Citrus Sinensis ID: 017906

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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----
Protein Sequence
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIEP
Secondary Structure (PSIPRED)
cEEEEEcccccEEEEEEcccccHHHHHHHHHHHcccccccccccEEEEcccccccccHHHHcccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHHccccccHHHHHHHHHHcHHHHHHHHHcHHHHHHHHccccccccccccccccccccccccccHHHHHcccc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEEEEccHHHHHHHHHHHHHHcccccccHHHcEEEEccEEEcccccHHHcccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccHHHHHHHHHccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHHHcHHHHHHHHHHHHcccHHHHHHHHHcHHHHHHHHcccccccccccccccccccccEEEEcHHHHHHccc
Coil and Loop (DISEMBL)
MKVFVKTlkgthfeievkpedkvsdVKKNIetvqgsdvypasQQMLIHqgkvlkdvttleenkvaENSFVVVMLTKskvsssgastvsaapanqaqttssapptstqptttsqtpaptvappqsvpesapppaapapapapapapapapapvssvsdvYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYsgipeqtavppvarasaggqagnppaqtqaqqpaapaptsgpnanpldlfpqglpnmgsnagagtLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLinepveggegnvLGQLAsampqavtvtpeereaiep
Flexible Loop (DISEMBL)
mkvfvktlkgthfeievkpedkvsdvkKNIETvqgsdvypasqQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSssgastvsaapanqaqttssapptstqpTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASampqavtvtpeereaiep
Low Complexity Region (SEG)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLtkskvsssgastvsaAPANqaqttssapptstqptttsqtpaptvappqsvpesapppaapapapapapapapapapvssvsDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARasaggqagnppaqtqaqqpaapaptsgpNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIEP
Disordered region (IsUnstruct)
****VKTLKGTHFEI**********************VYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT*****************************************************************************************NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI**************************************************************LDFLR***QFQALRTMVQANPQILQPML*******PHLMRLIQEHQTDFLRLINEPVE******************************
Disordered Region (DISOPRED)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM****************************************************************************************************************************************************************************************************************************************************IQEHQTDFL**************************************
Disordered Region (DISEMBL)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS******************************************************************************SDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVA***************************GPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASA*****************
Disordered Region (DISPRO)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS*****************************************************************************************VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQT********************************************************GTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP*****************QAVTVTPEEREAIE*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAIEP
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	364	2.2.26 [Sep-21-2011]
Q84L31	419	Putative DNA repair prote	yes	no	0.953	0.828	0.674	1e-135
Q84L30	378	Putative DNA repair prote	no	no	0.925	0.891	0.681	1e-121
Q40742	392	Probable DNA repair prote	yes	no	0.945	0.877	0.609	1e-108
Q84L33	371	Putative DNA repair prote	no	no	0.898	0.881	0.562	3e-98
Q84L32	368	Putative DNA repair prote	no	no	0.898	0.888	0.515	6e-93
P54727	409	UV excision repair protei	yes	no	0.931	0.828	0.372	2e-49
P54728	416	UV excision repair protei	yes	no	0.914	0.800	0.345	2e-47
Q4KMA2	415	UV excision repair protei	yes	no	0.934	0.819	0.347	2e-47
Q29RK4	408	UV excision repair protei	yes	no	0.914	0.816	0.345	8e-46
P54725	363	UV excision repair protei	no	no	0.840	0.842	0.356	9e-40

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

 Score =  483 bits (1242), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 267/396 (67%), Positives = 304/396 (76%), Gaps = 49/396 (12%)

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 SSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 212
            S  DVYGQAASNL AGSNLE+T+QQILDMGGG+WDRETV+ ALRAA+NNPERAVEYLY+
Sbjct: 168 GSQGDVYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLYT 227

Query: 213 GIPEQTAVPPVARA-SAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSN 271
           GIPEQ  VPPVAR  ++ GQ  NPPAQTQ  QPAA AP SGPNANPLDLFPQGLPN+G N
Sbjct: 228 GIPEQAEVPPVARPPASAGQPANPPAQTQ--QPAA-APASGPNANPLDLFPQGLPNVGGN 284

Query: 272 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 331
            GAGTLDFLRNSQQFQALR MVQANPQ+LQPMLQELGKQNP+LMRLIQ+HQ DFLRLINE
Sbjct: 285 PGAGTLDFLRNSQQFQALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLINE 344

Query: 332 PVEGG--EGNVLGQLASAM--PQAVTVTPEEREAIE 363
           PVEGG   GN+LGQ+A+ M  PQA+ VT EEREAIE
Sbjct: 345 PVEGGGESGNLLGQMAAGMPQPQAIQVTHEEREAIE 380

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 =  436 bits (1122), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 248/364 (68%), Positives = 278/364 (76%), Gaps = 27/364 (7%)

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 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSV-SDVYGQAASNLVAGSNLEATVQQI 179
            PQ        P A  P P    A A APA  +SV +DVYGQAASNLVAG+ LE+TVQQI
Sbjct: 101 TPQ-----VSAPTASVPVPTSGTATAAAPATAASVQTDVYGQAASNLVAGTTLESTVQQI 155

Query: 180 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 239
           LDMGGGSWDR+TV+RALRAA+NNPERAVEYLYSGIP Q  +PPVA+A A G+    P   
Sbjct: 156 LDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPATGEQAANPLAQ 215

Query: 240 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQI 299
             Q  A  A T GPNANPL+LFPQG+P   + AGAG LDFLRNSQQFQALR MVQANPQI
Sbjct: 216 PQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQFQALRAMVQANPQI 275

Query: 300 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEER 359
           LQPMLQELGKQNP L+RLIQEHQ DFLRLINEPVE GE NV+ QL +AMPQAVTVTPEER
Sbjct: 276 LQPMLQELGKQNPQLVRLIQEHQADFLRLINEPVE-GEENVMEQLEAAMPQAVTVTPEER 334

Query: 360 EAIE 363
           EAIE
Sbjct: 335 EAIE 338

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 =  392 bits (1006), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 223/366 (60%), Positives = 264/366 (72%), Gaps = 22/366 (6%)

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 APPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQI 179
           AP  +VP +    +AP P    +PAPA A   VSS +D YGQA SNLVAGSNLEAT+Q I
Sbjct: 112 APATTVPVTV---SAPTPTATASPAPAVA---VSSEADNYGQATSNLVAGSNLEATIQSI 165

Query: 180 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 239
           L+MGGG WDR+ V+ AL AA+NNPERAVEYLYSG+PEQ  + PV   S   Q  NP   +
Sbjct: 166 LEMGGGIWDRDIVLHALSAAFNNPERAVEYLYSGVPEQMDI-PVPPPSI--QPANPTQAS 222

Query: 240 QAQQPAAPAP-TSGPNANPLDLFPQGLPNMGSN-AGAGTLDFLRNSQQFQALRTMVQANP 297
           QA QPAAP+  +SGPNA+PLDLFPQ LPN  ++ AG G LD LRN+ QF+ L ++VQANP
Sbjct: 223 QATQPAAPSILSSGPNASPLDLFPQALPNASTDAAGLGNLDALRNNAQFRTLLSLVQANP 282

Query: 298 QILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG-GEGNVLGQLASAMPQAVTVTP 356
           QILQP+LQELGKQNP +++LIQE+Q +FL LINEP EG  E N+L Q   AMPQ + VTP
Sbjct: 283 QILQPLLQELGKQNPQILQLIQENQAEFLHLINEPAEGDDEENLLDQFPEAMPQTIAVTP 342

Query: 357 EEREAI 362
           EE EAI
Sbjct: 343 EENEAI 348

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 =  358 bits (920), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 207/368 (56%), Positives = 249/368 (67%), Gaps = 41/368 (11%)

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 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
           P  S  +S+P PA+P PA     A           +D YGQAAS LV+GS+LE  VQQI+
Sbjct: 109 P--STTQSSPVPASPIPAQEQPAAQ----------TDTYGQAASTLVSGSSLEQMVQQIM 156

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE--QTAVP-PVARASAGGQAGNPPA 237
           +MGGGSWD+ETV RALRAAYNNPERAV+YLYSGIP+  + AVP P A+ +  G A     
Sbjct: 157 EMGGGSWDKETVTRALRAAYNNPERAVDYLYSGIPQTAEVAVPVPEAQIAGSGAA----- 211

Query: 238 QTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANP 297
                 P APA + GPN++PLDLFPQ       +   GTL+FLRN+ QFQ LRTMV +NP
Sbjct: 212 ------PVAPA-SGGPNSSPLDLFPQETVAAAGSGDLGTLEFLRNNDQFQQLRTMVHSNP 264

Query: 298 QILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG--GEGNVLGQLASAMPQAVTVT 355
           QILQPMLQELGKQNP L+RLIQE+Q +FL+L+NEP EG  GEG++  Q    MP A+ VT
Sbjct: 265 QILQPMLQELGKQNPQLLRLIQENQAEFLQLVNEPYEGSDGEGDMFDQPEQEMPHAINVT 324

Query: 356 PEEREAIE 363
           P E+EAI+
Sbjct: 325 PAEQEAIQ 332

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 =  341 bits (874), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 188/365 (51%), Positives = 236/365 (64%), Gaps = 38/365 (10%)

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+T   +++   AP+  
Sbjct: 61  ENKVTEEGFLVVMLSKSKTASS------AGPS-----STQPTSTTTSTISSTTLAAPSTT 109

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
              +VP S   P    P               ++ SD YGQAAS LV+GS++E  VQQI+
Sbjct: 110 QSIAVPASNSTPVQEQP---------------TAQSDTYGQAASTLVSGSSIEQMVQQIM 154

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ 240
           +MGGGSWD+ETV RALRAAYNNPERAV+YLYSGIPE   +P    +  G           
Sbjct: 155 EMGGGSWDKETVTRALRAAYNNPERAVDYLYSGIPETVTIPATNLSGVGS---------- 204

Query: 241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQIL 300
            ++  AP P+ GPN++PLDLFPQ   +  +    GTL+FLR + QFQ LR+MV +NPQIL
Sbjct: 205 GRELTAPPPSGGPNSSPLDLFPQEAVSDAAGGDLGTLEFLRGNDQFQQLRSMVNSNPQIL 264

Query: 301 QPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNV--LGQLASAMPQAVTVTPEE 358
           QPMLQELGKQNP L+RLIQE+Q +FL+L+NEP EG +G+V    Q    MP +V VTPEE
Sbjct: 265 QPMLQELGKQNPQLLRLIQENQAEFLQLLNEPYEGSDGDVDIFDQPDQEMPHSVNVTPEE 324

Query: 359 REAIE 363
           +E+IE
Sbjct: 325 QESIE 329

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 =  196 bits (499), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 147/395 (37%), Positives = 209/395 (52%), Gaps = 56/395 (14%)

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---PAPAPAPAPAPV-------------SSVSDVYGQA 162
             P    P SA   + PAPA A     PA  PA  PV             SS S+++  A
Sbjct: 121 STPASITPASATASSEPAPASAAKQEKPAEKPAETPVATSPTATDSTSGDSSRSNLFEDA 180

Query: 163 ASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP---EQTA 219
            S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP   E  A
Sbjct: 181 TSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQA 237

Query: 220 V--PPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTL 277
           V  PP A ++   Q+    A            +SG           G P          L
Sbjct: 238 VVDPPQAASTGAPQSSAVAAAAATTTATTTTTSSG-----------GHP----------L 276

Query: 278 DFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG- 336
           +FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV+   
Sbjct: 277 EFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAG 336

Query: 337 --------EGNVLGQLASAMPQAVTVTPEEREAIE 363
                       + +  S     + VTP+E+EAIE
Sbjct: 337 GQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAIE 371

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 =  190 bits (482), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 141/408 (34%), Positives = 205/408 (50%), Gaps = 75/408 (18%)

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 --------TTTSQTPAPTVAPPQSVPESAPPPAAPAPAPA-----PAPAPAPAPAPVSSV 155
                   T  S  PA T A  +  P  A  P  PA  PA      +PAPA +    SS 
Sbjct: 114 TPALPPTSTPASTAPASTTASSEPAPAGATQPEKPAEKPAQTPVLTSPAPADSTPGDSSR 173

Query: 156 SDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
           S+++  A S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP
Sbjct: 174 SNLFEDATSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIP 230

Query: 216 ----EQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSN 271
                Q  V P            PP       P +PA  +                  + 
Sbjct: 231 GDRESQAVVDP------------PPQAVSTGTPQSPAVAAAAATT--------TATTTTT 270

Query: 272 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 331
           +G   L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NE
Sbjct: 271 SGGHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNE 330

Query: 332 PV-EGGE---------------GNVLGQLASAMPQAVTVTPEEREAIE 363
           PV E G                G  + +  S     + VTP+E+EAIE
Sbjct: 331 PVQEAGSQGGGGGGGGGGGGGGGGGIAEAGSGHMNYIQVTPQEKEAIE 378

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 =  190 bits (482), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 139/400 (34%), Positives = 204/400 (51%), Gaps = 60/400 (15%)

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 PTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPA-----PAPAPAPAPAPVSSVSDVYGQA 162
            T  S TPA T A  +  P  A  P  PA  PA      +PAPA +    SS S+++  A
Sbjct: 121 STPASTTPASTTASSEPAPTGATQPEKPAEKPAQTPVLTSPAPADSTPGDSSRSNLFEDA 180

Query: 163 ASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP----EQT 218
            S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP     Q 
Sbjct: 181 TSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQA 237

Query: 219 AVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLD 278
            V P            PP       P +PA  +                  + +G   L+
Sbjct: 238 VVDP------------PPQAVSTGTPQSPAVAAAAATT--------TATTTTTSGGHPLE 277

Query: 279 FLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG-- 336
           FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV+    
Sbjct: 278 FLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGG 337

Query: 337 -------------EGNVLGQLASAMPQAVTVTPEEREAIE 363
                         G  + +  S     + VTP+E+EAIE
Sbjct: 338 QGGGGGGGGGGGGGGGGIAEAGSGHMNYIQVTPQEKEAIE 377

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 =  184 bits (467), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 138/400 (34%), Positives = 200/400 (50%), Gaps = 67/400 (16%)

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 --------TTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSV-----S 156
                     S TPAPT A  +  P SA     PA  P   P      +  S+      S
Sbjct: 115 PASAPTPTPVSVTPAPTTASSEPAPASAAKQEKPAERPVETPVATTPTSTDSTSGDSSRS 174

Query: 157 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP- 215
           +++  A S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP 
Sbjct: 175 NLFEDATSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPG 231

Query: 216 ---EQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNA 272
               Q  V P   AS G    +  A            +SG           G P      
Sbjct: 232 DRESQAVVDPPPAASTGAPQSSVAAAAATTTATTTTTSSG-----------GHP------ 274

Query: 273 GAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP 332
               L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEP
Sbjct: 275 ----LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEP 330

Query: 333 VEGGEGNVLGQLASAMPQA---------VTVTPEEREAIE 363
           V+   G   G    +   A         + VTP+E+EAIE
Sbjct: 331 VQEAGGQGGGGGGGSGGIAEAGGGHMNYIQVTPQEKEAIE 370

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 =  164 bits (415), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 134/376 (35%), Positives = 196/376 (52%), Gaps = 70/376 (18%)

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--------EASPTAAPESSTSFPPAPTSGM- 111

Query: 123 QSVPESAPPPAA---PAPAPAPAPAPAPAPAPVSSVSDVYG----QAASNLVAGSNLEAT 175
                S PPPAA    +P+   AP  +P     S  S         AAS LV GS  E  
Sbjct: 112 -----SHPPPAAREDKSPSEESAPTTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETM 166

Query: 176 VQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNP 235
           + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP           S   + G+ 
Sbjct: 167 LTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP----------GSPEPEHGSV 213

Query: 236 PAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQA 295
                ++QPA  A                       AG   L+FLR+  QFQ +R ++Q 
Sbjct: 214 QESQVSEQPATEA-----------------------AGENPLEFLRDQPQFQNMRQVIQQ 250

Query: 296 NPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP------VEGGEGNVLGQLASAMP 349
           NP +L  +LQ+LG++NP L++ I  HQ  F++++NEP      +   EG V G +    P
Sbjct: 251 NPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEPPGELADISDVEGEV-GAIGEEAP 309

Query: 350 QA--VTVTPEEREAIE 363
           Q   + VTP+E+EAIE
Sbjct: 310 QMNYIQVTPQEKEAIE 325

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	364
225452017	381	PREDICTED: putative DNA repair protein R	0.939	0.897	0.746	1e-145
255551362	381	uv excision repair protein rad23, putati	0.939	0.897	0.743	1e-145
224079274	385	predicted protein [Populus trichocarpa]	0.942	0.890	0.726	1e-137
5640111	389	RAD23 protein [Solanum lycopersicum var.	0.936	0.876	0.731	1e-136
363807216	400	uncharacterized protein LOC100813881 [Gl	0.980	0.892	0.746	1e-135
358248820	392	uncharacterized protein LOC100809066 [Gl	0.967	0.897	0.741	1e-135
297832888	417	hypothetical protein ARALYDRAFT_477488 [	0.953	0.832	0.687	1e-134
356575534	402	PREDICTED: putative DNA repair protein R	0.989	0.895	0.693	1e-134
224127650	384	predicted protein [Populus trichocarpa]	0.928	0.880	0.716	1e-134
15232924	419	putative DNA repair protein RAD23-3 [Ara	0.953	0.828	0.674	1e-134

>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 =  521 bits (1342), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 271/363 (74%), Positives = 300/363 (82%), Gaps = 21/363 (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 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
            P+ +PE       PAPA AP+         +SS SD+YGQAASNLVAG+NLE T+QQIL
Sbjct: 119 LPEVIPE-------PAPAVAPS---------ISSDSDIYGQAASNLVAGNNLEVTIQQIL 162

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ 240
           DMGGGSWDR+TV+RALRAAYNNPERAVEYLYSGIPEQ   PP AR  A G A N P Q  
Sbjct: 163 DMGGGSWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEGPPAARPPASGLAVNLPTQA- 221

Query: 241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQIL 300
            Q P     +SGPNANPLDLFPQGLP+MGSNA AGTLDFLRNS QFQALR MVQANPQIL
Sbjct: 222 PQGPQTTVASSGPNANPLDLFPQGLPSMGSNASAGTLDFLRNSPQFQALRAMVQANPQIL 281

Query: 301 QPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEERE 360
           QPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVE GEGNVLGQL + +PQAVT+TPEERE
Sbjct: 282 QPMLQELGKQNPHLMRLIQEHQADFLRLINEPVE-GEGNVLGQLGT-VPQAVTITPEERE 339

Query: 361 AIE 363
           +IE
Sbjct: 340 SIE 342

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 =  520 bits (1339), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 270/363 (74%), Positives = 296/363 (81%), Gaps = 21/363 (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 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
            PQS  ES                  P   PVSS +D+YGQAASNLVAGSNLEATVQQIL
Sbjct: 121 LPQSAAES-----------------TPVVNPVSSETDIYGQAASNLVAGSNLEATVQQIL 163

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ 240
           DMGGGSWDRETV RALRAA+NNPERAVEYLYSGIPEQ  V P+ RA + GQA  P A   
Sbjct: 164 DMGGGSWDRETVARALRAAFNNPERAVEYLYSGIPEQPEVQPLPRAPSSGQAAIPSA--T 221

Query: 241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQIL 300
           AQ+PAAP  + G NANPLDLFPQGLP +GS   AGTLDFLRNSQQFQALR MVQANPQIL
Sbjct: 222 AQEPAAPT-SGGANANPLDLFPQGLPTIGSTTSAGTLDFLRNSQQFQALRAMVQANPQIL 280

Query: 301 QPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEERE 360
           QPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVE G+GN+LGQLASA+PQ+V+VTPEERE
Sbjct: 281 QPMLQELGKQNPHLMRLIQEHQADFLRLINEPVE-GDGNLLGQLASAVPQSVSVTPEERE 339

Query: 361 AIE 363
           AIE
Sbjct: 340 AIE 342

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 =  493 bits (1268), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 266/366 (72%), Positives = 293/366 (80%), Gaps = 23/366 (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 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
            PQS  ES+P     A                   +++YGQAASNLVAGSNLEAT+Q+IL
Sbjct: 121 LPQSAAESSPAVVTSALLD----------------TNMYGQAASNLVAGSNLEATIQEIL 164

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAG---GQAGNPPA 237
           DMGGG W+RETV+RALRAA+NNPERA++YLYSGIPEQ  VPPVA+   G   G A NPPA
Sbjct: 165 DMGGGDWNRETVVRALRAAFNNPERAIDYLYSGIPEQAEVPPVAQVVQGPASGNAVNPPA 224

Query: 238 QTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANP 297
              A QP   AP SGPNANPLDLFPQG  + GSNAG G LDFLRNSQQFQALR MVQANP
Sbjct: 225 L--APQPVV-APNSGPNANPLDLFPQGHHSTGSNAGTGNLDFLRNSQQFQALRAMVQANP 281

Query: 298 QILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPE 357
           QILQPMLQELGKQNP+LMRLIQEHQ DFLRLINEPVE GEGNVLGQLASAMPQAVTVTPE
Sbjct: 282 QILQPMLQELGKQNPYLMRLIQEHQADFLRLINEPVE-GEGNVLGQLASAMPQAVTVTPE 340

Query: 358 EREAIE 363
           EREAIE
Sbjct: 341 EREAIE 346

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  490 bits (1262), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 272/372 (73%), Positives = 291/372 (78%), Gaps = 31/372 (8%)

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

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTST-QPTTTSQTPAPTV 119
           ENKVAENSFVV+ML+K+KVSS+G S++SAA +N AQ     P  ST Q   T  TP  T 
Sbjct: 61  ENKVAENSFVVIMLSKNKVSSTGTSSISAALSNTAQ-----PDGSTDQARQTITTPQATA 115

Query: 120 APPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQI 179
           A PQS  ESAP PA    A              SSV+DVY QAASNLVAGSNLE TVQQI
Sbjct: 116 ALPQSASESAPTPAPVPAAA-------------SSVTDVYDQAASNLVAGSNLETTVQQI 162

Query: 180 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAV--------PPVARASAGGQ 231
           LDMGGGSWDR+TV+RALRAAYNNPERAV+YLYSGIPEQT +         P   A A  Q
Sbjct: 163 LDMGGGSWDRDTVVRALRAAYNNPERAVDYLYSGIPEQTEIPPVARAPAAPAVTAPASAQ 222

Query: 232 AGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRT 291
           A NP AQ  +Q      P+SGPNANPLDLFPQGL N GSNAGAG LDFLRNS QFQALR 
Sbjct: 223 AINPAAQDASQ---LAVPSSGPNANPLDLFPQGLTNAGSNAGAGNLDFLRNSPQFQALRA 279

Query: 292 MVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQA 351
           MVQANPQILQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVE GEGNVLGQ A A+PQA
Sbjct: 280 MVQANPQILQPMLQELGKQNPHLMRLIQEHQPDFLRLINEPVE-GEGNVLGQTAGAIPQA 338

Query: 352 VTVTPEEREAIE 363
           VTVTPEEREAIE
Sbjct: 339 VTVTPEEREAIE 350

Source: Solanum lycopersicum var. cerasiforme

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  488 bits (1256), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 274/367 (74%), Positives = 297/367 (80%), Gaps = 10/367 (2%)

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 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSV--SDVYGQAASNLVAGSNLEATVQQ 178
               V      PA      APAPAPAP  +  SSV  SD+YGQAASNLVAGSNLE T+QQ
Sbjct: 117 SATPVTAPTAAPAPAPAPAAPAPAPAPIFSG-SSVPESDIYGQAASNLVAGSNLEGTIQQ 175

Query: 179 ILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQ 238
           ILDMGGGSWDR+TV+R LRAAYNNPERAVEYLYSGIPEQ   PPV    A  Q  NPPA 
Sbjct: 176 ILDMGGGSWDRDTVVRTLRAAYNNPERAVEYLYSGIPEQAEAPPVTGVPASAQPSNPPAD 235

Query: 239 T-QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSN-AGAGTLDFLRNSQQFQALRTMVQAN 296
           T QA QPA+  P+SGPNANPLDLFPQGLPN+GS  AGAG+LDFLRNSQQFQALR MVQAN
Sbjct: 236 TPQAAQPAS-VPSSGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQAN 294

Query: 297 PQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTP 356
           PQILQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVEGGEGN+LGQLA  MPQAVTVTP
Sbjct: 295 PQILQPMLQELGKQNPHLMRLIQEHQVDFLRLINEPVEGGEGNILGQLAGTMPQAVTVTP 354

Query: 357 EEREAIE 363
           EER+AIE
Sbjct: 355 EERQAIE 361

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  486 bits (1251), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 270/364 (74%), Positives = 293/364 (80%), Gaps = 12/364 (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 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
            P  V   A P +A APAP  + +  P        SD+YGQAASNLVAGSNLE T+QQIL
Sbjct: 117 TPTPVTAPAAPASAAAPAPISSGSAVPE-------SDIYGQAASNLVAGSNLEGTIQQIL 169

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ 240
           DMGGGSWDR+TV+RALRAAYNNPERAVEYLYSGIPEQ   PPV R  A  Q  NPPA   
Sbjct: 170 DMGGGSWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEAPPVTREPASAQPANPPAAAP 229

Query: 241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSN-AGAGTLDFLRNSQQFQALRTMVQANPQI 299
                A  P+SGPNANPLDLFPQGLPN+GS  AGAG+LDFLRNSQQFQALR MVQANPQI
Sbjct: 230 QAAQPASVPSSGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANPQI 289

Query: 300 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEER 359
           LQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVEGGEGN+LGQLASAMPQAVTVTPEER
Sbjct: 290 LQPMLQELGKQNPHLMRLIQEHQVDFLRLINEPVEGGEGNILGQLASAMPQAVTVTPEER 349

Query: 360 EAIE 363
           +AIE
Sbjct: 350 QAIE 353

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 =  485 bits (1249), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 271/394 (68%), Positives = 302/394 (76%), Gaps = 47/394 (11%)

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

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAP--- 117
           ENKVAENSF+VVML KSK +S+GAS+ SA          S PP+++QP+ + QTPA    
Sbjct: 61  ENKVAENSFIVVMLNKSKPASTGASSASAG----TSQAKSTPPSTSQPSISPQTPASVAA 116

Query: 118 -----------------------TVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSS 154
                                  TV  P  +PE       P PA  P+  PAP  AP  S
Sbjct: 117 PVAPAPTRAPPPAPTPAPVAATETVTTP--IPE-------PVPATIPSSTPAPDSAPAGS 167

Query: 155 VSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI 214
             DVYGQAASNL AGSNLE+T+QQILDMGGG+WDRETV+RALRAA+NNPERAVEYLY+GI
Sbjct: 168 QGDVYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVRALRAAFNNPERAVEYLYTGI 227

Query: 215 PEQTAVPPVARASAG-GQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAG 273
           PEQ  VPPVARA A  GQ  NP AQTQ  QPAA AP SGPNANPLDLFPQGLPN+G N G
Sbjct: 228 PEQAEVPPVARAPASFGQPANPSAQTQ--QPAA-APASGPNANPLDLFPQGLPNVGGNPG 284

Query: 274 AGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV 333
           AGTLDFLRNSQQFQALR MVQANPQ+LQPMLQELGKQNP+LMRLIQ+HQ DFLRLINEPV
Sbjct: 285 AGTLDFLRNSQQFQALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLINEPV 344

Query: 334 EGG--EGNVLGQLASAM--PQAVTVTPEEREAIE 363
           EGG   GN+LGQ+A+ M  PQA+ VTPEEREAIE
Sbjct: 345 EGGGESGNLLGQMAAGMPQPQAIQVTPEEREAIE 378

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  485 bits (1249), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 253/365 (69%), Positives = 287/365 (78%), Gaps = 5/365 (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 ++  P  +    AP  A
Sbjct: 61  ENKVAENTFIVIMLSKSKSTSGEGSTTSTALSTKAPQTSTVPAST--PPVSVAPQAPAPA 118

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
              ++P S   P +             +       SD+YGQAASNLVAGSNLE T+QQIL
Sbjct: 119 ATGALPASVTAPVSSPSPAPAPAPAPISSGTAVEGSDIYGQAASNLVAGSNLEGTIQQIL 178

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT- 239
           DMGGGSWDR+TV+RALRAAYNNPERAVEYLY+GIPEQ   P VARA    Q  NPPA   
Sbjct: 179 DMGGGSWDRDTVVRALRAAYNNPERAVEYLYTGIPEQAEAPLVARAPVSAQPTNPPADAP 238

Query: 240 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSN-AGAGTLDFLRNSQQFQALRTMVQANPQ 298
           Q  QPAA   ++GPNANPLDLFPQGLPN+GS  AGAG+LDFLRNSQQFQALR MVQANPQ
Sbjct: 239 QTAQPAA-VTSAGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANPQ 297

Query: 299 ILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEE 358
           ILQPMLQELGKQNPHLMRLI++HQ DFLRLINEP EGGEGN+LGQ+AS MPQAVTVTPEE
Sbjct: 298 ILQPMLQELGKQNPHLMRLIRDHQADFLRLINEPAEGGEGNILGQMASGMPQAVTVTPEE 357

Query: 359 REAIE 363
           R+AIE
Sbjct: 358 RQAIE 362

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 =  483 bits (1243), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 265/370 (71%), Positives = 295/370 (79%), Gaps = 32/370 (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 TPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLE 173
                     S+P +   P++ + A  PA A + A        D+YGQAASNLVAGSNLE
Sbjct: 118 ----------SLPSNVTQPSSTSQAAVPAAAFSDA--------DMYGQAASNLVAGSNLE 159

Query: 174 ATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAG 233
           AT+QQILDMGGGSW+RETV+RALRAA+NNPERAVEYLYSGIPEQ  VPPVA+  A G A 
Sbjct: 160 ATIQQILDMGGGSWNRETVVRALRAAFNNPERAVEYLYSGIPEQAEVPPVAQGPASGVAV 219

Query: 234 NPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMV 293
           NPPAQ Q         + GPNANPLDLFPQGLP+ GSNAGAG LDFLRNSQQFQALR MV
Sbjct: 220 NPPAQAQQPAAPP---SGGPNANPLDLFPQGLPSTGSNAGAGNLDFLRNSQQFQALRAMV 276

Query: 294 QANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVT 353
           QANPQILQPMLQELGKQNPHLMRLIQEHQ DFLRLINEPVE GEGNVLGQLASA+PQ VT
Sbjct: 277 QANPQILQPMLQELGKQNPHLMRLIQEHQPDFLRLINEPVE-GEGNVLGQLASAVPQTVT 335

Query: 354 VTPEEREAIE 363
           VTPEEREAI+
Sbjct: 336 VTPEEREAID 345

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 =  483 bits (1242), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 267/396 (67%), Positives = 304/396 (76%), Gaps = 49/396 (12%)

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 SSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 212
            S  DVYGQAASNL AGSNLE+T+QQILDMGGG+WDRETV+ ALRAA+NNPERAVEYLY+
Sbjct: 168 GSQGDVYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLYT 227

Query: 213 GIPEQTAVPPVARA-SAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSN 271
           GIPEQ  VPPVAR  ++ GQ  NPPAQTQ  QPAA AP SGPNANPLDLFPQGLPN+G N
Sbjct: 228 GIPEQAEVPPVARPPASAGQPANPPAQTQ--QPAA-APASGPNANPLDLFPQGLPNVGGN 284

Query: 272 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 331
            GAGTLDFLRNSQQFQALR MVQANPQ+LQPMLQELGKQNP+LMRLIQ+HQ DFLRLINE
Sbjct: 285 PGAGTLDFLRNSQQFQALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLINE 344

Query: 332 PVEGG--EGNVLGQLASAM--PQAVTVTPEEREAIE 363
           PVEGG   GN+LGQ+A+ M  PQA+ VT EEREAIE
Sbjct: 345 PVEGGGESGNLLGQMAAGMPQPQAIQVTHEEREAIE 380

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	364
TAIR|locus:2076944	419	RAD23C "RADIATION SENSITIVE23C	0.563	0.489	0.725	1e-107
TAIR|locus:2177376	378	RAD23D "RADIATION SENSITIVE23D	0.565	0.544	0.724	4.1e-102
TAIR|locus:2200522	368	RAD23A "RADIATION SENSITIVE23A	0.541	0.535	0.555	1.5e-77
RGD|1309899	351	Rad23a "RAD23 homolog A (S. ce	0.255	0.264	0.421	7.9e-43
ZFIN|ZDB-GENE-040426-1487	382	rad23b "RAD23 homolog B (S. ce	0.535	0.510	0.355	1.1e-42
UNIPROTKB|D4AD39	363	Rad23a "RAD23a homolog (S. cer	0.25	0.250	0.43	1.7e-42
UNIPROTKB|P54727	409	RAD23B "UV excision repair pro	0.502	0.447	0.348	1.8e-42
UNIPROTKB|A3KMV2	362	RAD23A "UV excision repair pro	0.255	0.256	0.411	2.1e-42
MGI|MGI:105126	363	Rad23a "RAD23a homolog (S. cer	0.25	0.250	0.42	2.2e-42
UNIPROTKB|P54725	363	RAD23A "UV excision repair pro	0.25	0.250	0.42	2.9e-42

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

 Score = 755 (270.8 bits), Expect = 1.0e-107, Sum P(2) = 1.0e-107
 Identities = 153/211 (72%), Positives = 167/211 (79%)

Query:   157 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE 216
             DVYGQAASNL AGSNLE+T+QQILDMGGG+WDRETV+ ALRAA+NNPERAVEYLY+GIPE
Sbjct:   172 DVYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLYTGIPE 231

Query:   217 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 276
             Q  VPPVAR                            NANPLDLFPQGLPN+G N GAGT
Sbjct:   232 QAEVPPVARPPASAGQPANPPAQTQQPAAAPASGP--NANPLDLFPQGLPNVGGNPGAGT 289

Query:   277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG 336
             LDFLRNSQQFQALR MVQANPQ+LQPMLQELGKQNP+LMRLIQ+HQ DFLRLINEPVEGG
Sbjct:   290 LDFLRNSQQFQALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLINEPVEGG 349

Query:   337 --EGNVLGQLASAMPQ--AVTVTPEEREAIE 363
                GN+LGQ+A+ MPQ  A+ VT EEREAIE
Sbjct:   350 GESGNLLGQMAAGMPQPQAIQVTHEEREAIE 380

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 = 748 (268.4 bits), Expect = 4.1e-102, Sum P(2) = 4.1e-102
 Identities = 150/207 (72%), Positives = 163/207 (78%)

Query:   157 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE 216
             DVYGQAASNLVAG+ LE+TVQQILDMGGGSWDR+TV+RALRAA+NNPERAVEYLYSGIP 
Sbjct:   133 DVYGQAASNLVAGTTLESTVQQILDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPA 192

Query:   217 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 276
             Q  +PPVA+                            NANPL+LFPQG+P   + AGAG 
Sbjct:   193 QAEIPPVAQAPATGEQAANPLAQPQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGN 252

Query:   277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG 336
             LDFLRNSQQFQALR MVQANPQILQPMLQELGKQNP L+RLIQEHQ DFLRLINEPVEG 
Sbjct:   253 LDFLRNSQQFQALRAMVQANPQILQPMLQELGKQNPQLVRLIQEHQADFLRLINEPVEGE 312

Query:   337 EGNVLGQLASAMPQAVTVTPEEREAIE 363
             E NV+ QL +AMPQAVTVTPEEREAIE
Sbjct:   313 E-NVMEQLEAAMPQAVTVTPEEREAIE 338

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 = 559 (201.8 bits), Expect = 1.5e-77, Sum P(2) = 1.5e-77
 Identities = 116/209 (55%), Positives = 142/209 (67%)

Query:   157 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE 216
             D YGQAAS LV+GS++E  VQQI++MGGGSWD+ETV RALRAAYNNPERAV+YLYSGIPE
Sbjct:   131 DTYGQAASTLVSGSSIEQMVQQIMEMGGGSWDKETVTRALRAAYNNPERAVDYLYSGIPE 190

Query:   217 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 276
                +P                                N++PLDLFPQ   +  +    GT
Sbjct:   191 TVTIP----------ATNLSGVGSGRELTAPPPSGGPNSSPLDLFPQEAVSDAAGGDLGT 240

Query:   277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGG 336
             L+FLR + QFQ LR+MV +NPQILQPMLQELGKQNP L+RLIQE+Q +FL+L+NEP EG 
Sbjct:   241 LEFLRGNDQFQQLRSMVNSNPQILQPMLQELGKQNPQLLRLIQENQAEFLQLLNEPYEGS 300

Query:   337 EGNV--LGQLASAMPQAVTVTPEEREAIE 363
             +G+V    Q    MP +V VTPEE+E+IE
Sbjct:   301 DGDVDIFDQPDQEMPHSVNVTPEEQESIE 329

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

RGD|1309899 Rad23a "RAD23 homolog A (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 203 (76.5 bits), Expect = 7.9e-43, Sum P(3) = 7.9e-43
 Identities = 43/102 (42%), Positives = 64/102 (62%)

Query:   270 SNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLI 329
             + AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++
Sbjct:   224 TEAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQML 283

Query:   330 NEP------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIE 363
             NEP      +   EG V G L    PQ   + VTP+E+EAIE
Sbjct:   284 NEPPGELADISDVEGEV-GALGEEAPQMNYIQVTPQEKEAIE 324

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

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

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

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

ZFIN|ZDB-GENE-040426-1487 rad23b "RAD23 homolog B (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 312 (114.9 bits), Expect = 1.1e-42, Sum P(2) = 1.1e-42
 Identities = 75/211 (35%), Positives = 115/211 (54%)

Query:   157 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE 216
             +++ +A S LV G + E  V +I+ MG   ++R+ V+ ALRA++NNP+RAVEYL +GIP 
Sbjct:   146 NIFEEATSALVTGQSYENMVTEIMLMG---YERDRVVAALRASFNNPDRAVEYLLTGIPA 202

Query:   217 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 276
             +     V                               ++P    P   P+  S  GA  
Sbjct:   203 EGEGSVVGAVDAVSPSGSTPASAPAPAISTGL------SSPSSTAP-AQPSSAS--GANP 253

Query:   277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV-EG 335
             L+FLRN  QF  +R ++Q NP +L  +LQ++G++NP L++ I  HQ  F++++NEPV E 
Sbjct:   254 LEFLRNQPQFLQMRQIIQQNPSLLPALLQQIGRENPQLLQQISSHQEQFIQMLNEPVQEA 313

Query:   336 GEGNVLGQLASA---MPQAVTVTPEEREAIE 363
             G+G   G +A A       + VTP+E+EAIE
Sbjct:   314 GQGGGAGGVAEAGGGHMNYIQVTPQEKEAIE 344

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

 Score = 202 (76.2 bits), Expect = 1.7e-42, Sum P(3) = 1.7e-42
 Identities = 43/100 (43%), Positives = 63/100 (63%)

Query:   272 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 331
             AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct:   227 AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 286

Query:   332 P------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIE 363
             P      +   EG V G L    PQ   + VTP+E+EAIE
Sbjct:   287 PPGELADISDVEGEV-GALGEEAPQMNYIQVTPQEKEAIE 325

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|P54727 RAD23B "UV excision repair protein RAD23 homolog B" [Homo sapiens (taxid:9606)]

 Score = 297 (109.6 bits), Expect = 1.8e-42, Sum P(2) = 1.8e-42
 Identities = 77/221 (34%), Positives = 116/221 (52%)

Query:   157 DVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP- 215
             +++  A S LV G + E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL  GIP 
Sbjct:   175 NLFEDATSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPG 231

Query:   216 --EQTAV--PPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSN 271
               E  AV  PP A                                             ++
Sbjct:   232 DRESQAVVDPPQAASTGAPQSSAVAAAAATTTATTTT---------------------TS 270

Query:   272 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 331
             +G   L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NE
Sbjct:   271 SGGHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNE 330

Query:   332 PVE--GGEGNVLGQLASAMPQA-------VTVTPEEREAIE 363
             PV+  GG+G   G  +  + +A       + VTP+E+EAIE
Sbjct:   331 PVQEAGGQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAIE 371

GO:0003684 "damaged DNA binding" evidence=IEA

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

GO:0000502 "proteasome complex" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0071942 "XPC complex" evidence=IDA

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

GO:0000715 "nucleotide-excision repair, DNA damage recognition" evidence=IDA;TAS

GO:0031593 "polyubiquitin binding" evidence=IDA

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

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

GO:0000718 "nucleotide-excision repair, DNA damage removal" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

 Score = 201 (75.8 bits), Expect = 2.1e-42, Sum P(3) = 2.1e-42
 Identities = 42/102 (41%), Positives = 64/102 (62%)

Query:   270 SNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLI 329
             + AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++
Sbjct:   224 TEAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQML 283

Query:   330 NEP------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIE 363
             NEP      +   EG V G +    PQ   + VTP+E+EAIE
Sbjct:   284 NEPPGELVDISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIE 324

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 = 200 (75.5 bits), Expect = 2.2e-42, Sum P(3) = 2.2e-42
 Identities = 42/100 (42%), Positives = 63/100 (63%)

Query:   272 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 331
             AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct:   227 AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 286

Query:   332 P------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIE 363
             P      +   EG V G +    PQ   + VTP+E+EAIE
Sbjct:   287 PPGELADISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIE 325

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 = 200 (75.5 bits), Expect = 2.9e-42, Sum P(3) = 2.9e-42
 Identities = 42/100 (42%), Positives = 63/100 (63%)

Query:   272 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 331
             AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct:   227 AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 286

Query:   332 P------VEGGEGNVLGQLASAMPQA--VTVTPEEREAIE 363
             P      +   EG V G +    PQ   + VTP+E+EAIE
Sbjct:   287 PPGELADISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIE 325

