVD   57 (72)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHTTSCCSS
T ss_pred             HHHHhhcCCcCCChHHhhhccCcchhhcccchhhhhhccc
Confidence            7899999999999999999999999999999999877755

>d1ttea1 a.5.2.1 (A:161-215) Ubiquitin-protein ligase ubc1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-protein ligase ubc1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.63  E-value=0.098  Score=36.15  Aligned_cols=23  Identities=13%  Similarity=0.514  Sum_probs=21.5

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHH
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRA  199 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrA  199 (403)
                      ...|.++++||   |+|+.|+..||-
T Consensus        10 ~~~V~~f~~mG---F~rdKvI~VLrr   32 (55)
T d1ttea1          10 HDLIDEFESQG---FEKDKIVEVLRR   32 (55)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CCchhHHHHHHH
Confidence            57899999999   999999999996

>d1aipc1 a.5.2.2 (C:2-53) Elongation factor Ts (EF-Ts), N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=89.61  E-value=0.27  Score=33.67  Aligned_cols=36  Identities=28%  Similarity=0.298  Sum_probs=31.1

Q ss_pred             HHHHHHHHc-CCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          175 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       175 ~~v~~i~~M-G~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      +.|.+|-+. |   +.=-+|..||..+.+|-|+|+|||-.
T Consensus         4 elvK~LR~~Tg---a~~~dcKkAL~e~~gD~ekA~e~Lr~   40 (52)
T d1aipc1           4 ELIKKLREATG---AGMMDVKRALEDAGWDEEKAVQLLRE   40 (52)
T ss_dssp             HHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            467777775 7   88899999999999999999999953

>d1xb2b1 a.5.2.2 (B:56-111) Elongation factor Ts (EF-Ts), N-terminal domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=89.51  E-value=0.27  Score=34.18  Aligned_cols=37  Identities=14%  Similarity=0.192  Sum_probs=32.4

Q ss_pred             HHHHHHHHHc-CCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          174 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       174 e~~v~~i~~M-G~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      -++|.+|-+. |   +.=-+|..||..+-+|-|.|+|||..
T Consensus         5 ~~lvk~LRe~Tg---a~~~dcKkAL~e~~gD~ekA~e~Lrk   42 (56)
T d1xb2b1           5 KELLMKLRRKTG---YSFINCKKALETCGGDLKQAESWLHK   42 (56)
T ss_dssp             HHHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            3578888886 7   88899999999999999999999963

>d1xo3a_ d.15.3.3 (A:) C9orf74 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: C9orf74 homolog
domain: C9orf74 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.71  E-value=0.36  Score=37.07  Aligned_cols=69  Identities=14%  Similarity=0.137  Sum_probs=42.0

Q ss_pred             CEEEEEeCCC--------cEEEEEeC---CCCcHHHHHHHHHHHhCCCCCCCCCcEEEeCC-------eecCCCCc---c
Q 015628            1 MKVFVKTLKG--------THFEIEVK---PEDKVSDVKKNIETVQGSDVYPASQQMLIHQG-------KVLKDVTT---L   59 (403)
Q Consensus         1 MkI~VKtl~g--------~~~~ieV~---~~~TV~dLK~kI~~~~g~~~ip~~~QkLiy~G-------kiL~D~~t---L   59 (403)
                      |+|+|+...|        +.+.++++   ...||.+|-+.+.++++.     .+-+|+..+       -++-++..   +
T Consensus         5 m~V~V~F~g~L~~lf~~~r~~~v~l~~~~~~~TV~dll~~L~~~~p~-----~~~~l~~~~~~lr~~v~v~vN~~di~~l   79 (101)
T d1xo3a_           5 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLK-----ERPELFIQGDSVRPGILVLINDADWELL   79 (101)
T ss_dssp             CEEEEEECSSGGGGGTTCCCEEEECCSSSCCCCHHHHHHHHHHHHCC-----SCGGGSCCTTSCCSSEEEEETTEEHHHH
T ss_pred             eEEEEEEechHHHHhCCcceEEEEcCCCCCCcCHHHHHHHHHHhCCc-----chhhhhccCcCeeeeEEEEEcCcceecc
Confidence            8999997442        44566664   347999999999998762     122221111       11112211   1


Q ss_pred             --cccccCCCcEEEEEE
Q 015628           60 --EENKVAENSFVVVML   74 (403)
Q Consensus        60 --sd~gI~~~s~I~v~v   74 (403)
                        -++.|++||.|.++-
T Consensus        80 ~gl~t~l~dgDeV~~~p   96 (101)
T d1xo3a_          80 GELDYQLQDQDSILFIS   96 (101)
T ss_dssp             TTTSCCCCTTCEEEEEE
T ss_pred             CCCccCcCCCCEEEEeC
Confidence              256799999998874