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

---

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	0.6092	0.9450	0.8775	yes	no
Q29RK4	RD23B_BOVIN	No assigned EC number	0.345	0.9148	0.8161	yes	no
P54727	RD23B_HUMAN	No assigned EC number	0.3721	0.9313	0.8288	yes	no
P54728	RD23B_MOUSE	No assigned EC number	0.3455	0.9148	0.8004	yes	no
O74803	RHP23_SCHPO	No assigned EC number	0.3128	0.8681	0.8586	yes	no
Q84L31	RD23C_ARATH	No assigned EC number	0.6742	0.9532	0.8281	yes	no
Q4KMA2	RD23B_RAT	No assigned EC number	0.3475	0.9340	0.8192	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	364
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	3e-82
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	2e-34
smart00213	72	smart00213, UBQ, Ubiquitin homologues	4e-20
pfam09280	59	pfam09280, XPC-binding, XPC-binding domain	9e-20
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	4e-18
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	8e-18
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	2e-10
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	5e-10
pfam00627	37	pfam00627, UBA, UBA/TS-N domain	5e-10
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-09
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	2e-09
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	5e-09
cd01803	76	cd01803, Ubiquitin, Ubiquitin	1e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-08
cd00194	38	cd00194, UBA, Ubiquitin Associated domain	5e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-07
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-07
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	3e-07
smart00165	37	smart00165, UBA, Ubiquitin associated domain	9e-07
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	9e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-06
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	1e-06
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	1e-06
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-06
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	2e-06
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	5e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	7e-06
PRK10672	361	PRK10672, PRK10672, rare lipoprotein A; Provisiona	7e-06
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	8e-06
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	9e-06
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	9e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-05
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	1e-05
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-05
PRK06302	155	PRK06302, PRK06302, acetyl-CoA carboxylase biotin	2e-05
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	2e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-05
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	3e-05
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	3e-05
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	5e-05
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	5e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	6e-05
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	6e-05
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	6e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	9e-05
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-04
PRK06302	155	PRK06302, PRK06302, acetyl-CoA carboxylase biotin	1e-04
pfam10152	147	pfam10152, DUF2360, Predicted coiled-coil domain-c	1e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	2e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	2e-04
cd01812	71	cd01812, BAG1_N, Ubiquitin-like domain of BAG1	2e-04
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	2e-04
PLN02983	274	PLN02983, PLN02983, biotin carboxyl carrier protei	2e-04
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	3e-04
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	3e-04
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	3e-04
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	3e-04
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	4e-04
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	4e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	5e-04
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	5e-04
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	6e-04
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	6e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	7e-04
PRK05704	407	PRK05704, PRK05704, dihydrolipoamide succinyltrans	7e-04
PRK14960	702	PRK14960, PRK14960, DNA polymerase III subunits ga	7e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	8e-04
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	8e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.001
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	0.001
PRK11901	327	PRK11901, PRK11901, hypothetical protein; Reviewed	0.001
COG4982	866	COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein]	0.001
PRK11892	464	PRK11892, PRK11892, pyruvate dehydrogenase subunit	0.001
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	0.001
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.002
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	0.002
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	0.002
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	0.002
pfam04652	315	pfam04652, DUF605, Vta1 like	0.002
TIGR03593	366	TIGR03593, yidC_nterm, membrane protein insertase,	0.002
PRK05641	153	PRK05641, PRK05641, putative acetyl-CoA carboxylas	0.002
PRK11633	226	PRK11633, PRK11633, cell division protein DedD; Pr	0.002
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	0.002
PRK12438	991	PRK12438, PRK12438, hypothetical protein; Provisio	0.002
PRK14959	624	PRK14959, PRK14959, DNA polymerase III subunits ga	0.002
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.002
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.003
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	0.003
PRK11892	464	PRK11892, PRK11892, pyruvate dehydrogenase subunit	0.003
PRK11633	226	PRK11633, PRK11633, cell division protein DedD; Pr	0.003
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.003
PRK12799	421	PRK12799, motB, flagellar motor protein MotB; Revi	0.003
pfam12526	115	pfam12526, DUF3729, Protein of unknown function (D	0.003
PRK10547	670	PRK10547, PRK10547, chemotaxis protein CheA; Provi	0.003
PRK09111	598	PRK09111, PRK09111, DNA polymerase III subunits ga	0.003
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	0.004
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	0.004
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	0.004
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	0.004
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.004
cd01793	74	cd01793, Fubi, Fubi ubiquitin-like protein	0.004
TIGR02813	2582	TIGR02813, omega_3_PfaA, polyketide-type polyunsat	0.004
PRK06975	656	PRK06975, PRK06975, bifunctional uroporphyrinogen-	0.004

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

 Score =  255 bits (652), Expect = 3e-82
 Identities = 135/372 (36%), Positives = 197/372 (52%), Gaps = 39/372 (10%)

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  +   +  +A P        ++ PT T     S     + A
Sbjct: 61  EYKIKEKDFVVVMVSKPKTGTGKVAPPAATP--------TSAPTPTPSPPASPASGMSAA 112

Query: 121 PPQSVPESAPPP-AAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQI 179
           P  +V E +P   +A A AP       P+             AAS LV GS  E T+++I
Sbjct: 113 PASAVEEKSPSEESATATAPESPSTSVPSSGSD---------AASTLVVGSERETTIEEI 163

Query: 180 LDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 239
           ++MG   ++RE V RALRAA+NNP+RAVEYL +GIPE    P   + +A   A       
Sbjct: 164 MEMG---YEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAASTAAATTETP 220

Query: 240 QAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQI 299
           Q       A   G             P   +  G   L+FLRN  QFQ LR +VQ NPQ+
Sbjct: 221 QHGSVFEQAAQGGTEQ----------PATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQL 270

Query: 300 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG--GEGNVLGQLASAMPQA------ 351
           L P+LQ++G++NP L++ I +H   FL+++NEPV     E ++ G + +           
Sbjct: 271 LPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGELASESDMEGGVGAIAEAGLPQMNQ 330

Query: 352 VTVTPEEREAIE 363
           + VTPEE+EAIE
Sbjct: 331 IQVTPEEKEAIE 342

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 =  120 bits (304), Expect = 2e-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 = 4e-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 = 81.5 bits (202), Expect = 9e-20
 Identities = 36/59 (61%), Positives = 48/59 (81%)

Query: 277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG 335
           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 = 4e-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 = 8e-18
 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 = 56.0 bits (135), Expect = 2e-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 = 5e-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|201355 pfam00627, UBA, UBA/TS-N domain

 Score = 53.6 bits (130), Expect = 5e-10
 Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 3/38 (7%)

Query: 173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL 210
           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|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 59.1 bits (144), Expect = 2e-09
 Identities = 29/97 (29%), Positives = 42/97 (43%), Gaps = 5/97 (5%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTV--APPQSVPESAPPPAAPAP 137
           S++  +  +AA A  A   ++AP            PA     APP+    +A   A  AP
Sbjct: 40  STAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAP 99

Query: 138 APAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEA 174
             A A A   A A    V+ + G AA+  VA  N++A
Sbjct: 100 PAAAAAAAPAAAAVEDEVTPLRGAAAA--VA-KNMDA 133

Length = 1228

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

 Score = 53.2 bits (128), 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|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 57.6 bits (140), Expect = 5e-09
 Identities = 26/79 (32%), Positives = 33/79 (41%)

Query: 73  MLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPP 132
                   S+ A T +AA A  A +  +A P +  P   +  P    AP      +A   
Sbjct: 32  FFADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAA 91

Query: 133 AAPAPAPAPAPAPAPAPAP 151
           AA APA  PA A A APA 
Sbjct: 92  AAAAPAAPPAAAAAAAPAA 110

Length = 1228

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 51.0 bits (122), 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 = 56.1 bits (136), Expect = 2e-08
 Identities = 23/81 (28%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 90  APANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAP 149
             +  A T ++A   +      +   A   A P   P +A  PAAP P PA A A A AP
Sbjct: 38  PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAP-PKPAAAAAAAAAP 96

Query: 150 APVSSVSDVYGQAASNLVAGS 170
           A   + +     AA+ +    
Sbjct: 97  AAPPAAAAAAAPAAAAVEDEV 117

Length = 1228

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

 Score = 55.7 bits (135), Expect = 2e-08
 Identities = 24/82 (29%), Positives = 35/82 (42%)

Query: 98  TSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSD 157
            S+A PT+      +   AP  AP    P +  P    A APA  P PA A A  ++ + 
Sbjct: 39  GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAA 98

Query: 158 VYGQAASNLVAGSNLEATVQQI 179
               AA+   A + +E  V  +
Sbjct: 99  PPAAAAAAAPAAAAVEDEVTPL 120

Length = 1228

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

 Score = 48.2 bits (116), Expect = 5e-08
 Identities = 19/41 (46%), Positives = 26/41 (63%), Gaps = 3/41 (7%)

Query: 172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 212
            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|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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 52.7 bits (127), Expect = 2e-07
 Identities = 40/157 (25%), Positives = 51/157 (32%), Gaps = 38/157 (24%)

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

Query: 160 GQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTA 219
              A +    +   A                                        P   A
Sbjct: 450 AGGAPSPPPAAAPSAQPA-------------------------------------PAPAA 472

Query: 220 VPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNAN 256
            P    A A      P        PAAPA  +G +  
Sbjct: 473 APEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDA 509

Length = 824

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

 Score = 52.4 bits (126), Expect = 2e-07
 Identities = 27/97 (27%), Positives = 37/97 (38%), Gaps = 6/97 (6%)

Query: 78  KVSSSGASTVSAAPAN----QAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESA--PP 131
           K +++  +   A        +A   ++AP                 A   + P +A  P 
Sbjct: 365 KPAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPA 424

Query: 132 PAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVA 168
           P A   A APA APA APA V+       QAA   VA
Sbjct: 425 PVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVA 461

Length = 618

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

 Score = 51.8 bits (124), Expect = 3e-07
 Identities = 43/203 (21%), Positives = 60/203 (29%), Gaps = 17/203 (8%)

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

Query: 134 ------------APAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLE-ATVQQIL 180
                         APAPAPAPA APA A   + +     AA+   A +    A      
Sbjct: 433 LAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPA 492

Query: 181 DMGGGSWDRETVIRALRAAY-NNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT 239
           D     W+      A  A    +   A     S     TA P  A  +        PA  
Sbjct: 493 DDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPR 552

Query: 240 QAQQPAAPAPTSGPNANPLDLFP 262
            A           P A+   L  
Sbjct: 553 AAAATEPVVAPRPPRASASGLPD 575

Length = 700

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

 Score = 44.8 bits (107), Expect = 9e-07
 Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 3/39 (7%)

Query: 172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL 210
            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|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like

 Score = 45.6 bits (109), Expect = 9e-07
 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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 50.4 bits (121), Expect = 1e-06
 Identities = 44/220 (20%), Positives = 55/220 (25%), Gaps = 50/220 (22%)

Query: 82  SGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAP 141
              +   A P+      +   P+       S  PAP  A       +  P    APAPA 
Sbjct: 433 PAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAA 492

Query: 142 APAPAPAPAPVSSVSDV------------------------------------------- 158
           APA   APA  +   D                                            
Sbjct: 493 APAAPAAPAAPAGADDAATLRERWPEILAAVPKRSRKTWAILLPEATVLGVRGDTLVLGF 552

Query: 159 -YGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ 217
             G  A    +  N E  V  + +  GG W  E V+     A                  
Sbjct: 553 STGGLARRFASPGNAEVLVTALAEELGGDWQVEAVVGPAPGAAGGEGPPAP------ASS 606

Query: 218 TAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANP 257
                 AR +A      P A   A   AAPA  S   A  
Sbjct: 607 GPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPG 646

Length = 824

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

 Score = 50.0 bits (120), Expect = 1e-06
 Identities = 31/115 (26%), Positives = 41/115 (35%), Gaps = 4/115 (3%)

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

Query: 148 APAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGG--GSWD--RETVIRALRA 198
            P    + +     A +   A     A      D       W      V +  R 
Sbjct: 475 EPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRERWPEILAAVPKRSRK 529

Length = 824

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

 Score = 46.4 bits (110), 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|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.9 bits (120), Expect = 1e-06
 Identities = 39/181 (21%), Positives = 60/181 (33%), Gaps = 6/181 (3%)

Query: 91  PANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPA 150
           PA         P ++    +   T APT A       + PPP A AP  APA       +
Sbjct: 361 PAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTS 420

Query: 151 PVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL 210
            + +      +A     A  +  A   +   +        +V  A  A    P +   Y 
Sbjct: 421 QLLAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAPAKKEAYR 480

Query: 211 Y-SGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAP-APTSGPNANPLDLFPQ-GLPN 267
           + +  P +    PVA   A  +A       +  + AA  A  +        L  Q GLP 
Sbjct: 481 WKATNPVEVKKEPVATPKALKKA---LEHEKTPELAAKLAAEAIERDPWAALVSQLGLPG 537

Query: 268 M 268
           +
Sbjct: 538 L 538

Length = 647

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

 Score = 49.3 bits (118), Expect = 2e-06
 Identities = 29/110 (26%), Positives = 46/110 (41%), Gaps = 7/110 (6%)

Query: 77  SKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPE-------SA 129
           +  +S+ A+  +AAP       ++A P +      +        P Q+ PE        A
Sbjct: 408 AAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVA 467

Query: 130 PPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQI 179
           P PA  + APAPA APA A    +   DV+      L A   + A  +++
Sbjct: 468 PEPAVASAAPAPAAAPAAARLTPTEEGDVWHATVQQLAAAEAITALAREL 517

Length = 618

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

 Score = 49.4 bits (118), Expect = 2e-06
 Identities = 21/78 (26%), Positives = 34/78 (43%)

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

Query: 139 PAPAPAPAPAPAPVSSVS 156
             PA        PVS VS
Sbjct: 447 VRPAQFKEEKKIPVSKVS 464

Length = 614

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

 Score = 47.9 bits (114), Expect = 5e-06
 Identities = 25/115 (21%), Positives = 38/115 (33%), Gaps = 7/115 (6%)

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

Query: 131 PPAAPAPAPAPAPAP----APAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILD 181
           P +AP    A  P         PAP              L     LEA  +QIL 
Sbjct: 425 PESAPKLTRAAIPVDEKPKYTPPAPPKEEEKALIADGDVL---EQLEAIWKQILR 476

Length = 585

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

 Score = 47.7 bits (114), Expect = 7e-06
 Identities = 36/180 (20%), Positives = 51/180 (28%), Gaps = 12/180 (6%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAP 139
           +++  +  SAAPA         P     P  +            + P + PP  APA   
Sbjct: 632 AAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPA 691

Query: 140 APAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAA 199
           APA A    PAP  + +   GQA                                A    
Sbjct: 692 APAGAAPAQPAPAPAATPPAGQADDPAAQ------------PPQAAQGASAPSPAADDPV 739

Query: 200 YNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLD 259
              PE       +G P Q   PP    +A   A  PP+    ++  A       +     
Sbjct: 740 PLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRR 799

Length = 824

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

 Score = 47.0 bits (112), Expect = 7e-06
 Identities = 26/81 (32%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

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

Query: 136 APAPAPAPAPAPAPAPVSSVS 156
           + APA APA A   A  +S S
Sbjct: 265 SSAPATAPAAAAPQAAATSSS 285

Length = 361

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

 Score = 46.9 bits (112), Expect = 8e-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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 47.6 bits (113), Expect = 9e-06
 Identities = 49/187 (26%), Positives = 58/187 (31%), Gaps = 11/187 (5%)

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

Query: 143  PAPAPA-PAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMG-----GGSWDRETVIRAL 196
             APA A P   S    +    ++   A           L +G     GG   R    R+ 
Sbjct: 2812 LAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSP 2871

Query: 197  RAAYNNP-----ERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTS 251
             A    P      R      S   E  A+PP            PP Q Q Q P  P P  
Sbjct: 2872 AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQP 2931

Query: 252  GPNANPL 258
             P   P 
Sbjct: 2932 PPPPPPR 2938

Length = 3151

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

 Score = 47.3 bits (113), Expect = 9e-06
 Identities = 26/99 (26%), Positives = 35/99 (35%), Gaps = 8/99 (8%)

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

Query: 144 APAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDM 182
              P+P P +         A+N     NLE   QQIL  
Sbjct: 421 PTEPSPTPPA--------NAANAPPSLNLEELWQQILAK 451

Length = 620

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

 Score = 47.3 bits (113), Expect = 1e-05
 Identities = 40/172 (23%), Positives = 47/172 (27%), Gaps = 17/172 (9%)

Query: 87  VSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPA 146
           V       A       P S+ P   +  PA   AP       AP  AA APA A A    
Sbjct: 587 VVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAP-AAPAPAGAAAAPAEASAAPAP 645

Query: 147 PAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERA 206
              AP      V    AS+   G   +A                    A  A        
Sbjct: 646 GVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAA-------- 697

Query: 207 VEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPL 258
                   P Q A  P A   AG          QA Q A+    +  +  PL
Sbjct: 698 --------PAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPL 741

Length = 824

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

 Score = 46.9 bits (112), Expect = 1e-05
 Identities = 24/100 (24%), Positives = 34/100 (34%), Gaps = 4/100 (4%)

Query: 70  VVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPES- 128
           + + L     S+S  +     P       +  PP      T      P   P  +   S 
Sbjct: 506 IKLNLESQSGSASNTAKTPPPPQKSPPPPAPTPPLPQPTATAPPPTPPPPPPTATQASSN 565

Query: 129 --APPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNL 166
             A  PA  +P P     P P+P   SS  +   +AA NL
Sbjct: 566 APAQIPADSSPPPPIPEEPTPSPTKDSSP-EEIDKAAKNL 604

Length = 620

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

 Score = 46.4 bits (110), Expect = 2e-05
 Identities = 35/149 (23%), Positives = 42/149 (28%), Gaps = 30/149 (20%)

Query: 106 TQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASN 165
             P T +  P    AP  + P +A P  A  PA   A   A A A   + +      A  
Sbjct: 372 AGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPA-- 429

Query: 166 LVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVP-PVA 224
                                        AL AA     R      +  P   A P   A
Sbjct: 430 ---------------------------PEALAAARQASARGPGGAPAPAPAPAAAPAAAA 462

Query: 225 RASAGGQAGNPPAQTQAQQPAAPAPTSGP 253
           R +A G      A   A   AAPA    P
Sbjct: 463 RPAAAGPRPVAAAAAAAPARAAPAAAPAP 491

Length = 700

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

 Score = 43.6 bits (104), Expect = 2e-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|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 45.3 bits (107), Expect = 2e-05
 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 = 45.7 bits (109), Expect = 3e-05
 Identities = 27/91 (29%), Positives = 41/91 (45%), Gaps = 5/91 (5%)

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

Query: 134 APAPAPAPAPAPAPAPAPVSSVSDVYGQAAS 164
           AP+P PA AP+  PAPAP ++       A +
Sbjct: 453 APSPPPAAAPSAQPAPAPAAAPEPTAAPAPA 483

Length = 824

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

 Score = 45.6 bits (109), Expect = 3e-05
 Identities = 24/102 (23%), Positives = 33/102 (32%), Gaps = 17/102 (16%)

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

Query: 130 PPPAAPA--------------PAPAPAPAPAPAPAPVSSVSD 157
           P   +                 A    PA A    PV+S  +
Sbjct: 416 PETTSQLLAARQQLQRAQGATKAKKSEPAAASRARPVNSALE 457

Length = 647

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

 Score = 45.1 bits (107), Expect = 3e-05
 Identities = 25/81 (30%), Positives = 28/81 (34%), Gaps = 10/81 (12%)

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

Query: 144 APAPAPAPVSSVSDVYGQAAS 164
             A AP   S+       A  
Sbjct: 428 PAAAAPPARSADPAAAASAGD 448

Length = 576

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

 Score = 44.7 bits (106), Expect = 5e-05
 Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

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

Query: 135 PAPAPAPAPAPAPAPAP 151
           PA APA        PA 
Sbjct: 438 PAAAPAAVALAPAPPAQ 454

Length = 618

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

 Score = 44.2 bits (105), Expect = 5e-05
 Identities = 23/94 (24%), Positives = 28/94 (29%), Gaps = 3/94 (3%)

Query: 72  VMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPP 131
           V L  S  +    +   AAP +   T S  P  +T P          V  P     +   
Sbjct: 162 VPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQ---ANVD 218

Query: 132 PAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASN 165
            AA     APA     AP P          A  N
Sbjct: 219 TAATPAPAAPATPDGAAPLPTDQAGVSTPAADPN 252

Length = 331

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

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 22/72 (30%), Positives = 25/72 (34%), Gaps = 3/72 (4%)

Query: 82  SGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAP 141
                   A A  A   S+A      P       A   A   +   +A P  APAPAPAP
Sbjct: 383 RRLGVAGGAGAPAAAAPSAAAAA---PAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAP 439

Query: 142 APAPAPAPAPVS 153
           AP      AP  
Sbjct: 440 APPSPAGNAPAG 451

Length = 824

>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|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 44.3 bits (105), Expect = 6e-05
 Identities = 22/70 (31%), Positives = 28/70 (40%), Gaps = 1/70 (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 PAPAPAPVSS 154
             P P PV+ 
Sbjct: 175 AKPPPTPVAR 184

Length = 418

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

 Score = 44.2 bits (105), Expect = 9e-05
 Identities = 17/81 (20%), Positives = 25/81 (30%), Gaps = 5/81 (6%)

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

Query: 143 PAPAPAPAPVSSVSDVYGQAA 163
                APA  +         +
Sbjct: 443 SPAGNAPAGGAPSPPPAAAPS 463

Length = 824

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

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 33/146 (22%), Positives = 44/146 (30%), Gaps = 20/146 (13%)

Query: 122 PQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILD 181
           P +  E+A P     PA   A APA AP   ++       A +   A +           
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAA----APAPAAAPAAAASAPAAPPAAA 421

Query: 182 MGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ- 240
                            A   P  A        P   A+ P   A A  +    P +   
Sbjct: 422 PPA---------PVAAPAAAAPAAAPA----AAPAAVALAPAPPAQAAPETVAIPVRVAP 468

Query: 241 --AQQPAAPAPTSGPNANPLDLFPQG 264
             A   AAPAP + P A  L    +G
Sbjct: 469 EPAVASAAPAPAAAPAAARLTPTEEG 494

Length = 618

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

 Score = 41.3 bits (98), Expect = 1e-04
 Identities = 17/41 (41%), Positives = 19/41 (46%)

Query: 113 QTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
              AP      + P +A P AA A A APA APA A A   
Sbjct: 38  APVAPVAQQAAAAPVAAAPAAAAAAAAAPAAAPAAAAAEAE 78

Length = 155

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

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 20/63 (31%), Positives = 24/63 (38%), Gaps = 1/63 (1%)

Query: 95  AQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSS 154
              T    P       T+  P P   P ++   S PPP APA  PA     APA   V+ 
Sbjct: 51  EDVTVQTTPPPPASAITNGGPPPP-PPARAEAASPPPPEAPAEPPAEPEPEAPAENTVTV 109

Query: 155 VSD 157
             D
Sbjct: 110 AKD 112

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

 Score = 43.4 bits (103), Expect = 2e-04
 Identities = 29/181 (16%), Positives = 36/181 (19%), Gaps = 1/181 (0%)

Query: 80  SSSGASTVSAAPANQAQ-TTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPA 138
               A   S  P   A+    +AP     P       AP  A     P  A P   P   
Sbjct: 598 EGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHV 657

Query: 139 PAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRA 198
             P  +      P  +               +                       +A   
Sbjct: 658 AVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDP 717

Query: 199 AYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPL 258
           A   P+ A             VP              PAQ       APA        P 
Sbjct: 718 AAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPS 777

Query: 259 D 259
            
Sbjct: 778 P 778

Length = 824

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

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 34/161 (21%), Positives = 49/161 (30%), Gaps = 19/161 (11%)

Query: 89  AAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAP---APAPAP 145
           A  A +  +              +  PA    P        P  AA A AP   APA AP
Sbjct: 432 ALAAARQASARGPGGAPAPAPAPAAAPAAAARPA--AAGPRPVAAAAAAAPARAAPAAAP 489

Query: 146 APAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPER 205
           APA        ++  + AS   A            D     W  E++     A  ++   
Sbjct: 490 APADDDPPPWEELPPEFASPAPAQP----------DAAPAGWVAESIPDPATADPDDAFE 539

Query: 206 AVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAA 246
            +    +  P     P  A A+    A  PP  + +  P  
Sbjct: 540 TL----APAPAAAPAPRAAAATEPVVAPRPPRASASGLPDM 576

Length = 700

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

 Score = 42.8 bits (101), Expect = 2e-04
 Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 2/63 (3%)

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 APV 152
             V
Sbjct: 445 QAV 447

Length = 614

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

 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 37/184 (20%), Positives = 53/184 (28%), Gaps = 13/184 (7%)

Query: 74   LTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPA 133
            LT+  V+S   S  S           +A          + +PA  + PP     ++  P 
Sbjct: 2783 LTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPP-----TSAQPT 2837

Query: 134  APAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVI 193
            AP P P P P   P    V+   DV  +  S   A          +  +   +  R T  
Sbjct: 2838 APPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTES 2897

Query: 194  RALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGP 253
             AL           +      P      P        Q   PP     +     APT+ P
Sbjct: 2898 FALPPDQPERPPQPQ-----APPPPQPQPQPPPPPQPQ---PPPPPPPRPQPPLAPTTDP 2949

Query: 254  NANP 257
                
Sbjct: 2950 AGAG 2953

Length = 3151

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

 Score = 43.0 bits (102), Expect = 2e-04
 Identities = 35/205 (17%), Positives = 55/205 (26%), Gaps = 23/205 (11%)

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

Query: 133 AAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASN---------------LVAGSNLEATVQ 177
           A P       PA A    P  ++ +++ Q  +                LV+  +  A + 
Sbjct: 419 AEPTEPSPTPPANAANAPPSLNLEELWQQILAKLELPSTRMLLSQQAELVSLDSNRAVIA 478

Query: 178 ---QILDMGGGSWDRETVIR-ALRAAYNNPERAV-EYLYSGIPEQTAVPPVARASAGGQA 232
                L M      R+ ++  A         +   E            PP  + S    A
Sbjct: 479 VSPNWLGMVQS---RKPLLEQAFAKVLGRSIKLNLESQSGSASNTAKTPPPPQKSPPPPA 535

Query: 233 GNPPAQTQAQQPAAPAPTSGPNANP 257
             PP          P P   P    
Sbjct: 536 PTPPLPQPTATAPPPTPPPPPPTAT 560

Length = 620

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

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 23/85 (27%), Positives = 30/85 (35%), Gaps = 3/85 (3%)

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 APAPAPAPVSSVSDVYGQAASNLVA 168
           A APA        DV       L A
Sbjct: 420 AAAPAGLA-LRWRDVLAALKMQLRA 443

Length = 504

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

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 25/53 (47%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 103 PTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPA-PAPAPAPVSS 154
           P    P    Q P P   PP S P + P P+APA +P P PA P PA AP SS
Sbjct: 144 PPPPAPVVMMQPPPPHAMPPASPPAAQPAPSAPASSPPPTPASPPPAKAPKSS 196

Length = 274

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

 Score = 41.9 bits (99), Expect = 3e-04
 Identities = 17/100 (17%), Positives = 27/100 (27%), Gaps = 1/100 (1%)

Query: 73  MLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQT-PAPTVAPPQSVPESAPP 131
            L+++   S    T +          ++   T+   + T     AP  A          P
Sbjct: 153 ELSQNSGQSVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAP 212

Query: 132 PAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSN 171
             A     A     APA    ++         S   A  N
Sbjct: 213 SQANVDTAATPAPAAPATPDGAAPLPTDQAGVSTPAADPN 252

Length = 331

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

 Score = 42.5 bits (101), Expect = 3e-04
 Identities = 18/45 (40%), Positives = 22/45 (48%)

Query: 120 APPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAAS 164
               + P +A P AA A APAPAPA A APA  +  +      A 
Sbjct: 199 PAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPGKAP 243

Length = 547

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

 Score = 42.1 bits (100), Expect = 3e-04
 Identities = 18/38 (47%), Positives = 21/38 (55%)

Query: 119 VAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVS 156
           VA       +AP  AAPA A A APAPAPA A   + +
Sbjct: 194 VAAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAA 231

Length = 547

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

 Score = 42.1 bits (100), Expect = 3e-04
 Identities = 16/53 (30%), Positives = 19/53 (35%)

Query: 104 TSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVS 156
            +      +  PA       +    AP PAA A   A APA A AP      S
Sbjct: 194 VAAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPGKAPHAS 246

Length = 547

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

 Score = 41.6 bits (98), Expect = 4e-04
 Identities = 18/88 (20%), Positives = 26/88 (29%), Gaps = 3/88 (3%)

Query: 88  SAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAP---PPAAPAPAPAPAPA 144
           S+A  +Q    S    TST     +                 P      APA  P     
Sbjct: 150 SSAELSQNSGQSVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAV 209

Query: 145 PAPAPAPVSSVSDVYGQAASNLVAGSNL 172
            AP+ A V + +     A +     + L
Sbjct: 210 VAPSQANVDTAATPAPAAPATPDGAAPL 237

Length = 331

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

 Score = 42.1 bits (99), Expect = 4e-04
 Identities = 36/174 (20%), Positives = 47/174 (27%), Gaps = 12/174 (6%)

Query: 77  SKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPA 136
                +GA     A A  A   S+ P  +          AP  A   +   +  PPAAPA
Sbjct: 372 VPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPA 431

Query: 137 PA------------PAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGG 184
           P              AP PA A A A   S  D            ++  A+         
Sbjct: 432 PPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFE 491

Query: 185 GSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQ 238
            +        A  AA  +            P   A P          A  P A+
Sbjct: 492 PAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAAAPAAR 545

Length = 830

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

 Score = 41.7 bits (98), Expect = 5e-04
 Identities = 16/66 (24%), Positives = 22/66 (33%), Gaps = 1/66 (1%)

Query: 100 SAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPA-APAPAPAPAPAPAPAPAPVSSVSDV 158
           +AP  S     +      + A   S P+SA  PA  P       PA  P   P ++   V
Sbjct: 388 AAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAV 447

Query: 159 YGQAAS 164
                 
Sbjct: 448 RPAQFK 453

Length = 614

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

 Score = 41.8 bits (98), Expect = 5e-04
 Identities = 34/154 (22%), Positives = 48/154 (31%), Gaps = 6/154 (3%)

Query: 116 APTVAPPQSVPESAPPPAA-PAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEA 174
           AP    P  V  + P P A  A A   +  PA      ++ + +  +AA+   A      
Sbjct: 367 APGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAP 426

Query: 175 TVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGN 234
                        D      A   A  N   + +   S   E+ A PP    SA   A +
Sbjct: 427 PAAPAPPATADRGDDAADGDAPVPAKANARASAD---SRCDERDAQPPADSGSASAPASD 483

Query: 235 --PPAQTQAQQPAAPAPTSGPNANPLDLFPQGLP 266
             P A  +    AA    + P A P    P    
Sbjct: 484 APPDAAFEPAPRAAAPSAATPAAVPDARAPAAAS 517

Length = 830

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

 Score = 41.3 bits (97), Expect = 6e-04
 Identities = 31/155 (20%), Positives = 53/155 (34%), Gaps = 13/155 (8%)

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

Query: 140 APAPAPAPAPAPVSSVSDVYGQ---AASNLVAGSNLEATVQQI-LDMGGGSW-------- 187
            PA A +      + V+ V G+     ++L  GS L  +   + +    GS+        
Sbjct: 439 DPAAAASAGDRWRAFVAFVKGKKPALGASLEQGSPLGVSAGLLEIGFPEGSFELSAMQDP 498

Query: 188 DRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPP 222
           D    ++AL   +      +  +        A PP
Sbjct: 499 DSRAELKALAEQFFGRPTRLR-ITVLAAPPGAAPP 532

Length = 576

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

 Score = 37.8 bits (88), Expect = 6e-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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.5 bits (98), Expect = 7e-04
 Identities = 19/78 (24%), Positives = 30/78 (38%)

Query: 80  SSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAP 139
              G +  + APA  A + ++A P +      +   A     P + P+ AP PA     P
Sbjct: 383 RRLGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPP 442

Query: 140 APAPAPAPAPAPVSSVSD 157
           +PA       AP    + 
Sbjct: 443 SPAGNAPAGGAPSPPPAA 460

Length = 824

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

 Score = 41.0 bits (97), Expect = 7e-04
 Identities = 25/105 (23%), Positives = 35/105 (33%), Gaps = 27/105 (25%)

Query: 81  SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAP------------PQSVPES 128
             GA+  +AA A  A   ++A P   Q    ++     ++P              +V  +
Sbjct: 77  DEGAAAGAAAAAAAAAAAAAAAPAQAQAAAAAEQSNDALSPAARKLAAENGLDASAVKGT 136

Query: 129 ---------------APPPAAPAPAPAPAPAPAPAPAPVSSVSDV 158
                          A   AAPA   A APA APAP        V
Sbjct: 137 GKGGRVTKEDVLAALAAAAAAPAAPAAAAPAAAPAPLGARPEERV 181

Length = 407

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

 Score = 41.2 bits (96), Expect = 7e-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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.5 bits (97), Expect = 8e-04
 Identities = 39/188 (20%), Positives = 54/188 (28%), Gaps = 12/188 (6%)

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

Query: 148  APAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNN----- 202
               P +       +        S      +        S  +    RA R    +     
Sbjct: 2640 PHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLA 2699

Query: 203  ----PERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPL 258
                P    E     +   T +PP   A+       P A      PA PA   GP     
Sbjct: 2700 DPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPAR 2759

Query: 259  DLFPQGLP 266
                 G P
Sbjct: 2760 PPTTAGPP 2767

Length = 3151

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

 Score = 40.0 bits (94), Expect = 8e-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|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 1/85 (1%)

Query: 91  PANQAQTTSSAPP-TSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAP 149
           PA  A+  + A   T  +P   +   AP      +   +A P AA +   AP  A  PAP
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAP 425

Query: 150 APVSSVSDVYGQAASNLVAGSNLEA 174
               + +      A+   A +   A
Sbjct: 426 VAAPAAAAPAAAPAAAPAAVALAPA 450

Length = 618

>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|237015 PRK11901, PRK11901, hypothetical protein; Reviewed

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 17/70 (24%), Positives = 26/70 (37%)

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

Query: 141 PAPAPAPAPA 150
           P    A A A
Sbjct: 228 PKSGAASARA 237

Length = 327

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

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 24/60 (40%), Positives = 26/60 (43%)

Query: 109 TTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVA 168
           T   + PA   A P +   SAP PAA APAP  A APA A             A   LVA
Sbjct: 5   TDAKEEPAKEEATPPAPAASAPAPAAAAPAPVAAAAPAAAGPRPDDEPFKASDALHALVA 64

Length = 866

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

 Score = 40.3 bits (95), 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|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 38.3 bits (89), Expect = 0.001
 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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 44/196 (22%), Positives = 56/196 (28%), Gaps = 14/196 (7%)

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

Query: 137  ------------PAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGG 184
                         +PA   APAP   P    +   G A       +              
Sbjct: 2719 TPLPPGPAAARQASPALPAAPAPPAVPAGPATPG-GPARPARPPTTAGPPAPAPPAAPAA 2777

Query: 185  GSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQP 244
            G   R T       + +       +  +  P     P  A   A   AG  P  T A QP
Sbjct: 2778 GPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSA-QP 2836

Query: 245  AAPAPTSGPNANPLDL 260
             AP P  GP    L L
Sbjct: 2837 TAPPPPPGPPPPSLPL 2852

Length = 3151

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

 Score = 39.4 bits (93), Expect = 0.002
 Identities = 20/53 (37%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 116 APTVAPPQSVPESAPPPAAPAPAPAPAPAPAP-APAPVSSVSDVYGQAASNLV 167
           A   A       +    AA APAPAPA A AP A AP ++ +      AS  V
Sbjct: 197 AAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPGKAPHASPAV 249

Length = 547

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

 Score = 39.3 bits (92), Expect = 0.002
 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|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 38.3 bits (89), Expect = 0.002
 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|218191 pfam04652, DUF605, Vta1 like

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 4/77 (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 APAPAPAPAPAPVSSVS 156
            PA  P P    V  +S
Sbjct: 239 GPAAPPPPPVQQVPPLS 255

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|234273 TIGR03593, yidC_nterm, membrane protein insertase, YidC/Oxa1 family, N-terminal domain

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 17/58 (29%), Positives = 25/58 (43%)

Query: 102 PPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVY 159
            P   +P   +QT +   A   + P +APP A    A A A A A     ++  +DV 
Sbjct: 26  GPPPPKPPAAAQTASAQSATAAATPAAAPPAADAPAAAAAADAAAATAKRITVKTDVL 83

Essentially all bacteria have a member of the YidC family, whose C-terminal domain is modeled by TIGR03592. The two copies are found in endospore-forming bacteria such as Bacillus subtilis appear redundant during vegetative growth, although the member designated spoIIIJ (stage III sporulation protein J) has a distinct role in spore formation. YidC, its mitochondrial homolog Oxa1, and its chloroplast homolog direct insertion into the bacterial/organellar inner (or only) membrane. This model describes an N-terminal sequence region, including a large periplasmic domain lacking in YidC members from Gram-positive species. The multifunctional YidC protein acts both with and independently of the Sec system [Protein fate, Protein and peptide secretion and trafficking]. Length = 366

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

 Score = 38.3 bits (89), Expect = 0.002
 Identities = 17/40 (42%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 115 PAPTVAPPQSVPESAPPPAAP-APAPAPAPAPAPAPAPVS 153
               V      P  AP PA P AP P    APAPAPA   
Sbjct: 44  DLSAVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPAPASAG 83

Length = 153

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

 Score = 39.2 bits (92), Expect = 0.002
 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|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 84  ASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPT-VAPPQSVPESAPPPAAPAPAPAPA 142
           A   +AAPA      ++AP   ++P   +  PAP  V   + +        A A APA  
Sbjct: 52  APPAAAAPAAAQPPPAAAPAAVSRPAAPAAEPAPWLVEHAKRLTAQREQLVARAAAPAAP 111

Query: 143 PAPAPAPAPVSSVSDVYGQAASN 165
            A APA     + ++   +  + 
Sbjct: 112 EAQAPAAPAERAAAENAARRLAR 134

Length = 484

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

 Score = 39.8 bits (93), Expect = 0.002
 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|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.7 bits (92), Expect = 0.002
 Identities = 28/103 (27%), Positives = 39/103 (37%), Gaps = 3/103 (2%)

Query: 88  SAAPANQAQTTSSAPPTSTQPTTTS-QTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPA 146
           +           +AP     P++ +  TPAP+ AP   VP    PPA P     P PAP 
Sbjct: 396 TIPTPGTQGPQGTAPAAGMTPSSAAPATPAPSAAPSPRVPWDDAPPAPPRSGIPPRPAPR 455

Query: 147 -PAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWD 188
            P  +PV    D    A+       +   T +     G  +WD
Sbjct: 456 MPEASPVPGAPDSVASASDAPPTLGDPSDTAEHT-PSGPRTWD 497

Length = 624

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

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 18/73 (24%), Positives = 24/73 (32%), Gaps = 2/73 (2%)

Query: 77  SKVSSSGASTVSAAPANQAQTTSSAPPTS--TQPTTTSQTPAPTVAPPQSVPESAPPPAA 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 = 39.5 bits (92), Expect = 0.003
 Identities = 20/83 (24%), Positives = 24/83 (28%)

Query: 75   TKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAA 134
             +  V       VS +  + A                   P P   PP       PPP  
Sbjct: 2879 ARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPR 2938

Query: 135  PAPAPAPAPAPAPAPAPVSSVSD 157
            P P  AP   PA A  P  +V  
Sbjct: 2939 PQPPLAPTTDPAGAGEPSGAVPQ 2961

Length = 3151

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

 Score = 39.0 bits (92), Expect = 0.003
 Identities = 15/43 (34%), Positives = 17/43 (39%), Gaps = 1/43 (2%)

Query: 116 APTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDV 158
           A   A P +    A   AA     A APA A A A    V +V
Sbjct: 81  AAAAAAPAAAAAPAAAAAAAPAPAAAAPAAA-AAAAGGGVVEV 122

Length = 547

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

 Score = 39.1 bits (92), Expect = 0.003
 Identities = 11/48 (22%), Positives = 16/48 (33%)

Query: 110 TTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSD 157
           + S   A   A  ++   +    AA A   A     APA       +D
Sbjct: 83  SASDAGAAPAAAAEAAAAAPAAAAAAAAKKAAPAPAAPAAPAAEVAAD 130

Length = 464

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

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 17/64 (26%), Positives = 23/64 (35%), Gaps = 1/64 (1%)

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

Query: 148 APAP 151
            P P
Sbjct: 114 KPKP 117

Length = 226

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

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 33/188 (17%), Positives = 55/188 (29%), Gaps = 7/188 (3%)

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

Query: 133 AAPAPAPAPAPAPAP---APAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDR 189
             PA A    P  +    A A   + +     A     + S+  ++       G      
Sbjct: 197 TPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGP----E 252

Query: 190 ETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAP 249
                   A    P R  E      P     P  + +S   ++ +P   +    PA  +P
Sbjct: 253 NECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSP 312

Query: 250 TSGPNANP 257
            +  +++ 
Sbjct: 313 RASSSSSS 320

Length = 1352

>gnl|CDD|183756 PRK12799, motB, flagellar motor protein MotB; Reviewed

 Score = 38.9 bits (90), Expect = 0.003
 Identities = 17/98 (17%), Positives = 32/98 (32%)

Query: 78  KVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAP 137
           ++ + G   V+A   + A T SSA   S+    +      +V    +    A   A  + 
Sbjct: 292 QIDTHGTVPVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSVTTQSATTTQASAVALSSA 351

Query: 138 APAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEAT 175
              P+    P    + +   V  Q        +   +T
Sbjct: 352 GVLPSDVTLPGTVALPAAEPVNMQPQPMSTTETQQSST 389

Length = 421

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

 Score = 36.6 bits (85), Expect = 0.003
 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|236712 PRK10547, PRK10547, chemotaxis protein CheA; Provisional

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 14/60 (23%), Positives = 19/60 (31%)

Query: 96  QTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSV 155
           Q T      + Q      T    V+P  SVP      A  APA           +  +S+
Sbjct: 221 QITFETAVAAPQEKAEETTEVVEVSPKISVPPVLKLAAEQAPAGRVEREKTARSSESTSI 280

Length = 670

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

 Score = 39.1 bits (92), Expect = 0.003
 Identities = 17/88 (19%), Positives = 27/88 (30%), Gaps = 1/88 (1%)

Query: 78  KVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAP 137
           ++     S             +   P +      +        P  ++       AA A 
Sbjct: 386 RLQEGPPSPGGGGGGPPGGGGAPGAPAAAAAPGAAAAAPAAGGPAAALAAVPDAAAAAAA 445

Query: 138 APAPAPAPAPAPAPVSSVSDVYGQAASN 165
            PAPA AP PA   ++S  D+   A   
Sbjct: 446 PPAPAAAPQPAV-RLNSFEDIVALAEEK 472

Length = 598

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

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 18/83 (21%), Positives = 26/83 (31%), Gaps = 3/83 (3%)

Query: 92  ANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAP 151
            + A T + A P  T PT +      T   P   P+     A  AP+ A     A     
Sbjct: 170 TDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQ---NAVVAPSQANVDTAATPAPA 226

Query: 152 VSSVSDVYGQAASNLVAGSNLEA 174
             +  D      ++    S   A
Sbjct: 227 APATPDGAAPLPTDQAGVSTPAA 249

Length = 331

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

 Score = 38.7 bits (90), 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|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 36.7 bits (85), Expect = 0.004
 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|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 38.5 bits (90), Expect = 0.004
 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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 32/178 (17%), Positives = 51/178 (28%), Gaps = 12/178 (6%)

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

Query: 139  PAPAPA-PAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALR 197
             AP    P        +V+    + A  +V   +  A +++  +        E V+    
Sbjct: 921  AAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAE------TAEVVVAEPE 974

Query: 198  AAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNA 255
                     V  + + +   TAV P    +   +A        A    APAP   P A
Sbjct: 975  VVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVEHNHATAPMTRAPAPEYVPEA 1032

Length = 1068

>gnl|CDD|176388 cd01793, Fubi, Fubi ubiquitin-like protein

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FV+    TH  +EV  ++ VSD+K ++  ++G        Q+L+  G  L+D  TL 
Sbjct: 1  MQLFVRAQN-TH-TLEVTGQETVSDIKAHVAGLEG---IDVEDQVLLLAGVPLEDDATLG 55

Query: 61 ENKVAENS 68
          +  V E  
Sbjct: 56 QCGVEELC 63

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. Length = 74

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

 Score = 39.2 bits (91), Expect = 0.004
 Identities = 47/210 (22%), Positives = 73/210 (34%), Gaps = 25/210 (11%)

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

Query: 102  --PPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAP-APAPVSSVSDV 158
              PP  +     S   A  +AP   VP + P   +    P+ A A AP A    S++  V
Sbjct: 1156 VSPPVVSAAPAQSVATAVAMAPVAEVPIAVPVQQSVDYMPSVAQAAAPQASVNDSAIQQV 1215

Query: 159  YGQ--AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYN-----NPE------- 204
              +  A         LE  +    D+G  S  R  ++ +++   N     NPE       
Sbjct: 1216 MMEVVAEKTGYPTEMLELEMDMEADLGIDSIKRVEILGSVQEIINDLPELNPEDLAELRT 1275

Query: 205  --RAVEYLYSGIPEQTAVPPVARASAGGQA 232
                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|235899 PRK06975, PRK06975, bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 18/64 (28%), Positives = 22/64 (34%), Gaps = 3/64 (4%)

Query: 89  AAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPA 148
           A  A Q  T + AP   T    +      T  P  +    APPP  PA  P P       
Sbjct: 266 ADAAAQPATAAPAPSRMTDTNDSKS---VTSQPAAAAAAPAPPPNPPATPPEPPARRGRG 322

Query: 149 PAPV 152
            A +
Sbjct: 323 SAAL 326

Length = 656

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	364
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	99.88
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.77
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.75
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.73
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.72
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.72
PTZ00044	76	ubiquitin; Provisional	99.71
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.69
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.69
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.69
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.68
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.68
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.68
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.67
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.67
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.66
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.65
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.65
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.64
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.64
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.62
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.59
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.57
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.54
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.54
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.46
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.46
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.45
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.43
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.37
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.29
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.27
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.26
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.21
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.03
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	99.02
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.89
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	98.88
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	98.84
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	98.82
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	98.79
PLN02560	308	enoyl-CoA reductase	98.79
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	98.75
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	98.72
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.65
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.61
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.42
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.38
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.18
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.14
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.13
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	97.98
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	97.7
KOG4495	110	consensus RNA polymerase II transcription elongati	97.64
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.53
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	97.1
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	97.09
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	97.08
KOG4583	391	consensus Membrane-associated ER protein involved	97.08
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.05
KOG0944	763	consensus Ubiquitin-specific protease UBP14 [Postt	96.9
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	96.85
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	96.81
smart00727	41	STI1 Heat shock chaperonin-binding motif.	96.75
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	96.69
KOG0013	231	consensus Uncharacterized conserved protein [Funct	96.61
COG5417	81	Uncharacterized small protein [Function unknown]	96.6
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	96.53
KOG1639	297	consensus Steroid reductase required for elongatio	96.43
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	96.41
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	96.33
KOG0418	200	consensus Ubiquitin-protein ligase [Posttranslatio	96.32
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	96.23
PF13019	162	Telomere_Sde2: Telomere stability and silencing	96.17
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	95.89
smart00546	43	CUE Domain that may be involved in binding ubiquit	95.85
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	95.67
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	94.81
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	94.56
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	94.47
PF09288	55	UBA_3: Fungal ubiquitin-associated domain ; InterP	93.76
KOG0012	380	consensus DNA damage inducible protein [Replicatio	93.36
PRK06437	67	hypothetical protein; Provisional	93.2
PF14453	57	ThiS-like: ThiS-like ubiquitin	93.11
PF11626	87	Rap1_C: TRF2-interacting telomeric protein/Rap1 -	93.01
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	92.76
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	92.67
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	92.43
PF06972	60	DUF1296: Protein of unknown function (DUF1296); In	92.09
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	91.94
PF07499	47	RuvA_C: RuvA, C-terminal domain; InterPro: IPR0111	91.82
PRK08364	70	sulfur carrier protein ThiS; Provisional	91.49
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	91.36
PRK06488	65	sulfur carrier protein ThiS; Validated	90.91
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	89.85
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	89.56
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	88.85
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	88.53
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	88.36
PF12754	309	Blt1: Cell-cycle control medial ring component; In	88.01
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	86.86
PRK05863	65	sulfur carrier protein ThiS; Provisional	86.26
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	86.07
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	85.88
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	85.41
PRK05659	66	sulfur carrier protein ThiS; Validated	85.37
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	84.71
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	84.28
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	83.57
PRK08053	66	sulfur carrier protein ThiS; Provisional	83.16
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	82.9
KOG0944	763	consensus Ubiquitin-specific protease UBP14 [Postt	82.33
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	81.94
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	81.88
PF08938	79	HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This	81.83
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	81.65
PF11069	98	DUF2870: Protein of unknown function (DUF2870); In	81.65
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	81.42
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	80.96

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=100.00  E-value=1.3e-75  Score=581.01  Aligned_cols=328  Identities=41%  Similarity=0.699  Sum_probs=221.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+...|++.+++++|||||+||+|+|+++|++|+|+++++|+||++|+|..
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            89999999999999999999999999999999988545899999999999999999999999999999999999998874


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCcccc
Q 017906           81 SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPA-PAPAPAPVSSVSDVY  159 (364)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  159 (364)
                      +...+++...+.+++.++. ..+   .+......++++.++     ..+      .+.+ .+++ +...+.+.+. ....
T Consensus        81 ~~~~~~~~~~~~~~p~~~~-~~~---~~~~~~~~~~~~~~~-----~~~------~~~~-~~~~~~~~~~~~~~~-~~~~  143 (378)
T TIGR00601        81 TGKSAPPAATPTSAPTPTP-SPP---ASPASGMSAAPASAV-----EEK------SPSE-ESATATAPESPSTSV-PSSG  143 (378)
T ss_pred             CCCCCCCCCCCCCCCCCCC-CCC---CCCCCCCCCCCCCCC-----ccc------cccC-CCCCCCCCCCCCccc-cccC
Confidence            3222111101101011100 000   000000000000000     000      0000 0000 0000000000 0001


Q ss_pred             ccccccccCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCCCCCCCccccccCCCCCCCCCCcc
Q 017906          160 GQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT  239 (364)
Q Consensus       160 ~~~~s~l~~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~~~~~~~~~~~~~~~~~~~~~~~~  239 (364)
                      ..+.|+||+|++||++|++||+||   |+|+||+|||||||||||||||||++|||++++...+    ...    +... 
T Consensus       144 ~~~~s~l~~g~~~e~~I~~i~eMG---f~R~qV~~ALRAafNNPdRAVEYL~tGIP~~~~~~~~----~~~----~~~~-  211 (378)
T TIGR00601       144 SDAASTLVVGSERETTIEEIMEMG---YEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEP----VQQ----TAAS-  211 (378)
T ss_pred             CCcccccccchHHHHHHHHHHHhC---CCHHHHHHHHHHHhCCHHHHHHHHHhCCCcccccccc----CCC----cccc-
Confidence            246789999999999999999999   9999999999999999999999999999988652111    100    0000 


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCcCCCCCCCC------CCCCCCchHhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHH
Q 017906          240 QAQQPAAPAPTSGPNANPLDLFPQGLPNMG------SNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPH  313 (364)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~------~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~  313 (364)
                      .     . ....+....+ |||++++.++.      .+.|+++|+|||++|||++||++||+||++|++|||||+++||+
T Consensus       212 ~-----~-~~~~~~~~~~-~lf~~a~~~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLqql~~~nP~  284 (378)
T TIGR00601       212 T-----A-AATTETPQHG-SVFEQAAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQ  284 (378)
T ss_pred             c-----c-cccCCCCCCc-chhhhhhcccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHHHHHhhCHH
Confidence            0     0 0111112222 99998864321      01245699999999999999999999999999999999999999


Q ss_pred             HHHHHHHCHHHHHHHhcCCCCC--CCCccc---ccccC-CCCc--ceecCHHHHhhcCC
Q 017906          314 LMRLIQEHQTDFLRLINEPVEG--GEGNVL---GQLAS-AMPQ--AVTVTPEEREAIEP  364 (364)
Q Consensus       314 L~~~I~~n~e~Fl~~l~e~~~~--~~g~~~---~~~~~-~~~~--~i~lT~ee~~AIeR  364 (364)
                      |+|+|++|||+||+|||++.++  ++++..   ++..+ +.++  .|+||+||++||+|
T Consensus       285 l~q~I~~n~e~Fl~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~lT~eE~~AIeR  343 (378)
T TIGR00601       285 LLQQISQHPEQFLQMLNEPVGELAGESDMEGGVGAIAEAGLPQMNQIQVTPEEKEAIER  343 (378)
T ss_pred             HHHHHHHCHHHHHHHhcCcccccccccccccccccccccCcccccccccCHHHHHHHHH
Confidence            9999999999999999998532  112111   11111 1112  69999999999998

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=2.8e-76  Score=562.26  Aligned_cols=303  Identities=55%  Similarity=0.853  Sum_probs=232.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+++|.+|+|+|.+++||.+||++|+...|.+ +|++.|||||+||+|+|+.++.+|+|+++++|+||++|+|..
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 017906           81 SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYG  160 (364)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (364)
                      ....     ++.+  .+   +          ...+..+.+|.. +.+..       ..+ .++       ..++....++
T Consensus        80 ~t~~-----ap~s--~~---~----------~~~p~~~~ap~~-s~a~~-------~s~-~~~-------~~~~~~~~~~  123 (340)
T KOG0011|consen   80 STQV-----APQS--SA---A----------THLPKAAEAPPS-SAAED-------ASP-ATP-------AQTSQEDTYE  123 (340)
T ss_pred             ccCC-----CCCC--cc---c----------cCCCccCCCCCc-ccccc-------CCC-Ccc-------ccccccchhh
Confidence            1110     0000  00   0          000011111100 00000       000 000       0112234467


Q ss_pred             cccccccCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCCCCCCCccccccCCCCCCCCCCccc
Q 017906          161 QAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ  240 (364)
Q Consensus       161 ~~~s~l~~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~~~~~~~~~~~~~~~~~~~~~~~~~  240 (364)
                      .+.|+|++|.++|.+|.+||+||   |+||+|+|||||||||||||||||++|||+....+.+...++..          
T Consensus       124 ~aas~Lv~G~~~e~~V~~Im~MG---y~re~V~~AlRAafNNPeRAVEYLl~GIP~~~~~~~~~~~~~~~----------  190 (340)
T KOG0011|consen  124 IAASTLVVGSEYEQTVQQIMEMG---YDREEVERALRAAFNNPERAVEYLLNGIPEDAEVPEPEKSTAAA----------  190 (340)
T ss_pred             hhhhhhhccchhHHHHHHHHHhC---ccHHHHHHHHHHhhCChhhhHHHHhcCCcccccCCcccCCcccC----------
Confidence            78999999999999999999999   99999999999999999999999999999986655532111100          


Q ss_pred             cCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCchHhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHH
Q 017906          241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQE  320 (364)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I~~  320 (364)
                              +....+.++.++|++.+....   |+++|+|||++|||++||++||+||+||++||||||++||+|+|+|++
T Consensus       191 --------~~~p~~~~p~~~~~~~~~~~~---~~~~l~fLr~~~qf~~lR~~iqqNP~ll~~~Lqqlg~~nP~L~q~Iq~  259 (340)
T KOG0011|consen  191 --------AELPANAQPLDLFPQGAVEAS---GGDPLEFLRNQPQFQQLRQMIQQNPELLHPLLQQLGKQNPQLLQLIQE  259 (340)
T ss_pred             --------CCCCCCCChhhcCCccchhhh---cCCchhhhhccHHHHHHHHHHhhCHHHHHHHHHHHhhhCHHHHHHHHH
Confidence                    000002345788888664443   348999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHhcCCCCCCCCcccccccCCCC-cceecCHHHHhhcCC
Q 017906          321 HQTDFLRLINEPVEGGEGNVLGQLASAMP-QAVTVTPEEREAIEP  364 (364)
Q Consensus       321 n~e~Fl~~l~e~~~~~~g~~~~~~~~~~~-~~i~lT~ee~~AIeR  364 (364)
                      ||++||+|||||.+|+++++.+..+..++ ++|+||+||++||+|
T Consensus       260 nqe~Fl~mlnep~~~~~~~~~~~~~~~~~~~~I~vtpee~eAIeR  304 (340)
T KOG0011|consen  260 NQEAFLQLLNEPVEGGDGGGTGAPAAEGPGHQIQVTPEEKEAIER  304 (340)
T ss_pred             HHHHHHHHhhcccccccccccccccccCCcceEecCHHHHHHHHH
Confidence            99999999999998755555555554454 689999999999998

>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=99.88  E-value=4.3e-23  Score=153.74  Aligned_cols=58  Identities=60%  Similarity=1.070  Sum_probs=54.6

Q ss_pred             hHhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHCHHHHHHHhcCCCC
Q 017906          277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVE  334 (364)
Q Consensus       277 l~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I~~n~e~Fl~~l~e~~~  334 (364)
                      |+|||++|+|++||++||+||++|++|||+|+++||+|+++|++|||+|++||+++.+
T Consensus         1 L~~Lr~~Pqf~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~n~e~Fl~ll~~~~~   58 (59)
T PF09280_consen    1 LEFLRNNPQFQQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQNPEEFLRLLNEPAE   58 (59)
T ss_dssp             CGGGTTSHHHHHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHHTHHHHHHHHHSTS-
T ss_pred             ChHHHcChHHHHHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHHCHHHHHHHHcCCCC
Confidence            6899999999999999999999999999999999999999999999999999999754

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=99.77  E-value=2.2e-18  Score=133.97  Aligned_cols=73  Identities=27%  Similarity=0.403  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+++|+++.++|++++||.+||++|+++.|   +++++|+|+|+||.|+|+.+|++|||+++++|+++++.
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   99999999999999999999999999999999999863

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=99.75  E-value=9.1e-18  Score=130.88  Aligned_cols=75  Identities=55%  Similarity=0.790  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCC--CCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVY--PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~i--p~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|++|.++|++++||.+||++|+...|   +  ++++|+|+|+|+.|+|+.+|++|||++|++|++++++++
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=99.73  E-value=1.1e-17  Score=131.87  Aligned_cols=74  Identities=22%  Similarity=0.354  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCcE-EEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTH-FEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~-~~ie-V~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|++ +.|+ +++++||.+||++|++..|   +++++|||+|+||+|+|+.+|++|||+++++|+|+++..
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   999999999999999999999999999999999998753

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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.72  E-value=2.7e-17  Score=127.90  Aligned_cols=73  Identities=27%  Similarity=0.369  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+.  +++.++|++++||.+||.+|+++.|   +|+++|+|+|+||.|+|+++|++|+|+++++||++++.+.
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            89999974  7899999999999999999999999   9999999999999999999999999999999999998653

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.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.72  E-value=2.2e-17  Score=128.58  Aligned_cols=71  Identities=18%  Similarity=0.328  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||++.|+.+.++|++++||.+||++|+...|   +++++|||+|+|++|+|+++|++|||+++++||+..
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   999999999999999999999999999999999874

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.

>PTZ00044 ubiquitin; Provisional

Probab=99.71  E-value=4.8e-17  Score=126.62  Aligned_cols=74  Identities=28%  Similarity=0.446  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|+++.++|++++||.+||.+|+...|   +|++.|+|+|+|+.|+|+.+|++|+|+++++||++++.+
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

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.69  E-value=7.8e-17  Score=133.54  Aligned_cols=75  Identities=33%  Similarity=0.546  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+++.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+.+|++|+|+++++|+++++.+.
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.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.69  E-value=8.2e-17  Score=126.72  Aligned_cols=73  Identities=23%  Similarity=0.407  Sum_probs=69.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+.+|+.+.|+|+++.||.+||++|+++.+   +++++|||+|+||+|+|+ +|++|||+++++|+|+....
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   999999999999999998 99999999999999998653

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.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.69  E-value=2e-16  Score=122.47  Aligned_cols=74  Identities=36%  Similarity=0.557  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   ++++.|+|+|+|+.|+|+++|++|+|+++++|+|+++.+
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   999999999999999999999999999999999998764

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.

>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2

Probab=99.68  E-value=1.3e-16  Score=124.08  Aligned_cols=72  Identities=22%  Similarity=0.271  Sum_probs=69.5

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+||++.|+++.|+|++++||.+||++|+...|   +++++|+|+|+||.|+|+++|++|||+++++|+++++..
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   999999999999999999999999999999999998764

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.

>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2

Probab=99.68  E-value=1.1e-16  Score=126.48  Aligned_cols=74  Identities=28%  Similarity=0.401  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkL--if~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|+++.++|++++||.+||++|+...|   +++++|||  +|+|++|+|+++|++|||+++++|+|++++-
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=99.68  E-value=2.2e-16  Score=122.26  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+.+|+.+.|+|++++||.+||++|+..+|   ++++.|+|+|+|+.|+|+++|++|+|+++++|+|+++.+
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~   74 (76)
T cd01803           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (76)
T ss_pred             CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhC---CCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcc
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999864

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

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.67  E-value=1.6e-16  Score=122.65  Aligned_cols=69  Identities=28%  Similarity=0.462  Sum_probs=66.7

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      +.||.++|+++.++|++++||.+||.+|++..|   +++++|+|+|+|++|+|+.+|++|+|+++++|||++
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   999999999999999999999999999999999987

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=99.67  E-value=3.3e-16  Score=120.04  Aligned_cols=72  Identities=36%  Similarity=0.459  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+++|+++.++|++++||.+||++|+..+|   ++++.|+|+|+|+.|+|+.+|++|||+++++|+|+.+
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=99.66  E-value=2.5e-16  Score=121.04  Aligned_cols=70  Identities=30%  Similarity=0.546  Sum_probs=67.5

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+||++.|+++.++|++++||.+||++|+++.|   +++++|+|+|+|+.|+|+.+|++|||+++++|||+.|
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=99.65  E-value=4.8e-16  Score=119.85  Aligned_cols=71  Identities=32%  Similarity=0.428  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+.+|+ +.|+|++++||.+||++|++..|   ++.++|+|+|+||+|+|+++|++|||+++++||++++
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.

>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=99.65  E-value=1.2e-15  Score=153.49  Aligned_cols=75  Identities=29%  Similarity=0.444  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      ++|+||+.++ ++.|.|..+.||.+||++|...++   +++++++|||.||+|+|+++|..|||++|.+|||+++....
T Consensus        16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~---a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~~~   90 (493)
T KOG0010|consen   16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFG---APPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQPR   90 (493)
T ss_pred             eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcC---CChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccCCC
Confidence            5799999988 899999999999999999999998   89999999999999999999999999999999999866543

>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=99.64  E-value=6.3e-16  Score=117.90  Aligned_cols=69  Identities=38%  Similarity=0.603  Sum_probs=66.1

Q ss_pred             EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         6 Ktl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+++|+.|.|+|++++||.+||++|+...+   ++++.|+|+|+|++|+|+.+|++|||+++++|+|+++++
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~---~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~~   69 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETG---IPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKPR   69 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHT---STGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESSE
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccc---cccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEecC
Confidence            689999999999999999999999999999   999999999999999999999999999999999988753

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 ....

>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein

Probab=99.64  E-value=6.6e-16  Score=121.79  Aligned_cols=73  Identities=21%  Similarity=0.207  Sum_probs=64.6

Q ss_pred             CEEEEEeCCCcE--EEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhc--cCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTH--FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENK--VAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~--~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~g--Ik~~s~I~v~v   74 (364)
                      |.|+||+.+|++  |.+++++++||.+||++|+...+.. +++++|||||+||+|+|+.+|++|+  ++++.+|||+.
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            589999999998  5555689999999999999987522 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.

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.62  E-value=1.2e-15  Score=118.97  Aligned_cols=70  Identities=29%  Similarity=0.414  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe---CCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif---~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|| ++|++|.|+|++++||.+||++|++.+|   +|+++|||+|   +||+|+|+.+|++|+|+++++|+||.
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 7999999999999999999999999999   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=99.59  E-value=3.3e-15  Score=115.51  Aligned_cols=68  Identities=34%  Similarity=0.435  Sum_probs=64.4

Q ss_pred             EEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CChhhhccCCCCEEEEE
Q 017906            3 VFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVM   73 (364)
Q Consensus         3 I~VKtl-~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~-~tL~d~gIk~~s~I~v~   73 (364)
                      |+||+. +|+++.|+|++++||.+||.+|+.+.|   +|+++|+|+|+||.|+|+ .+|++|||+++++|++.
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=99.57  E-value=9.1e-15  Score=111.97  Aligned_cols=70  Identities=29%  Similarity=0.421  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||+. |+.+.++|++++||.+||++|+..+|   +++++|||+|+|+.|+|+++|++|||++|++|+|+.
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 89999999999999999999999999   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=99.54  E-value=6.1e-15  Score=108.42  Aligned_cols=70  Identities=36%  Similarity=0.548  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |.|.||+++|+.+.|++++.++|..+|++|+++.|   ||+.+|||||.||.+.|+++-++|++.-|+++|++
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   99999999999999999999999999999999874

>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120

Probab=99.54  E-value=2.2e-14  Score=112.17  Aligned_cols=68  Identities=26%  Similarity=0.396  Sum_probs=65.1

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         8 l~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      ++|+++.|+|++++||.+||.+|+..+|   +|++.|+|+|+|+.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999998754

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=99.46  E-value=7e-15  Score=120.21  Aligned_cols=76  Identities=37%  Similarity=0.583  Sum_probs=73.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |.++++++.|++++++|++++||..||.+|....|   +|++.|+|+|+||+|+|..||++|||...++||++.+.+..
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   99999999999999999999999999999999999887764

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.46  E-value=4.6e-13  Score=107.54  Aligned_cols=75  Identities=16%  Similarity=0.265  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |.|+|++.+|+.+.|+|.+++||..||.+++++.|   +++++++|+|+|+.|+|+.|+.+|+|.++++|+|+++.+.
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            68999999999999999999999999999999999   9999999999999999999999999999999999987653

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.

>smart00213 UBQ Ubiquitin homologues

Probab=99.45  E-value=2.8e-13  Score=100.71  Aligned_cols=64  Identities=42%  Similarity=0.649  Sum_probs=61.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS   68 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s   68 (364)
                      |+|+||+.+ +.+.++|++++||.+||.+|+..+|   ++++.|+|+|+|+.|.|+++|++|||++++
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 7999999999999999999999999   999999999999999999999999999875

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

>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]

Probab=99.43  E-value=9.1e-14  Score=121.06  Aligned_cols=77  Identities=35%  Similarity=0.553  Sum_probs=73.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+|+++.++++.++|..++||..+|.+|++..|   ||+++|+|||.|+.|+|.++|+||+|+..++|+++++.+...
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   999999999999999999999999999999999999876544

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.37  E-value=7.2e-13  Score=103.37  Aligned_cols=55  Identities=25%  Similarity=0.237  Sum_probs=49.1

Q ss_pred             CCCcHHHHHHHHHHHhCCCCC-CCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906           19 PEDKVSDVKKNIETVQGSDVY-PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus        19 ~s~TV~dLK~kI~~~~g~~~i-p~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      .++||.+||++|+++.+.. + ++++|||||+||+|+|+++|++|||+++++|||+.
T Consensus        19 ~~~TV~~LK~kI~~~~~eg-i~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          19 GGYQVSTLKQLIAAQLPDS-LPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             ccCcHHHHHHHHHHhhccC-CCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            4689999999999996322 5 58999999999999999999999999999999985

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.

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.29  E-value=1.2e-11  Score=93.15  Aligned_cols=68  Identities=43%  Similarity=0.663  Sum_probs=64.4

Q ss_pred             EEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            4 FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         4 ~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      +||..+|+.+.++++++.||.+||++|+..+|   ++++.|+|+|+|+.|+|+.+|.+|+|++++.|+++.
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            37878899999999999999999999999999   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=99.27  E-value=1.4e-11  Score=96.47  Aligned_cols=65  Identities=18%  Similarity=0.274  Sum_probs=59.0

Q ss_pred             EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCChhhhccC-CCCEEEEEE
Q 017906            6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVA-ENSFVVVML   74 (364)
Q Consensus         6 Ktl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~-D~~tL~d~gIk-~~s~I~v~v   74 (364)
                      |...|+++.|+|++++||.+||.+|+.+.|   +|++.|+| |+|+.|. |+++|++|||+ +|+++++.+
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            445678999999999999999999999999   99999999 9999985 67999999999 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.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.26  E-value=1e-11  Score=103.38  Aligned_cols=77  Identities=17%  Similarity=0.236  Sum_probs=62.6

Q ss_pred             EEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCC--CCCC--CCCeEEEeCCeecCCCCChhhhc------cCCCCEE
Q 017906            2 KVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGS--DVYP--ASQQMLIHQGKVLKDVTTLEENK------VAENSFV   70 (364)
Q Consensus         2 kI~VKtl~gk~~-~ieV~~s~TV~dLK~kI~~~~g~--~~ip--~~~qkLif~GkiL~D~~tL~d~g------Ik~~s~I   70 (364)
                      .|.||..+|..+ .+.+.+++||.+||++|++..+.  ..+|  +++|||||+||+|+|++||++|+      +....++
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            577887788543 46778999999999999966642  1144  99999999999999999999999      7777899


Q ss_pred             EEEEecCC
Q 017906           71 VVMLTKSK   78 (364)
Q Consensus        71 ~v~v~k~k   78 (364)
                      ||+++.+.
T Consensus        86 Hvvlr~~~   93 (113)
T cd01814          86 HVVVQPPL   93 (113)
T ss_pred             EEEecCCC
Confidence            99887654

NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.

>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins

Probab=99.21  E-value=5.4e-11  Score=91.48  Aligned_cols=71  Identities=24%  Similarity=0.391  Sum_probs=65.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~-~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|++.+|+.+.+.|.++++|..|++++++..+   ++. +.++|+|+|+.|+++.|+++|||+++++|.|++
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 999999999999999999999999999999874

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=99.03  E-value=6.1e-10  Score=90.62  Aligned_cols=62  Identities=21%  Similarity=0.238  Sum_probs=57.1

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCChhhhccCCCCEEEEEEec
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~-D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      ...++|++++||.+||.+|...++   +++.+|||+|+|+.|. |.++|++|||..++.|.+.+..
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~---V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llide   78 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFS---VAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADE   78 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhc---CCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecC
Confidence            467889999999999999999999   9999999999999995 5789999999999999998754

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=99.02  E-value=4.5e-10  Score=76.03  Aligned_cols=36  Identities=50%  Similarity=0.723  Sum_probs=33.8

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHH
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL  210 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL  210 (364)
                      +++.|+.|++||   |++++|++||+++.||.|+||+||
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            578999999999   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 ....

>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=98.89  E-value=1.6e-08  Score=75.48  Aligned_cols=72  Identities=39%  Similarity=0.585  Sum_probs=68.2

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      ++++++.|+.+.+++....+|..+|.+|....|   ++.+.|+|+|.|+.|.|+.+|.+|+|..++++++..+.+
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

>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A

Probab=98.88  E-value=1.6e-08  Score=85.00  Aligned_cols=68  Identities=22%  Similarity=0.283  Sum_probs=52.6

Q ss_pred             EEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCC----CCCCCCeEEEeCCeecCCCCChhhhccCCCCE
Q 017906            2 KVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSD----VYPASQQMLIHQGKVLKDVTTLEENKVAENSF   69 (364)
Q Consensus         2 kI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~----~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~   69 (364)
                      .|+++..+|+ +-.+.+++++||.+||+.|......+    ...++.+||||.||+|+|+++|++|.+..+++
T Consensus         4 ~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~   76 (111)
T PF13881_consen    4 ELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGET   76 (111)
T ss_dssp             EEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSE
T ss_pred             EEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCC
Confidence            5778888998 78899999999999999999876432    13456889999999999999999999987763

>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B

Probab=98.84  E-value=1.7e-08  Score=80.59  Aligned_cols=71  Identities=25%  Similarity=0.316  Sum_probs=59.1

Q ss_pred             EEEEEeCC-CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEE-EeCCe-----ec-CCCCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLK-GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQGK-----VL-KDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~-gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkL-if~Gk-----iL-~D~~tL~d~gIk~~s~I~v~   73 (364)
                      +|.|+... ....+..+++++||.+||.+|+..+|   ++++.|+| +|.|+     .| +|+++|.+|++++|..|||+
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 33445569999999999999999999   99999999 58888     46 67889999999999999998


Q ss_pred             Ee
Q 017906           74 LT   75 (364)
Q Consensus        74 v~   75 (364)
                      -.
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.

>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]

Probab=98.82  E-value=5.1e-09  Score=113.25  Aligned_cols=70  Identities=26%  Similarity=0.400  Sum_probs=67.4

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      .|+|||++.++.+|.|...+||++||.+|.++.+   |+.+.|||||.|++|.|++++++|+| +|.+|||+-|
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 8999999877

>cd00194 UBA Ubiquitin Associated domain

Probab=98.79  E-value=9.7e-09  Score=69.52  Aligned_cols=38  Identities=50%  Similarity=0.733  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      +++.|++|++||   |+|++|++||+++.||.++|++||+.
T Consensus         1 ~~~~v~~L~~mG---f~~~~~~~AL~~~~~d~~~A~~~L~~   38 (38)
T cd00194           1 DEEKLEQLLEMG---FSREEARKALRATNNNVERAVEWLLE   38 (38)
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            367899999999   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.

>PLN02560 enoyl-CoA reductase

Probab=98.79  E-value=1.6e-08  Score=99.01  Aligned_cols=71  Identities=32%  Similarity=0.427  Sum_probs=62.7

Q ss_pred             CEEEEEeCCCcEE---EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---C----eecCCCCChhhhccCCCCEE
Q 017906            1 MKVFVKTLKGTHF---EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G----KVLKDVTTLEENKVAENSFV   70 (364)
Q Consensus         1 MkI~VKtl~gk~~---~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~---G----kiL~D~~tL~d~gIk~~s~I   70 (364)
                      |+|+||..+|+.+   +|+|+++.||++||++|+++.+.  +++++|||++.   |    +.|+|+++|++||++++++|
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            8999998889887   79999999999999999999872  47899999983   3    48899999999999999988


Q ss_pred             EEE
Q 017906           71 VVM   73 (364)
Q Consensus        71 ~v~   73 (364)
                      ++-
T Consensus        79 y~k   81 (308)
T PLN02560         79 VFK   81 (308)
T ss_pred             EEE
Confidence            764

>smart00165 UBA Ubiquitin associated domain

Probab=98.75  E-value=1.3e-08  Score=68.58  Aligned_cols=37  Identities=51%  Similarity=0.791  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      +++.|++|++||   |++++|.+||+.+.||.++|++||+
T Consensus         1 ~~~~v~~L~~mG---f~~~~a~~aL~~~~~d~~~A~~~L~   37 (37)
T smart00165        1 DEEKIDQLLEMG---FSREEALKALRAANGNVERAAEYLL   37 (37)
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence            367899999999   9999999999999999999999995

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=98.72  E-value=4.2e-08  Score=81.78  Aligned_cols=73  Identities=21%  Similarity=0.276  Sum_probs=61.6

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhcc-------CCCCEEEE
Q 017906            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-------AENSFVVV   72 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gI-------k~~s~I~v   72 (364)
                      |-++++....| ++.+++.++.||.+||++|+....   .|++.|+|+..+.+|+|+++|+|||+       ....+|-+
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            45555544444 677899999999999999999998   99999999977789999999999999       55777877


Q ss_pred             EEec
Q 017906           73 MLTK   76 (364)
Q Consensus        73 ~v~k   76 (364)
                      .+++
T Consensus        78 a~r~   81 (119)
T cd01788          78 AFRS   81 (119)
T ss_pred             EEec
Confidence            7775

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=1.1e-07  Score=76.13  Aligned_cols=73  Identities=23%  Similarity=0.318  Sum_probs=57.8

Q ss_pred             EEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC----C---eec-CCCCChhhhccCCCCEEE
Q 017906            2 KVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ----G---KVL-KDVTTLEENKVAENSFVV   71 (364)
Q Consensus         2 kI~VKtl~g--k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~----G---kiL-~D~~tL~d~gIk~~s~I~   71 (364)
                      +|+|.....  +.++..++.++||.+||.+|+..+|   ++++.|+|.|.    +   ..| +|+++|.+||+++|..||
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            567775554  4888999999999999999999999   99999999765    2   124 568999999999999999


Q ss_pred             EEEecC
Q 017906           72 VMLTKS   77 (364)
Q Consensus        72 v~v~k~   77 (364)
                      |.-..+
T Consensus        80 V~D~~p   85 (87)
T PF14560_consen   80 VVDTNP   85 (87)
T ss_dssp             EEE-T-
T ss_pred             EEeCCC
Confidence            986543

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=98.61  E-value=1.2e-07  Score=74.25  Aligned_cols=69  Identities=23%  Similarity=0.253  Sum_probs=54.6

Q ss_pred             EEEEEeCC-CcEEEEEeC-CCCcHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecCCCCChhhhccCCCCEEEE
Q 017906            2 KVFVKTLK-GTHFEIEVK-PEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~-gk~~~ieV~-~s~TV~dLK~kI~~~~g~~~ip~~~qkL--if~GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      .|.++..+ .....++++ ++.||.+||+.|+...+.  +++++|+|  .+.|++|.|+.+|.+|||+++++|+|
T Consensus         2 ~i~~~~~~~k~~~~~~~~~~~aTV~dlk~~i~~~~~~--~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801           2 EILDAKRSDKPIGKLKVSSGDATIADLKKLIAKSSPQ--LTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             eeeccccCcCceeecccCCCCccHHHHHHHHHHHcCC--CCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            56666555 333334444 889999999999998652  57899888  58999999999999999999998876

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.

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.42  E-value=1.4e-06  Score=61.46  Aligned_cols=67  Identities=31%  Similarity=0.457  Sum_probs=60.5

Q ss_pred             EEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         5 VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+..++..+.+.+..+.||.+||++|..+.|   ++++.++|+++|+.+.+...+.+|++.+++.|+++.
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   889999999999999999888999999999998864

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=98.38  E-value=6e-07  Score=71.18  Aligned_cols=69  Identities=28%  Similarity=0.359  Sum_probs=44.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---Ceec--CCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---GKVL--KDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~---GkiL--~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |-|.||+.+| .+.|+|++++||.+||++|.+..+   ++...+.|..+   ...|  .++++|+++||+.|+.|+|.
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            6788888777 889999999999999999999999   88888888533   1234  46899999999999998763

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=98.18  E-value=4.2e-06  Score=84.82  Aligned_cols=72  Identities=22%  Similarity=0.367  Sum_probs=66.6

Q ss_pred             EEEEEeCCCcEEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            2 KVFVKTLKGTHFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         2 kI~VKtl~gk~~~ie-V~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      .|.|| +.|+.|.++ ++.++|+..||.+|...+|   ++|++||++++|+.|.|+-.+..++||++.+|+||.+.-
T Consensus         5 ~v~VK-W~gk~y~v~~l~~d~t~~vlKaqlf~LTg---V~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e   77 (473)
T KOG1872|consen    5 TVIVK-WGGKKYPVETLSTDETPSVLKAQLFALTG---VPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAE   77 (473)
T ss_pred             eEeee-ecCccccceeccCCCchHHHHHHHHHhcC---CCccceeEEEecccccccccccccccCCCCEEEeecccc
Confidence            36677 899999998 9999999999999999999   999999999999999999899999999999999997653

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=98.14  E-value=3.5e-06  Score=81.51  Aligned_cols=74  Identities=27%  Similarity=0.394  Sum_probs=64.3

Q ss_pred             CEEEEEeC---CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTL---KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl---~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |.+.|+.-   .-..+.|+|+.+..|.+||+.++.+.|   +|++++|+||.||.|.|+.++..+.+...+.+|+|..++
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            67777744   223588999999999999999999999   999999999999999999999999999889999885444

>cd01811 OASL_repeat1 2'-5' oligoadenylate synthetase-like protein, repeat 1 of 2

Probab=98.13  E-value=1.4e-05  Score=61.94  Aligned_cols=71  Identities=18%  Similarity=0.309  Sum_probs=61.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--eecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G--KVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~---G--kiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      ++|+||-+.+..+.+.|+|..+|..||.+|....+   ++ ..|||.|.   |  ..|.+..+|++|||-.+-.|.|+-.
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---CS-GLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLET   76 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhC---cc-cceEEEeecCCcccccccccccHhhhcceeccEEEEEec
Confidence            58999999999999999999999999999999999   54 59999983   3  3578999999999998877777643

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=97.98  E-value=2.8e-06  Score=63.95  Aligned_cols=69  Identities=19%  Similarity=0.308  Sum_probs=60.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      .+.+...-|++..|.+.+++||+|+|+.|+.++|   ..++.+.|---+.+++|.-+|++|.|++|-.+.+.
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            5667777899999999999999999999999999   66888888766678899999999999999887765

>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]

Probab=97.70  E-value=0.00025  Score=58.06  Aligned_cols=72  Identities=14%  Similarity=0.234  Sum_probs=64.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      +|.|+..++....|.|..+.....|++..++..|   +....+|++|+|+.+.+..|-.++++++++.|-++...
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            4666665666778999999999999999999999   88999999999999999999999999999999988654

>KOG4495 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription]

Probab=97.64  E-value=7.3e-05  Score=60.64  Aligned_cols=60  Identities=22%  Similarity=0.298  Sum_probs=49.2

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe-CC-eecCCCCChhhhccCC
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-QG-KVLKDVTTLEENKVAE   66 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif-~G-kiL~D~~tL~d~gIk~   66 (364)
                      |.|| ....++.++.+++.||.+||.+++....   -|++.|+|+. .- ..|+|.++|+|||...
T Consensus         5 ~~Vr-R~kttif~da~es~tV~elK~~l~gi~~---~Pvn~qrL~kmd~eqlL~D~ktL~d~gfts   66 (110)
T KOG4495|consen    5 LRVR-RHKTTIFTDAKESSTVFELKRKLEGILK---RPVNEQRLYKMDTEQLLDDGKTLGDCGFTS   66 (110)
T ss_pred             eeee-ecceeEEeecCccccHHHHHHHHHHHHh---CCCcchheeecCHHHHhhccchhhhccccc
Confidence            4444 2344688899999999999999999998   8999999976 33 6789999999998753

>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi

Probab=97.53  E-value=0.00035  Score=57.43  Aligned_cols=60  Identities=17%  Similarity=0.228  Sum_probs=47.2

Q ss_pred             EEEEEeCCC-cEEEEEeC--CCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhh
Q 017906            2 KVFVKTLKG-THFEIEVK--PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN   62 (364)
Q Consensus         2 kI~VKtl~g-k~~~ieV~--~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~   62 (364)
                      .|+||..++ ..+.++|.  .+.||..||+.|....+.+ ..-.++||||+||+|.|...|...
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  7899999999999998533 666789999999999998877664

They contain a characteristic GFDRL sequence motif.

>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs)

Probab=97.10  E-value=0.00087  Score=46.38  Aligned_cols=41  Identities=32%  Similarity=0.330  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      +++.|+.|.+|=- .|+++.+.++|++.-+|.|+||++|+.|
T Consensus         1 ~~~~v~~L~~mFP-~~~~~~I~~~L~~~~~~ve~ai~~LL~~   41 (42)
T PF02845_consen    1 REEMVQQLQEMFP-DLDREVIEAVLQANNGDVEAAIDALLEM   41 (42)
T ss_dssp             CHHHHHHHHHHSS-SS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHCC-CCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            4678999999921 1999999999999999999999999865

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.

>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []

Probab=97.09  E-value=0.0011  Score=52.03  Aligned_cols=71  Identities=18%  Similarity=0.271  Sum_probs=50.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC---CeEEE-eCCeecCCCCChhhhccCCCCEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS---QQMLI-HQGKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~---~qkLi-f~GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      +|+|..-+|+.+.+.+..+.+|.+|...|.+..+.......   ..+|. -+|..|+++.+|.++||.+|+.+++
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            57777655689999999999999999999998873212222   35676 7899999999999999999999986

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.

>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=97.08  E-value=0.0038  Score=48.92  Aligned_cols=68  Identities=22%  Similarity=0.299  Sum_probs=57.3

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCC-eEEE--eCCeecCCC--CChhhhccCCCCEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQ-QMLI--HQGKVLKDV--TTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~-qkLi--f~GkiL~D~--~tL~d~gIk~~s~I~v   72 (364)
                      +|.||..+|+.+...+..++||.+|...|.....   .+... .+|+  |-.+.|.++  ++|+++|+..+.+|+|
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 7786  677888543  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 ....

>KOG4583 consensus Membrane-associated ER protein involved in stress response (contains ubiquitin-like domain) [Posttranslational modification, protein turnover, chaperones]

Probab=97.08  E-value=7.3e-05  Score=72.99  Aligned_cols=76  Identities=20%  Similarity=0.207  Sum_probs=57.2

Q ss_pred             EEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCC--EEEEEEecC
Q 017906            2 KVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS--FVVVMLTKS   77 (364)
Q Consensus         2 kI~VKtl~gk--~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s--~I~v~v~k~   77 (364)
                      .++||..+++  ...|..+..+||++||..++.....+ --..+|||||.||.|.|...|.|+-+|...  ++||+...+
T Consensus        11 ~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPsk-pl~~dqrliYsgkllld~qcl~d~lrkq~k~Hv~hlvcnsk   89 (391)
T KOG4583|consen   11 TLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSK-PLELDQRLIYSGKLLLDHQCLTDWLRKQVKEHVKHLVCNSK   89 (391)
T ss_pred             EEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCC-CchhhHHHHhhccccccchhHHHHHHHHHHHHHHHHhcCCC
Confidence            4667766554  46677888999999999999997644 335689999999999999999998766543  455554443


Q ss_pred             C
Q 017906           78 K   78 (364)
Q Consensus        78 k   78 (364)
                      .
T Consensus        90 ~   90 (391)
T KOG4583|consen   90 E   90 (391)
T ss_pred             C
Confidence            3

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.05  E-value=0.0042  Score=48.75  Aligned_cols=68  Identities=13%  Similarity=0.135  Sum_probs=55.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCChhhhccCCCCEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~D---~~tL~d~gIk~~s~I~v   72 (364)
                      +|.||..+|+.+......++||.+|.+.|....+   ......+|+  |-.|.|.+   +++|.++|+....+|+|
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  67788854   47999999988887765

Present in FAF1 and Shp1p.