>d2f4mb1 a.189.1.1 (B:275-332) XPC-binding domain of Rad23 homolog B (Hhr23b) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: XPC-binding domain
superfamily: XPC-binding domain
family: XPC-binding domain
domain: XPC-binding domain of Rad23 homolog B (Hhr23b)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.39  E-value=0.11  Score=36.39  Aligned_cols=35  Identities=26%  Similarity=0.490  Sum_probs=24.6

Q ss_pred             hCcHHHH--HHHHHHHhCccchHHHHHHHHhhC-HHHHHHHHH
Q 015628          282 RNSQQFQ--ALRTMVQANPQILQPMLQELGKQN-PHLMRLIQE  321 (403)
Q Consensus       282 r~~pqf~--~lR~~vq~NP~lL~~~lq~i~~~n-P~l~~lI~~  321 (403)
                      .+||++.  -|.++.++||++++     +.++| .+|+++|++
T Consensus        19 q~nP~~L~~lLqql~~~NP~L~q-----~I~~nqe~Fl~llne   56 (58)
T d2f4mb1          19 QQNPSLLPALLQQIGRENPQLLQ-----QISQHQEHFIQMLNE   56 (58)
T ss_dssp             HHCGGGHHHHHHHHHHHCHHHHH-----HHHHSHHHHHHHHTS
T ss_pred             HHCHHHHHHHHHHHHhhCHHHHH-----HHHHCHHHHHHHHcC
Confidence            3477764  57888899998776     44556 677887754

>d1efub3 a.5.2.2 (B:1-54) Elongation factor Ts (EF-Ts), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.29  E-value=0.46  Score=32.68  Aligned_cols=36  Identities=22%  Similarity=0.237  Sum_probs=31.4

Q ss_pred             HHHHHHHHc-CCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          175 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       175 ~~v~~i~~M-G~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      ..|..|-+. |   +.=-+|..||..+-+|-|.|+|||..
T Consensus         6 ~~iK~LR~~Tg---ag~~dCKkAL~e~~gD~ekA~e~Lr~   42 (54)
T d1efub3           6 SLVKELRERTG---AGMMDCKKALTEANGDIELAIENMRK   42 (54)
T ss_dssp             HHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            467888776 7   88889999999999999999999963

>d1mn3a_ a.5.2.4 (A:) Vacuolar protein sorting-associated protein vps9 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Vacuolar protein sorting-associated protein vps9
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.24  E-value=0.26  Score=34.01  Aligned_cols=39  Identities=18%  Similarity=0.181  Sum_probs=36.2

Q ss_pred             ccHHHHHHHHHHc--CCCCCCHHHHHHHHHHhhCChHHHHHHHH
Q 015628          171 SNLEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLY  212 (403)
Q Consensus       171 ~~~e~~v~~i~~M--G~~~f~R~qv~~ALrAafnNPdRAvEyL~  212 (403)
                      .++++.++.|.+|  .   ++++=++.-|++.-+|.|+||+.|+
T Consensus        10 ~e~~e~~~~Lk~MFP~---~D~~VI~~VL~a~~G~vd~aidaLL   50 (54)
T d1mn3a_          10 NERKDTLNTLQNMFPD---MDPSLIEDVCIAKKSRIEPCVDALL   50 (54)
T ss_dssp             HHHHHHHHHHHHHCTT---SCHHHHHHHHSCSSCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4678999999999  5   8999999999999999999999997

>d1ufza_ a.5.9.1 (A:) HBS1-like protein {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: HBS1-like domain
family: HBS1-like domain
domain: HBS1-like protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.24  E-value=0.55  Score=34.96  Aligned_cols=45  Identities=9%  Similarity=0.265  Sum_probs=38.2

Q ss_pred             ccCCHHHHHH----HHHHHH-cC--CChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015628          353 VTVTPEEREA----IERLEA-MG--FDRALVLEVFFACNKNEELAANYLLDH  397 (403)
Q Consensus       353 ~~lt~ee~~a----i~rL~~-lG--F~~~~~~~a~~ac~~ne~~a~~~L~~~  397 (403)
                      -+|++.+++.    |+.+.+ +|  .++.+.++|.+.|+-|.+.|.|++|+.
T Consensus        24 ~~Ls~~d~aRL~SCldqmR~VvGDsvpe~~lv~avlk~dydvekALd~vL~~   75 (83)
T d1ufza_          24 HQLSEIDQARLYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQ   75 (83)
T ss_dssp             HHCCHHHHHHHHHHHHHHHHHTTTTSCHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             hhcCHHHHHHHHHHHHHHHHHHcccCCHHHHHHHHHHccCCHHHHHHHHHhc
Confidence            4688888876    556665 47  799999999999999999999999964

>d2cp8a1 a.5.2.1 (A:8-48) Migration-inducing protein 19 NBR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Migration-inducing protein 19 NBR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.77  E-value=0.8  Score=29.33  Aligned_cols=35  Identities=29%  Similarity=0.448  Sum_probs=31.7