>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]

Probab=96.90  E-value=0.0006  Score=72.00  Aligned_cols=43  Identities=40%  Similarity=0.652  Sum_probs=40.2

Q ss_pred             cchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCC
Q 017906          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  215 (364)
Q Consensus       170 ~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP  215 (364)
                      +..|+.|..|++||   |.|.|++.||++..||.+|||||+++-+-
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            46789999999999   99999999999999999999999998855

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=96.85  E-value=0.0091  Score=46.44  Aligned_cols=67  Identities=27%  Similarity=0.339  Sum_probs=53.6

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~D---~~tL~d~gIk~~s~I~v~   73 (364)
                      +|.||..+|+.+......++||.+|.+-|.....   . ....+|+  |-.|.|.|   +.+|+++|+. .+.+++.
T Consensus         4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~---~-~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~-~s~~~~~   75 (77)
T cd01767           4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGP---P-AEPFTLMTSFPRRVLTDLDYELTLQEAGLV-NEVVFQR   75 (77)
T ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCC---C-CCCEEEEeCCCCccCCCCCccCcHHHcCCc-cceEEEE
Confidence            6889999999999999999999999999987654   2 4567776  66788854   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.

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=96.81  E-value=0.0092  Score=47.10  Aligned_cols=67  Identities=22%  Similarity=0.341  Sum_probs=53.8

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC-CCChhhhccCCCCEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENSFVV   71 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~D-~~tL~d~gIk~~s~I~   71 (364)
                      +|.||..+|+.+...+..++||.+|++.|....+.  .......|+  |-.|.|.| +.||+|.|+.+ +.|+
T Consensus         6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~--~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~-s~v~   75 (79)
T cd01770           6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPE--FAARPFTLMTAFPVKELSDESLTLKEANLLN-AVIV   75 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCC--CCCCCEEEecCCCCcccCCCCCcHHHCCCcC-cEEE
Confidence            68899999999999999999999999999987641  223566776  77888854 78999999986 4443

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.

>smart00727 STI1 Heat shock chaperonin-binding motif

Probab=96.75  E-value=0.0016  Score=44.72  Aligned_cols=36  Identities=47%  Similarity=0.652  Sum_probs=31.2

Q ss_pred             HhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHH
Q 017906          278 DFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLI  318 (364)
Q Consensus       278 ~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I  318 (364)
                      ..|+ +|+|+++.+-+++||+++..+++.    ||+++++|
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 999999999999999999998877    99998865

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=96.69  E-value=0.014  Score=45.97  Aligned_cols=67  Identities=19%  Similarity=0.358  Sum_probs=55.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCChhhhccCCCCEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~D---~~tL~d~gIk~~s~I~v   72 (364)
                      +|.||..+|+.+......++||.+|++.|....+   . ....+|+  |-.|.+.+   +++|.++|+....+|+|
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            6889999999998899999999999999986654   2 2567776  77898853   58999999998887776

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.

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.61  E-value=0.0037  Score=57.71  Aligned_cols=62  Identities=26%  Similarity=0.369  Sum_probs=54.6

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         9 ~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      +++.|.+.+...+||.++|.++....|   +.+-.|+++|+|+.|.|...|..|+|..+...+|.
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg---~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlq  216 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEG---VDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQ  216 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhc---cchhhheeeccCCceeccccceeeeecCCCEEEEE
Confidence            466788889999999999999999999   66889999999999999999999999999544443

>COG5417 Uncharacterized small protein [Function unknown]

Probab=96.60  E-value=0.0093  Score=46.43  Aligned_cols=68  Identities=7%  Similarity=0.185  Sum_probs=56.0

Q ss_pred             EEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCC--CCCCCeEEEeCCeecCCCCChhhhccCCCCEEEE
Q 017906            5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDV--YPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         5 VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~--ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      ++..+|++|.+.+....+|+.|-..+.+....+.  ..-..+|+.-++++|.++..|.+|+|.+|+.+.+
T Consensus        11 ~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei   80 (81)
T COG5417          11 FTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI   80 (81)
T ss_pred             eEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence            4677899999999999999999988887765321  2224678889999999999999999999998875

>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=96.53  E-value=0.011  Score=45.04  Aligned_cols=63  Identities=17%  Similarity=0.210  Sum_probs=46.5

Q ss_pred             eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEE
Q 017906            7 TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         7 tl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      ..+++.+.|.|.++.++.++-+..+.++|   +..++-.|.|++|.|+-+..+.-.|+-+|..+.+
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            36788999999999999999999999999   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.

>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]

Probab=96.43  E-value=0.0071  Score=57.31  Aligned_cols=71  Identities=17%  Similarity=0.202  Sum_probs=54.4

Q ss_pred             CEEEEEeCCCc-EEE-EEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEE----EeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGT-HFE-IEVKPEDKVSDVKKNIETVQGSDVYPASQQML----IHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk-~~~-ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkL----if~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |.|+++..++. ..+ .+.....||.|++++|..+..+  +.+..+|+    --+||.|.|+.+|++|+..++.+|+|-
T Consensus         1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k--~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~vK   77 (297)
T KOG1639|consen    1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLK--ITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIYVK   77 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhc--cCccchhheeeccCCCccccchhHHHHhccCCCCEEEEe
Confidence            78999877662 333 6777889999999888877653  55544444    347999999999999999999877663

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=96.41  E-value=0.0038  Score=63.10  Aligned_cols=40  Identities=33%  Similarity=0.493  Sum_probs=37.0

Q ss_pred             cchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       170 ~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      ++-.++|++|++||   |+|..|+.|-.|+..|=+.|+.||+.
T Consensus       335 ~eE~~AIeRL~~LG---F~r~~viqaY~ACdKNEelAAn~Lf~  374 (378)
T TIGR00601       335 PEEKEAIERLCALG---FDRGLVIQAYFACDKNEELAANYLLS  374 (378)
T ss_pred             HHHHHHHHHHHHcC---CCHHHHHHHHHhcCCcHHHHHHHHHh
Confidence            34467999999999   99999999999999999999999985

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).

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=96.33  E-value=0.033  Score=44.40  Aligned_cols=69  Identities=19%  Similarity=0.338  Sum_probs=59.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC---CCCChhhhccCCCCEEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~---D~~tL~d~gIk~~s~I~v~v   74 (364)
                      +|.||..+|+.+.-....++++.+|...|.. .|   .+.+..+|+  |--|.|.   .+.+|+++|+....+|+|--
T Consensus         7 ~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g---~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq~   80 (82)
T cd01773           7 RLMLRYPDGKREQIALPEQAKLLALVRHVQS-KG---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE   80 (82)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cC---CCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEec
Confidence            6899999999999999999999999999988 56   678899997  6677773   35899999999999888743

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.

>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.32  E-value=0.0046  Score=56.10  Aligned_cols=46  Identities=26%  Similarity=0.296  Sum_probs=43.6

Q ss_pred             cccCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          165 NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       165 ~l~~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .+..+..+.+.|.+|.+||   |+|+.++.+|+-...|-.+|.|+|++|
T Consensus       155 ~~~~~~~~~~~v~~l~~mG---f~~~~~i~~L~~~~w~~~~a~~~~~s~  200 (200)
T KOG0418|consen  155 RLPDDPWDKKKVDSLIEMG---FSELEAILVLSGSDWNLADATEQLLSG  200 (200)
T ss_pred             CCCCCchhHHHHHHHHHhc---ccHHHHHHHhhccccchhhhhHhhccC
Confidence            3778899999999999999   999999999999999999999999987

>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]

Probab=96.23  E-value=0.018  Score=46.52  Aligned_cols=68  Identities=16%  Similarity=0.192  Sum_probs=59.1

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |.|...+|..+.+.|..+.+...|-+..+...|+   ..+.+|++|+|+.++-++|-.|+++.+++.|.++
T Consensus        27 Lkvv~qd~telfFkiKktT~f~klm~af~~rqGK---~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav   94 (103)
T COG5227          27 LKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGK---NMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAV   94 (103)
T ss_pred             eEEecCCCCEEEEEEeccchHHHHHHHHHHHhCc---CcceeEEEEcceecCCCCChhhcCCccchHHHHH
Confidence            4455556778889999999999999999999994   4789999999999999999999999999877654

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=96.17  E-value=0.037  Score=49.50  Aligned_cols=76  Identities=17%  Similarity=0.221  Sum_probs=54.7

Q ss_pred             CEEEEEeCCC----cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCC-eEEEe-CCeec--CCCCChhhhccCCCC----
Q 017906            1 MKVFVKTLKG----THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQ-QMLIH-QGKVL--KDVTTLEENKVAENS----   68 (364)
Q Consensus         1 MkI~VKtl~g----k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~-qkLif-~GkiL--~D~~tL~d~gIk~~s----   68 (364)
                      |+|+|+++.|    .++.+.+..+.||.+|+.+|....+   ++... ..|.+ .++.|  .++..+.++.-...+    
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    5889999999999999999999999   66666 33444 34444  456677777544432    


Q ss_pred             EEEEEEecCCC
Q 017906           69 FVVVMLTKSKV   79 (364)
Q Consensus        69 ~I~v~v~k~k~   79 (364)
                      +|.|+++....
T Consensus        78 ~l~l~~rl~GG   88 (162)
T PF13019_consen   78 TLRLSLRLRGG   88 (162)
T ss_pred             EEEEEEeccCC
Confidence            45555555443

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=95.89  E-value=0.064  Score=42.95  Aligned_cols=68  Identities=16%  Similarity=0.170  Sum_probs=55.3

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC--CeecC--------CCCChhhhccCCCCEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GKVLK--------DVTTLEENKVAENSFVV   71 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~--GkiL~--------D~~tL~d~gIk~~s~I~   71 (364)
                      +|.||..+|+.+.-....++||.+|..-|.. .+   ..++...|+++  -|.|.        .+.||++.||....+|+
T Consensus         6 ~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~---~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L~   81 (85)
T cd01774           6 KIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LK---ETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLF   81 (85)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CC---CCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEE
Confidence            6899999999998899999999999999964 44   45678888854  47775        36799999999877776


Q ss_pred             EE
Q 017906           72 VM   73 (364)
Q Consensus        72 v~   73 (364)
                      |-
T Consensus        82 V~   83 (85)
T cd01774          82 VQ   83 (85)
T ss_pred             Ee
Confidence            63

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.

>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs)

Probab=95.85  E-value=0.023  Score=39.33  Aligned_cols=39  Identities=26%  Similarity=0.406  Sum_probs=35.7

Q ss_pred             hHHHHHHHHHc--CCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .++.|..|.+|  .   ++++.|++.|++.-+|.|+|++.|+.|
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            46789999999  5   899999999999999999999999976

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)

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=95.67  E-value=0.092  Score=41.54  Aligned_cols=67  Identities=21%  Similarity=0.261  Sum_probs=57.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC---CCCChhhhccCCCCEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~---D~~tL~d~gIk~~s~I~v   72 (364)
                      +|.||..+|+.+.-....++++.+|...|... |   ++....+|+  |--|.+.   .+.+|++.|+....+|+|
T Consensus         6 ~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~---~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~V   77 (80)
T cd01771           6 KLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-G---YPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLIL   77 (80)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-C---CCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEE
Confidence            68899999999988999999999999999864 6   667788886  7778874   257999999998888876

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.

>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]

Probab=94.81  E-value=0.072  Score=49.31  Aligned_cols=70  Identities=19%  Similarity=0.221  Sum_probs=53.7

Q ss_pred             EEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEE-EeCC-----eecC-CCCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQG-----KVLK-DVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkL-if~G-----kiL~-D~~tL~d~gIk~~s~I~v~   73 (364)
                      +|.|.+...+ .+......+.||.+||.|++..+|   .+++.++| +|.|     ..|. ++..|..|+..+|..||++
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            4555543322 234457789999999999999999   88999998 4665     2454 5789999999999999988


Q ss_pred             E
Q 017906           74 L   74 (364)
Q Consensus        74 v   74 (364)
                      -
T Consensus        80 D   80 (234)
T KOG3206|consen   80 D   80 (234)
T ss_pred             e
Confidence            5

>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]

Probab=94.56  E-value=0.044  Score=53.94  Aligned_cols=40  Identities=30%  Similarity=0.429  Sum_probs=37.2

Q ss_pred             chHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      +-.++|.+|+.||   |+|.-|+.|--|+..|=+-|.+||+.-
T Consensus       297 ee~eAIeRL~alG---F~ralViqayfACdKNEelAAN~Ll~~  336 (340)
T KOG0011|consen  297 EEKEAIERLEALG---FPRALVIQAYFACDKNEELAANYLLSH  336 (340)
T ss_pred             HHHHHHHHHHHhC---CcHHHHHHHHHhcCccHHHHHHHHHhh
Confidence            4467999999999   999999999999999999999999864

>PF15044 CLU_N: Mitochondrial function, CLU-N-term

Probab=94.47  E-value=0.065  Score=42.03  Aligned_cols=56  Identities=23%  Similarity=0.351  Sum_probs=46.3

Q ss_pred             eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhh-ccCCCCEEEEEE
Q 017906           17 VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN-KVAENSFVVVML   74 (364)
Q Consensus        17 V~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~-gIk~~s~I~v~v   74 (364)
                      |.++++|.+||+.|......  .......|.|+|+.|+|...|+++ |++++..|.|+.
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            56789999999999987552  456788999999999998889888 588888888763

>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=93.76  E-value=0.07  Score=39.28  Aligned_cols=23  Identities=35%  Similarity=0.679  Sum_probs=19.5

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHH
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRA  198 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrA  198 (364)
                      ...|+++++||   |+|+.|+.|||.
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.

>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]

Probab=93.36  E-value=0.12  Score=51.63  Aligned_cols=69  Identities=14%  Similarity=0.141  Sum_probs=60.1

Q ss_pred             CEEEEEeC--CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCC--CCChhhhccCCCCEEEE
Q 017906            1 MKVFVKTL--KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKD--VTTLEENKVAENSFVVV   72 (364)
Q Consensus         1 MkI~VKtl--~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D--~~tL~d~gIk~~s~I~v   72 (364)
                      |.++|.+.  ..++|.|+|..+-....|+..+....|   +..+..-|+|+++.|.+  ...|..||++.+++|.+
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            67777665  667899999999999999999999999   88999999999999965  46799999999988754

>PRK06437 hypothetical protein; Provisional

Probab=93.20  E-value=0.63  Score=35.42  Aligned_cols=54  Identities=22%  Similarity=0.327  Sum_probs=43.2

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         9 ~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      .++...++++...||.+|-+.    .+   ++.....+..+|+++.     .++-|++|+.|.++-
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            445677888888999988765    47   7788899999999997     555688899988763

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=93.11  E-value=0.49  Score=35.17  Aligned_cols=55  Identities=20%  Similarity=0.305  Sum_probs=39.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|.   |+.  ++++.+.|+.+||+++..         +.-.+||+|-..+++.     -++++|.|+++-
T Consensus         1 M~I~vN---~k~--~~~~~~~tl~~lr~~~k~---------~~DI~I~NGF~~~~d~-----~L~e~D~v~~Ik   55 (57)
T PF14453_consen    1 MKIKVN---EKE--IETEENTTLFELRKESKP---------DADIVILNGFPTKEDI-----ELKEGDEVFLIK   55 (57)
T ss_pred             CEEEEC---CEE--EEcCCCcCHHHHHHhhCC---------CCCEEEEcCcccCCcc-----ccCCCCEEEEEe
Confidence            667664   554  677788899999987433         2336799999887754     467789998864

>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=93.01  E-value=0.15  Score=40.90  Aligned_cols=36  Identities=28%  Similarity=0.482  Sum_probs=31.6

Q ss_pred             HHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCC
Q 017906          176 VQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  214 (364)
Q Consensus       176 V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GI  214 (364)
                      |+.+.+.|   |+++.|.+||+++-.++..|..|+++++
T Consensus         1 i~~~~~~g---~~~~~v~~aL~~tSgd~~~a~~~vl~~l   36 (87)
T PF11626_consen    1 IKHYEELG---YSREFVTHALYATSGDPELARRFVLNFL   36 (87)
T ss_dssp             -HHHHHHT---B-HHHHHHHHHHTTTBHHHHHHHHHHCH
T ss_pred             CchHHHhC---CCHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            56788999   9999999999999999999999999883

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.

>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain

Probab=92.76  E-value=0.65  Score=35.73  Aligned_cols=68  Identities=21%  Similarity=0.184  Sum_probs=50.6

Q ss_pred             EEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe----CC--eecCCCCChhhhccCCCCEEEEEE
Q 017906            5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH----QG--KVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         5 VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif----~G--kiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+.++|...+++|+.+.|+.+|=..|+...+.  ...+-.-|.|    +|  .-|+.+++|.+...+......+..
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l--~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~~~~~~~l~f   74 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGL--KEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKKNNPPFTLYF   74 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTT--SSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBTSSSSEEEEE
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCC--CCccEEEEEEeecCCCcceeccCcccHHHHcCCCCCCEEEEE
Confidence            67789999999999999999999999999993  3455667777    23  346888999998777334333333

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 ....

>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=92.67  E-value=0.16  Score=52.47  Aligned_cols=42  Identities=36%  Similarity=0.522  Sum_probs=38.1

Q ss_pred             CcchHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      -..|..-.+++-+||   | +|+.-++||+|.+.+.++|||-|+.+
T Consensus       451 e~r~q~QLeQL~~MG---F~nre~nlqAL~atgGdi~aAverll~s  493 (493)
T KOG0010|consen  451 EERYQTQLEQLNDMG---FLDREANLQALRATGGDINAAVERLLGS  493 (493)
T ss_pred             hHHHHHHHHHHHhcC---CccHHHHHHHHHHhcCcHHHHHHHHhcC
Confidence            356788899999999   9 99999999999999999999999853

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=92.43  E-value=0.52  Score=36.82  Aligned_cols=66  Identities=11%  Similarity=0.160  Sum_probs=45.6

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC--CCeEEEeCCeecCCCCChhhhccCCCCEEE
Q 017906            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGSDVYPA--SQQMLIHQGKVLKDVTTLEENKVAENSFVV   71 (364)
Q Consensus         1 MkI~VKtl~------g-k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~--~~qkLif~GkiL~D~~tL~d~gIk~~s~I~   71 (364)
                      |+|+|+.+.      | ....+++....||.+|++.|......  +..  ....+..+|+...++     +-|++|+.|.
T Consensus         2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~--l~~~~~~~~vavN~~~v~~~-----~~l~dgDeVa   74 (82)
T PLN02799          2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPS--LEEVRSCCVLALNEEYTTES-----AALKDGDELA   74 (82)
T ss_pred             eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChh--HHHHhhCcEEEECCEEcCCC-----cCcCCCCEEE
Confidence            778888653      4 45677888889999999999876420  111  223466788887533     4578899998


Q ss_pred             EE
Q 017906           72 VM   73 (364)
Q Consensus        72 v~   73 (364)
                      ++
T Consensus        75 i~   76 (82)
T PLN02799         75 II   76 (82)
T ss_pred             Ee
Confidence            86

>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=92.09  E-value=0.39  Score=35.88  Aligned_cols=41  Identities=29%  Similarity=0.370  Sum_probs=37.3

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .-++|+.|-|.-|+ +..+++-..|+-++++||.||+-||+-
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            46799999998766 899999999999999999999999963

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=91.94  E-value=0.77  Score=35.25  Aligned_cols=57  Identities=11%  Similarity=0.135  Sum_probs=41.5

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCC-CCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGS-DVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~-~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      ...++++...||.+|.+.+...++. .........+..+|+....     ++-|++|+.|.++
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~~-----~~~l~~gD~v~i~   74 (80)
T cd00754          17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVRL-----DTPLKDGDEVAII   74 (80)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcCC-----CcccCCCCEEEEe
Confidence            4667887789999999999987541 0012345667789998873     4568889999887

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.

>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=91.82  E-value=0.23  Score=35.15  Aligned_cols=37  Identities=22%  Similarity=0.463  Sum_probs=29.8

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      .++.+.-|+.+|   |.+.++.+|++....+++.-+|.++
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            578999999999   9999999999998756666677665

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=91.49  E-value=1.3  Score=33.93  Aligned_cols=53  Identities=26%  Similarity=0.458  Sum_probs=40.7

Q ss_pred             CCc--EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            9 KGT--HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         9 ~gk--~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      +|+  ...++++...||.+|.+.+    +   ++.....+..+|+++..     +.-+++|+.|.++
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            455  5678888889999998765    5   66677788899999854     4557889988876

>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=91.36  E-value=0.21  Score=51.19  Aligned_cols=58  Identities=21%  Similarity=0.166  Sum_probs=49.6

Q ss_pred             EEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906           15 IEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus        15 ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      ++.....|-.+|..+|.++.|   ++-...|.|.+||+|.-.+||.+-|++.+..+.|++.
T Consensus        54 ~k~sL~i~Gselqa~iakklg---i~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~~  111 (568)
T KOG2561|consen   54 KKCSLHITGSELQALIAKKLG---IKENHVKCIINGKILSCRKTLAEQGLKINQELMVAVG  111 (568)
T ss_pred             hhcccccccHHHHHHHHHHcC---CchhhhheeeccceeecccchhhhhhhhhhHHHHHhc
Confidence            455566788899999999999   8888899999999999999999999988776666554

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=90.91  E-value=0.95  Score=33.87  Aligned_cols=60  Identities=13%  Similarity=0.258  Sum_probs=42.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|   +|+.+.+  + ..||.+|.+.+    +   +......+-++++++. .....+.-+++||.|.++-
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            56665   4777776  3 35899988764    5   5566677889999986 2334566789999998873

>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=89.85  E-value=1.1  Score=35.69  Aligned_cols=37  Identities=16%  Similarity=0.169  Sum_probs=34.4

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCe
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK   51 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~Gk   51 (364)
                      ++.|.|.++.+..+|+.+|.++.+   ++.+..+|.|+..
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            899999999999999999999999   9899999999653

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=89.56  E-value=1.2  Score=35.87  Aligned_cols=74  Identities=18%  Similarity=0.177  Sum_probs=50.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC----Ceec-CCCCChhhh-c---cCCCCEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ----GKVL-KDVTTLEEN-K---VAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~----GkiL-~D~~tL~d~-g---Ik~~s~I~v   72 (364)
                      .+++|+.+|+.+.|.+.+++.+.+|+..|..+.|.+........|.|-    -++| .-+.-|.+| .   .....+|.+
T Consensus         2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D~DL~e~v~iar~~g~~~v~L   81 (86)
T cd06409           2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSDSDLVAAVLVARSAGLKKLDL   81 (86)
T ss_pred             cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEeccchHHHHHHHHHHcCCCEEEE
Confidence            468899999999999999999999999999999933122257777773    2333 333444444 2   233445655


Q ss_pred             EEe
Q 017906           73 MLT   75 (364)
Q Consensus        73 ~v~   75 (364)
                      ++.
T Consensus        82 ~v~   84 (86)
T cd06409          82 HLH   84 (86)
T ss_pred             EEe
Confidence            553

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

>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=88.85  E-value=0.52  Score=48.45  Aligned_cols=42  Identities=21%  Similarity=0.389  Sum_probs=38.6

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCCC
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~~  217 (364)
                      ...|.+|+.||   |++-..+.||++.-||-|.|.++|+--++..
T Consensus       430 ~~~la~Lv~mG---F~e~~A~~ALe~~gnn~~~a~~~L~~s~~n~  471 (568)
T KOG2561|consen  430 GISLAELVSMG---FEEGKARSALEAGGNNEDTAQRLLSASVANE  471 (568)
T ss_pred             hhhHHHHHHhc---cccchHHHHHHhcCCcHHHHHHHHHHhCCCC
Confidence            45799999999   9999999999999999999999999888754

>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=88.53  E-value=1.3  Score=30.66  Aligned_cols=37  Identities=24%  Similarity=0.397  Sum_probs=30.5

Q ss_pred             HHHHHHHHHc-CCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          173 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       173 e~~V~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      ++.|.+.|+. |   -+++.++.-|+.+.+|.++||+.-+.
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            4678899986 6   79999999999999999999986653

>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=88.36  E-value=2.9  Score=33.18  Aligned_cols=71  Identities=14%  Similarity=0.147  Sum_probs=48.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCeEEEeCCe-----ecCCCCChhh----hccCCCCEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQGK-----VLKDVTTLEE----NKVAENSFV   70 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~-~~qkLif~Gk-----iL~D~~tL~d----~gIk~~s~I   70 (364)
                      |+|++. .+|..+.|.+.++.+..+|+.+|.++++   +.. ..+.|-|..-     .|..+.-|.+    |......+|
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 4677899999999999999999999998   543 5677777432     1333334444    344455667


Q ss_pred             EEEEe
Q 017906           71 VVMLT   75 (364)
Q Consensus        71 ~v~v~   75 (364)
                      .+++.
T Consensus        77 ~l~v~   81 (82)
T cd06407          77 RLLVH   81 (82)
T ss_pred             EEEee
Confidence            66653

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

>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=88.01  E-value=0.15  Score=49.93  Aligned_cols=60  Identities=25%  Similarity=0.390  Sum_probs=0.0

Q ss_pred             EEEEEeCCCcEEEEEeC---C--CCcHHHHHHHHHH----------HhCCCCCCCCCeE-----EEeCCeecCCCCChhh
Q 017906            2 KVFVKTLKGTHFEIEVK---P--EDKVSDVKKNIET----------VQGSDVYPASQQM-----LIHQGKVLKDVTTLEE   61 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~---~--s~TV~dLK~kI~~----------~~g~~~ip~~~qk-----Lif~GkiL~D~~tL~d   61 (364)
                      .|++|.+.+-.+.|.+.   +  +.+|.+||..++.          +.+   +|.+++|     |+|+.|.+.|.++|.+
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            46667666655544332   2  5789999999999          777   9999999     9999999999999988


Q ss_pred             hcc
Q 017906           62 NKV   64 (364)
Q Consensus        62 ~gI   64 (364)
                      +.-
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.

>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function

Probab=86.86  E-value=3  Score=31.84  Aligned_cols=67  Identities=16%  Similarity=0.209  Sum_probs=52.8

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE-eCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-HQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         9 ~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi-f~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      +|+...++.+....+.-+..+--+..|...-|++...|- -+|.+|+-++.++|||+.++-++++.++
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLK   71 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLK   71 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEee
Confidence            578888888888888888777777766333567776664 5788999999999999999998887654

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=86.26  E-value=2.7  Score=31.57  Aligned_cols=60  Identities=17%  Similarity=0.255  Sum_probs=42.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|   +|+.+.+  ....||.+|-+.    .+   ++.....+.+++.++..+. ...+ +++||.|-++-
T Consensus         1 m~i~v---NG~~~~~--~~~~tl~~ll~~----l~---~~~~~vav~~N~~iv~r~~-~~~~-L~~gD~ieIv~   60 (65)
T PRK05863          1 MIVVV---NEEQVEV--DEQTTVAALLDS----LG---FPEKGIAVAVDWSVLPRSD-WATK-LRDGARLEVVT   60 (65)
T ss_pred             CEEEE---CCEEEEc--CCCCcHHHHHHH----cC---CCCCcEEEEECCcCcChhH-hhhh-cCCCCEEEEEe
Confidence            56665   4776555  467788877664    46   7788999999999885422 2245 89999998864

>smart00295 B41 Band 4

Probab=86.07  E-value=6.8  Score=34.97  Aligned_cols=61  Identities=21%  Similarity=0.214  Sum_probs=46.4

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCeEEEeC---C---eecCCCCChhhhccC
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQ---G---KVLKDVTTLEENKVA   65 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~-~~qkLif~---G---kiL~D~~tL~d~gIk   65 (364)
                      .|.|..++|....|.++.+.||.+|...|+.+.|   +.. ...-|.+-   +   .-|+...+|.+...+
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            5788889999999999999999999999999999   532 33344431   2   346667788877655

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.

>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A

Probab=85.88  E-value=4.6  Score=32.69  Aligned_cols=62  Identities=13%  Similarity=0.198  Sum_probs=42.0

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--e--CCe-ecCC-CCChhhhccCCCCEEEEEEec
Q 017906           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--H--QGK-VLKD-VTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus        11 k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f--~Gk-iL~D-~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      ..++..+...+||..+++.+.+.+.   + ....||-  |  ++. .|.+ +.||.|.+|.+|-.|++=.+.
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            3677788999999999999999998   8 6677883  2  222 3644 679999999999877765544

>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer

Probab=85.41  E-value=2  Score=32.57  Aligned_cols=60  Identities=15%  Similarity=0.150  Sum_probs=47.0

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      ...+.+....||.+|.+.+....+.. .......+..+|+.+.+  ...+.-+++++.|.++-
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            66788899999999999999886411 12367888899999987  35666788999998873

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 ....

>PRK05659 sulfur carrier protein ThiS; Validated

Probab=85.37  E-value=3.9  Score=30.39  Aligned_cols=61  Identities=13%  Similarity=0.251  Sum_probs=43.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|   +|+.+  ++....||.+|-+.    .+   ++.....+.++|+++.-. ...+.-+++|+.|-++-
T Consensus         1 m~i~v---NG~~~--~~~~~~tl~~lL~~----l~---~~~~~vav~vNg~iv~r~-~~~~~~l~~gD~vei~~   61 (66)
T PRK05659          1 MNIQL---NGEPR--ELPDGESVAALLAR----EG---LAGRRVAVEVNGEIVPRS-QHASTALREGDVVEIVH   61 (66)
T ss_pred             CEEEE---CCeEE--EcCCCCCHHHHHHh----cC---CCCCeEEEEECCeEeCHH-HcCcccCCCCCEEEEEE
Confidence            55555   47755  55667898888765    46   778888889999888633 23344588999988764

>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal

Probab=84.71  E-value=5.3  Score=30.94  Aligned_cols=58  Identities=19%  Similarity=0.277  Sum_probs=41.9

Q ss_pred             CCc-EEEEEeCCC-CcHHHHHHHHHHHhCCCCCC--CCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            9 KGT-HFEIEVKPE-DKVSDVKKNIETVQGSDVYP--ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         9 ~gk-~~~ieV~~s-~TV~dLK~kI~~~~g~~~ip--~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      .|+ ...+++..+ .||.+|+..+....+.  +-  .....+..+|+.+.+     +.-|++|+.|.++
T Consensus        13 ~g~~~~~~~~~~~~~tv~~L~~~L~~~~p~--l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~   74 (80)
T TIGR01682        13 AGTDEETLELPDESTTVGELKEHLAKEGPE--LAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFI   74 (80)
T ss_pred             hCCCeEEEECCCCCcCHHHHHHHHHHhCch--hhhhccceEEEECCEEcCC-----CcCcCCCCEEEEe
Confidence            344 357888876 8999999999988641  11  134567789988875     4568889999887

The C-terminal Gly-Gly of this model is critical to function.

>smart00666 PB1 PB1 domain

Probab=84.28  E-value=4.8  Score=30.97  Aligned_cols=45  Identities=16%  Similarity=0.178  Sum_probs=37.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~G   50 (364)
                      +|.|+. ++..+.+.|..+.|..+|+.+|..+++   +.....+|-|..
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            456664 667888999999999999999999998   656788888864

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.

>PF11620 GABP-alpha: GA-binding protein alpha chain; InterPro: IPR024668 GA-binding protein alpha is a transcription factor capable of interacting with purine rich repeats (GA repeats)

Probab=83.57  E-value=3.2  Score=33.33  Aligned_cols=62  Identities=18%  Similarity=0.137  Sum_probs=43.5

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      .+...++-...+..||..++.+.+   +.-+.-.+......|+.+++|-+-+|+-...|.+.+--
T Consensus         4 vI~q~mDI~epl~~Lk~lLe~Rl~---~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQi   65 (88)
T PF11620_consen    4 VIMQHMDIREPLSTLKKLLERRLG---ISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQI   65 (88)
T ss_dssp             EEEEEEESSSBGGGHHHHSHHHH----S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEEE
T ss_pred             eEEEEEecCCcHHHHHHHHHHhhC---CCcCCCeEEeccceecCCccHHHhhccccCEEEEEEEE
Confidence            345567777899999999999999   66778888888878999999999999998888887654

This N-terminal domain found in the transcription factor GABP alpha consists of a five-stranded beta-sheet crossed by a distorted helix and has been termed OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300 [].; PDB: 2JUO_A.

>PRK08053 sulfur carrier protein ThiS; Provisional

Probab=83.16  E-value=6.6  Score=29.47  Aligned_cols=61  Identities=7%  Similarity=0.176  Sum_probs=42.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|.   |+.+.+  ....||.+|.+.    .+   +......+-++++++.. ....++-+++|+.|.++-
T Consensus         1 m~i~vN---g~~~~~--~~~~tl~~ll~~----l~---~~~~~vaVavN~~iv~r-~~w~~~~L~~gD~Ieii~   61 (66)
T PRK08053          1 MQILFN---DQPMQC--AAGQTVHELLEQ----LN---QLQPGAALAINQQIIPR-EQWAQHIVQDGDQILLFQ   61 (66)
T ss_pred             CEEEEC---CeEEEc--CCCCCHHHHHHH----cC---CCCCcEEEEECCEEeCh-HHcCccccCCCCEEEEEE
Confidence            666664   776555  567789988865    34   44566788899999852 223444588999988763

>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]

Probab=82.90  E-value=1.7  Score=45.56  Aligned_cols=40  Identities=30%  Similarity=0.580  Sum_probs=35.5

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCCC
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIP  215 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GIP  215 (364)
                      ...|.+|++||   |+.+.+.|||-+.-| +-+.|+.||.-.+-
T Consensus       559 qs~I~qL~~mG---fp~~~~~rAL~~tgNqDaEsAMNWLFqHMd  599 (749)
T COG5207         559 QSLIRQLVDMG---FPEEDAARALGITGNQDAESAMNWLFQHMD  599 (749)
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHhhccCcchHHHHHHHHhhcc
Confidence            56899999999   999999999998776 68899999997753

>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]

Probab=82.33  E-value=1.9  Score=46.45  Aligned_cols=42  Identities=24%  Similarity=0.408  Sum_probs=36.9

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHH-cCChHHHHHHHHhCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAA-YNNPERAVEYLYSGIPE  216 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAa-fnNpdRAvEyL~~GIP~  216 (364)
                      .+..|.+|++||   |+.+.|.|||... ..+-+-|..||+.-+-+
T Consensus       571 d~s~i~qL~~MG---Fp~eac~rAly~tgN~~aEaA~NWl~~HMdD  613 (763)
T KOG0944|consen  571 DRSVISQLVEMG---FPEEACRRALYYTGNSGAEAASNWLMEHMDD  613 (763)
T ss_pred             hHHHHHHHHHcC---CCHHHHHHHHhhhcCccHHHHHHHHHHhccC
Confidence            467899999999   9999999999998 55789999999988643

>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=81.94  E-value=5.9  Score=31.92  Aligned_cols=46  Identities=17%  Similarity=0.262  Sum_probs=36.5

Q ss_pred             EEEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCe
Q 017906            2 KVFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK   51 (364)
Q Consensus         2 kI~VKtl-~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~Gk   51 (364)
                      +|+||.. .|..+.|.|.++.+..+|..+|.++++   +. ..++|-|...
T Consensus         2 ~ikVKv~~~~Dv~~i~v~~~i~f~dL~~kIrdkf~---~~-~~~~iKykDE   48 (86)
T cd06408           2 KIRVKVHAQDDTRYIMIGPDTGFADFEDKIRDKFG---FK-RRLKIKMKDD   48 (86)
T ss_pred             cEEEEEEecCcEEEEEcCCCCCHHHHHHHHHHHhC---CC-CceEEEEEcC
Confidence            3555554 678999999999999999999999999   63 5667766554

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

>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown

Probab=81.88  E-value=3.6  Score=35.23  Aligned_cols=60  Identities=17%  Similarity=0.174  Sum_probs=44.1

Q ss_pred             EeCC-CCcHHHHHHHHHHHhCCC-------CCCCCCeEEEeC-----------------Ceec---CCCCChhhhccCCC
Q 017906           16 EVKP-EDKVSDVKKNIETVQGSD-------VYPASQQMLIHQ-----------------GKVL---KDVTTLEENKVAEN   67 (364)
Q Consensus        16 eV~~-s~TV~dLK~kI~~~~g~~-------~ip~~~qkLif~-----------------GkiL---~D~~tL~d~gIk~~   67 (364)
                      .|+. +.||.+|++.|.+.....       .+.-+.+||++.                 ..+|   +++++|.+|||.+.
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 899999999998775311       134456677653                 2577   77899999999999


Q ss_pred             CEEEEEEe
Q 017906           68 SFVVVMLT   75 (364)
Q Consensus        68 s~I~v~v~   75 (364)
                      ..|-++..
T Consensus       101 TEiSfF~~  108 (122)
T PF10209_consen  101 TEISFFNM  108 (122)
T ss_pred             ceeeeeCH
Confidence            88887654

>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins

Probab=81.83  E-value=0.81  Score=35.97  Aligned_cols=27  Identities=33%  Similarity=0.434  Sum_probs=23.7

Q ss_pred             C-CHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          187 W-DRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       187 f-~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      . ++.+++.||...|+|+++||.||++-
T Consensus        43 ~~~e~~i~eal~~~~fDvekAl~~Ll~~   70 (79)
T PF08938_consen   43 VPPEEQIKEALWHYYFDVEKALDYLLSK   70 (79)
T ss_dssp             C--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence            5 89999999999999999999999987

; PDB: 1UFZ_A 3IZQ_1.

>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]

Probab=81.65  E-value=2.2  Score=43.10  Aligned_cols=65  Identities=23%  Similarity=0.354  Sum_probs=52.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC-CCChhhhccCCCC
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENS   68 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~D-~~tL~d~gIk~~s   68 (364)
                      .|-||..+|+.+...++.+.||.||+..|......  .....+-|+  |--|.|.| +.||++-|+.+..
T Consensus       307 sIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~--~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsv  374 (380)
T KOG2086|consen  307 SIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPG--DSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSV  374 (380)
T ss_pred             eEEEEecCCceeeeeccCcccHHHHHHHHHhcCCC--CcCCceeeeecCCCcccCCcchhHHhccchhhh
Confidence            47889899999999999999999999999998762  333455555  66788855 7899999998743

>PF11069 DUF2870: Protein of unknown function (DUF2870); InterPro: IPR021298 This is a eukaryotic family of proteins with unknown function

Probab=81.65  E-value=2.2  Score=35.12  Aligned_cols=33  Identities=27%  Similarity=0.309  Sum_probs=23.0

Q ss_pred             EEEeCCeecCCCCChhhh-ccCCCCEEEEEEecC
Q 017906           45 MLIHQGKVLKDVTTLEEN-KVAENSFVVVMLTKS   77 (364)
Q Consensus        45 kLif~GkiL~D~~tL~d~-gIk~~s~I~v~v~k~   77 (364)
                      .|-|.||.|..+++|++| |-.+...|+|-+.++
T Consensus         3 ~LW~aGK~l~~~k~l~dy~GkNEKtKiivKl~~~   36 (98)
T PF11069_consen    3 QLWWAGKELQRGKKLSDYIGKNEKTKIIVKLQKR   36 (98)
T ss_pred             eEEeccccccCCCcHHHhcCCCcceeEEEEeccC
Confidence            578999999999999999 223344555444443

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=81.42  E-value=10  Score=29.77  Aligned_cols=58  Identities=12%  Similarity=0.268  Sum_probs=40.2

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCC---CCCC-----CCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGS---DVYP-----ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~---~~ip-----~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      ...++++ ..||.+|.+.|.++++.   ..+.     .....+..+|+..+++..   .-|++|+.|.++
T Consensus        17 ~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~   82 (88)
T TIGR01687        17 SEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIF   82 (88)
T ss_pred             eEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEe
Confidence            5677886 89999999999988541   0011     123566788888765432   458899999887

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.

>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases

Probab=80.96  E-value=4.7  Score=31.27  Aligned_cols=45  Identities=20%  Similarity=0.158  Sum_probs=38.1

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~G   50 (364)
                      +.|-..+|+.-.+.|.+..||.++-.++.++.|   +.++...|.+.|
T Consensus         2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~---l~~~~~~v~~~~   46 (72)
T cd01760           2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRG---LNPECCDVFLLG   46 (72)
T ss_pred             EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcC---CCHHHEEEEEec
Confidence            456677899999999999999999999999999   777777766543

The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	364
1oqy_A	368	Structure Of The Dna Repair Protein Hhr23a Length =		3e-20
1uel_A	95	Solution Structure Of Ubiquitin-Like Domain Of Hhr2		8e-12
1p1a_A	85	Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Le		1e-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		3e-09
2wyq_A	85	The Crystal Structure Of The Ubiquitin-Like (Ubl) D		5e-08
1p98_A	78	High-Resolution Nmr Structure Of The Ubl-Domain Of		8e-08
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		1e-06
1tp4_A	97	Solution Structure Of The Xpc Binding Domain Of Hhr		1e-06
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		2e-06
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		3e-06
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		3e-06
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		4e-06
3jvz_X	81	E2~ubiquitin-Hect Length = 81		4e-06
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		5e-06
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		5e-06
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		5e-06
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		6e-06
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		6e-06
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		6e-06
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		6e-06
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		6e-06
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		7e-06
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		7e-06
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		7e-06
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		7e-06
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		7e-06
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		7e-06
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		7e-06
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		8e-06
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		8e-06
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		8e-06
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		8e-06
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		8e-06
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		9e-06
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		9e-06
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		9e-06
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		9e-06
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		1e-05
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		1e-05
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		1e-05
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		1e-05
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		1e-05
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		1e-05
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		1e-05
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		1e-05
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-05
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		2e-05
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		2e-05
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		2e-05
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		2e-05
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-05
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		2e-05
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-05
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		2e-05
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		3e-05
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		3e-05
1ndd_B	76	Structure Of Nedd8 Length = 76		3e-05
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		3e-05
3h7s_A	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		3e-05
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		3e-05
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		3e-05
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		3e-05
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		3e-05
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		4e-05
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		4e-05
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		4e-05
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		5e-05
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		5e-05
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		5e-05
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		5e-05
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		6e-05
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		1e-04
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-04
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		1e-04
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		1e-04
4hk2_A	78	U7ub25.2540 Length = 78		1e-04
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		2e-04
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		3e-04
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		3e-04
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		6e-04
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		8e-04
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		8e-04

>pdb|1OQY|A Chain A, Structure Of The Dna Repair Protein Hhr23a Length = 368

Iteration: 1
 Score = 96.3 bits (238), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 76/215 (35%), Positives = 107/215 (49%), Gaps = 55/215 (25%)
Query: 162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI-----PE 216
           AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GI     PE
Sbjct: 158 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIPGSPEPE 214
Query: 217 QTAVPPVARXXXXXXXXXXXXXXXXXXXXXXXXXXXXNANPLDLFPQGLPNMGSNAGAGT 276
             +V                                 +  P              AG   
Sbjct: 215 HGSV----------------------------QESQVSEQP----------ATEAAGENP 236
Query: 277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP---- 332
           L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NEP    
Sbjct: 237 LEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEPPGEL 296
Query: 333 --VEGGEGNVLGQLASAMPQA--VTVTPEEREAIE 363
             +   EG V G +    PQ   + VTP+E+EAIE
Sbjct: 297 ADISDVEGEV-GAIGEEAPQMNYIQVTPQEKEAIE 330

>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 = 8e-12,   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 = 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: 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: 277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVE 334
           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 = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 44/57 (77%)
Query: 277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV 333
           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 = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/51 (54%), Positives = 36/51 (70%), Gaps = 3/51 (5%)
Query: 165 NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
            LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct: 1   TLVTGSEYETMLTEIMSMG---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 = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 47/72 (65%)
Query: 3  VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN 62
          + +KTL+   F+I ++P++ V  +K+ IE  +G D +P + Q LI+ GK+L D   + + 
Sbjct: 8  ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 67
Query: 63 KVAENSFVVVML 74
          ++ E +FVVVM+
Sbjct: 68 RIDEKNFVVVMV 79

>pdb|1P98|A Chain A, High-Resolution Nmr Structure Of The Ubl-Domain Of Hhr23a Length = 78

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 47/72 (65%)
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 KVAENSFVVVML 74
          ++ E +FVVVM+
Sbjct: 65 RIDEKNFVVVMV 76

>pdb|3V6C|B Chain B, Crystal Structure Of Usp2 In Complex With Mutated Ubiquitin Length = 91

Iteration: 1
 Score = 53.1 bits (126), 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 = 1e-06,   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: 272 AGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 331
           AG   L+FLR+  QFQ +R ++Q NP +L  +LQ+LG++NP L++ I  HQ  F++++NE
Sbjct: 7   AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNE 66
Query: 332 P 332
           P
Sbjct: 67  P 67

>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 = 49.7 bits (117), 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|3K9O|B Chain B, The Crystal Structure Of E2-25k And Ubb+1 Complex Length = 96

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: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 59 DYNIQKESTLHLVL 72

>pdb|2OJR|A Chain A, Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag Length = 111

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-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 = 49.3 bits (116), 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: 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 = 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: 6  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 62
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 63 DYNIQKESTLHLVL 76

>pdb|4AP4|C Chain C, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 80

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: 5  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 61
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 62 DYNIQKESTLHLVL 75

>pdb|2K6D|B Chain B, Cin85 Sh3-C Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 48.5 bits (114), 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|3U30|A Chain A, Crystal Structure Of A Linear-Specific Ubiquitin Fab Bound To Linear Ubiquitin Length = 172

Iteration: 1
 Score = 48.5 bits (114), 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|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 = 48.5 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: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 59 DYNIQKESTLHLVL 72

>pdb|2KHW|B Chain B, Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex Length = 79

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: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|3DVG|X Chain X, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 80

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: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|3DVG|Y Chain Y, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 79

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 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|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: Compositional matrix adjust.
 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|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|2ZNV|C Chain C, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 77

Iteration: 1
 Score = 48.5 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|1AAR|A Chain A, Structure Of A Diubiquitin Conjugate And A Model For Interaction With Ubiquitin Conjugating Enzyme (E2) Length = 76

Iteration: 1
 Score = 48.1 bits (113), 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|2ZVN|A Chain A, Nemo Cozi Domain Incomplex With Diubiquitin In P212121 Space Group Length = 154

Iteration: 1
 Score = 48.1 bits (113), 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: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 59
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 60 DYNIQKESTLHLVL 73

>pdb|3B08|A Chain A, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With Linear Di- Ubiquitin Length = 152

Iteration: 1
 Score = 48.1 bits (113), 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|2XK5|B Chain B, Crystal Structure Of K6-Linked Diubiquitin Length = 76

Iteration: 1
 Score = 48.1 bits (113), 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---IPPQQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3NOB|A Chain A, Structure Of K11-Linked Di-Ubiquitin Length = 78

Iteration: 1
 Score = 48.1 bits (113), 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: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 59
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 60 DYNIQKESTLHLVL 73

>pdb|1XD3|B Chain B, Crystal Structure Of Uchl3-Ubvme Complex Length = 75

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|1CMX|B Chain B, Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases Length = 76

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|4I6L|B Chain B, Crystal Structure Of Otub1 In Complex With Ubiquitin Variant Length = 76

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 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|2GBR|A Chain A, Crystal Structure Of The 35-36 Moad Insertion Mutant Of Ubiquitin Length = 81

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 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|3RUL|A Chain A, New Strategy To Analyze Structures Of Glycopeptide-Target Complexes Length = 79

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|2Y5B|B Chain B, Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde Length = 152

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-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|3ONS|A Chain A, Crystal Structure Of Human Ubiquitin In A New Crystal Form Length = 72

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-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|3LDZ|F Chain F, Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin Length = 73

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-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 = 47.8 bits (112), Expect = 9e-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|1ZGU|B Chain B, Solution Structure Of The Human Mms2-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 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|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: Compositional matrix adjust.
 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|2ZCB|A Chain A, Crystal Structure Of Ubiquitin P37aP38A Length = 76

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   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     A QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IAADQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1UD7|A Chain A, Solution Structure Of The Designed Hydrophobic Core Mutant Of Ubiquitin, 1d7 Length = 76

Iteration: 1
 Score = 47.4 bits (111), 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|4HJK|A Chain A, U7ub7 Disulfide Variant Length = 77

Iteration: 1
 Score = 47.4 bits (111), 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|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: Compositional matrix adjust.
 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|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant Of Ubiquitin Length = 88

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 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|3MTN|B Chain B, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 85

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   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|1YIW|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin 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
          +++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|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 = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 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|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 = 47.0 bits (110), Expect = 2e-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|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 = 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: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 69
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 70 DYKILGGSVLHLVL 83

>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 = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 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|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: Compositional matrix adjust.
 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|1C3T|A Chain A, Rotamer Strain As A Determinant Of Protein Structural Specificity Length = 76

Iteration: 1
 Score = 46.6 bits (109), 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|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: Compositional matrix adjust.
 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|2BKR|B Chain B, Nedd8 Nedp1 Complex Length = 77

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 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|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: 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: 23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 79
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 80 DYNIQKESTLHLVL 93

>pdb|2O6V|B Chain B, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

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+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|1NDD|B Chain B, Structure Of Nedd8 Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 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 = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 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|3H7S|A Chain A, Crystal Structures Of K63-Linked Di- And Tri-Ubiquitin Reveal A Highly Extended Chain Architecture Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 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|1S1Q|B Chain B, Tsg101(Uev) Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-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: 2  QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSD 58
Query: 62 NKVAENSFVVVML 74
            + + S + ++L
Sbjct: 59 YNIQKESTLHLVL 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 = 46.2 bits (108), Expect = 3e-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|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 = 45.8 bits (107), 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: 21 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 77
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 78 DYNIQKESTLHLVL 91

>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 = 45.8 bits (107), Expect = 3e-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: 4  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|1OTR|B Chain B, Solution Structure Of A Cue-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-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|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 = 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
          +++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|1ZW7|A Chain A, Elimination Of The C-Cap In Ubiquitin Structure, Dynamics And Thermodynamic Consequences Length = 82

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-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|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-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|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 = 45.4 bits (106), Expect = 5e-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|1OGW|A Chain A, Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Length = 76

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-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+P D + +VK  I+  +G    P  QQ LI  GK  +D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQXEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S   ++L
Sbjct: 58 DYNIQKESTXHLVL 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 = 45.4 bits (106), Expect = 5e-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|4GSW|A Chain A, Crystal Structure Of Ubiquitin From Entamoeba Histolytica To 2.15 Angstrom Length = 80

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-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 = 44.3 bits (103), Expect = 1e-04,   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 = 44.3 bits (103), Expect = 1e-04,   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|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 = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 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|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 = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 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|4HK2|A Chain A, U7ub25.2540 Length = 78

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   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 = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 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|3ZF7|SS Chain s, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 128

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 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|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1 Length = 76

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-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|1GJZ|A Chain A, Solution Structure Of A Dimeric N-Terminal Fragment Of Human Ubiquitin Length = 53

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVL 53
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQL 52

>pdb|2KDI|A Chain A, Solution Structure Of A UbiquitinUIM FUSION PROTEIN Length = 114

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-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 = 41.2 bits (95), 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

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	364
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	9e-63
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	2e-37
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	3e-37
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	1e-31
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	3e-31
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	3e-25
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	2e-24
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	6e-24
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	1e-23
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	7e-23
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	5e-22
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	5e-22
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	2e-21
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-21
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	6e-21
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	7e-21
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	1e-20
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	1e-20
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	3e-20
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	3e-20
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	5e-20
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	6e-20
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	2e-19
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	2e-19
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	3e-19
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	2e-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
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	3e-18
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	3e-18
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	9e-18
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	4e-17
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	8e-17
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	1e-16
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	3e-16
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	3e-16
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	2e-15
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	3e-15
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	3e-15
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	5e-15
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	9e-15
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	2e-14
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	7e-08
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	2e-14
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	8e-14
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	4e-13
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	4e-07
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	6e-13
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	2e-12
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	4e-09
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	3e-11
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	2e-09
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	3e-09
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	4e-09
1we6_A	111	Splicing factor, putative; structural genomics, ub	9e-09
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	1e-08
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	1e-08
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	2e-07
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	2e-07
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	2e-07
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	3e-06
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	4e-06
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	6e-06
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	6e-06
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	1e-05
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	2e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-05
2uv9_A	1878	Fatty acid synthase alpha subunits; fungal, dehydr	3e-05
2uv8_A	1887	Fatty acid synthase subunit alpha (FAS2); fatty ac	4e-05
2uv8_A	1887	Fatty acid synthase subunit alpha (FAS2); fatty ac	2e-04
2uv8_A	1887	Fatty acid synthase subunit alpha (FAS2); fatty ac	3e-04
2uv8_A	1887	Fatty acid synthase subunit alpha (FAS2); fatty ac	7e-04
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	5e-05
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	8e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	1e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	2e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	5e-04
3nwa_A	703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	1e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	2e-04
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	6e-04
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	8e-04
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	9e-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 =  204 bits (518), Expect = 9e-63
 Identities = 111/370 (30%), Positives = 174/370 (47%), Gaps = 54/370 (14%)

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+P    ++++S PP  T   +     A    
Sbjct: 68  DYRIDEKNFVVVMVTKTKAGQGTSAPPEASPTAAPESSTSFPPAPTSGMSHPPPAARE-- 125

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
                        +   AP  +P       P S  S     AAS LV GS  E  + +I+
Sbjct: 126 ---------DKSPSEESAPTTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETMLTEIM 176

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ 240
            MG   ++RE V+ ALRA+YNNP RAVEYL +GIP                         
Sbjct: 177 SMG---YERERVVAALRASYNNPHRAVEYLLTGIPG-----------------------S 210

Query: 241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQIL 300
            +        S  +  P              AG   L+FLR+  QFQ +R ++Q NP +L
Sbjct: 211 PEPEHGSVQESQVSEQP----------ATEAAGENPLEFLRDQPQFQNMRQVIQQNPALL 260

Query: 301 QPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVE-------GGEGNVLGQLASAMPQAVT 353
             +LQ+LG++NP L++ I  HQ  F++++NEP                    +     + 
Sbjct: 261 PALLQQLGQENPQLLQQISRHQEQFIQMLNEPPGELADISDVEGEVGAIGEEAPQMNYIQ 320

Query: 354 VTPEEREAIE 363
           VTP+E+EAIE
Sbjct: 321 VTPQEKEAIE 330

>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 =  129 bits (326), Expect = 2e-37
 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 (323), 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 =  114 bits (287), Expect = 1e-31
 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 (282), Expect = 3e-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 = 3e-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 = 94.3 bits (235), Expect = 2e-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

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 93.2 bits (232), Expect = 6e-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

>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 = 92.3 bits (229), Expect = 1e-23
 Identities = 29/70 (41%), Positives = 47/70 (67%)

Query: 273 GAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP 332
               L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEP
Sbjct: 2   SHMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEP 61

Query: 333 VEGGEGNVLG 342
           V+   G   G
Sbjct: 62  VQEAGGQGGG 71

>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 = 89.5 bits (222), Expect = 7e-23
 Identities = 27/60 (45%), Positives = 44/60 (73%)

Query: 274 AGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV 333
              L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV
Sbjct: 1   GHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 60

>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 = 5e-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 = 90.3 bits (224), Expect = 5e-22
 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

>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 = 88.2 bits (218), Expect = 2e-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

>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 = 86.2 bits (214), Expect = 2e-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

>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 = 6e-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

>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 = 7e-21
 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 = 1e-20
 Identities = 28/50 (56%), Positives = 36/50 (72%), Gaps = 3/50 (6%)

Query: 166 LVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
           LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct: 2   LVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 48

>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 = 84.4 bits (209), 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

>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 = 3e-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

>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 = 83.1 bits (206), Expect = 3e-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

>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 = 5e-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 = 83.0 bits (205), Expect = 6e-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 = 80.7 bits (200), Expect = 2e-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

>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 = 2e-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

>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 = 80.5 bits (199), 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

>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 = 79.0 bits (195), Expect = 2e-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 = 78.5 bits (194), 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 = 78.7 bits (194), 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 = 3e-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 = 77.0 bits (190), Expect = 9e-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 = 75.1 bits (185), Expect = 4e-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

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score = 73.6 bits (181), Expect = 8e-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: 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 = 73.6 bits (181), 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

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 75.2 bits (184), Expect = 3e-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

>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 = 72.8 bits (179), Expect = 3e-16
 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

>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

>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 = 69.7 bits (171), Expect = 3e-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

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 70.6 bits (173), Expect = 3e-15
 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

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 69.3 bits (170), Expect = 5e-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 = 68.2 bits (167), Expect = 9e-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

>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 = 69.3 bits (169), Expect = 2e-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 = 50.4 bits (120), Expect = 7e-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

>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 = 2e-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

>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 = 65.4 bits (160), Expect = 8e-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 = 66.2 bits (161), Expect = 4e-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 = 4e-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 = 6e-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 = 63.8 bits (155), 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 = 54.2 bits (130), Expect = 4e-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 = 59.0 bits (143), Expect = 3e-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

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 55.8 bits (134), 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

>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 = 52.7 bits (126), Expect = 3e-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 = 52.7 bits (126), Expect = 4e-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

>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 = 51.7 bits (124), Expect = 9e-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

>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 = 51.2 bits (122), Expect = 1e-08
 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

>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 = 50.9 bits (122), Expect = 1e-08
 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 = 47.9 bits (114), Expect = 2e-07
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 4/81 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
            V VK  K     +E+  ++     K  +  + G      ++Q ++ +G  LKD     
Sbjct: 8  YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTG---VQPARQKVMVKGGTLKD-DDWG 63

Query: 61 ENKVAENSFVVVMLTKSKVSS 81
            K+     V++M +   +  
Sbjct: 64 NIKMKNGMTVLMMGSADALPE 84

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 47.6 bits (113), 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: 173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAG 229
           E  V  I+ MG   + R+  ++ALRA  N+ ERAV++++S I +  A   ++  S+G
Sbjct: 10  EDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMSGPSSG 63

>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 = 43.7 bits (103), Expect = 3e-06
 Identities = 8/40 (20%), Positives = 24/40 (60%), Gaps = 3/40 (7%)

Query: 173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 212
           +++V  +L  G   +  +   +AL+A+  + E+A +++++
Sbjct: 30  QSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFN 66

>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 = 4e-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

>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 = 43.3 bits (102), Expect = 6e-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

>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 = 43.4 bits (102), Expect = 6e-06
 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

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 43.5 bits (102), Expect = 1e-05
 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

>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 = 42.0 bits (98), 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

>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 = 45.2 bits (106), Expect = 3e-05
 Identities = 26/190 (13%), Positives = 46/190 (24%), Gaps = 15/190 (7%)

Query: 94  QAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
           QAQ       T  Q       P    A   S  +   PP    P+        PA   + 
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70

Query: 154 SVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG 213
              D    + +++   +        ++D       +  V                     
Sbjct: 71  QQIDQATTSMNDMHLHN------VPLVDPNAYMQPQVPVQMGTPLQQQQQ---------P 115

Query: 214 IPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAG 273
           +       P A      +  N            P  T      P  + P     + S   
Sbjct: 116 MAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELS 175

Query: 274 AGTLDFLRNS 283
             + D++R++
Sbjct: 176 NASPDYIRST 185

>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 = 45.3 bits (107), Expect = 3e-05
 Identities = 22/63 (34%), Positives = 25/63 (39%), Gaps = 1/63 (1%)

Query: 107 QPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPA-PVSSVSDVYGQAASN 165
                   P PT A   S   +     A   APA APAPAPA A P + V D    A   
Sbjct: 91  DVEPIEDEPEPTPAAASSADAAPAAAPAAPAAPAAAPAPAPASAGPAAPVQDAPVTATDV 150

Query: 166 LVA 168
           + A
Sbjct: 151 IRA 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 = 44.6 bits (105), Expect = 4e-05
 Identities = 13/50 (26%), Positives = 21/50 (42%)

Query: 109 TTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDV 158
           T      A    P +    +  P A+     A APAP  A AP ++ +++
Sbjct: 91  TPDPSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEI 140

>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 = 42.7 bits (100), Expect = 2e-04
 Identities = 20/50 (40%), Positives = 24/50 (48%)

Query: 106 TQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSV 155
                  + PA   AP  +   SAP PAA APAP  A APA A A ++  
Sbjct: 94  PSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADE 143

>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 = 41.9 bits (98), Expect = 3e-04
 Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 1/62 (1%)

Query: 107 QPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNL 166
            P+  +    P      + P  A    APA A     A A   A  + ++D   +A+  L
Sbjct: 93  DPSELAAKEEPAKEEAPA-PTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVKASLLL 151

Query: 167 VA 168
             
Sbjct: 152 HV 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 = 40.7 bits (95), Expect = 7e-04
 Identities = 11/58 (18%), Positives = 17/58 (29%)

Query: 98  TSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSV 155
           T      + +     +          +   +A  PA  A A   A A   A  PV + 
Sbjct: 91  TPDPSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVKAS 148

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 41.2 bits (96), Expect = 5e-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

>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 = 40.6 bits (94), Expect = 8e-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

>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 = 42.4 bits (99), Expect = 1e-04
 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 = 42.1 bits (98), Expect = 2e-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 = 40.9 bits (95), Expect = 5e-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

>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 = 42.6 bits (100), Expect = 1e-04
 Identities = 20/95 (21%), Positives = 27/95 (28%), Gaps = 3/95 (3%)

Query: 82  SGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAP 141
           +   T   A A QA   ++  P +  P      P     P ++     P P  PA   A 
Sbjct: 6   TSPGTPGVAAATQA---ANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDNAT 62

Query: 142 APAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATV 176
             A                  A+  V      ATV
Sbjct: 63  VAAGHATLREHLRDIKAENTDANFYVCPPPTGATV 97

>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 = 2e-04
 Identities = 26/104 (25%), Positives = 33/104 (31%), Gaps = 1/104 (0%)

Query: 60  EENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTV 119
           E++K AE        + +  S+  A         Q      A           Q   P  
Sbjct: 345 EDDKDAETEIPAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQG 404

Query: 120 APPQS-VPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQA 162
            PPQ   P+  PP   P P     P  AP  AP   V +   QA
Sbjct: 405 YPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAAPPQGVDNQAYQA 448

>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 = 6e-04
 Identities = 24/91 (26%), Positives = 32/91 (35%), Gaps = 1/91 (1%)

Query: 96  QTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSV 155
                    +         P P+ A P + P SA   A  A   A   A   AP+P SS 
Sbjct: 15  MANLPNGYMTDLQRPQPPPPPPSAASPGATPGSAAASAERAS-TAAPVASPAAPSPGSSG 73

Query: 156 SDVYGQAASNLVAGSNLEATVQQILDMGGGS 186
              +  + SN V  +   A       +GGGS
Sbjct: 74  GGGFFSSLSNAVKQTTAAAAATFSEQVGGGS 104

>2lbc_A Ubiquitin carboxyl-terminal hydrolase 13; tandem UBA of USP13; NMR {Homo sapiens} Length = 126

 Score = 38.0 bits (87), Expect = 8e-04
 Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 3/36 (8%)

Query: 177 QQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 212
             I  MG   + R   I+ALRA  NN ERA+++++S
Sbjct: 83  AIITSMG---FQRNQAIQALRATNNNLERALDWIFS 115

>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 = 37.7 bits (87), Expect = 9e-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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	364
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	100.0
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	99.91
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	99.91
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	99.9
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.79
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.77
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.77
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.76
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.76
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.75
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.75
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.75
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.74
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.74
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.74
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.74
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.73
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.73
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.73
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.73
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.72
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.72
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.72
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.71
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.71
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.71
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.71
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.71
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.71
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.71
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.71
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.71
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.7
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.7
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.7
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.7
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.69
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.69
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	99.69
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.69
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.68
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.68
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.68
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.68
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.67
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.67
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.67
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.67
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.49
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.66
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.66
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.65
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.64
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.64
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.64
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.63
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.62
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.62
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.62
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.62
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.62
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.62
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.62
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.62
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.62
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.61
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.61
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.6
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.6
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.6
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.59
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.59
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.57
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.56
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.56
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.55
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.55
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.54
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.53
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.52
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.5
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.46
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.42
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.42
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.42
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.38
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.38
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.36
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	99.35
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.35
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	99.34
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	99.34
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.33
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	99.32
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	99.28
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.28
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.28
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.26
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.26
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	99.25
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	99.24
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.24
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.21
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	99.2
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	99.19
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.19
2dna_A	67	Unnamed protein product; ubiquitin associated doma	99.19
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.16
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.14
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.12
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	99.11
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	99.1
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	99.1
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.09
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	99.06
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	99.05
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	99.05
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	98.98
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	98.98
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	98.97
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	98.96
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	98.9
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	98.89
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	98.87
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	98.83
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	98.79
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	98.71
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	98.61
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.57
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	98.55
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	98.53
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	98.5
2pjh_A	80	Protein NPL4, nuclear protein localization protein	98.49
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	98.47
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	98.4
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	98.37
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	98.29
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	98.27
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	98.24
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	98.2
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	98.11
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.04
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	98.02
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	97.94
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	97.93
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	97.91
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	97.82
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	97.7
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	97.65
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	97.62
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	97.6
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	97.59
2cos_A	54	Serine/threonine protein kinase LATS2; UBA domain,	97.57
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	97.48
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	97.34
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	97.31
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.25
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	96.71
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	96.41
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	96.28
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	95.93
2pwq_A	216	Ubiquitin conjugating enzyme; structural genomics	95.85
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	95.6
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	95.33
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	95.3
2dhy_A	67	CUE domain-containing protein 1; structural genomi	95.29
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	94.71
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	94.69
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	94.55
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	94.42
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	94.38
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	93.86
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	93.42
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	93.22
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	93.06
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	92.16
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	91.8
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	91.32
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	90.77
1ip9_A	85	BEM1 protein; ubiquitin alpha/beta roll, signaling	89.58
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	89.15
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	88.83
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	87.97
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	87.95
4dbg_B	162	Ring finger protein 31; ubiquitin fold, ubiquitina	87.85
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	87.36
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	87.26
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	87.22
2llw_A	71	Heat shock protein STI1; DP domain, alpha helix, c	86.35
1q02_A	52	Sequestosome 1; helical bundle, protein binding; N	86.05
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	85.55
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	85.18
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	85.17
2k5p_A	78	THis protein, thiamine-biosynthesis protein; NESG,	84.68
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	84.48
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	84.27
2lnm_A	62	Protein TIC 40, chloroplastic; translocon, import,	84.21
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	83.37
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	81.54
1ixs_A	62	Holliday junction DNA helicase RUVA; heterodimeric	80.93
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	80.67
3onh_A	127	Ubiquitin-activating enzyme E1-like; ligase, SUMO	80.4
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	80.16

>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=9e-66  Score=509.40  Aligned_cols=312  Identities=34%  Similarity=0.585  Sum_probs=211.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHH---hCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETV---QGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~---~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.+   .|   +++++|||||+||+|+|+++|++|+|+++++|++|+.|.
T Consensus         8 M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~g---ip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~   84 (368)
T 1oqy_A            8 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDA---FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKT   84 (368)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSS---CCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECC
T ss_pred             EEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCC---CChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecC
Confidence            899999999999999999999999999999994   56   999999999999999999999999999999997787776


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 017906           78 KVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPP--QSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSV  155 (364)
Q Consensus        78 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (364)
                      +..+.....+...+.+++++   .++.+   +...+.+++...+.  .+.+..       .+.+..+|..+...++..+.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~---~~~~~---~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~p~~~~~~~~~~~~  151 (368)
T 1oqy_A           85 KAGQGTSAPPEASPTAAPES---STSFP---PAPTSGMSHPPPAAREDKSPSE-------ESAPTTSPESVSGSVPSSGS  151 (368)
T ss_dssp             CSSSCCCCCSSCCCCCSSSC---CCSCC---CSSSCCCCCCCSSSSCCCCCSC-------SCCCCSSTTCSCCCSCSCCC
T ss_pred             CCCCCCCCCcccCCCCCccc---cCCCC---CCCCCCCCCCCccccccCCccc-------cCCCCCCCCccccccccccc
Confidence            65433111111111110110   00000   00000000000000  000000       00000011111111111111


Q ss_pred             ccccccccccccCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCCCCCCCccccccCCCCCCCC
Q 017906          156 SDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNP  235 (364)
Q Consensus       156 ~~~~~~~~s~l~~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~~~~~~~~~~~~~~~~~~~~  235 (364)
                      ...++.+.|+||+|+++|++|++||+||   |+|++|++|||++|||||||||||++|||++.+...+    .    ..+
T Consensus       152 ~~~~~~~~s~l~~g~~~~~~i~~l~~MG---f~~~~~~~AL~a~~nn~~~A~e~L~~gip~~~~~~~~----~----~~~  220 (368)
T 1oqy_A          152 SGREEDAASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIPGSPEPEHG----S----VQE  220 (368)
T ss_dssp             SCCCCCCCTTTCCTTTHHHHHHHHHTTT---CCSHHHHHHHHHSCSSTTHHHHTTTTSSTTCSSCCCC----C----CCC
T ss_pred             ccccccccccccCCcchHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCcccccccC----C----ccc
Confidence            2335567899999999999999999999   9999999999999999999999999999987442210    0    000


Q ss_pred             CCccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCchHhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHH
Q 017906          236 PAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLM  315 (364)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~  315 (364)
                      . ..        ....                +.++++.++|+|||++|||++||++||+||++|++|||||+++||+|+
T Consensus       221 ~-~~--------~~~~----------------~~~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~l~~~lq~l~~~nP~l~  275 (368)
T 1oqy_A          221 S-QV--------SEQP----------------ATEAAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLL  275 (368)
T ss_dssp             C-CS--------SCCC----------------CSSCCSCCTTHHHHHSHHHHHHHHSTTTCTTHHHHHHTTTTTTCHHHH
T ss_pred             c-cc--------cccc----------------CccccccchHHHHhcChHHHHHHHHHHhChHHHHHHHHHHHhhCHHHH
Confidence            0 00        0000                011234578999999999999999999999999999999999999999


Q ss_pred             HHHHHCHHHHHHHhcCCCCCC-CCc----cccccc--CCCCcceecCHHHHhhcCC
Q 017906          316 RLIQEHQTDFLRLINEPVEGG-EGN----VLGQLA--SAMPQAVTVTPEEREAIEP  364 (364)
Q Consensus       316 ~~I~~n~e~Fl~~l~e~~~~~-~g~----~~~~~~--~~~~~~i~lT~ee~~AIeR  364 (364)
                      ++|++||++||+||+++++++ .+.    ..+..+  .....+|+||+||+++|+|
T Consensus       276 ~~I~~n~~~Fl~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~t~ee~eaI~r  331 (368)
T 1oqy_A          276 QQISRHQEQFIQMLNEPPGELADISDVEGEVGAIGEEAPQMNYIQVTPQEKEAIER  331 (368)
T ss_dssp             HHHHHHHHHHHHHHHSCCCCSCSSCCCSSSSCCCSCCCTTCSSCCCCTTTHHHHHH
T ss_pred             HHHHHCHHHHHHHHcCcccccccccccccccccccccCCccccccCCCcCHHHHHH
Confidence            999999999999999986431 110    011111  1123479999999999987

>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=99.91  E-value=4.7e-25  Score=168.64  Aligned_cols=62  Identities=44%  Similarity=0.880  Sum_probs=59.2

Q ss_pred             CCchHhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHCHHHHHHHhcCCCCC
Q 017906          274 AGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEG  335 (364)
Q Consensus       274 ~~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I~~n~e~Fl~~l~e~~~~  335 (364)
                      +++|+|||++|+|++||++||+||++|++|||+|+++||+|+++|++|||+||+||+|+.++
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            45799999999999999999999999999999999999999999999999999999998764

>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=99.90  E-value=6e-24  Score=157.90  Aligned_cols=59  Identities=46%  Similarity=0.935  Sum_probs=56.9

Q ss_pred             CchHhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHCHHHHHHHhcCCC
Q 017906          275 GTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV  333 (364)
Q Consensus       275 ~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I~~n~e~Fl~~l~e~~  333 (364)
                      ++|+|||++|+|++||++||+||++|++|||+|+++||+|+++|++|||+||+||+|++
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            46899999999999999999999999999999999999999999999999999999874

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.79  E-value=1.7e-19  Score=148.66  Aligned_cols=78  Identities=24%  Similarity=0.397  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +++++|||+|+||+|+|+++|++|||++|++|+|++++++..
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   999999999999999999999999999999999999877644


Q ss_pred             C
Q 017906           81 S   81 (364)
Q Consensus        81 ~   81 (364)
                      +
T Consensus        79 ~   79 (106)
T 3m62_B           79 K   79 (106)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.77  E-value=3.1e-18  Score=138.05  Aligned_cols=78  Identities=45%  Similarity=0.705  Sum_probs=73.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHH---hCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETV---QGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~---~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|+.|.|+|++++||.+||++|+..   .|   +++++|||+|+||.|+|+++|++|||++|++|+|+++++
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 017906           78 KVSS   81 (364)
Q Consensus        78 k~~~   81 (364)
                      +..+
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=99.77  E-value=1.6e-18  Score=137.77  Aligned_cols=78  Identities=35%  Similarity=0.518  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+..+|   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+...
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             C
Q 017906           81 S   81 (364)
Q Consensus        81 ~   81 (364)
                      .
T Consensus        78 ~   78 (88)
T 4fbj_B           78 G   78 (88)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.76  E-value=1.4e-18  Score=138.06  Aligned_cols=75  Identities=28%  Similarity=0.380  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.++|   +++++|||+|+||.|+|+++|++|+| ++++|||+++.+..
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 89999999886543

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.76  E-value=2e-18  Score=133.81  Aligned_cols=74  Identities=24%  Similarity=0.320  Sum_probs=71.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+
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=99.75  E-value=5.1e-18  Score=132.97  Aligned_cols=76  Identities=36%  Similarity=0.640  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHH---hCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETV---QGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~---~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|+.|.++|++++||.+||++|+..   .|   +++++|||+|+|+.|+|+++|++|+|+++++|+|+++++
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   77   999999999999999999999999999999999999876


Q ss_pred             CC
Q 017906           78 KV   79 (364)
Q Consensus        78 k~   79 (364)
                      ++
T Consensus        83 ~~   84 (85)
T 2wyq_A           83 KA   84 (85)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.75  E-value=3.8e-18  Score=134.86  Aligned_cols=72  Identities=36%  Similarity=0.517  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCee-cCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV-LKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~Gki-L~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|||+|+||. |+|+++|++|+|+++++|+|+++
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

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.75  E-value=4.4e-18  Score=135.78  Aligned_cols=74  Identities=39%  Similarity=0.646  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+..+|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.+
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

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.74  E-value=3.2e-18  Score=139.41  Aligned_cols=74  Identities=27%  Similarity=0.459  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCcEEEE--EeCCCCcHHHHHHHH-HHHhCCCCCCCCCeEEEeCCeecCCCCChhhhcc-CCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEI--EVKPEDKVSDVKKNI-ETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~i--eV~~s~TV~dLK~kI-~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gI-k~~s~I~v~v~k   76 (364)
                      |+|+||+++|++|.|  +|++++||.+||++| +...|   +++++|||||+||+|+|+.+|++|+| ++|++|+||+++
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 017906           77 S   77 (364)
Q Consensus        77 ~   77 (364)
                      +
T Consensus        97 p   97 (98)
T 4a20_A           97 N   97 (98)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.74  E-value=6e-18  Score=136.00  Aligned_cols=71  Identities=27%  Similarity=0.379  Sum_probs=69.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||++.|+++.|+|++++||.+||++|+++.|   +|+++|||+|+||+|+|+.+|++|+|++|++|++..
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   999999999999999999999999999999999874

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.74  E-value=3e-18  Score=136.68  Aligned_cols=74  Identities=28%  Similarity=0.455  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCcEEEEEeC--CCCcHHHHHHHH-HHHhCCCCCCCCCeEEEeCCeecCCCCChhhhcc-CCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVK--PEDKVSDVKKNI-ETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~--~s~TV~dLK~kI-~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gI-k~~s~I~v~v~k   76 (364)
                      |+|+||+++|++|.|+|+  +++||.+||++| +...|   +|+++|||||+||+|+|+.+|++|+| .++++|+|++++
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            899999999999988765  999999999999 99989   99999999999999999999999999 699999999875


Q ss_pred             C
Q 017906           77 S   77 (364)
Q Consensus        77 ~   77 (364)
                      .
T Consensus        79 ~   79 (87)
T 2lxa_A           79 N   79 (87)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.74  E-value=1.1e-17  Score=134.23  Aligned_cols=77  Identities=36%  Similarity=0.589  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+++|+.|.|+|++++||.+||++|+..+|   +++++|||+|+|+.|+|+++|++|+|+++++|+|+++.+...
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

>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=99.73  E-value=1.9e-17  Score=135.98  Aligned_cols=76  Identities=26%  Similarity=0.324  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+.+|+ |.|+|++++||.+||++|+..+|   +++++|||+|+||.|+|+++|++|+|+++++|||+++++...
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            78999998885 89999999999999999999999   999999999999999999999999999999999999876543

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.3e-17  Score=135.07  Aligned_cols=75  Identities=36%  Similarity=0.577  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.++|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
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=99.73  E-value=2.1e-17  Score=125.95  Aligned_cols=74  Identities=36%  Similarity=0.562  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+.+|+.+.++|++++||.+||++|+...|   ++++.|+|+|+|+.|+|+.+|++|+|+++++|+|+++.+
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~---i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~   74 (76)
T 1ndd_A            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALR   74 (76)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHC---cChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999998765

>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=99.73  E-value=9.9e-18  Score=131.99  Aligned_cols=75  Identities=36%  Similarity=0.546  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+..+|   +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999988653

>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=99.72  E-value=1.9e-17  Score=127.77  Aligned_cols=73  Identities=22%  Similarity=0.349  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCcEE-EEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHF-EIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~-~ie-V~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+++|+.+ .|+ |++++||.+||++|+...|   +|+++|+|+|+|+.|+|+++|++|||+++++|+|+++.
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 999 9999999999999999999   99999999999999999999999999999999999875

>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=99.72  E-value=8.3e-18  Score=137.29  Aligned_cols=71  Identities=17%  Similarity=0.281  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||+++|+++.|+|++++||.+||++|+++.|   +++++|||+|.||+|+|+.+|++|+|+++++|+|..
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

>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=99.72  E-value=3.7e-17  Score=124.59  Aligned_cols=75  Identities=37%  Similarity=0.601  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+.+|+.+.++|++++||.+||++|+...|   +++++|+|+|+|+.|+|+.+|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999987653

>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=99.71  E-value=2e-17  Score=129.28  Aligned_cols=76  Identities=36%  Similarity=0.546  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|+++.|+|++++||.+||++|++.++   +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+..
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

>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=99.71  E-value=1.8e-17  Score=136.31  Aligned_cols=76  Identities=20%  Similarity=0.364  Sum_probs=72.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|++|.|+|++++||.+||.+|+...|   +++++|||+|+||.|+|+++|++|||++|++|||+++++..
T Consensus        24 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~~~~   99 (106)
T 1ttn_A           24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG---VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQ   99 (106)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTC---CCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSSC
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHC---cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            78999999999999999999999999999999999   99999999999999999999999999999999999987654

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.8e-17  Score=127.29  Aligned_cols=73  Identities=27%  Similarity=0.424  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.
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   99999999999999999999999999999999999865

>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=99.71  E-value=5.4e-17  Score=128.41  Aligned_cols=76  Identities=20%  Similarity=0.295  Sum_probs=72.1

Q ss_pred             CEEEEEeCCC-cEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKG-THFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~g-k~~~i-eV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++| ++|.| +|++++||.+||++|+...|   +++++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+.
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 69999 59999999999999999999   9999999999999999999999999999999999998765


Q ss_pred             C
Q 017906           79 V   79 (364)
Q Consensus        79 ~   79 (364)
                      .
T Consensus        85 G   85 (89)
T 1wy8_A           85 G   85 (89)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.71  E-value=2.2e-17  Score=127.81  Aligned_cols=75  Identities=19%  Similarity=0.268  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+++.|+|++++||.+||++|+++.|   +++++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999997653

>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=99.71  E-value=3.4e-17  Score=127.78  Aligned_cols=76  Identities=37%  Similarity=0.577  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|++|.|+|++++||.+||++|++.++   +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+..
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

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.71  E-value=2.3e-17  Score=130.97  Aligned_cols=75  Identities=24%  Similarity=0.310  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+.+.|+|++++||.+||++|+...|   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999988654

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.71  E-value=2.8e-17  Score=129.93  Aligned_cols=71  Identities=30%  Similarity=0.411  Sum_probs=68.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.++|   +|+++|||+|+||.|+|+.+|++||| +|++||+++|
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

>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=99.71  E-value=4.5e-17  Score=128.22  Aligned_cols=75  Identities=29%  Similarity=0.467  Sum_probs=72.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+++.++|++++||.+||++|++..+   +++++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+.
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---i~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~G   82 (87)
T 1wh3_A            8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGS   82 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTC---CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhC---CChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccC
Confidence            78999999999999999999999999999999999   9999999999999999999999999999999999998765

>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=99.70  E-value=5e-17  Score=130.23  Aligned_cols=76  Identities=20%  Similarity=0.215  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHh--CCCCCCCCCeEEEeCCeecCCCCChhhh--ccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQ--GSDVYPASQQMLIHQGKVLKDVTTLEEN--KVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk--~~~ieV~~s~TV~dLK~kI~~~~--g~~~ip~~~qkLif~GkiL~D~~tL~d~--gIk~~s~I~v~v   74 (364)
                      |+|+||+.+|+  .+.|+|++++||.+||++|+..+  +   +++++|||||+||+|+|+++|++|  +|+++++|||++
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             ecCCC
Q 017906           75 TKSKV   79 (364)
Q Consensus        75 ~k~k~   79 (364)
                      +.+..
T Consensus        85 ~~~gg   89 (93)
T 1wgd_A           85 NVKSG   89 (93)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77654

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=99.70  E-value=4.7e-17  Score=129.27  Aligned_cols=75  Identities=33%  Similarity=0.604  Sum_probs=69.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+++.++|++++||.+||++|++..|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999988654

>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=99.70  E-value=2e-17  Score=136.31  Aligned_cols=77  Identities=22%  Similarity=0.234  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC---------------CCeEEEeCCeecC-CCCChhhhcc
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA---------------SQQMLIHQGKVLK-DVTTLEENKV   64 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~---------------~~qkLif~GkiL~-D~~tL~d~gI   64 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+++.+   +++               +.|+|||+||+|. |+++|++|||
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 6799999999


Q ss_pred             CCCCEEEEEEecCCCC
Q 017906           65 AENSFVVVMLTKSKVS   80 (364)
Q Consensus        65 k~~s~I~v~v~k~k~~   80 (364)
                      +++++|||+.+.+...
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

>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=99.70  E-value=5.9e-17  Score=130.21  Aligned_cols=74  Identities=28%  Similarity=0.320  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~-~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|+.|.|+|++++||.+||++|+...      +++|||+|+||.|+|+ ++|++|+|+++++|||++++++.
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 INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ------ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGA   81 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST------TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC------cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCCC
Confidence            7899999999999999999999999999998873      7899999999999999 99999999999999999887654


Q ss_pred             C
Q 017906           80 S   80 (364)
Q Consensus        80 ~   80 (364)
                      .
T Consensus        82 ~   82 (95)
T 1wia_A           82 A   82 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.69  E-value=4.5e-17  Score=131.82  Aligned_cols=75  Identities=19%  Similarity=0.268  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+++.|+|++++||.+||++|+.+.|   +++++|||+|+|+.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999998753

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.69  E-value=8.8e-17  Score=129.62  Aligned_cols=75  Identities=31%  Similarity=0.370  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~-~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++| ++.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+ ++|++|+|+++++|+|+++.+..
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            6899999888 899999999999999999999999   999999999999999999 99999999999999999987654

>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=99.69  E-value=2.3e-17  Score=117.81  Aligned_cols=49  Identities=57%  Similarity=1.000  Sum_probs=47.2

Q ss_pred             cccCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCC
Q 017906          165 NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  216 (364)
Q Consensus       165 ~l~~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~  216 (364)
                      +|++|+.+++.|++|++||   |+|++|++|||+++||++||||||++|||+
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

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.69  E-value=1.3e-16  Score=122.42  Aligned_cols=71  Identities=30%  Similarity=0.517  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+ +|+.+.++|++++||.+||++|+...|   +++++|+|+|+|+.|+|+++|++|||++|++|+|+.+
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

>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=99.68  E-value=1.1e-16  Score=130.75  Aligned_cols=76  Identities=20%  Similarity=0.334  Sum_probs=69.9

Q ss_pred             CEEEEEeCCC----cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKG----THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~g----k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~-~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+.++    ++|.|+|++++||.+||++|+.++|   +++++|||+|+||.|+|+ ++|++|+|+++++|+|+++
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   999999999999999887 7999999999999999987


Q ss_pred             cCCC
Q 017906           76 KSKV   79 (364)
Q Consensus        76 k~k~   79 (364)
                      .+..
T Consensus        85 ~~gg   88 (102)
T 1v5o_A           85 DNVG   88 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6544