Q ss_pred             HHHHHHHHcCCCCC-CHHHHHHHHHHhhCChHHHHHHHH
Q 015628          175 ATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLY  212 (403)
Q Consensus       175 ~~v~~i~~MG~~~f-~R~qv~~ALrAafnNPdRAvEyL~  212 (403)
                      .+...|+|||   | +|.-=.+=|+.-.||-..+|.-|+
T Consensus         4 ~lM~~L~EMG---F~DR~lNq~LL~KH~~nl~~vV~eLl   39 (41)
T d2cp8a1           4 ALMAHLFEMG---FCDRQLNLRLLKKHNYNILQVVTELL   39 (41)
T ss_dssp             HHHHHHHHHT---CCCHHHHHHHHTTTTTCHHHHHHHHH
T ss_pred             HHHHHHHHhC---cchhHHHHHHHHHccCcHHHHHHHHH
Confidence            4788999999   9 999999999999999999998775

>d1wgra_ d.15.1.5 (A:) Growth factor receptor-bound protein 7, GRB-7 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: Growth factor receptor-bound protein 7, GRB-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.35  E-value=2.4  Score=32.13  Aligned_cols=71  Identities=18%  Similarity=0.137  Sum_probs=46.1

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CcEEE--e--CC--eecCCCCcccc----cccCCCcEEE
Q 015628            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLI--H--QG--KVLKDVTTLEE----NKVAENSFVV   71 (403)
Q Consensus         3 I~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~~-~QkLi--y--~G--kiL~D~~tLsd----~gI~~~s~I~   71 (403)
                      |.|-..+|....|.|+.++|+.+|-+.+..+.+..   .. ..-|+  +  .|  +.|.|...+-+    ......  -.
T Consensus        12 vkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~---~~~~f~L~E~~~~~~leR~L~d~E~vl~v~~~W~~~~~--~r   86 (100)
T d1wgra_          12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHAL---SDETWGLVECHPHLALERGLEDHESVVEVQAAWPVGGD--SR   86 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCC---CCCCCCEEEEETTTTEEEEECSSSCHHHHHTTSCSSSC--CE
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCC---CCCCeEEEEecCCCcceeecCchHhHHHHHHcCCCCCC--CE
Confidence            45556789999999999999999999999999843   22 22222  2  23  77888654333    333333  34


Q ss_pred             EEEecCC
Q 015628           72 VMLTKSK   78 (403)
Q Consensus        72 v~v~k~k   78 (403)
                      +++||.-
T Consensus        87 ~v~rkny   93 (100)
T d1wgra_          87 FVFRKNF   93 (100)
T ss_dssp             EEECSCC
T ss_pred             EEEeecC
Confidence            5555543

>d2dkla1 a.5.2.1 (A:8-79) Trinucleotide repeat containing 6c protein, TNRC6C {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Trinucleotide repeat containing 6c protein, TNRC6C
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.31  E-value=1.2  Score=32.01  Aligned_cols=37  Identities=30%  Similarity=0.452  Sum_probs=33.9

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhhCChHHHHHHHHc
Q 015628          174 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  213 (403)
Q Consensus       174 e~~v~~i~~MG~~~f~R~qv~~ALrAafnNPdRAvEyL~~  213 (403)
                      ...|.++..||   |.|+..+.+|+..-+|-+-|+--|+-
T Consensus        15 np~~KQfsnMG---f~re~~e~~l~sN~m~L~~a~~~l~d   51 (72)
T d2dkla1          15 SRLIKQLTDMG---FPREPAEEALKSNNMNLDQAMSALLE   51 (72)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             hHHHHHHhhcC---CcCCChHHhhhccCcchhhcccchhh
Confidence            56899999999   99999999999999999999988864

>d1ef1a3 d.15.1.4 (A:4-87) Moesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Moesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.21  E-value=2.5  Score=31.15  Aligned_cols=70  Identities=17%  Similarity=0.179  Sum_probs=50.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCcEEEe---CCe--ecCCCCcccccccCCCcEEEEEE
Q 015628            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIH---QGK--VLKDVTTLEENKVAENSFVVVML   74 (403)
Q Consensus         1 MkI~VKtl~g~~~~ieV~~~~TV~dLK~kI~~~~g~~~ip~-~~QkLiy---~Gk--iL~D~~tLsd~gI~~~s~I~v~v   74 (403)
                      |+|.|.++++ .+++.|+...+..+|=.+|....+   +.. +-.=|-|   .|.  =|+.++.|..+.++.+..+++..
T Consensus         2 ~~v~V~~LD~-~~~~~v~~~a~G~~l~~~Vc~~l~---L~E~dYFGL~y~d~~~~~~WLd~~k~l~kq~~~~~~~~~l~F   77 (84)
T d1ef1a3           2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIG---LREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKF   77 (84)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHT---CCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEE
T ss_pred             EEEEEEEcCC-EEEEEEcCCChHHHHHHHHHHHcC---CcccccceEEEECCCCCeEeccCCCchhhhccCCCCCEEEEE
Confidence            6789999997 589999999999999999999999   432 2223333   332  26778888888666666444443