>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=99.68  E-value=1.2e-16  Score=132.52  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+.|.|+|++++||.+||.+|+.++|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
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            78999999999999999999999999999999999   9999999999999999999999999999999999998753

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.68  E-value=1.8e-16  Score=128.00  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+.+|+.+.|+|++++||.+||++|+...|   +++++|+|+|+||.|+|+++|++|||+++++|+|+++.+.
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

>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=99.68  E-value=7e-17  Score=129.88  Aligned_cols=75  Identities=27%  Similarity=0.322  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+. |+.|.|+|++++||.+||++|+..++   +++++|||+|+||.|+|+++|++|+|+++++|||+++.+..
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

>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=1.4e-16  Score=129.97  Aligned_cols=71  Identities=20%  Similarity=0.132  Sum_probs=64.7

Q ss_pred             EEEEEeCC----CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            2 KVFVKTLK----GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         2 kI~VKtl~----gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      .|.|+..+    +++|.|+|++++||.+||++|+++.|   +|+++|||||+||+|+|+++|++|+|+++++|+||+.
T Consensus        17 ti~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~g---ip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti~vl~l   91 (100)
T 1wju_A           17 TIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG---LQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLEL   91 (100)
T ss_dssp             EEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTT---CCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECC
T ss_pred             EEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHC---cCHHHeEEEeCCeECCCCCcHHHcCCCCCCEEEEEEE
Confidence            36677666    77999999999999999999999999   9999999999999999999999999999999965543

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.67  E-value=1.9e-16  Score=129.15  Aligned_cols=74  Identities=30%  Similarity=0.353  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+. |+.|.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+++++.
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

>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=99.67  E-value=1.5e-16  Score=129.59  Aligned_cols=75  Identities=27%  Similarity=0.324  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+.+|+ |.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|+++++|+|+++.+..
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            78999999885 79999999999999999999999   99999999999999999999999999999999999887653

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.67  E-value=2e-16  Score=134.17  Aligned_cols=76  Identities=29%  Similarity=0.329  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||++ |+.|.|+|++++||.+||++|+.++|   +++++|||+|+||+|+|+++|++|+|+++++|+|+++++...
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

>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=99.49  E-value=4.7e-18  Score=130.43  Aligned_cols=75  Identities=27%  Similarity=0.408  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+.+|++|.++|++++||.+||++|+...|   ++++.|+|+|+|+.|+|+++|++|||+++++|+|+++.+.
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   9999999999999999999999999999999999988653

>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=99.66  E-value=3.1e-16  Score=131.33  Aligned_cols=75  Identities=20%  Similarity=0.229  Sum_probs=64.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHH------hCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCE--EEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETV------QGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSF--VVV   72 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~------~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~--I~v   72 (364)
                      |+|+||+++|++++|+|++++||.+||++|+..      .+.. +++++|||||.||+|+|+++|++|+|+.+++  |||
T Consensus        17 m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p-~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlhL   95 (116)
T 1wgh_A           17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQV-SSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHL   95 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCC-CCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCC-CChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEE
Confidence            789999999999999999999999999999994      3411 3699999999999999999999999987764  555


Q ss_pred             EEec
Q 017906           73 MLTK   76 (364)
Q Consensus        73 ~v~k   76 (364)
                      +++.
T Consensus        96 vlr~   99 (116)
T 1wgh_A           96 VARE   99 (116)
T ss_dssp             EECS
T ss_pred             EccC
Confidence            5544

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.66  E-value=2.4e-16  Score=126.64  Aligned_cols=73  Identities=22%  Similarity=0.342  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+  |+++.|+|++++||.+||++|++..|   +|+++|+|+|+||.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999987653

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.65  E-value=6.1e-16  Score=137.59  Aligned_cols=77  Identities=35%  Similarity=0.549  Sum_probs=73.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+++|++|+|+++++|||+++.+...
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   999999999999999999999999999999999999877543

>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=99.64  E-value=3.6e-16  Score=126.56  Aligned_cols=72  Identities=21%  Similarity=0.276  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~-~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+|| +.|+.| .|+|++++||.+||++|++.+|   +++++|||+|+||.|+|+ +|++|+|+++++|+||.+..
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 99999999999999987544

>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=99.64  E-value=6.8e-16  Score=127.13  Aligned_cols=74  Identities=23%  Similarity=0.152  Sum_probs=68.4

Q ss_pred             CEEEEEeCCC---cEEEEEeC--------C-CCcHHHHHHHHHHHh--CCCCCCCCC-eEEEeCCeecCCCCChhhhccC
Q 017906            1 MKVFVKTLKG---THFEIEVK--------P-EDKVSDVKKNIETVQ--GSDVYPASQ-QMLIHQGKVLKDVTTLEENKVA   65 (364)
Q Consensus         1 MkI~VKtl~g---k~~~ieV~--------~-s~TV~dLK~kI~~~~--g~~~ip~~~-qkLif~GkiL~D~~tL~d~gIk   65 (364)
                      |+|+||+.++   ++|.|+|+        + ++||.+||++|+..+  |   +++++ |||||+||.|+|+++|++|+|+
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 017906           66 ENSFVVVMLTKS   77 (364)
Q Consensus        66 ~~s~I~v~v~k~   77 (364)
                      ++++|||+++.+
T Consensus        90 ~g~~i~lv~~~~  101 (107)
T 1x1m_A           90 PGSTVHVLRKSW  101 (107)
T ss_dssp             TTCEEEEEESSC
T ss_pred             CCCEEEEEeCCC
Confidence            999999998764

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.64  E-value=9.8e-16  Score=126.90  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999998653

>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=99.63  E-value=5.3e-16  Score=130.07  Aligned_cols=72  Identities=22%  Similarity=0.290  Sum_probs=67.7

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccC-------CCCEEEE
Q 017906            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVA-------ENSFVVV   72 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk-------~~s~I~v   72 (364)
                      |.++|+...++ ++.|+|++++||.+||++|+.+.|   +|+++|||||+||+|+|+++|++|||+       .+++|+|
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            77888877776 599999999999999999999999   999999999999999999999999999       6999999


Q ss_pred             EEe
Q 017906           73 MLT   75 (364)
Q Consensus        73 ~v~   75 (364)
                      +++
T Consensus        78 ~lr   80 (118)
T 2fnj_B           78 AFR   80 (118)
T ss_dssp             EEB
T ss_pred             Eec
Confidence            998

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.62  E-value=6.1e-16  Score=131.21  Aligned_cols=74  Identities=20%  Similarity=0.253  Sum_probs=65.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHH------HhCCCCC--CCCCeEEEeCCeecCCCCChhhhccCCCCE--E
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIET------VQGSDVY--PASQQMLIHQGKVLKDVTTLEENKVAENSF--V   70 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~------~~g~~~i--p~~~qkLif~GkiL~D~~tL~d~gIk~~s~--I   70 (364)
                      |+|+||+++|++++|+|++++||.+||++|+.      +.+   +  ++++|||||+||+|+|+++|++|+|+++++  |
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            68999999999999999999999999999999      455   5  589999999999999999999999998885  4


Q ss_pred             EEEEecC
Q 017906           71 VVMLTKS   77 (364)
Q Consensus        71 ~v~v~k~   77 (364)
                      ||+++.+
T Consensus        95 hlv~r~~  101 (125)
T 2gow_A           95 HLVARET  101 (125)
T ss_dssp             EEEECSC
T ss_pred             EEEecCC
Confidence            5555443

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.62  E-value=1.7e-15  Score=126.32  Aligned_cols=76  Identities=33%  Similarity=0.522  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      ++|+||+++|+++.|+|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+..
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

>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=99.62  E-value=1.1e-15  Score=133.40  Aligned_cols=76  Identities=24%  Similarity=0.292  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|+++.|+|++++||.+||++|+.+.|   +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+..
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   99999999999999999999999999999999999987653

>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=99.62  E-value=7.3e-16  Score=128.97  Aligned_cols=73  Identities=22%  Similarity=0.286  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCC-------CCEEEE
Q 017906            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAE-------NSFVVV   72 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~-------~s~I~v   72 (364)
                      |.|+|+...++ ++.++|++++||.+||++|+.+.|   +|+++|||||+||+|+|+++|++|||++       +++|+|
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 788999999999999999999999   9999999999999999999999999999       999999


Q ss_pred             EEec
Q 017906           73 MLTK   76 (364)
Q Consensus        73 ~v~k   76 (364)
                      +++.
T Consensus        78 vlr~   81 (118)
T 4ajy_B           78 AFRA   81 (118)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.62  E-value=1.1e-15  Score=129.58  Aligned_cols=79  Identities=16%  Similarity=0.262  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhC--CCCCCC--CCeEEEeCCeecCCCCChhhhccCCC------CE
Q 017906            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQG--SDVYPA--SQQMLIHQGKVLKDVTTLEENKVAEN------SF   69 (364)
Q Consensus         1 MkI~VKtl~gk~~-~ieV~~s~TV~dLK~kI~~~~g--~~~ip~--~~qkLif~GkiL~D~~tL~d~gIk~~------s~   69 (364)
                      |+|+||+++|+.| .+++++++||.+||++|+...+  +..+|+  ++|||||+||+|+|+++|++|+|.++      .+
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            6899999999988 6999999999999999965432  112775  79999999999999999999999998      46


Q ss_pred             EEEEEecCCC
Q 017906           70 VVVMLTKSKV   79 (364)
Q Consensus        70 I~v~v~k~k~   79 (364)
                      +||+++.+..
T Consensus        97 mhlVlrl~g~  106 (126)
T 1se9_A           97 MHVIIQAPVT  106 (126)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEeccCCc
Confidence            7777776643

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.62  E-value=5.5e-16  Score=126.37  Aligned_cols=71  Identities=20%  Similarity=0.239  Sum_probs=64.2

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHh-CCCCCCCCCeEEEeCCeecCCCCChhhh--ccCCCCEEEEE
Q 017906            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQ-GSDVYPASQQMLIHQGKVLKDVTTLEEN--KVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk--~~~ieV~~s~TV~dLK~kI~~~~-g~~~ip~~~qkLif~GkiL~D~~tL~d~--gIk~~s~I~v~   73 (364)
                      |+|+||+++|+  .+.|+|++++||.+||++|+.+. |.  +++++|||||+||+|+|+++|++|  +|+++++|+|+
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  67899999999999999999974 51  446999999999999999999999  99999999874

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.62  E-value=2.9e-16  Score=128.20  Aligned_cols=72  Identities=29%  Similarity=0.517  Sum_probs=68.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+ +|+.|.|+|++++||.+||++|+..+|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.
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            5688997 899999999999999999999999999   99999999999999999999999999999999998754

>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=99.62  E-value=1.4e-15  Score=121.38  Aligned_cols=72  Identities=25%  Similarity=0.409  Sum_probs=68.2

Q ss_pred             CEEEEEeCCCcEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE---eCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~i-eV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi---f~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||. .|++|.| +|++++||.+||++|++++|   +|+++|||+   |+||.|+|+.+|++|+|+++++|+||...
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   99999999999999999999999998754

>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=99.62  E-value=1.9e-15  Score=120.61  Aligned_cols=73  Identities=29%  Similarity=0.408  Sum_probs=67.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCC-----CcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCC-CCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPE-----DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKD-VTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s-----~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D-~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||+ .|+.|.|+|+++     +||.+||++|+..+|   +|+++|||+|+||.|+| +++|++|+|+++++|+|+.
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 588999999995     999999999999999   99999999999999988 6689999999999999987


Q ss_pred             ecC
Q 017906           75 TKS   77 (364)
Q Consensus        75 ~k~   77 (364)
                      ++.
T Consensus        84 ~~~   86 (92)
T 1wxv_A           84 KKN   86 (92)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            554

>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=99.61  E-value=1.2e-15  Score=126.39  Aligned_cols=76  Identities=24%  Similarity=0.324  Sum_probs=72.0

Q ss_pred             CEEEEEeC---CCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTL---KGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl---~gk~~~ieV~~-s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+.   +|+.+.|+|++ ++||.+||++|+..+|   +|+++|+|+|+|++|+|+++|++|+|+++++|+|+++.
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   88999999998 9999999999999999   99999999999999999999999999999999999987


Q ss_pred             CCC
Q 017906           77 SKV   79 (364)
Q Consensus        77 ~k~   79 (364)
                      +..
T Consensus       105 ~GG  107 (111)
T 1we6_A          105 RSG  107 (111)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.61  E-value=2.1e-15  Score=133.66  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.++|   +++++|||+|+|+.|+|+++|++|+|+++++|+|+++.+
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   999999999999999999999999999999999998764

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.60  E-value=2.8e-15  Score=118.50  Aligned_cols=70  Identities=24%  Similarity=0.436  Sum_probs=66.3

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      +++++++|+.|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++
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

>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=2.8e-15  Score=130.85  Aligned_cols=73  Identities=30%  Similarity=0.420  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE-e-CCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-H-QGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi-f-~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+++|++|.++|++++||.+||++|+..+|   +|+++|||+ | +|+.|+|+++|++|+|+++++|+++++.
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            79999999999999999999999999999999999   999999999 9 7999999999999999999999999873

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.60  E-value=1.9e-15  Score=136.68  Aligned_cols=77  Identities=35%  Similarity=0.543  Sum_probs=73.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+..+|   +|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+++.+...
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

>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=99.59  E-value=1.3e-15  Score=122.96  Aligned_cols=71  Identities=23%  Similarity=0.365  Sum_probs=65.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+|| +.|++|.|+|++++||.+||++|+..+|   +|+++|||+|+||.| |+.+|++|+|+++++|+|+.++
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            678999 6789999999999999999999999999   999999999999999 5569999999999999998654

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.59  E-value=4.5e-15  Score=122.07  Aligned_cols=73  Identities=19%  Similarity=0.250  Sum_probs=68.5

Q ss_pred             CEEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhcc-CCCCEEEEEEec
Q 017906            1 MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~g--k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gI-k~~s~I~v~v~k   76 (364)
                      |+|+|++..+  .+++|+|++++||.+||++|++++|   +|++.|||+|+|+.|+|+++|.+||| ++|++|||++..
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            6899999875  6899999999999999999999999   99999999999999999999999999 599999999854

>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=99.57  E-value=1.8e-16  Score=134.57  Aligned_cols=76  Identities=36%  Similarity=0.555  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|++|.|+|++++||.+||.+|+..+|   +|++.|+|+|+|+.|+|+.+|++|+|+++++|+|+++.+..
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=99.56  E-value=1.2e-14  Score=124.85  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|+.+.++|++++||.+||++|+..+|   +|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+.+.+
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g---ip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~   74 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCT
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHC---cChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeecc
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999998643

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.1e-14  Score=121.40  Aligned_cols=74  Identities=24%  Similarity=0.282  Sum_probs=67.7

Q ss_pred             EEEEE-eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            2 KVFVK-TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         2 kI~VK-tl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      .|+|+ ...++.|.++++++.||.+||++|+...+   +|++.|+|||+||+|+|+.+|++|||++|.+|||+++...
T Consensus        17 tvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~---iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~~   91 (118)
T 2daf_A           17 TVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLG---IPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFSTN   91 (118)
T ss_dssp             EEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHT---CCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEESC
T ss_pred             EEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhC---CChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecCC
Confidence            45555 55688999999999999999999999999   9999999999999999999999999999999999987643

>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=99.55  E-value=1.7e-14  Score=124.02  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=71.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|+.|.++|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999998753

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.55  E-value=8.2e-15  Score=129.78  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |.|+||+++|+++.++|++++||.+||++|+.++|   +|+++|+|+|+|+.|+|+++|.+|+|+++++|||+++.+.
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            57999999999999999999999999999999999   9999999999999999999999999999999999988653

>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=99.54  E-value=2e-14  Score=119.69  Aligned_cols=76  Identities=24%  Similarity=0.338  Sum_probs=69.6

Q ss_pred             CEEEEEeC----------CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEE
Q 017906            1 MKVFVKTL----------KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFV   70 (364)
Q Consensus         1 MkI~VKtl----------~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I   70 (364)
                      ++|+|+..          +|+++.|+|++++||.+||.+|+...|   +++++|+|+|+|+.|+|+.+|++|+|+++++|
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          478999999999999999999999999   99999999999999999999999999999999


Q ss_pred             EEEEecCCC
Q 017906           71 VVMLTKSKV   79 (364)
Q Consensus        71 ~v~v~k~k~   79 (364)
                      ||+++.+..
T Consensus       103 ~lv~rl~GG  111 (115)
T 1we7_A          103 HLALKERSG  111 (115)
T ss_dssp             EEEECCCSC
T ss_pred             EEEEEcCCC
Confidence            999987754

>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=99.53  E-value=1.1e-15  Score=133.89  Aligned_cols=76  Identities=36%  Similarity=0.555  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|++|.|+|++++||.+||.+|+...|   +|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+++.+..
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GG   76 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (152)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCC
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999987654

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=9e-15  Score=116.59  Aligned_cols=69  Identities=20%  Similarity=0.265  Sum_probs=63.5

Q ss_pred             CEEEEEeCCCcEE--EE-EeCCCCcHHHHHHHHHHH-hCCCCCCCCCeEEEeC--CeecCCCCChhhhccCCCCEEEE
Q 017906            1 MKVFVKTLKGTHF--EI-EVKPEDKVSDVKKNIETV-QGSDVYPASQQMLIHQ--GKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         1 MkI~VKtl~gk~~--~i-eV~~s~TV~dLK~kI~~~-~g~~~ip~~~qkLif~--GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      |+|+||+++|+.+  .| +|++++||.+||++|++. .|   +++++|||+|.  ||+|+|+++|++|+|+++++|||
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            7899999998775  58 999999999999999995 67   99999999976  99999999999999999999876

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=2.6e-14  Score=116.71  Aligned_cols=71  Identities=20%  Similarity=0.314  Sum_probs=65.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif--~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |.+++++++|++|.|+|++++||.+||.+|++++|   +|+++|||+|  .|+ |+|+.+|++|+|+.+++|||++.
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            56778889999999999999999999999999999   9999999996  565 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=99.46  E-value=1e-13  Score=133.84  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=69.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|+.+.|+|++++||.+||++|+.+.|   +++++|||+|+||+|+|+++|++|+|+++++|+|+++.+
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

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.42  E-value=1.5e-13  Score=109.15  Aligned_cols=73  Identities=15%  Similarity=0.070  Sum_probs=63.9

Q ss_pred             EEEEE--eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe-------CCeecCCCCChhhhccCCCCEEEE
Q 017906            2 KVFVK--TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-------QGKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VK--tl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif-------~GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      +|.|.  ..+.+.+++.+++++||.+||.+|+.++|   +|+++|||+|       .|+.|+|+++|++|||++|++|||
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            34454  34556788999999999999999999999   9999999997       488999999999999999999999


Q ss_pred             EEecC
Q 017906           73 MLTKS   77 (364)
Q Consensus        73 ~v~k~   77 (364)
                      +-+.|
T Consensus        81 vd~~P   85 (86)
T 4b6w_A           81 VDLQP   85 (86)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            97654

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.42  E-value=2.2e-13  Score=112.19  Aligned_cols=71  Identities=20%  Similarity=0.234  Sum_probs=65.4

Q ss_pred             CEEEEEeCCCcEEEEEeC-CCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCe-----------e----cCCCCChhhhcc
Q 017906            1 MKVFVKTLKGTHFEIEVK-PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-----------V----LKDVTTLEENKV   64 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~-~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~Gk-----------i----L~D~~tL~d~gI   64 (364)
                      |+|+||+.+|+. .|+|+ +++||.+||++|+.+++   ++++.|+|+|.|+           .    ++|+++|++|||
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   9999999999998           4    588999999999


Q ss_pred             CCCCEEEEEEe
Q 017906           65 AENSFVVVMLT   75 (364)
Q Consensus        65 k~~s~I~v~v~   75 (364)
                      ++|++|||...
T Consensus        84 ~~G~~L~l~~~   94 (107)
T 1wf9_A           84 AHGSMVYLAYE   94 (107)
T ss_dssp             CTTCEEECCCS
T ss_pred             CCCCEEEEEeC
Confidence            99999998765

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.42  E-value=5.9e-13  Score=107.59  Aligned_cols=70  Identities=17%  Similarity=0.195  Sum_probs=62.4

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC--Ce---ec-CCCCChhhhccCCCCEEEE
Q 017906            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GK---VL-KDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         1 MkI~VKtl~gk--~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~--Gk---iL-~D~~tL~d~gIk~~s~I~v   72 (364)
                      ++|+|+...++  .++++|++++||.+||++|+.++|   +|+++|||+|.  |+   .| +|+++|++|+|++|++|+|
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            36788876654  789999999999999999999999   99999999998  55   34 8999999999999999998


Q ss_pred             E
Q 017906           73 M   73 (364)
Q Consensus        73 ~   73 (364)
                      +
T Consensus        93 v   93 (95)
T 2kjr_A           93 V   93 (95)
T ss_dssp             E
T ss_pred             E
Confidence            6

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.38  E-value=1.1e-12  Score=106.42  Aligned_cols=71  Identities=11%  Similarity=0.018  Sum_probs=62.4

Q ss_pred             EEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC---ee----cCCCCChhhhccCCCCEEEE
Q 017906            2 KVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~g--k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~G---ki----L~D~~tL~d~gIk~~s~I~v   72 (364)
                      +|+|+....  +.++++|++++||.+||.+|+.++|   +|+++|||+|.|   +.    ++|+++|++|+|++|++|+|
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            567776443  4789999999999999999999999   999999999988   33    48899999999999999999


Q ss_pred             EEe
Q 017906           73 MLT   75 (364)
Q Consensus        73 ~v~   75 (364)
                      +-.
T Consensus        93 vd~   95 (97)
T 2kj6_A           93 IDL   95 (97)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            864

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.38  E-value=4.2e-14  Score=127.56  Aligned_cols=71  Identities=21%  Similarity=0.257  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|++|.|+|++++||.+||.+|+...|   +|+++|+|||+|++|+|+.+|+     ++++|||+++.+..
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     88999999987643

>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=99.36  E-value=1.4e-12  Score=104.87  Aligned_cols=73  Identities=22%  Similarity=0.209  Sum_probs=63.6

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC---ee----cCCCCChhhhccCCCCEEEE
Q 017906            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~G---ki----L~D~~tL~d~gIk~~s~I~v   72 (364)
                      ++|+|+..... .++++|++++||.+||.+|+..+|   +|+++|||+|.|   +.    |+|+++|.+|||+++++|||
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            36788876553 689999999999999999999999   999999999986   54    58999999999999999998


Q ss_pred             EEec
Q 017906           73 MLTK   76 (364)
Q Consensus        73 ~v~k   76 (364)
                      +...
T Consensus        85 ~d~~   88 (95)
T 1v6e_A           85 IDHS   88 (95)
T ss_dssp             BCCS
T ss_pred             EECC
Confidence            7643

>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.35  E-value=1e-12  Score=90.93  Aligned_cols=40  Identities=23%  Similarity=0.327  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  214 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GI  214 (364)
                      .++.|++|++||   |+|++|++||++++||+++|++||++||
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            478999999999   9999999999999999999999999986

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.35  E-value=1.3e-12  Score=103.10  Aligned_cols=71  Identities=17%  Similarity=0.304  Sum_probs=63.5

Q ss_pred             CEEEEEeCCCcEEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC--CeecC---CCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GKVLK---DVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ie-V~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~--GkiL~---D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||+.+|+. .|+ |++++||.+||.+|+++.|   +++++|+|+|+  +|.|+   |+++|++|||++|++|+|..
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            899999999954 587 9999999999999999999   99999999987  48874   68899999999999998865


Q ss_pred             e
Q 017906           75 T   75 (364)
Q Consensus        75 ~   75 (364)
                      .
T Consensus        77 ~   77 (86)
T 2kzr_A           77 D   77 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1vej_A Riken cDNA 4931431F19; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.34  E-value=1.2e-12  Score=100.74  Aligned_cols=46  Identities=17%  Similarity=0.340  Sum_probs=42.9

Q ss_pred             CcchHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhCCCCC
Q 017906          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~GIP~~  217 (364)
                      ...|++.|++|++||   | +|+.+++||+++++|++||||||++|||+.
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            456999999999999   9 899999999999999999999999998864

>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=99.34  E-value=1.2e-12  Score=100.69  Aligned_cols=44  Identities=36%  Similarity=0.389  Sum_probs=40.8

Q ss_pred             CcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCC
Q 017906          169 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  215 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP  215 (364)
                      ...+++.|++||+||   |+|++|++|||+++||+|||||||++|+.
T Consensus        26 ~~~~ee~I~~L~eMG---F~r~~a~~AL~~~~~nve~Ave~Ll~~~~   69 (73)
T 1vg5_A           26 VAASEEQIQKLVAMG---FDRTQVEVALAAADDDLTVAVEILMSQSG   69 (73)
T ss_dssp             SCCCHHHHHHHHTTT---CCHHHHHHHHHHHTSCHHHHHHHHHTCSC
T ss_pred             CcccHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHHCCC
Confidence            345899999999999   99999999999999999999999999944

>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=99.33  E-value=3.1e-12  Score=103.16  Aligned_cols=76  Identities=14%  Similarity=0.206  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+.+|+.+.|.|.+++++..||++++++.|   ++++.+||+|.|+.|.++.|+++|+|.++++|+|+++.+..
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

>2bwb_A Ubiquitin-like protein DSK2; UBA, signaling protein; 2.3A {Saccharomyces cerevisiae} SCOP: a.5.2.1 PDB: 2bwe_A

Probab=99.32  E-value=1.6e-12  Score=91.37  Aligned_cols=40  Identities=30%  Similarity=0.473  Sum_probs=38.0

Q ss_pred             chHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          171 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .|+..|++|++||   | +|+.+++||+++++|++||||||++|
T Consensus         6 ~~~~~i~~L~~MG---F~d~~~~~~AL~~~~gnv~~Ave~L~~~   46 (46)
T 2bwb_A            6 RYEHQLRQLNDMG---FFDFDRNVAALRRSGGSVQGALDSLLNG   46 (46)
T ss_dssp             HTHHHHHHHHHTT---CCCHHHHHHHHHHHTTCHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHcc
Confidence            5899999999999   9 79999999999999999999999986

>2knz_A Ubiquilin-4; cytoplasm, endoplasmic reticulum, nucleus, phosphoprotein, protein binding; NMR {Mus musculus}

Probab=99.28  E-value=3.4e-12  Score=92.32  Aligned_cols=43  Identities=26%  Similarity=0.375  Sum_probs=40.7

Q ss_pred             cchHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhCCC
Q 017906          170 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIP  215 (364)
Q Consensus       170 ~~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~GIP  215 (364)
                      ..|++.|++|++||   | +|+.|++||++++||++||||||++|++
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            45899999999999   9 9999999999999999999999999865

>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=99.28  E-value=1.4e-11  Score=94.25  Aligned_cols=71  Identities=15%  Similarity=0.227  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||+.+|+.+.+.|..++++..|+++++++.|   +++..++|+|.|+.|.++.|.++|++.+|++|+|++
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   999999999999999999999999999999999873

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.28  E-value=3e-12  Score=124.55  Aligned_cols=72  Identities=18%  Similarity=0.285  Sum_probs=66.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE---eCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi---f~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+|| ++|++|.|+|++++||.+||++|++++|   +|+++||||   |+||+|+|+.+|++|+|++|++|+||.+.
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~   80 (320)
T 3shq_A            6 VVVIVK-WSGKEYPVDLTDQDTVEVLRHEIFRKTQ---VRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGST   80 (320)
T ss_dssp             EEEEEE-ETTEEEEEEEETTSBHHHHHHHHHHHHC---CCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECCC
T ss_pred             EEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEccc
Confidence            578999 6899999999999999999999999999   999999999   89999999999999999999999999654

>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=99.26  E-value=1.2e-11  Score=104.12  Aligned_cols=74  Identities=14%  Similarity=0.130  Sum_probs=64.3

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC---ee----cCCCCChhhhccCCCCEEEE
Q 017906            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~G---ki----L~D~~tL~d~gIk~~s~I~v   72 (364)
                      |+|+|+...+. .++++|++++||.+||.+|+..+|   +|+++|||+|.|   +.    ++|+++|.+|||.+|++|||
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            46788876553 688999999999999999999999   999999999987   43    48999999999999999999


Q ss_pred             EEecC
Q 017906           73 MLTKS   77 (364)
Q Consensus        73 ~v~k~   77 (364)
                      +...+
T Consensus        84 vd~~p   88 (122)
T 1t0y_A           84 VDVTG   88 (122)
T ss_dssp             EECTT
T ss_pred             EeCCC
Confidence            87543

>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=99.26  E-value=1.9e-11  Score=97.96  Aligned_cols=75  Identities=15%  Similarity=0.224  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+.+|+.+.|.|.+++++..||++++++.|   +++..+||+|.|+.|.++.|+++|++.++++|.|++....
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   9999999999999999999999999999999999987654

>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=99.25  E-value=7.3e-12  Score=98.36  Aligned_cols=44  Identities=27%  Similarity=0.381  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh--C-CCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS--G-IPEQT  218 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~--G-IP~~~  218 (364)
                      .++.|++||+||   |+|++|++|||+++||++||+|||++  | ||+.+
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            588999999999   99999999999999999999999999  7 77654

>2jy5_A Ubiquilin-1; UBA, alternative splicing, cytoplasm, nucleus, phosphoprotein, proteasome, signaling protein; NMR {Homo sapiens} PDB: 2jy6_B

Probab=99.24  E-value=1e-11  Score=89.45  Aligned_cols=42  Identities=26%  Similarity=0.411  Sum_probs=39.6

Q ss_pred             CcchHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      ...|++.|++|++||   | +|+.|++||++++||++||||||++|
T Consensus         9 ~~~~~~~l~~L~~MG---F~~~~~~~~AL~~t~gn~e~A~e~L~~~   51 (52)
T 2jy5_A            9 EVRFQQQLEQLSAMG---FLNREANLQALIATGGDINAAIERLLGS   51 (52)
T ss_dssp             TTTTHHHHHHHHHTT---CCCHHHHHHHHHHHTTCHHHHHHHHTTC
T ss_pred             hhHHHHHHHHHHHcC---CCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            356899999999999   9 99999999999999999999999976

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.24  E-value=4.2e-11  Score=93.29  Aligned_cols=70  Identities=13%  Similarity=0.236  Sum_probs=67.1

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |+|+|++.+|+ .+.|.|..++++..|+.+++++.|   ++++.+||+|.|+.|.++.|+++|++.++++|+|+
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   89999999999999999999999999999999986

>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=99.21  E-value=4.4e-11  Score=96.09  Aligned_cols=74  Identities=15%  Similarity=0.231  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+|++.+|+.+.|.|..++++..|+.+++++.|   ++++.+||+|.|+.|.++.|+++|+|.++++|+|++...
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            57899999999999999999999999999999999   899999999999999999999999999999999998754

>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=99.20  E-value=1.6e-11  Score=91.83  Aligned_cols=42  Identities=29%  Similarity=0.369  Sum_probs=39.3

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  216 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~  216 (364)
                      .++.|++|++||   |+|++|++|||+++||++||+|||+++..+
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            588999999999   999999999999999999999999999543

>1wr1_B Ubiquitin-like protein DSK2; UBA domain, UBA-ubiquitin complex, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.19  E-value=1.5e-11  Score=90.44  Aligned_cols=42  Identities=29%  Similarity=0.446  Sum_probs=39.5

Q ss_pred             CcchHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      ...|++.|++|++||   | +|+.+++||+++++|++||||||++|
T Consensus        14 e~~~~~qi~~L~~MG---F~d~~~~~~AL~~~~gnve~Ave~L~~~   56 (58)
T 1wr1_B           14 EERYEHQLRQLNDMG---FFDFDRNVAALRRSGGSVQGALDSLLNG   56 (58)
T ss_dssp             HHHTHHHHHHHHHHT---CCCHHHHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            356899999999999   9 79999999999999999999999998

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.19  E-value=5.2e-11  Score=97.72  Aligned_cols=75  Identities=15%  Similarity=0.229  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+|++.+|+.+.|.|..++++..|+.+++++.|   +++..+||+|.|+.|.++.|+.+|+|.++++|+|++....
T Consensus        25 I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~g---i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~G   99 (104)
T 1wz0_A           25 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG---LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTS   99 (104)
T ss_dssp             EEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHT---CCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCCC
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhC---CCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            57999999999999999999999999999999999   8999999999999999999999999999999999987654

>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.19  E-value=2.1e-11  Score=91.88  Aligned_cols=45  Identities=18%  Similarity=0.198  Sum_probs=41.6

Q ss_pred             cchHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhCCCCC
Q 017906          170 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (364)
Q Consensus       170 ~~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~GIP~~  217 (364)
                      ..|+..|++|++||   | +|+.+++|||++++|++||||||++++++.
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            45899999999999   9 888889999999999999999999998864

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.16  E-value=1.7e-11  Score=91.66  Aligned_cols=43  Identities=40%  Similarity=0.677  Sum_probs=40.5

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~~  217 (364)
                      .++.|++||+||   |+|++|++|||+++||++||+|||+.++++.
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            688999999999   9999999999999999999999999997753

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.14  E-value=8.1e-11  Score=97.52  Aligned_cols=75  Identities=15%  Similarity=0.248  Sum_probs=70.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+|++.+|+.+.|.|..++++..||.+++++.|   ++++.+||+|.|+.|.++.|+++|+|.++++|+|++....
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            67999999999999999999999999999999999   9999999999999999999999999999999999987643

>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=99.12  E-value=1.4e-10  Score=95.42  Aligned_cols=73  Identities=11%  Similarity=0.157  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+|++ +|+.+.|.|..++++..|+.+++++.|   +++..+||+|.|+.|.++.|.++|++.++++|.|++...
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            5789999 999999999999999999999999999   889999999999999999999999999999999998754

>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=99.11  E-value=7.1e-11  Score=90.88  Aligned_cols=41  Identities=20%  Similarity=0.455  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  215 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP  215 (364)
                      .++.|++|++||   |+|++|++|||+++||++||||||+++..
T Consensus        29 ~~~~v~~L~~MG---F~~~~a~~AL~~t~~nve~Ave~L~~~~~   69 (73)
T 1wiv_A           29 DQSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFNNSG   69 (73)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHHSCC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHhCCC
Confidence            578999999999   99999999999999999999999999843

>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=99.10  E-value=4.3e-11  Score=89.80  Aligned_cols=45  Identities=22%  Similarity=0.358  Sum_probs=40.7

Q ss_pred             cchHHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCCCCC
Q 017906          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  217 (364)
Q Consensus       170 ~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GIP~~  217 (364)
                      ...+..|++|++||   |+|+.|++||++++| |+++|+|||+.++++.
T Consensus         7 ~~~e~~v~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~wL~~h~~d~   52 (64)
T 2crn_A            7 GSSPSLLEPLLAMG---FPVHTALKALAATGRKTAEEALAWLHDHCNDP   52 (64)
T ss_dssp             CCSCSSHHHHHHTS---CCHHHHHHHHHHHTSCCHHHHHHHHHHHSSST
T ss_pred             CCCHHHHHHHHHcC---CCHHHHHHHHHHhCCCCHHHHHHHHHhCCCCc
Confidence            34567899999999   999999999999999 9999999999998753

>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} SCOP: a.5.2.1

Probab=99.10  E-value=7.3e-11  Score=79.93  Aligned_cols=38  Identities=29%  Similarity=0.490  Sum_probs=36.3

Q ss_pred             chHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      ++++.|++|++||   |+|++|++||+++.||+++|++||+
T Consensus         3 ~~~~~i~~L~~mG---f~~~~a~~AL~~~~~n~e~A~~~L~   40 (40)
T 1z96_A            3 GLNSKIAQLVSMG---FDPLEAAQALDAANGDLDVAASFLL   40 (40)
T ss_dssp             CHHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             hHHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHC
Confidence            5788999999999   9999999999999999999999995

>2dag_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5 (USP 5), UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=1.1e-10  Score=90.16  Aligned_cols=43  Identities=21%  Similarity=0.370  Sum_probs=40.1

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  217 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GIP~~  217 (364)
                      .++.|++||+||   |+|++|++|||+++| |+++|+|||+.++++.
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 7999999999998764

>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=99.06  E-value=9.8e-11  Score=87.87  Aligned_cols=42  Identities=19%  Similarity=0.344  Sum_probs=38.6

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHc-CChHHHHHHHHhCCCCC
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAY-NNPERAVEYLYSGIPEQ  217 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAaf-nNpdRAvEyL~~GIP~~  217 (364)
                      ++.|++||+||   |+|++|++|||+++ +|+++|++||+.++++.
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            45899999999   99999999999995 89999999999998764

>2ekk_A UBA domain from E3 ubiquitin-protein ligase HUWE1; ubiquitin associated domain, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.05  E-value=1.3e-10  Score=81.87  Aligned_cols=38  Identities=37%  Similarity=0.597  Sum_probs=35.7

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      +++.|++|++||   |+|++|++|||++ ||+++|+|||++.
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            588999999999   9999999999999 7999999999864

>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=99.05  E-value=1e-10  Score=87.81  Aligned_cols=40  Identities=23%  Similarity=0.408  Sum_probs=37.6

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCCC
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIP  215 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GIP  215 (364)
                      +..|++||+||   |+|++|++|||+++| |+++|||||++++-
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            56899999999   999999999999998 99999999998854

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.98  E-value=1.2e-09  Score=87.92  Aligned_cols=72  Identities=18%  Similarity=0.238  Sum_probs=62.0

Q ss_pred             EEEEEe---CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC------ee-c-CCCCChhhhccCCCCEE
Q 017906            2 KVFVKT---LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG------KV-L-KDVTTLEENKVAENSFV   70 (364)
Q Consensus         2 kI~VKt---l~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~G------ki-L-~D~~tL~d~gIk~~s~I   70 (364)
                      +|+|+.   .+|+.+.+.+..++||.+||.+|+..+|   +|+..|||+|.+      .+ | +|.++|.+|+|.+|++|
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 67889999999999999


Q ss_pred             EEEEec
Q 017906           71 VVMLTK   76 (364)
Q Consensus        71 ~v~v~k   76 (364)
                      ||....
T Consensus        88 ~V~d~~   93 (97)
T 1wjn_A           88 LVRWSG   93 (97)
T ss_dssp             EEECCS
T ss_pred             EEEecC
Confidence            998744

>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.98  E-value=4.7e-10  Score=88.33  Aligned_cols=43  Identities=23%  Similarity=0.366  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~~  217 (364)
                      .++.|++||+||   |+|++|++|||+++||+++|+|||+.++.+.
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            588999999999   9999999999999999999999999997653

>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=98.97  E-value=5.4e-10  Score=88.19  Aligned_cols=43  Identities=26%  Similarity=0.365  Sum_probs=39.8

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  217 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GIP~~  217 (364)
                      .+..|++||+||   |+|++|++|||+++| |+++|++||++++++.
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            588999999999   999999999999985 9999999999998753

>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.96  E-value=5.8e-10  Score=81.82  Aligned_cols=39  Identities=28%  Similarity=0.577  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      -++.|..|++||   |.++|+.+||++.-||.+||+|||++-
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            367899999999   999999999999999999999999975

>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=98.90  E-value=1.5e-09  Score=78.62  Aligned_cols=41  Identities=29%  Similarity=0.442  Sum_probs=37.4

Q ss_pred             chHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhCC
Q 017906          171 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGI  214 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~GI  214 (364)
                      .|++.|++|++||   | +|+.+++||+++.+|.+||||||+++.
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            4899999999999   9 666689999999999999999999874

>2lbc_A Ubiquitin carboxyl-terminal hydrolase 13; tandem UBA of USP13; NMR {Homo sapiens}

Probab=98.89  E-value=1.6e-09  Score=91.56  Aligned_cols=41  Identities=41%  Similarity=0.608  Sum_probs=39.7

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  215 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP  215 (364)
                      .+..|++|++||   |+|++|++|||+++||++||+|||++|++
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            588999999999   99999999999999999999999999987

>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=98.87  E-value=2.2e-09  Score=88.29  Aligned_cols=42  Identities=33%  Similarity=0.509  Sum_probs=39.4

Q ss_pred             chHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhCCC
Q 017906          171 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIP  215 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~GIP  215 (364)
                      .|++.|++|++||   | +|+.+++||+++++|++||||||++|.+
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            5899999999999   9 8899999999999999999999999854

>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=98.83  E-value=1.5e-08  Score=84.46  Aligned_cols=73  Identities=19%  Similarity=0.273  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+|++.+|+.+.|.|..++++..|+...+++.|   ++...+||+|.|+.|.++.|.+++++.++++|.|++..
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            46888888899999999999999999999999999   99999999999999999999999999999999998754

>2dkl_A Trinucleotide repeat containing 6C protein; TNRC6C, KIAA1582 protein, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.79  E-value=5.1e-09  Score=82.75  Aligned_cols=38  Identities=29%  Similarity=0.430  Sum_probs=36.9

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      ++.|++|++||   |+|++|++||++.++|+++|+|||+..
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            88999999999   999999999999999999999999987

>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=98.71  E-value=2.8e-09  Score=75.06  Aligned_cols=41  Identities=22%  Similarity=0.327  Sum_probs=38.5

Q ss_pred             chHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCC
Q 017906          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  214 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GI  214 (364)
                      +.+++|++|++||   |+|.+|++||.+.-+|.++|++||+++.
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

>2ooa_A E3 ubiquitin-protein ligase CBL-B; alpha-helical domain; 1.56A {Homo sapiens} PDB: 2oob_A 2jnh_A 2do6_A

Probab=98.61  E-value=4.7e-08  Score=69.35  Aligned_cols=38  Identities=34%  Similarity=0.424  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      .+..|+.||+||   |+|++|++||+.+-||.|-|..+|+.
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            467999999999   99999999999999999999999973

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.57  E-value=1.8e-07  Score=84.99  Aligned_cols=76  Identities=11%  Similarity=0.116  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      ++|+|+ .+|+.+.|.|..++++..||+..+++.|   ++...+||+|.|+.|.++.|.+++++.+|++|.|+.......
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            467887 5889999999999999999999999999   999999999999999999999999999999999999876544

>2d9s_A CBL E3 ubiquitin protein ligase; UBA domain, dimer, protein binding, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.55  E-value=8.6e-08  Score=68.31  Aligned_cols=38  Identities=26%  Similarity=0.401  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      .|..|..||+||   |+|++|++||+.+-||.|-|..+|+.
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            466799999999   99999999999999999999999984

>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=98.53  E-value=1.2e-07  Score=85.17  Aligned_cols=75  Identities=11%  Similarity=0.121  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+|+ .+|+.+.|.|..++++..|++..+++.|   ++...++|+|.|+.|.++.|.+++++.++++|.|++.....
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            457776 4888999999999999999999999999   89999999999999999999999999999999999876553

>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=98.50  E-value=7.6e-08  Score=80.53  Aligned_cols=39  Identities=18%  Similarity=0.313  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      +.+.|.+|++||   |++++|+.||+...||.|||||||+++
T Consensus        76 ~~~~v~~L~eMG---F~~~~a~~AL~~~~nd~erAlewL~~~  114 (118)
T 4ae4_A           76 FLQLMSKFKEMG---FELKDIKEVLLLHNNDQDNALEDLMAR  114 (118)
T ss_dssp             HHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence            567899999999   999999999999999999999999986

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=98.49  E-value=8.1e-08  Score=74.89  Aligned_cols=69  Identities=10%  Similarity=0.181  Sum_probs=57.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCee---c--CCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV---L--KDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~Gki---L--~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |.|.||+.+| .+.|+|++++||.+||.+|.+.++   ++.+.+.|.++-..   |  .++.+|+++||+.|+.|+|.
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            6788998777 888999999999999999999999   87788776554332   3  47889999999999999874

>2oo9_A E3 ubiquitin-protein ligase CBL; alpha-helical domain, homodimer; 2.10A {Homo sapiens}

Probab=98.47  E-value=2.2e-07  Score=63.95  Aligned_cols=41  Identities=29%  Similarity=0.447  Sum_probs=38.5

Q ss_pred             CcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          169 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      |..+|..|..||+||   |+|+.|++||-.+-||.+-|-+.|+.
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   99999999999999999999999973

>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=98.40  E-value=1.6e-06  Score=66.87  Aligned_cols=70  Identities=16%  Similarity=0.224  Sum_probs=65.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~-~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      .+.++..+...+.|.|..+.+|.+|-+..+.+.|   |+.+ .++|.|.|..|+.+.++.+|++.+++.|-||+
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            4667777777899999999999999999999999   9899 99999999999999999999999999999985

>2juj_A E3 ubiquitin-protein ligase CBL; alpha helix, UBA domain, calcium, cytoplasm, metal- binding, phosphorylation, proto-oncogene, SH2 domain; NMR {Homo sapiens}

Probab=98.37  E-value=4e-07  Score=65.04  Aligned_cols=39  Identities=26%  Similarity=0.344  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .|..|..||+||   |+|+.|++||+.+-||.+-|-.+|+.=
T Consensus         7 ~e~~Ia~L~smG---fsr~da~~AL~ia~Ndv~~AtNiLlEf   45 (56)
T 2juj_A            7 LSSEIENLMSQG---YSYQDIQKALVIAQNNIEMAKNILREF   45 (56)
T ss_dssp             HHHHHHHHHTTT---CCHHHHHHHHHHTTTCSHHHHHHHHHS
T ss_pred             ChHHHHHHHHcC---CCHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            678999999999   999999999999999999999999853

>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=98.29  E-value=5.3e-07  Score=81.85  Aligned_cols=43  Identities=33%  Similarity=0.470  Sum_probs=40.2

Q ss_pred             cCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          167 VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       167 ~~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      ..+..+++.|++|++||   |+|++|+.||+...+|.++|+|||++
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            34668999999999999   99999999999999999999999985

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=98.27  E-value=4e-06  Score=67.70  Aligned_cols=70  Identities=10%  Similarity=0.202  Sum_probs=64.0

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      ++|+|+..+|+ .+.|.|..++++..|....+++.|   ++....+|+|.|..|..+.|..++++.++++|.|+
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            35777777784 789999999999999999999999   88999999999999999999999999999999886

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=98.24  E-value=1.3e-07  Score=86.01  Aligned_cols=75  Identities=11%  Similarity=0.122  Sum_probs=0.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+| +.+|+.+.|.|..++++..|++..+++.|   +++..+||+|+|+.|.++.|.+++++.+|++|.|+......
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 67888999999999999999999999999   99999999999999999999999999999999999876553

>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=98.20  E-value=1.9e-06  Score=70.04  Aligned_cols=44  Identities=27%  Similarity=0.571  Sum_probs=41.3

Q ss_pred             cchHHHHHHHHHc-CCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCC
Q 017906          170 SNLEATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  216 (364)
Q Consensus       170 ~~~e~~V~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~  216 (364)
                      .++++.|..||+| |   |++++|+.||..+.++.++|++||+.|.++
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            3578999999999 9   999999999999999999999999999874

>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=98.11  E-value=2.9e-06  Score=70.94  Aligned_cols=39  Identities=33%  Similarity=0.634  Sum_probs=36.7

Q ss_pred             chHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      .-.+.|+.|++||   |+++.|++||++..||+++|+|||+.
T Consensus         7 ~e~~~v~~l~~MG---Fp~~~~~kAl~~~g~~~e~amewL~~   45 (118)
T 4ae4_A            7 SERQCVETVVNMG---YSYECVLRAMKAAGANIEQILDYLFA   45 (118)
T ss_dssp             HHHHHHHHHHHTT---CCHHHHHHHHHHHCSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC---CCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            3578999999999   99999999999999999999999985

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.04  E-value=2.5e-05  Score=62.59  Aligned_cols=72  Identities=11%  Similarity=0.197  Sum_probs=66.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      +.|+|+ .+|..+.|.|..++....|.+..+.+.|   +.++.++++|.|..+.++.|-.++++.++++|.|++.+
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            367788 4788999999999999999999999999   88999999999999999999999999999999999865

>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=98.02  E-value=4.7e-06  Score=59.94  Aligned_cols=42  Identities=24%  Similarity=0.342  Sum_probs=39.1

Q ss_pred             CcchHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .+.|...+.+|.+||   | +++..++|||...+|.++||++|+.+
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            456888999999999   9 99999999999999999999999975

>2lbc_A Ubiquitin carboxyl-terminal hydrolase 13; tandem UBA of USP13; NMR {Homo sapiens}

Probab=97.94  E-value=4.7e-06  Score=70.13  Aligned_cols=41  Identities=27%  Similarity=0.386  Sum_probs=37.7

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCCCC
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPE  216 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GIP~  216 (364)
                      +..|+.|++||   |++..|++|||++.| |.++|++||+...++
T Consensus         4 ~~~l~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~wL~~~~~d   45 (126)
T 2lbc_A            4 ESSVMQLAEMG---FPLEACRKAVYFTGNMGAEVAFNWIIVHMEE   45 (126)
T ss_dssp             THHHHHHHTTS---SCCHHHHHHHHHHTSCCHHHHHHHHHHGGGC
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHcCCCCHHHHHHHHHHhccc
Confidence            56899999999   999999999999988 899999999998654

>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=97.91  E-value=2.4e-05  Score=71.38  Aligned_cols=73  Identities=11%  Similarity=0.141  Sum_probs=67.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      .|+|+. +|+.+.|.|..++++..||+..+++.|   ++.++++|+|.|+.+.++.+..++.+.++++|.++.....
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   9999999999999999999999999999999999976655

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=97.82  E-value=6.1e-05  Score=60.34  Aligned_cols=63  Identities=16%  Similarity=0.109  Sum_probs=49.5

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeec--CCCCChhhhccC-CCCEEEEEE
Q 017906            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVL--KDVTTLEENKVA-ENSFVVVML   74 (364)
Q Consensus         9 ~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL--~D~~tL~d~gIk-~~s~I~v~v   74 (364)
                      ++..+.|.|.+++||..||++|++++|   |++++|+|+|.||.|  +.++.-..|--. ..+-|+++-
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            456788999999999999999999999   999999999999875  455556666433 334555543

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=97.70  E-value=5e-06  Score=81.61  Aligned_cols=74  Identities=11%  Similarity=0.150  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      +.|+|++ +|+.+.+.|..++++..|++..+++.|   ++.+.+|++|+|+.|.++.|.+++++++|++|.|+.....
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            3567776 677888999999999999999999999   8899999999999999999999999999999999987543

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=97.65  E-value=0.0002  Score=56.80  Aligned_cols=74  Identities=18%  Similarity=0.149  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |.|+|-..+++.++|.|.++.++.++-+..+.++|   +.+++-.|.|++|.|+-+..+.-.||-+|+.+.++.+.+
T Consensus        10 m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~g---l~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~s~   83 (90)
T 2al3_A           10 SAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQD---FNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVSR   83 (90)
T ss_dssp             CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTT---CCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSSS
T ss_pred             cEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhC---CChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEccC
Confidence            67899999999999999999999999999999999   888999999999999989999999999999999986544

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=97.62  E-value=8.5e-05  Score=57.94  Aligned_cols=70  Identities=13%  Similarity=0.226  Sum_probs=59.0

Q ss_pred             EEEEEe--CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC---CCeEEEeCCeecCCCCChhhhccCCCCEEEE
Q 017906            2 KVFVKT--LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA---SQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKt--l~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~---~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      +|+|..  ..++.|.+.|....||+.|+..+.+.++.. .+.   ...|+.-+|.+|.++..|.+|+|.+|+.|.+
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   3467788999999999999999999999876

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=97.60  E-value=0.00012  Score=61.80  Aligned_cols=68  Identities=25%  Similarity=0.255  Sum_probs=56.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-------------------------------------Ce
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-------------------------------------QQ   44 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~-------------------------------------~q   44 (364)
                      .|+|+.++|...++.|+.+.||.+++..|+.+.|   +...                                     ++
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   5422                                     33


Q ss_pred             EEEe--CCeecCCCCChhhhccCCCCEEEE
Q 017906           45 MLIH--QGKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus        45 kLif--~GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      ||-.  .+.-|+++++|.++||.++++|.+
T Consensus        90 kL~~dd~~~WLD~srtL~EQGI~e~~tllL  119 (128)
T 2kc2_A           90 KLHTDDELNWLDHGRTLREQGVEEHETLLL  119 (128)
T ss_dssp             SCCCSSSEEEECSSSCHHHHTCCTTSEEEE
T ss_pred             HhcccCCCCcccCCCcHHHcCCCCCCEEEE
Confidence            4421  235678899999999999999655

>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=97.59  E-value=1.7e-05  Score=78.28  Aligned_cols=41  Identities=22%  Similarity=0.353  Sum_probs=38.8

Q ss_pred             cchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       170 ~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      ++.++.|++|++||   |+|++|++||+++.+|.+||++||+++
T Consensus       323 ~ee~eaI~rL~~mG---F~~~~a~~al~a~~~n~e~A~~~L~~~  363 (368)
T 1oqy_A          323 PQEKEAIERLKALG---FPESLVIQAYFACEKNENLAANFLLSQ  363 (368)
T ss_dssp             TTTHHHHHHHHHHT---CCSHHHHHHTSSSSSCSSHHHHHHHHH
T ss_pred             CcCHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHhhC
Confidence            45788999999999   999999999999999999999999986

>2cos_A Serine/threonine protein kinase LATS2; UBA domain, structure genomics, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=97.57  E-value=9.4e-05  Score=52.78  Aligned_cols=39  Identities=28%  Similarity=0.395  Sum_probs=35.0

Q ss_pred             chHHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHh
Q 017906          171 NLEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYS  212 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~  212 (364)
                      ..-++++.|++||   |+++-|++||+..-| ..+-|+|||.-
T Consensus         8 vn~qmlq~L~eMG---Fd~erae~Alk~Tg~~Gle~AmewL~k   47 (54)
T 2cos_A            8 VNRQMLQELVNAG---CDQEMAGRALKQTGSRSIEAALEYISK   47 (54)
T ss_dssp             CCHHHHHHHHHHH---CCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcC---CCHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            3567899999999   999999999999877 79999999973

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=97.48  E-value=1.6e-05  Score=78.70  Aligned_cols=73  Identities=10%  Similarity=0.132  Sum_probs=0.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      .|+|+. +|+.+.|.|..++++..||+..+++.|   ++..+++|+|+|+.|.++.|.+++++.++++|.+++....
T Consensus        32 ~lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g---~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~g  104 (389)
T 4da1_A           32 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIG  104 (389)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             EEEEec-CCcEEEEEECCCChHHHHHHHHHHHhC---CCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeecccc
Confidence            466665 677788999999999999999999999   9999999999999999999999999999999999987654

>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=97.34  E-value=0.00018  Score=67.47  Aligned_cols=43  Identities=30%  Similarity=0.431  Sum_probs=40.2

Q ss_pred             cCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          167 VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       167 ~~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      +.+.+|++.|++|++||   |+|++|+.||+...+|-++|+|||+.
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            44678999999999999   99999999999999999999999985

>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=97.31  E-value=0.00085  Score=52.10  Aligned_cols=68  Identities=18%  Similarity=0.246  Sum_probs=57.8

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeec---CCCCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVL---KDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL---~D~~tL~d~gIk~~s~I~v~   73 (364)
                      +|.||..+|+.+.-....++||.+|+..|.. .+   +.....+|+  |-.|.|   +.+++|+++|+....+|+|-
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            6889999999888888999999999999988 56   667888998  567888   34789999999988888764

>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=97.25  E-value=0.0027  Score=51.91  Aligned_cols=71  Identities=13%  Similarity=0.209  Sum_probs=59.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC--C-CCChhhhccCCCCEEEEEEe
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--D-VTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~--D-~~tL~d~gIk~~s~I~v~v~   75 (364)
                      +|.||..+|+.+.-.+..++||.+|+..|....+   .+.....|+  |-.|.|.  | +++|+++|+....+|+|...
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            6889999999999999999999999999999877   556777886  6788886  3 68999999998877766543

>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=96.71  E-value=0.0038  Score=52.21  Aligned_cols=68  Identities=22%  Similarity=0.363  Sum_probs=58.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeec--CC-CCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVL--KD-VTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL--~D-~~tL~d~gIk~~s~I~v~   73 (364)
                      +|.||..+|+.+.-.+..++||.+|...|... +   +.....+|+  |-.|.|  .| +++|.++|+.....|+|.
T Consensus        45 ~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~---~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~  117 (124)
T 1wj4_A           45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-G---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-H---CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C---CCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEE
Confidence            68899999998888999999999999999886 6   667788887  668888  34 799999999988877765

>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=96.41  E-value=0.023  Score=46.20  Aligned_cols=68  Identities=16%  Similarity=0.145  Sum_probs=56.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC--CCCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--DVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~--D~~tL~d~gIk~~s~I~v~   73 (364)
                      +|.||..+|+.+.-.+..++||.+|...|... +   +.....+|+  |-.|.|.  .+++|+++||....+|+|-
T Consensus        25 ~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~---~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve   96 (109)
T 2cr5_A           25 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-G---YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVE   96 (109)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-T---CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C---CCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEE
Confidence            68899999998888888999999999999965 4   456778886  6678886  3789999999988777664

>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=96.28  E-value=0.015  Score=48.69  Aligned_cols=66  Identities=18%  Similarity=0.286  Sum_probs=54.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC-CCChhhhccCCCCE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENSF   69 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~D-~~tL~d~gIk~~s~   69 (364)
                      +|.||..+|+.+.-.+..++||.+|+..|..... + +......|+  |-.|.|.| +++|+++|+.+...
T Consensus        54 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~-~-~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psav  122 (127)
T 1s3s_G           54 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARP-A-MAATSFVLMTTFPNKELADENQTLKEANLLNAVI  122 (127)
T ss_dssp             CEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCS-G-GGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCc-C-CCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceE
Confidence            5889999999998899999999999999998642 0 445677886  67899975 69999999997433

>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=95.93  E-value=0.0076  Score=44.00  Aligned_cols=39  Identities=28%  Similarity=0.356  Sum_probs=36.9

Q ss_pred             hHHHHHHHHHc--CCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .|+.|..|.+|  .   ++++.|+..|++.-||.|+|++.|+.-
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            68999999999  6   899999999999999999999999976

>2pwq_A Ubiquitin conjugating enzyme; structural genomics consortium, SGC, ligase; 1.90A {Plasmodium yoelii}

Probab=95.85  E-value=0.0014  Score=60.00  Aligned_cols=41  Identities=24%  Similarity=0.293  Sum_probs=0.0

Q ss_pred             chHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCC
Q 017906          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  214 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GI  214 (364)
                      .+++.|+++++||   |+|++|++||+..-.+.++|+|.|+.|+
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            4588999999999   9999999999999999999999999884

>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=95.60  E-value=0.049  Score=42.53  Aligned_cols=70  Identities=14%  Similarity=0.208  Sum_probs=59.4

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe---CCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif---~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      ++.|.....+++.+.|++..++.+|--.|+++..   +.++...|..   .+..|+-+++|.||||++   ++.+-.++
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            5677777788899999999999999999999987   8888888874   456788899999999997   77766555

>1otr_A Protein CUE2; protein-protein complex, cell cycle; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.4

Probab=95.33  E-value=0.024  Score=39.82  Aligned_cols=39  Identities=15%  Similarity=0.236  Sum_probs=36.0

Q ss_pred             hHHHHHHHHHc--CCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      -+..|+.|+||  .   -+++.|.++|+++-+|.|||+..|+++
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            47889999999  4   599999999999999999999999987

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=95.30  E-value=0.05  Score=41.23  Aligned_cols=60  Identities=17%  Similarity=0.246  Sum_probs=46.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |+|+||....+...+++....||.+|-++    .|   ++++..-+..||+++..+.      +.+||.|.++
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            89999976444566899999999998765    67   8888888889999986555      2347877765

>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.29  E-value=0.035  Score=41.52  Aligned_cols=45  Identities=13%  Similarity=0.137  Sum_probs=39.1

Q ss_pred             CCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          168 AGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       168 ~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .+.+++..|+.|.+|= -.++++-|+..|++.-+|.|+|++-|+.-
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            4567899999999991 11799999999999999999999999864

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=94.71  E-value=0.2  Score=41.02  Aligned_cols=64  Identities=20%  Similarity=0.251  Sum_probs=46.2

Q ss_pred             CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCC------CCCeEEEe----CCeecCCC-------------CChhhhccCC
Q 017906           10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYP------ASQQMLIH----QGKVLKDV-------------TTLEENKVAE   66 (364)
Q Consensus        10 gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip------~~~qkLif----~GkiL~D~-------------~tL~d~gIk~   66 (364)
                      +..+.+.|-..+||.++|+||-+..-+. +|      ++.+.|-|    .|++|.|.             .||..|+|.+
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            4467888889999999999999775332 33      34566665    35677652             3788999999


Q ss_pred             CCEEEEEE
Q 017906           67 NSFVVVML   74 (364)
Q Consensus        67 ~s~I~v~v   74 (364)
                      |.+|.++-
T Consensus       102 gatl~l~~  109 (111)
T 4e71_A          102 GATLILSK  109 (111)
T ss_dssp             TCEEEEEE
T ss_pred             CCEEEEEe
Confidence            99998753

>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=94.69  E-value=0.024  Score=61.53  Aligned_cols=41  Identities=39%  Similarity=0.670  Sum_probs=37.8

Q ss_pred             cchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       170 ~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      ...++.|..|++||   |++++.++||++..||.+|||+||.+.
T Consensus       718 ~~~~e~i~~l~~mG---f~~~~a~~aL~~t~~~~eraidwlfs~  758 (854)
T 3ihp_A          718 PPPEDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSH  758 (854)
T ss_dssp             -CCHHHHHHHHTTT---CCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcC---CCHHHHHHHHHhhcCcHHHHHHhhhcC
Confidence            34678999999999   999999999999999999999999986

>2di0_A Activating signal cointegrator 1 complex subunit 2; ASCC2, CUE domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=94.55  E-value=0.11  Score=39.28  Aligned_cols=50  Identities=14%  Similarity=0.341  Sum_probs=43.4

Q ss_pred             cCCcchHHHHHHHHHc--CCCCCCHHHHHHHHHHHcCChHHHHHHHHhC-CCCCCC
Q 017906          167 VAGSNLEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG-IPEQTA  219 (364)
Q Consensus       167 ~~g~~~e~~V~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEyL~~G-IP~~~~  219 (364)
                      +.+.+.+..|.+|.++  -   |....|.++|..-.+|+++.|.+|+.| +|.++.
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   679999999999778999999999999 787653

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=94.42  E-value=0.23  Score=36.80  Aligned_cols=61  Identities=18%  Similarity=0.270  Sum_probs=45.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|.--. ....+++....||.+|.+.+    +   ++.....+..+|+++..+.     -+++|+.|.++-
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            567766322 24567788889999999875    5   5567777889999997654     588899998863

>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=94.38  E-value=0.16  Score=43.06  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=47.7

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCeEEEe----CCe-ecCCC-------------CChhhhccCC
Q 017906           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGK-VLKDV-------------TTLEENKVAE   66 (364)
Q Consensus        11 k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~------~~qkLif----~Gk-iL~D~-------------~tL~d~gIk~   66 (364)
                      ..+.+.|-..|||.++|+||-+..-++ +|.      +++-|-+    .|+ +|.|.             .||..|+|.+
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            457888989999999999999887644 543      3445554    344 46653             2899999999


Q ss_pred             CCEEEEEEec
Q 017906           67 NSFVVVMLTK   76 (364)
Q Consensus        67 ~s~I~v~v~k   76 (364)
                      |.+|.++-+.
T Consensus       120 ga~l~l~~~~  129 (138)
T 2r2o_A          120 GATVALVPCL  129 (138)
T ss_dssp             TCEEEEEEC-
T ss_pred             CCEEEEEECC
Confidence            9999887544

>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.2

Probab=93.86  E-value=0.093  Score=38.83  Aligned_cols=36  Identities=14%  Similarity=0.177  Sum_probs=33.1

Q ss_pred             HHHHHHHHHc-CCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          173 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       173 e~~V~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      .+.|..|.++ |   +...+|..||..+.+|.+.|++||-
T Consensus        10 ~~~Vk~LRe~TG---ag~~dcKkAL~e~~GDi~~Ai~~Lr   46 (64)
T 2cp9_A           10 KELLMKLRRKTG---YSFVNCKKALETCGGDLKQAEIWLH   46 (64)
T ss_dssp             CHHHHHHHHHHC---CCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            3579999997 7   8999999999999999999999996

>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=93.42  E-value=0.41  Score=43.73  Aligned_cols=61  Identities=13%  Similarity=0.249  Sum_probs=50.2

Q ss_pred             EEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CeEEEe-C----CeecCC-CCChhhhccCCCCEEEEEEec
Q 017906           13 FEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIH-Q----GKVLKD-VTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus        13 ~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~-~qkLif-~----GkiL~D-~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      +++.++..+||.+|+++++..++   ++.+ ..||-. .    ...|.| +.+|.+++|.++..|+|=++.
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            55778999999999999999999   8887 688853 2    245765 689999999999999887764

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=93.22  E-value=0.33  Score=43.95  Aligned_cols=62  Identities=13%  Similarity=0.240  Sum_probs=50.6

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CeEEE--e-CC--eecCC-CCChhhhccCCCCEEEEEEec
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLI--H-QG--KVLKD-VTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~-~qkLi--f-~G--kiL~D-~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      .+++.++..+||.+|+++++..++   ++.+ ..||-  | .+  ..|+| +++|.+++|.++..|+|=++.
T Consensus       141 ~~~~~~Sk~~ti~~l~~~~~~~~~---i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~r~  209 (217)
T 4a3p_A          141 VVTRRFSKADTIDTIEKEIRKIFS---IPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKN  209 (217)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHTT---CCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEECC
T ss_pred             ceEEEEcccchHHHHHHHHHHHhC---CCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEEec
Confidence            366788999999999999999999   8886 68883  3 23  34666 679999999999999887764

>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=93.06  E-value=0.57  Score=36.81  Aligned_cols=68  Identities=21%  Similarity=0.291  Sum_probs=47.7

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCC--CCC------CCCCeEEEeCCeecCCCCChhhhccC
Q 017906            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGS--DVY------PASQQMLIHQGKVLKDVTTLEENKVA   65 (364)
Q Consensus         1 MkI~VKtl~------g-k~~~ieV~~s~TV~dLK~kI~~~~g~--~~i------p~~~qkLif~GkiL~D~~tL~d~gIk   65 (364)
                      |+|+||.+.      | ....+++....||.+|.+.+......  ..+      ......+..||+.+..     ++-|+
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            678888663      3 46778888889999999999877420  000      0234567789988753     55688


Q ss_pred             CCCEEEEE
Q 017906           66 ENSFVVVM   73 (364)
Q Consensus        66 ~~s~I~v~   73 (364)
                      +|+.|.++
T Consensus        85 dGDeV~i~   92 (98)
T 1vjk_A           85 DGDVVGVF   92 (98)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEE
Confidence            99998876

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=92.16  E-value=0.38  Score=35.84  Aligned_cols=65  Identities=6%  Similarity=0.183  Sum_probs=45.0

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCC--CCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPA--SQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~--~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |+|+||.+..- .-.+++ ...||.+|++.+....+   +..  ....+..||+.+.+    .+.-+++|+.|.++
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            88999977532 134666 56899999999986533   221  45667778887543    24458899999887

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=91.80  E-value=0.85  Score=38.09  Aligned_cols=65  Identities=22%  Similarity=0.300  Sum_probs=47.3

Q ss_pred             CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCC------CCCeEEEe----CCe-ecCCC-------------CChhhhccC
Q 017906           10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYP------ASQQMLIH----QGK-VLKDV-------------TTLEENKVA   65 (364)
Q Consensus        10 gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip------~~~qkLif----~Gk-iL~D~-------------~tL~d~gIk   65 (364)
                      +..+.+.|-..|||.++|+||-+..-+. +|      ++.+.|-|    .|+ +|.|.             .||..|+|.
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            4567888889999999999999875432 33      35666765    234 36552             478899999


Q ss_pred             CCCEEEEEEe
Q 017906           66 ENSFVVVMLT   75 (364)
Q Consensus        66 ~~s~I~v~v~   75 (364)
                      +|.+|.+..+
T Consensus        95 dgatv~l~~~  104 (127)
T 3h6n_A           95 EGASLAMSLI  104 (127)
T ss_dssp             TTCEEEEEEC
T ss_pred             CCCEEEEEEc
Confidence            9999988744

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=91.32  E-value=0.65  Score=38.31  Aligned_cols=63  Identities=24%  Similarity=0.357  Sum_probs=45.0

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCeEEEe-CC---e-ecCCC-------------CChhhhccCCC
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH-QG---K-VLKDV-------------TTLEENKVAEN   67 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~------~~qkLif-~G---k-iL~D~-------------~tL~d~gIk~~   67 (364)
                      .+.+.|-..+||.++|+||-+..-+. +|.      +.+.|-| .|   + +|.|.             .||..|+|.+|
T Consensus        28 ~i~VkVLdCDTItQvKeKiLd~vyk~-~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  106 (117)
T 4e74_A           28 EVPVKILNCDTITQVKEKILDAIFKN-VPCSHRPKAADMDLEWRQGSGARMILQDEDITTKIENDWKRLNTLAHYQVPDG  106 (117)
T ss_dssp             CEEEEEETTSBHHHHHHHHHHHHTTT-SCGGGSCCGGGEEEEEECTTSCEEEECSSSTTCCC---CCCCCBHHHHTCCTT
T ss_pred             ceEeeeecCCchHHHHHHHHHHHhcC-CCcccCCCCCceeEEEecCCCCceEeecCCCccEecCcceEeccccccCCCCC
Confidence            47788889999999999999775332 433      3556654 23   3 35441             37899999999


Q ss_pred             CEEEEEEe
Q 017906           68 SFVVVMLT   75 (364)
Q Consensus        68 s~I~v~v~   75 (364)
                      .+|.++-+
T Consensus       107 atl~l~~~  114 (117)
T 4e74_A          107 SVVALVSK  114 (117)
T ss_dssp             CEEEEEEC
T ss_pred             CEEEEEeC
Confidence            99988754

>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=90.77  E-value=0.77  Score=44.40  Aligned_cols=71  Identities=13%  Similarity=0.067  Sum_probs=54.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCC-CCCCCCeEEEe------CCeecCCCCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSD-VYPASQQMLIH------QGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~-~ip~~~qkLif------~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      .+.|... +.+.++.++++.||.++.++|.++.... ..+.++--|..      +|+=|++.++|..|++.+++.|...
T Consensus         5 ~~~~~~~-~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~   82 (371)
T 3ivf_A            5 SLKISIG-NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYR   82 (371)
T ss_dssp             EEEEEET-TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEE
T ss_pred             EEEEEec-ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeecc
Confidence            3445543 6678899999999999999998886510 12456667766      4566888999999999999988765

>1ip9_A BEM1 protein; ubiquitin alpha/beta roll, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 1ipg_A 2kfk_A

Probab=89.58  E-value=0.54  Score=36.60  Aligned_cols=44  Identities=14%  Similarity=0.109  Sum_probs=33.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE-eCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-HQG   50 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi-f~G   50 (364)
                      |||.|- .++..|-|.|..+.+..+||.||..+..   +  +.+.|+ |++
T Consensus        13 ~KVK~y-y~DDIiAIrvP~di~~~~L~dKi~~RLk---~--~~~~l~~ykd   57 (85)
T 1ip9_A           13 TKIKFY-YKDDIFALMLKGDTTYKELRSKIAPRID---T--DNFKLQTKLF   57 (85)
T ss_dssp             EEEEEC-BTTCCEEEEECSCCCHHHHHHHHHHHHT---S--SCEEEEECCS
T ss_pred             eEEEEE-ecCcEEEEECCCCCCHHHHHHHHHHHhc---c--cceEEEEecC
Confidence            344444 3567899999999999999999999987   4  556554 443

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=89.15  E-value=2.6  Score=32.10  Aligned_cols=58  Identities=10%  Similarity=0.168  Sum_probs=41.3

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCC---CCC-----CCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906           11 THFEIEVKPEDKVSDVKKNIETVQGSD---VYP-----ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus        11 k~~~ieV~~s~TV~dLK~kI~~~~g~~---~ip-----~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      +...+++....||.+|++.+......-   .+.     .....+..||+....     ++-|++|+.|.++
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~~~~~~l~~~g~l~~~~~v~VN~~~v~~-----~~~l~~gDeV~i~   83 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPALESRVFGDDGELYDHINVLRNGEAAAL-----GEATAAGDELALF   83 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGGGHHHHBCTTSCBCTTSEEEETTEECCT-----TSBCCTTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcHHHHHHhccCCcccccEEEEECCEECCC-----CcccCCCCEEEEE
Confidence            567888888899999999998875310   000     023577789988865     4458889999887

>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=88.83  E-value=0.7  Score=35.83  Aligned_cols=45  Identities=11%  Similarity=0.028  Sum_probs=37.8

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~G   50 (364)
                      ++||-.-..++.|.|..+.+..+|+.+|.++.+   ++.+..+|.|+-
T Consensus         6 ~~VKV~~~~tvairvp~~~~y~~L~~~l~~kL~---l~~~~~~LsYk~   50 (83)
T 1oey_A            6 YTLKVHYKYTVVMKTQPGLPYSQVRDMVSKKLE---LRLEHTKLSYRP   50 (83)
T ss_dssp             EEEEEESSSEEEEEECTTCCHHHHHHHHHHHTT---CCGGGCCEEECC
T ss_pred             EEEEEEEEEEEEEECCCCCCHHHHHHHHHHHhC---CCcceeEEEeeC
Confidence            344433347899999999999999999999999   888999999965

>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=87.97  E-value=2.1  Score=39.72  Aligned_cols=75  Identities=16%  Similarity=0.135  Sum_probs=55.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe---CCe--ecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGK--VLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif---~Gk--iL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |.|.|..++| ++.|.|+...|+.+|-..|+...|.  ...+-.-|.|   +|.  -|+.++.|.+.+++.+..+.+..+
T Consensus         2 i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~L--~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l~fr   78 (294)
T 1ef1_A            2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGL--REVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFR   78 (294)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTC--CCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcCC--CCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEEEEE
Confidence            4688888888 7889999999999999999999993  2233445555   343  377788898887766666666666


Q ss_pred             cCC
Q 017906           76 KSK   78 (364)
Q Consensus        76 k~k   78 (364)
                      ++-
T Consensus        79 ~kf   81 (294)
T 1ef1_A           79 AKF   81 (294)
T ss_dssp             ESS
T ss_pred             EEE
Confidence            543

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=87.95  E-value=0.68  Score=36.08  Aligned_cols=57  Identities=9%  Similarity=0.239  Sum_probs=41.0

Q ss_pred             CCCcEEEEEeCCC-CcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            8 LKGTHFEIEVKPE-DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         8 l~gk~~~ieV~~s-~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      ++|+.  +++... .||.+|.+.+    +   ++.....+..+|+++..+ ...+.-|++||.|.++-
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            35665  445665 8999998875    5   556777888999998532 34455689999998873

>4dbg_B Ring finger protein 31; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens}

Probab=87.85  E-value=0.35  Score=41.86  Aligned_cols=38  Identities=24%  Similarity=0.203  Sum_probs=32.4

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      +...|.+|++.|  -|+|++|+.||+.+-.|.++|+--|-
T Consensus       102 R~~K~~eL~s~G--~~~~~~~~~aL~~~~Gdv~~Al~eLq  139 (162)
T 4dbg_B          102 RRRKVQELQSLG--FGPEEGSLQALFQHGGDVSRALTELQ  139 (162)
T ss_dssp             HHHHHHHHHHTT--CCGGGTHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhcC--CchHHHHHHHHHHcCCcHHHHHHHHH
Confidence            456788899999  33999999999999999999996663

>1h4r_A Merlin; FERM, neurofibromatosis, NF2, structural protein, cytoskeleton, anti-oncogene; 1.8A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1isn_A 3u8z_A

Probab=87.36  E-value=2.4  Score=39.84  Aligned_cols=74  Identities=15%  Similarity=0.053  Sum_probs=55.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe--CCe--ecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGK--VLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif--~Gk--iL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |.+.|..++| ++.|.|+.+.|+.+|-..|+...|.  ...+-.-|.|  +|.  -|+.++.|.+.+++.+..+.+..++
T Consensus        23 ~~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~L--~e~~~FgL~~~~~~~~~wL~~~~~i~~q~~~~~~~~~l~fr~   99 (314)
T 1h4r_A           23 FTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGL--RETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFLA   99 (314)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTC--CCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEEE
T ss_pred             eEEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhCC--CCCccceEEEEeCCcCeeCCCccCHHHcCCCCCCCEEEEEEE
Confidence            3578888898 7889999999999999999999993  2234445555  443  3788889998877666666666655


Q ss_pred             C
Q 017906           77 S   77 (364)
Q Consensus        77 ~   77 (364)
                      +
T Consensus       100 k  100 (314)
T 1h4r_A          100 K  100 (314)
T ss_dssp             S
T ss_pred             E
Confidence            4

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=87.26  E-value=1.7  Score=33.72  Aligned_cols=61  Identities=13%  Similarity=0.126  Sum_probs=52.2

Q ss_pred             EEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906           13 FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus        13 ~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      +.-.++-..++..||+.++.+.+   +.-+.-.+...+..|+++++|.|-+|+-...|.+.+--
T Consensus         5 i~qhmDI~epL~~Lk~LLe~Rl~---i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqi   65 (89)
T 2juo_A            5 VSQAIDINEPIGNLKKLLEPRLQ---CSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQV   65 (89)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHHC---SCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEE
T ss_pred             hhhhccccCcHHHHHHHHHHHhc---CCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEE
Confidence            34456667899999999999999   77888888888888999999999999988888887654

>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=87.22  E-value=0.43  Score=51.75  Aligned_cols=42  Identities=21%  Similarity=0.385  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCC-hHHHHHHHHhCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNN-PERAVEYLYSGIPE  216 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnN-pdRAvEyL~~GIP~  216 (364)
                      .+..|+.|++||   |++..+++||.+.-|+ .++|++||+..+-+
T Consensus       652 d~~~l~~L~~mG---f~~~~~~kal~~t~n~~~e~a~~wl~~hmdd  694 (854)
T 3ihp_A          652 DESVIIQLVEMG---FPMDACRKAVYYTGNSGAEAAMNWVMSHMDD  694 (854)
T ss_dssp             -CHHHHHHHHHT---CCHHHHHHHHHHTTSCCHHHHHHHHHHHTTS
T ss_pred             CHHHHHHHHhcC---CCHHHHHHHHhhcCCCchHHHhHHHhhccCc
Confidence            467899999999   9999999999999876 99999999987643

>2llw_A Heat shock protein STI1; DP domain, alpha helix, chaperone; NMR {Saccharomyces cerevisiae}

Probab=86.35  E-value=0.7  Score=34.73  Aligned_cols=36  Identities=28%  Similarity=0.445  Sum_probs=21.8

Q ss_pred             hhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHH
Q 017906          279 FLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQ  319 (364)
Q Consensus       279 ~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I~  319 (364)
                      .+.++|+|+++=+-+++||..+..++.     ||.++..|+
T Consensus        24 ~im~DP~~~~~lq~~~~NP~~~~k~~~-----nP~v~~~i~   59 (71)
T 2llw_A           24 AIMQDPVMQSILQQAQQNPAALQEHMK-----NPEVFKKIQ   59 (71)
T ss_dssp             HHHTCTHHHHHHHHHHHCHHHHHHHHH-----SHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHCHHHHHHHHh-----CHHHHHHHH
Confidence            345666666666666666666666543     666666654

>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=86.05  E-value=0.67  Score=32.65  Aligned_cols=38  Identities=24%  Similarity=0.386  Sum_probs=32.6

Q ss_pred             chHHHHHHHHHcCCCCCCHHH--HHHHHHHHcCChHHHHHHHH
Q 017906          171 NLEATVQQILDMGGGSWDRET--VIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f~r~q--v~~ALrAafnNpdRAvEyL~  211 (364)
                      ..++.|.+|++||   |+-+-  ..+.|.+..+|-.+|++-|-
T Consensus         9 rl~~al~qMl~MG---F~negGWLt~LL~~k~gDI~~aLD~lq   48 (52)
T 1q02_A            9 RLIESLSQMLSMG---FSDEGGWLTRLLQTKNYDIGAALDTIQ   48 (52)
T ss_dssp             HHHHHHHHHHTTT---CCCTTSHHHHHHHHTTTCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcC---CCccccHHHHHHHHccCCHHHHHHHhh
Confidence            4789999999999   96554  46999999999999999873

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=85.55  E-value=1.8  Score=31.52  Aligned_cols=62  Identities=18%  Similarity=0.078  Sum_probs=41.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|+..+|+.  +++....|+.+|-+.|....+     ....-...+|++.+-+     +-|++|+.|.++-
T Consensus         1 m~i~i~~p~g~~--~~~~~g~T~~dla~~i~~~l~-----~~~vaa~vNg~lvdl~-----~~L~~~~~Veivt   62 (73)
T 2kmm_A            1 MEVMVFTPKGEI--KRLPQGATALDFAYSLHSDLG-----DHCIGAKVNHKLVPLS-----YVLNSGDQVEVLS   62 (73)
T ss_dssp             CCEEEECTTCCE--EEECTTCBHHHHHHHHCSHHH-----HTEEEEEETTEECCTT-----CBCCSSSBEEEEE
T ss_pred             CeEEEEcCCCCE--EEcCCCCcHHHHHHHHhhccc-----cceEEEEECCEEeCCC-----cCcCCCCEEEEEE
Confidence            788998778876  456678999999888754432     1223334689877654     4456778777764

>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=85.17  E-value=2.3  Score=32.67  Aligned_cols=71  Identities=13%  Similarity=0.108  Sum_probs=44.1

Q ss_pred             CEEEEEeCC------CcEEEEEeCCCCcHHHHHHHHHHHhCCC--CC-C-------CCCeEEEeCCeecCCCCChhhhcc
Q 017906            1 MKVFVKTLK------GTHFEIEVKPEDKVSDVKKNIETVQGSD--VY-P-------ASQQMLIHQGKVLKDVTTLEENKV   64 (364)
Q Consensus         1 MkI~VKtl~------gk~~~ieV~~s~TV~dLK~kI~~~~g~~--~i-p-------~~~qkLif~GkiL~D~~tL~d~gI   64 (364)
                      |+|+|+.+.      |+...++++ ..||.+|+..+..++..-  .+ .       .....+..||+...+..- .+.-|
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-GDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVNIYVNDEDVRFSGG-LATAI   78 (93)
T ss_dssp             -CEEEECCGGGGGGTTTCSEEEEC-CSBHHHHHHHHHHHSTTHHHHHBCSSSTTSBCTTEEEEETTEEGGGTTG-GGCBC
T ss_pred             CEEEEEEeHHHHHHhCCCeEEecC-CCCHHHHHHHHHHHChhHHHHHhccccCCcccCCEEEEECCEEccCcCC-CCcCC
Confidence            788888542      433346654 579999999998875310  00 0       113566778887754222 24568


Q ss_pred             CCCCEEEEE
Q 017906           65 AENSFVVVM   73 (364)
Q Consensus        65 k~~s~I~v~   73 (364)
                      ++|+.|.++
T Consensus        79 ~~gDeV~i~   87 (93)
T 3dwg_C           79 ADGDSVTIL   87 (93)
T ss_dssp             CTTCEEEEE
T ss_pred             CCCCEEEEE
Confidence            999999887

>2k5p_A THis protein, thiamine-biosynthesis protein; NESG, GMR137, structural genomics, PSI-2, protein structure initiative; NMR {Geobacter metallireducens gs-15} PDB: 3cwi_A

Probab=84.68  E-value=0.97  Score=34.34  Aligned_cols=63  Identities=16%  Similarity=0.219  Sum_probs=44.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCC-CCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip-~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|   +|+.+.+......||.+|.+.    .+   ++ ....-+.++|.++.. ....++-+++||.|-++-
T Consensus         1 M~I~v---NGe~~e~~~~~~~Tl~~LL~~----l~---~~~~~~vAVavNg~iVpr-~~~~~~~L~dGD~IEIv~   64 (78)
T 2k5p_A            1 MNLTV---NGKPSTVDGAESLNVTELLSA----LK---VAQAEYVTVELNGEVLER-EAFDATTVKDGDAVEFLY   64 (78)
T ss_dssp             CEEEE---TTEEEECSSCSCEEHHHHHHH----HT---CSCTTTCCEEETTEECCT-THHHHCEECSSBCEEECC
T ss_pred             CEEEE---CCEEEEcCCCCCCcHHHHHHH----cC---CCCCCcEEEEECCEECCh-HHcCcccCCCCCEEEEEe
Confidence            66665   477654432156899999875    46   66 677778899999854 346667789999998763

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=84.48  E-value=1.4  Score=31.99  Aligned_cols=60  Identities=7%  Similarity=0.214  Sum_probs=42.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      |+|+|   +|+.+  ++....||.+|.+.+    +   ++.....+..+|+++..+ ...+.-+++|+.|.++
T Consensus         1 m~i~v---Ng~~~--~~~~~~tv~~ll~~l----~---~~~~~v~vavN~~~v~~~-~~~~~~L~~gD~v~i~   60 (66)
T 1f0z_A            1 MQILF---NDQAM--QCAAGQTVHELLEQL----D---QRQAGAALAINQQIVPRE-QWAQHIVQDGDQILLF   60 (66)
T ss_dssp             CCEEE---SSCEE--CCCTTCCHHHHHHHH----T---CCCSSEEEEETTEEECHH-HHTTCCCCTTEEECEE
T ss_pred             CEEEE---CCEEE--EcCCCCcHHHHHHHc----C---CCCCCEEEEECCEECCch-hcCCcCCCCCCEEEEE
Confidence            55555   47654  556778999999876    5   556777888999988532 2234458889988876

>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=84.27  E-value=1.1  Score=36.54  Aligned_cols=69  Identities=10%  Similarity=0.055  Sum_probs=41.5

Q ss_pred             CEEEEEeCC------C--cEEEEEeCC---CCcHHHHHHHHHHHhCCCCCCCCCeEEEeC-Ce------ecCCCCCh---
Q 017906            1 MKVFVKTLK------G--THFEIEVKP---EDKVSDVKKNIETVQGSDVYPASQQMLIHQ-GK------VLKDVTTL---   59 (364)
Q Consensus         1 MkI~VKtl~------g--k~~~ieV~~---s~TV~dLK~kI~~~~g~~~ip~~~qkLif~-Gk------iL~D~~tL---   59 (364)
                      |+|+|+...      |  +.+.|++..   ..||.+|...|.+.+.     ..+.+|+.. |+      +|-|+..+   
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            678887543      3  356788873   3699999999987752     223233211 21      22233321   


Q ss_pred             --hhhccCCCCEEEEEE
Q 017906           60 --EENKVAENSFVVVML   74 (364)
Q Consensus        60 --~d~gIk~~s~I~v~v   74 (364)
                        .++-+++|+.|.++-
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              346799999987753

>2lnm_A Protein TIC 40, chloroplastic; translocon, import, TIC40-NP, protein transport; NMR {Arabidopsis thaliana}

Probab=84.21  E-value=0.96  Score=32.82  Aligned_cols=45  Identities=13%  Similarity=0.187  Sum_probs=34.3

Q ss_pred             hHhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHCHHHHHHHhc
Q 017906          277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLIN  330 (364)
Q Consensus       277 l~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I~~n~e~Fl~~l~  330 (364)
                      +..+.++|+|.+.=+-|++||..+..++     +||.+.+.|+    .++.++.
T Consensus        14 ~~~~m~dP~~~~~lq~i~~NP~~~~~~~-----~dP~v~~~~~----~L~~~~~   58 (62)
T 2lnm_A           14 VAMAFQNPRVQAALMECSENPMNIMKYQ-----NDKEVMDVFN----KISQLFP   58 (62)
T ss_dssp             HHHHTTSHHHHHHHHHHTTCGGGHHHHT-----TCHHHHHHHH----HHHHHSS
T ss_pred             HHHHcCCHHHHHHHHHHHHCHHHHHHHH-----hChHHHHHHH----HHHHHhC
Confidence            4445588999999999999999887643     5999999884    3555553

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A

Probab=83.37  E-value=3.2  Score=42.92  Aligned_cols=76  Identities=13%  Similarity=0.089  Sum_probs=56.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--eecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G--KVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~---G--kiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |.|.|..++| ++.|.|+.+.|+.+|-..|+...|.  ...+-+-|.|.   |  ..|+.++.|.+.+++.+..+.+..+
T Consensus         5 i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~LgL--~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L~FR   81 (575)
T 2i1j_A            5 MNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIGL--REVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQFKFR   81 (575)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTC--CCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcCC--CCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEEEEE
Confidence            4678888888 7889999999999999999999993  22345566552   2  3477788898887777776666666


Q ss_pred             cCCC
Q 017906           76 KSKV   79 (364)
Q Consensus        76 k~k~   79 (364)
                      ++--
T Consensus        82 vkfy   85 (575)
T 2i1j_A           82 AKFY   85 (575)
T ss_dssp             ESSC
T ss_pred             EEEc
Confidence            6543

>3hm6_X Plexin-B1; structural genomics consortium, SGC, membrane, transmembrane receptor, cell membrane, glycoprotein, phosphoprotein; 2.40A {Homo sapiens} PDB: 3sua_D* 3su8_X*

Probab=81.54  E-value=4.3  Score=42.28  Aligned_cols=64  Identities=20%  Similarity=0.229  Sum_probs=44.9

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCeEEEe----CCe-ecCCC-------------CChhhhccCCC
Q 017906           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGK-VLKDV-------------TTLEENKVAEN   67 (364)
Q Consensus        12 ~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~------~~qkLif----~Gk-iL~D~-------------~tL~d~gIk~~   67 (364)
                      .+.+.|-..|||.++|+||-+..-++ +|.      +.+.|-|    .|+ +|.|.             .||..|+|.+|
T Consensus       275 ~i~VkVLdCDTItQVKeKiLDavYk~-~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  353 (644)
T 3hm6_X          275 GVPVKVLDCDTISQAKEKMLDQLYKG-VPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  353 (644)
T ss_dssp             CEEEEEETTSBHHHHHHHHHHHHTTT-SCGGGSCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBTTTTTCCTT
T ss_pred             ceeeEeeccCcHHHHHHHHHHHHHcC-CCcccCCCCCCcceEEeeCCCCceeecccCccceecCcceeecchhhcCCCCC
Confidence            47788889999999999999764322 333      4455554    233 46552             38999999999


Q ss_pred             CEEEEEEec
Q 017906           68 SFVVVMLTK   76 (364)
Q Consensus        68 s~I~v~v~k   76 (364)
                      ++|.++-+.
T Consensus       354 a~v~L~p~~  362 (644)
T 3hm6_X          354 ATVALVPCL  362 (644)
T ss_dssp             CEEEEEEC-
T ss_pred             cEEEEEecc
Confidence            999876443

>1ixs_A Holliday junction DNA helicase RUVA; heterodimeric protein complex, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.20A {Thermus thermophilus} SCOP: a.5.1.1

Probab=80.93  E-value=1.1  Score=32.75  Aligned_cols=28  Identities=11%  Similarity=0.192  Sum_probs=24.9

Q ss_pred             CcchHHHHHHHHHcCCCCCCHHHHHHHHHHH
Q 017906          169 GSNLEATVQQILDMGGGSWDRETVIRALRAA  199 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAa  199 (364)
                      +...++.|.-|+.+|   |.+.++.+|++..
T Consensus        14 ~~~~~ea~~AL~aLG---Y~~~ea~kav~~v   41 (62)
T 1ixs_A           14 SEAAEEAVMALAALG---FKEAQARAVVLDL   41 (62)
T ss_dssp             CHHHHHHHHHHHHTT---CCHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHcC---CCHHHHHHHHHHH
Confidence            445688999999999   9999999999886

>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=80.67  E-value=4.6  Score=31.54  Aligned_cols=46  Identities=7%  Similarity=0.111  Sum_probs=35.8

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCeEEEeCCe
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQGK   51 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~-~~qkLif~Gk   51 (364)
                      +|++. .+|..+.+.|+++.+..+|.++|.+.++   +.. +.+.|.|...
T Consensus         8 kvK~~-~~gdi~~~~v~~~i~~~~L~~kv~~~~~---~~~~~~f~lky~DE   54 (89)
T 1vd2_A            8 RVKAY-YRGDIMITHFEPSISFEGLCNEVRDMCS---FDNEQLFTMKWIDE   54 (89)
T ss_dssp             EEEEE-SSSCEEEEEECTTCCHHHHHHHHHHHTT---CCSSCCEEEEECCS
T ss_pred             EEEEE-eCCeEEEEECCCCCCHHHHHHHHHHHhC---CCCCCeEEEEEECC
Confidence            34444 4678899999999999999999999988   654 4477778653

>3onh_A Ubiquitin-activating enzyme E1-like; ligase, SUMO conjugation, UBC9; 1.60A {Saccharomyces cerevisiae} PDB: 3ong_A

Probab=80.40  E-value=4.8  Score=33.55  Aligned_cols=51  Identities=25%  Similarity=0.336  Sum_probs=37.9

Q ss_pred             CCcHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeec-----CC--CCChhhhccCCCCEEEEEE
Q 017906           20 EDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVL-----KD--VTTLEENKVAENSFVVVML   74 (364)
Q Consensus        20 s~TV~dLK~kI~~~~g~~~ip~~~qkLif--~GkiL-----~D--~~tL~d~gIk~~s~I~v~v   74 (364)
                      ..|+.+|-+.|..+.|   +. +.+.++-  ..+.|     +|  +++|+++||+.|++|.++-
T Consensus        19 ~~TL~dLV~~l~~~~g---y~-~eiSV~~~~~~rLLyD~DfDDnl~k~L~dLgv~~gsfLtv~D   78 (127)
T 3onh_A           19 KMKLSDFVVLIREKYS---YP-QDISLLDASNQRLLFDYDFEDLNDRTLSEINLGNGSIILFSD   78 (127)
T ss_dssp             HCBHHHHHHHHHHHHT---CC-SSEEEEETTTTEEEEETTBCTTTTSBTTTTTCCTTCEEEEEE
T ss_pred             ccCHHHHHHHHHHhcC---CC-CcEEEEecCCCCeEeCCCccccccCcHHHcCcCCCcEEEEEc
Confidence            4799999888988888   54 3555542  34454     23  5899999999999998875

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=80.16  E-value=6.3  Score=40.92  Aligned_cols=65  Identities=18%  Similarity=0.295  Sum_probs=45.8

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCC------CCCeEEEe----CCe-ecCCC-------------CChhhhccCC
Q 017906           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYP------ASQQMLIH----QGK-VLKDV-------------TTLEENKVAE   66 (364)
Q Consensus        11 k~~~ieV~~s~TV~dLK~kI~~~~g~~~ip------~~~qkLif----~Gk-iL~D~-------------~tL~d~gIk~   66 (364)
                      ..+.+.|-..|||.++|+||-+..-++ .|      ++++-|-|    .|+ +|.|.             .||..|+|.+
T Consensus       247 ~~i~vkVLdCDTItQVKeKiLdavYk~-~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~D  325 (627)
T 3ig3_A          247 AQVPVKVLNCDSITQAKDKLLDTVYKG-IPYSQRPKAEDMDLEWRQGRMARIILQDEDITTKIECDWKRVNSLAHYQVTD  325 (627)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHTTT-SCGGGSCCGGGEEEEEESCSSCEEEECSSSTTCCEETTEEECCBTTTTTCCT
T ss_pred             CceeeEeeccCcHHHHHHHHHHHHHcC-CCcccCCCCCccceeEeeCCCCceeeccCCccccccCceeEecchhhcCCCC
Confidence            467788889999999999999875322 33      34556654    233 35441             3789999999


Q ss_pred             CCEEEEEEec
Q 017906           67 NSFVVVMLTK   76 (364)
Q Consensus        67 ~s~I~v~v~k   76 (364)
                      |.+|.++-+.
T Consensus       326 ga~v~L~p~~  335 (627)
T 3ig3_A          326 GSLVALVPKQ  335 (627)
T ss_dssp             TCEEEEEEC-
T ss_pred             CceEEEEecc
Confidence            9999886543

---

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	364
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	1e-26
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	6e-23
d2f4mb1	58	a.189.1.1 (B:275-332) XPC-binding domain of Rad23	1e-22
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	6e-20
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	5e-19
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	4e-18
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	8e-18
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	9e-18
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	2e-17
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	5e-17
d1oqya1	41	a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Hum	2e-16
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	4e-16
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	4e-16
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	7e-16
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	9e-16
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	1e-15
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	2e-15
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	2e-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	3e-13
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	3e-13
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	5e-13
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	6e-13
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	1e-12
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	2e-12
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	3e-12
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	3e-12
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	1e-10
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	3e-10
d1wjia_	63	a.5.2.1 (A:) Tudor domain containing protein 3, TD	3e-10
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	1e-09
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	1e-09
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	1e-09
d1wiva_	73	a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress	8e-09
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	1e-08
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	3e-08
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	5e-08
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	7e-08
d1wgna_	63	a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1	1e-07
d1vg5a_	73	a.5.2.1 (A:) Rhomboid family protein At3g58460 {Th	1e-06
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	2e-05
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	3e-05
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	3e-05
d1whca_	64	a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus	2e-04
d2bwba1	44	a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharom	0.002
d2gqba1	130	a.282.1.1 (A:1-130) Hypothetical protein RPA2825 {	0.002

>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 = 1e-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 = 6e-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 = 87.4 bits (217), Expect = 1e-22
 Identities = 27/57 (47%), Positives = 44/57 (77%)

Query: 277 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV 333
           L+FLRN  QFQ +R ++Q NP +L  +LQ++G++NP L++ I +HQ  F++++NEPV
Sbjct: 2   LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 58

>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 = 80.7 bits (199), Expect = 6e-20
 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 = 78.4 bits (193), Expect = 5e-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

>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 = 75.7 bits (186), Expect = 4e-18
 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

>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 = 75.4 bits (185), Expect = 8e-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

>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 = 75.3 bits (185), Expect = 9e-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

>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 = 2e-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 = 5e-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

>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 = 70.0 bits (172), Expect = 2e-16
 Identities = 23/44 (52%), Positives = 31/44 (70%), Gaps = 3/44 (6%)

Query: 169 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 212
           GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +
Sbjct: 1   GSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLT 41

>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 = 70.3 bits (172), Expect = 4e-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

>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 = 70.3 bits (172), Expect = 4e-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

>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 = 69.5 bits (170), Expect = 7e-16
 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 = 9e-16
 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

>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 = 69.1 bits (169), Expect = 1e-15
 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 = 69.6 bits (170), Expect = 2e-15
 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

>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 = 68.5 bits (167), Expect = 2e-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

>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 = 68.0 bits (166), 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 = 63.1 bits (153), Expect = 3e-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 = 63.1 bits (153), Expect = 3e-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

>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 = 62.3 bits (151), Expect = 5e-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 = 6e-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

>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 = 60.4 bits (146), 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

>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 = 60.8 bits (147), Expect = 2e-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

>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 = 59.9 bits (145), Expect = 3e-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 = 59.3 bits (143), Expect = 3e-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

>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 = 55.6 bits (134), Expect = 1e-10
 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 = 54.1 bits (130), Expect = 3e-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

>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 = 53.2 bits (128), Expect = 3e-10
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAG 229
           E  ++ I +MG   + +E   +AL    NN E A+  L +   ++  + P +  S+G
Sbjct: 10  EKALKHITEMG---FSKEASRQALMDNGNNLEAALNVLLTSNKQKPVMGPPSGPSSG 63

>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 = 52.6 bits (126), Expect = 1e-09
 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

>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 = 52.3 bits (125), Expect = 1e-09
 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

>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 = 52.7 bits (126), Expect = 1e-09
 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

>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 = 49.8 bits (119), Expect = 8e-09
 Identities = 8/41 (19%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG 213
           +++V  +L  G   +  +   +AL+A+  + E+A +++++ 
Sbjct: 30  QSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFNN 67

>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 = 49.9 bits (119), Expect = 1e-08
 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

>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 = 48.2 bits (115), Expect = 3e-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

>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 = 48.3 bits (115), Expect = 5e-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

>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 = 7e-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

>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 = 1e-07
 Identities = 12/53 (22%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 160 GQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 212
           G  +   +   +    V+ +++MG   +  E V+RA++    N E+ ++YL++
Sbjct: 7   GAYSELQMLSPSERQCVETVVNMG---YSYECVLRAMKKKGENIEQILDYLFA 56

>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 = 43.8 bits (103), Expect = 1e-06
 Identities = 21/81 (25%), Positives = 30/81 (37%), Gaps = 19/81 (23%)

Query: 133 AAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETV 192
           +    AP    A  P      + S                E  +Q+++ MG   +DR  V
Sbjct: 6   SGSRQAPIANAAVLPQSQGRVAAS----------------EEQIQKLVAMG---FDRTQV 46

Query: 193 IRALRAAYNNPERAVEYLYSG 213
             AL AA ++   AVE L S 
Sbjct: 47  EVALAAADDDLTVAVEILMSQ 67

>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 = 40.7 bits (95), Expect = 2e-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

>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 = 40.2 bits (94), Expect = 3e-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

>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 = 40.7 bits (95), Expect = 3e-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 = 37.4 bits (87), Expect = 2e-04
 Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQTAVPPVARASAG 229
              ++ +++MG   + R    +AL    N   E A+++L     +     P++  S+G
Sbjct: 10  LTALESLIEMG---FPRGRAEKALALTGNQGIEAAMDWLMEHEDDPDVDEPLSGPSSG 64

>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 = 33.4 bits (77), Expect = 0.002
 Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 2/38 (5%)

Query: 176 VQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG 213
           ++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	364
d2f4mb1	58	XPC-binding domain of Rad23 homolog B (Hhr23b) {Hu	99.92
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.84
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.82
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.81
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.81
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.8
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.79
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.79
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.79
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.78
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.78
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.76
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.75
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.75
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.75
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.75
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.74
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.73
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.71
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.7
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.7
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.7
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.69
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.68
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.67
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.66
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.66
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.64
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.62
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.61
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	99.61
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.61
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.6
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.42
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.33
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.3
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	99.28
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.27
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	99.26
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.26
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	99.23
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	99.12
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.09
d1x3zb1	57	Rad23 STI1 domain {Baker's yeast (Saccharomyces ce	99.04
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	98.95
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	98.8
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	98.6
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	98.55
d2bwba1	44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.52
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	98.51
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	98.5
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.41
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	98.29
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	98.25
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	98.24
d3e46a1	42	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal	97.69
d1oqya2	44	DNA repair protein Hhr23a {Human (Homo sapiens) [T	97.47
d1z96a1	38	UBA-domain protein mud1 {Schizosaccharomyces pombe	97.16
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	97.13
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.13
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.8
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	96.55
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	96.46
d1wj7a1	91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	96.46
d2cosa1	41	Serine/threonine protein kinase LATS2 {Mouse (Mus	95.92
d1vega_	83	NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculu	95.14
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	94.98
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	93.96
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	93.19
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	93.18
d1ttea1	55	Ubiquitin-protein ligase ubc1 {Baker's yeast (Sacc	92.56
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	91.83
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	91.25
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	88.8
d2dkla1	72	Trinucleotide repeat containing 6c protein, TNRC6C	88.16
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	87.91
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	87.32
d2cp8a1	41	Migration-inducing protein 19 NBR1 {Human (Homo sa	87.11
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	86.17
d1ip9a_	85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	81.17
d2di0a1	63	Activating signal cointegrator 1 complex subunit 2	80.75

>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=99.92  E-value=3.8e-26  Score=165.33  Aligned_cols=58  Identities=47%  Similarity=0.960  Sum_probs=56.5

Q ss_pred             chHhhhCcHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHCHHHHHHHhcCCC
Q 017906          276 TLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV  333 (364)
Q Consensus       276 ~l~~Lr~~pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I~~n~e~Fl~~l~e~~  333 (364)
                      +|+|||++|||++||++||+||++|++|||+||++||+|+++|++|||+||+|||||+
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            6899999999999999999999999999999999999999999999999999999984

>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=99.84  E-value=1.2e-20  Score=150.61  Aligned_cols=80  Identities=45%  Similarity=0.727  Sum_probs=74.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~~   80 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+++.|.+.+++++|||||+||+|+|+++|++|||+++++|+|++++++..
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~~~   80 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAV   80 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCCCC
Confidence            99999999999999999999999999999999987544899999999999999999999999999999999999776543

>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=99.82  E-value=2.3e-20  Score=141.92  Aligned_cols=73  Identities=34%  Similarity=0.545  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+++|++|+++|++++||.+||++|+++.|   +++++|||+|+||.|+|+.+|++|||++|++||+++|.
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=99.81  E-value=5.2e-20  Score=144.69  Aligned_cols=76  Identities=29%  Similarity=0.446  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+++|++|+|+++++|||+++++..
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   99999999999999999999999999999999999877653

>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=99.81  E-value=5.8e-20  Score=140.75  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|++.|||+|+||.|+|+.+|++|||+++++|+|+++.+.
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

>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=99.80  E-value=7.1e-20  Score=141.23  Aligned_cols=75  Identities=27%  Similarity=0.406  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+.+|++|+|+|++++||.+||++|+++.|   +|++.|+|+|+||.|+|+++|++|+|+++++||++.|.+.
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   9999999999999999999999999999999999988764

>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=8.3e-20  Score=140.29  Aligned_cols=75  Identities=36%  Similarity=0.663  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|.+.+|+++|||+|+||+|+|+++|++|||+++++|+||++
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            799999999999999999999999999999999885448999999999999999999999999999999999974

>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=99.79  E-value=1.7e-19  Score=138.03  Aligned_cols=73  Identities=25%  Similarity=0.325  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+++|++++|+|++++||.+||++|+.+.|   +++++|+|+|+||.|+|+++|++|||++|++||+++|.
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

>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=99.79  E-value=1.3e-19  Score=140.14  Aligned_cols=75  Identities=20%  Similarity=0.376  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+++|++|.|+|++++||.+||.+|+.+.|   +|+++|||+|+||.|+|+++|++|||+++++|||+++++.
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   9999999999999999999999999999999999987654

>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=99.78  E-value=2.7e-19  Score=137.30  Aligned_cols=73  Identities=22%  Similarity=0.352  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCc-EEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGT-HFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk-~~~ie-V~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+++|+ +++++ |++++||.+||.+|+.+.|   +|++.|+|+|+||.|+|+.+|++|||+++++||+++|+
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=99.78  E-value=1.1e-19  Score=138.32  Aligned_cols=73  Identities=29%  Similarity=0.400  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~   77 (364)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+++|++|+| ++++|||+.+.|
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=99.76  E-value=1.3e-18  Score=133.46  Aligned_cols=72  Identities=21%  Similarity=0.327  Sum_probs=68.9

Q ss_pred             CEEEEEeCCC-cEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKG-THFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~g-k~~~i-eV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+++| +++++ +|++++||.+||.+|+.+.|   +|++.|+|+|+||.|+|+++|++|||+++++||+++|
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 57887 59999999999999999999   9999999999999999999999999999999999986

>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=99.75  E-value=1.4e-18  Score=140.54  Aligned_cols=75  Identities=21%  Similarity=0.380  Sum_probs=68.8

Q ss_pred             CEEEE----EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFV----KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~V----Ktl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~-D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+|    |++++++|.|+|++++||.+||++|+.+.|   +|+++|+|||+||.|. |+++|++|||++|++|+|+.+
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   9999999999999995 567999999999999988765


Q ss_pred             cCC
Q 017906           76 KSK   78 (364)
Q Consensus        76 k~k   78 (364)
                      +..
T Consensus        85 ~~~   87 (102)
T d1v5oa_          85 DNV   87 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=2.2e-18  Score=132.00  Aligned_cols=73  Identities=29%  Similarity=0.383  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif--~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      .+|+||+++|+.|.|+|++++||.+||.+|+.+.|   +|+++|||+|  +||+|+|+.+|++|||++|++|+|++++
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            37999999999999999999999999999999999   9999999999  7999999999999999999999999976

>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=99.75  E-value=1.8e-18  Score=131.54  Aligned_cols=71  Identities=27%  Similarity=0.388  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||+..|+++.|+|++++||.+||++|+.+.|   +++++|+|+|+||.|+|+.+|++|||++|++|+|+.
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~---i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~~   72 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIG---TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHC---CTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhc---ccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEEE
Confidence            68999999999999999999999999999999999   999999999999999999999999999999999864

>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=99.75  E-value=3.1e-18  Score=136.81  Aligned_cols=75  Identities=25%  Similarity=0.272  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~-D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+++|+.|.|+|++++||.+||++|+   .   +++++|||||+||+|. |.++|++|+|.+|++|||++++++.
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            7999999999999999999999999999985   3   5679999999999996 5689999999999999999887765


Q ss_pred             CC
Q 017906           80 SS   81 (364)
Q Consensus        80 ~~   81 (364)
                      ..
T Consensus        82 ~~   83 (95)
T d1wiaa_          82 AV   83 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.74  E-value=2.6e-18  Score=134.05  Aligned_cols=75  Identities=27%  Similarity=0.326  Sum_probs=70.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      |+|+||+.++ +|.|+|++++||.+||++|++++|   ++++.|+|+|+||.|+|+++|++|||++|++|+|++++++.
T Consensus         8 i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~g---i~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~~   82 (84)
T d1yqba1           8 IKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   82 (84)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             EEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHC---cCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCCC
Confidence            7899998755 689999999999999999999999   99999999999999999999999999999999999877643

>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=99.73  E-value=5.2e-18  Score=128.84  Aligned_cols=72  Identities=29%  Similarity=0.501  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+. +++|.|+|++++||.+||++|+...|   +|+++|+|+|+||.|+|+++|++|||++|++|||+.++
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   99999999999999999999999999999999998764

>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=99.71  E-value=6.4e-18  Score=135.13  Aligned_cols=74  Identities=20%  Similarity=0.204  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+||+.+++.+.|+|++++||.+||++|+..+|   +|+++|||||+||.|+|+ +|++|||++|++|+||.++..
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 799999999999999875544

>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=99.70  E-value=1.7e-17  Score=134.12  Aligned_cols=71  Identities=31%  Similarity=0.356  Sum_probs=67.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|+||+.++ ++.|+|++++||.+||++|+.++|   ++++.|+|+|+||+|+|+++|++|||++|++|||++|
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            6899998765 689999999999999999999999   9999999999999999999999999999999999875

>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=99.70  E-value=2.8e-17  Score=135.76  Aligned_cols=76  Identities=24%  Similarity=0.256  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHH--------HHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIE--------TVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~--------~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v   72 (364)
                      |+|+||+++|+++.|+|++++||.+||++|.        ++.+   +++++|||||.||+|+|+.+|++|+|.+|++++|
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            5799999999999999999999999999995        4455   8999999999999999999999999999998666


Q ss_pred             EEecCCC
Q 017906           73 MLTKSKV   79 (364)
Q Consensus        73 ~v~k~k~   79 (364)
                      ++..++.
T Consensus        94 hlv~r~~  100 (116)
T d1wgha_          94 HLVARET  100 (116)
T ss_dssp             EEEECSS
T ss_pred             EEEeCCC
Confidence            5555443

>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=99.70  E-value=1e-17  Score=134.93  Aligned_cols=71  Identities=17%  Similarity=0.281  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+||+..|++|.|+|++++||.+||++|+.++|   +|+++|||+|+||+|+|+.+|++|||++|++|+|+.
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

>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=99.69  E-value=1.2e-17  Score=130.02  Aligned_cols=72  Identities=28%  Similarity=0.363  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||+.++ .+.|+|++++||.+||++|++.++   ++++.|+|+|+||.|+|+++|++|||++|++|+|++|.
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            7899998755 679999999999999999999999   99999999999999999999999999999999998864

>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=99.68  E-value=6.9e-17  Score=126.55  Aligned_cols=68  Identities=26%  Similarity=0.387  Sum_probs=65.5

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         8 l~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      ++|++|.|+|++++||.+||.+|+.++|   +|+++|+|+|+|+.|+|+++|++|||++|++|||+++++.
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=99.67  E-value=1.5e-17  Score=135.13  Aligned_cols=77  Identities=21%  Similarity=0.235  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeE---------------EEeCCeecCCC-CChhhhcc
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM---------------LIHQGKVLKDV-TTLEENKV   64 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qk---------------Lif~GkiL~D~-~tL~d~gI   64 (364)
                      |+|+||+++|++|.|+|++++||.+||.+|++..+   +|+++||               |+|+|+.|.|+ .+|.+|||
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   9999987               99999999765 58999999


Q ss_pred             CCCCEEEEEEecCCCC
Q 017906           65 AENSFVVVMLTKSKVS   80 (364)
Q Consensus        65 k~~s~I~v~v~k~k~~   80 (364)
                      ++|++|||+.+.++..
T Consensus        85 ~~g~~l~lv~r~~~~~  100 (105)
T d1v2ya_          85 RNRDEVSFIKKLGQKS  100 (105)
T ss_dssp             CSSEEEEEEECSCSCC
T ss_pred             CCCCEEEEEEecCCCC
Confidence            9999999998766543

>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=99.66  E-value=4.6e-17  Score=131.08  Aligned_cols=75  Identities=23%  Similarity=0.243  Sum_probs=68.2

Q ss_pred             CEEEE--EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            1 MKVFV--KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         1 MkI~V--Ktl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      |+|+|  |...|++|.|+|+.++||.+||.+|+.+.|   +++++|||||+||+|+|+++|.+|||+++++|+|+..+..
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            35566  556899999999999999999999999999   9999999999999999999999999999999998876544

>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=99.66  E-value=2.1e-16  Score=127.14  Aligned_cols=78  Identities=17%  Similarity=0.264  Sum_probs=68.0

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCC--CCCC--CCCeEEEeCCeecCCCCChhhhccCCCC------E
Q 017906            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGS--DVYP--ASQQMLIHQGKVLKDVTTLEENKVAENS------F   69 (364)
Q Consensus         1 MkI~VKtl~gk~~-~ieV~~s~TV~dLK~kI~~~~g~--~~ip--~~~qkLif~GkiL~D~~tL~d~gIk~~s------~   69 (364)
                      |.|+||+++|+.+ .+.|++++||.+||++|+..+.+  ..+|  +++|||||+||+|+|+++|++|+|..|+      +
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            6899999999977 69999999999999999987321  1166  7799999999999999999999999997      8


Q ss_pred             EEEEEecCC
Q 017906           70 VVVMLTKSK   78 (364)
Q Consensus        70 I~v~v~k~k   78 (364)
                      +||++|.+.
T Consensus        88 mHlVvrpp~   96 (101)
T d1se9a_          88 MHVIIQAPV   96 (101)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999987654

>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=99.64  E-value=5.2e-16  Score=123.18  Aligned_cols=75  Identities=19%  Similarity=0.208  Sum_probs=64.8

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCC--EEEEEEec
Q 017906            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS--FVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk--~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s--~I~v~v~k   76 (364)
                      |+|+||+.+++  .|.|+|++++||.+||++|++..+.+ +++++|||||+||+|+|+.+|++|+++.++  +|||+++.
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            79999999876  48899999999999999999997633 889999999999999999999999876554  77776543

>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=99.62  E-value=4.4e-16  Score=122.63  Aligned_cols=73  Identities=25%  Similarity=0.404  Sum_probs=66.9

Q ss_pred             CEEEEEeCCCcEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE---eCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~i-eV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi---f~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+||. .|+.|.+ +|++++||.+||++|+.++|   +|+++||||   |.||+|+|+.+|.+|+|++|++|+|+.++
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   58999999999999999999999998764


Q ss_pred             C
Q 017906           77 S   77 (364)
Q Consensus        77 ~   77 (364)
                      .
T Consensus        84 ~   84 (90)
T d1v5ta_          84 E   84 (90)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.61  E-value=3.3e-16  Score=124.77  Aligned_cols=71  Identities=21%  Similarity=0.366  Sum_probs=66.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+|+ +++++|.|+|++++||.+||++|+..+|   +|+++|||+|+|+ |+|+++|++|+|+++++|+|+.+.
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 6889999999999999999999999999   9999999999997 999999999999999999998644

>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=99.61  E-value=7.4e-17  Score=109.01  Aligned_cols=41  Identities=56%  Similarity=0.985  Sum_probs=39.7

Q ss_pred             CcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          169 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      |+++|++|++||+||   |+|++|++|||+++||+|||+|||++
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

>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=99.61  E-value=1.1e-15  Score=118.29  Aligned_cols=73  Identities=30%  Similarity=0.383  Sum_probs=66.0

Q ss_pred             CEEEEEeCCCcEEEEEe-----CCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCChhhhccCCCCEEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEV-----KPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVML   74 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV-----~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~-D~~tL~d~gIk~~s~I~v~v   74 (364)
                      |+|+|+ ..++.|.|+|     ++++||.+||++|+..+|   +|+++|||+|+|+.|. |+++|++|||++|++|+|+.
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            689997 5778899888     568899999999999999   9999999999999996 56899999999999999998


Q ss_pred             ecC
Q 017906           75 TKS   77 (364)
Q Consensus        75 ~k~   77 (364)
                      ++.
T Consensus        78 ~~~   80 (81)
T d1wxva1          78 KKN   80 (81)
T ss_dssp             CCS
T ss_pred             ecC
Confidence            764

>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=99.60  E-value=4.8e-16  Score=127.29  Aligned_cols=76  Identities=24%  Similarity=0.318  Sum_probs=68.4

Q ss_pred             EEEEEeC-CCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCCC
Q 017906            2 KVFVKTL-KGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (364)
Q Consensus         2 kI~VKtl-~gk~~~ieV~~-s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k~   79 (364)
                      +|+|++. +|+++.|+|.+ ++||.+||.+|++++|   +|+++|||+|+||.|+|+.+|++|||+++++|||++|.+..
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            3445443 58999999986 8999999999999999   99999999999999999999999999999999999998864


Q ss_pred             C
Q 017906           80 S   80 (364)
Q Consensus        80 ~   80 (364)
                      +
T Consensus       108 ~  108 (111)
T d1we6a_         108 P  108 (111)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.53  E-value=1.8e-14  Score=116.26  Aligned_cols=72  Identities=21%  Similarity=0.279  Sum_probs=61.6

Q ss_pred             EEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCC-------EEEEEE
Q 017906            3 VFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS-------FVVVML   74 (364)
Q Consensus         3 I~VKtl~gk-~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s-------~I~v~v   74 (364)
                      |+|+...++ ++.|+|++++||.+||.+|+++.|   +++++|||||+||.|+|+++|++|||.+++       ++++.+
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            566655554 788999999999999999999999   999999999999999999999999996544       666666


Q ss_pred             ecC
Q 017906           75 TKS   77 (364)
Q Consensus        75 ~k~   77 (364)
                      +..
T Consensus        79 ~~~   81 (103)
T d2c9wb1          79 RAD   81 (103)
T ss_dssp             EET
T ss_pred             ecC
Confidence            533

>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=109.53  Aligned_cols=75  Identities=21%  Similarity=0.220  Sum_probs=67.2

Q ss_pred             CEEEEEe-CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCe-------ecCCCCChhhhccCCCCEEEE
Q 017906            1 MKVFVKT-LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-------VLKDVTTLEENKVAENSFVVV   72 (364)
Q Consensus         1 MkI~VKt-l~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~Gk-------iL~D~~tL~d~gIk~~s~I~v   72 (364)
                      |.|+|++ +++..++..+++++||.+||.||+..+|   +|++.|+|+|.|+       .++|+++|.+|+|.+|++|||
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            5789997 3666788999999999999999999999   9999999999887       578999999999999999999


Q ss_pred             EEecCC
Q 017906           73 MLTKSK   78 (364)
Q Consensus        73 ~v~k~k   78 (364)
                      +.+.+.
T Consensus        85 vd~~p~   90 (95)
T d1v6ea_          85 IDHSGS   90 (95)
T ss_dssp             BCCSCC
T ss_pred             EeCCCC
Confidence            976643

>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=99.33  E-value=1.4e-12  Score=99.77  Aligned_cols=73  Identities=11%  Similarity=0.141  Sum_probs=66.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEecCC
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k~k   78 (364)
                      +|+|+. +|+.+.|.|..++++..||+.++++.|   +++++++|+|+|+.|+++.|+++|+|+++++|+|+++...
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            456654 678888999999999999999999999   9999999999999999999999999999999999988653

>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=99.30  E-value=2e-12  Score=102.83  Aligned_cols=74  Identities=18%  Similarity=0.207  Sum_probs=63.6

Q ss_pred             EEEEEe---CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCee-------c-CCCCChhhhccCCCCEE
Q 017906            2 KVFVKT---LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV-------L-KDVTTLEENKVAENSFV   70 (364)
Q Consensus         2 kI~VKt---l~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~Gki-------L-~D~~tL~d~gIk~~s~I   70 (364)
                      +|+|+.   .+++.++++|+.++||.+||.+|+..+|   +|++.|+|+|.|+.       | +|+++|.+|||++|++|
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   4567899999999999999999999999   99999999998872       4 47899999999999999


Q ss_pred             EEEEecCC
Q 017906           71 VVMLTKSK   78 (364)
Q Consensus        71 ~v~v~k~k   78 (364)
                      +|....|+
T Consensus        88 ~V~~~~P~   95 (97)
T d1wjna_          88 LVRWSGPS   95 (97)
T ss_dssp             EEECCSSC
T ss_pred             EEEeCCCC
Confidence            99865543

>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=99.28  E-value=6.9e-12  Score=94.69  Aligned_cols=40  Identities=40%  Similarity=0.474  Sum_probs=38.2

Q ss_pred             chHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .+|+.|++||+||   |+|++|++||++++||+|||+|||+..
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            3689999999999   999999999999999999999999987

>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=99.27  E-value=2.1e-12  Score=102.13  Aligned_cols=57  Identities=26%  Similarity=0.138  Sum_probs=50.1

Q ss_pred             CCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEe
Q 017906           19 PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus        19 ~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      .++||.+||++|+.+.......+++|||||+||.|+|+++|++|||++|++||++.|
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            467999999999999763313469999999999999999999999999999999875

>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=99.26  E-value=1.5e-12  Score=95.61  Aligned_cols=43  Identities=28%  Similarity=0.557  Sum_probs=39.8

Q ss_pred             cchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC-CC
Q 017906          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG-IP  215 (364)
Q Consensus       170 ~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G-IP  215 (364)
                      +..++.|++||+||   |+|++|++||++++||++||||||++. +|
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   999999999999999999999999986 55

>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=99.26  E-value=7.8e-12  Score=95.12  Aligned_cols=73  Identities=19%  Similarity=0.273  Sum_probs=69.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      |+|+|++.+|+.+.+.|..+.++..||..++++.|   +++..++|+|+|+.|.++.|+++|+|++|++|+|+++.
T Consensus         3 I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~---~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q   75 (77)
T d2uyzb1           3 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ   75 (77)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC---CChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            57899999999999999999999999999999999   89999999999999999999999999999999999865

>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=99.23  E-value=5.2e-12  Score=92.74  Aligned_cols=43  Identities=28%  Similarity=0.372  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~~  217 (364)
                      .+++|++||+||   |+|++|++||++..||+++||+||+++..+.
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            488999999999   9999999999999999999999999997654

>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=2.6e-11  Score=91.45  Aligned_cols=39  Identities=21%  Similarity=0.507  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .++.|++||+||   |+|++|++|||++.||.+|||+||++.
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   999999999999999999999999987

>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=99.09  E-value=1.4e-10  Score=90.68  Aligned_cols=73  Identities=14%  Similarity=0.127  Sum_probs=61.0

Q ss_pred             EEEEEe-CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCe-------ecCCCCChhhhccCCCCEEEEE
Q 017906            2 KVFVKT-LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-------VLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKt-l~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~Gk-------iL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      .|.|.+ .++..++..++.++||.+||.+|+..+|   +|++.|+|+|.|+       .++|+++|.+|||++|++|||+
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            355553 2344467788999999999999999999   9999999999886       4578999999999999999998


Q ss_pred             EecC
Q 017906           74 LTKS   77 (364)
Q Consensus        74 v~k~   77 (364)
                      -+..
T Consensus        83 d~~~   86 (90)
T d1t0ya_          83 DVTG   86 (90)
T ss_dssp             ECTT
T ss_pred             eCCC
Confidence            6544

>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=99.04  E-value=1.5e-10  Score=79.27  Aligned_cols=49  Identities=27%  Similarity=0.546  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHCHHHHHHHhcCC
Q 017906          284 QQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEP  332 (364)
Q Consensus       284 pqf~~lR~~vq~nP~~L~~~Lqql~~~nP~L~~~I~~n~e~Fl~~l~e~  332 (364)
                      .++-+||++|..||+.|.++|+.|..++|+|++.|.+|||.|+.||.|.
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            3677999999999999999999999999999999999999999999864

>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=98.95  E-value=4e-10  Score=82.69  Aligned_cols=41  Identities=22%  Similarity=0.379  Sum_probs=37.8

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCCCC
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPE  216 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GIP~  216 (364)
                      +++|++|++||   |+|++|++||++..| |+++|||||+...-+
T Consensus        10 ~~~l~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~d   51 (64)
T d1whca_          10 LTALESLIEMG---FPRGRAEKALALTGNQGIEAAMDWLMEHEDD   51 (64)
T ss_dssp             CCHHHHHHTTT---CCHHHHHHHHHHHTSCCHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhCCCCHHHHHHHHHHCCCC
Confidence            67999999999   999999999999998 799999999998543

>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=98.80  E-value=1.3e-09  Score=76.23  Aligned_cols=37  Identities=24%  Similarity=0.484  Sum_probs=34.4

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHh
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYS  212 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~  212 (364)
                      +..|++|++||   |++++|++||++.-| |.++||+||+.
T Consensus        13 ~~~l~~L~~MG---F~~~~a~~AL~~t~n~~ve~A~~WLl~   50 (51)
T d2cpwa1          13 GSALDVLLSMG---FPRARAQKALASTGGRSVQTACDWLFS   50 (51)
T ss_dssp             CCHHHHHHHHT---CCHHHHHHHHHHTTTSCHHHHHHHHHS
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHHCCCCHHHHHHHHHc
Confidence            44799999999   999999999999988 99999999985

>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=98.60  E-value=1.1e-07  Score=70.88  Aligned_cols=70  Identities=16%  Similarity=0.238  Sum_probs=66.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEE
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~   73 (364)
                      ++|+|+..+|+.+.+.|..+.++..|....+...+   +++..++|+|+|..|..+.|.+++++++|+.|.|.
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            47888988999999999999999999999999999   88999999999999999999999999999999875

>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=98.55  E-value=5.8e-08  Score=64.07  Aligned_cols=39  Identities=23%  Similarity=0.342  Sum_probs=37.0

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .+.+|++|++||   |+++++++||+-...|-+-|+.||+-|
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            467999999999   999999999999999999999999976

>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=98.52  E-value=7e-08  Score=65.01  Aligned_cols=40  Identities=30%  Similarity=0.473  Sum_probs=38.1

Q ss_pred             chHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          171 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .|..-+++|-+||   | +++..++||+++..|.++|||+|++|
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            4788899999999   9 99999999999999999999999988

>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=98.51  E-value=4.8e-08  Score=75.11  Aligned_cols=41  Identities=27%  Similarity=0.362  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCCC
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIP  215 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GIP  215 (364)
                      .++.|++|++||   |+|..|++||++..| |.++|++||+...-
T Consensus        29 d~~~v~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~   70 (84)
T d1veka_          29 NEEIVAQLVSMG---FSQLHCQKAAINTSNAGVEEAMNWLLSHMD   70 (84)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHHcCCCHHHHHHHHHHcCC
Confidence            478999999999   999999999999987 99999999998743

>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=98.50  E-value=5.8e-08  Score=67.73  Aligned_cols=37  Identities=27%  Similarity=0.423  Sum_probs=34.3

Q ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHHhCC
Q 017906          175 TVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGI  214 (364)
Q Consensus       175 ~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~~GI  214 (364)
                      .|++|++||   |+|+++++||++.-| |.++||+||+...
T Consensus         5 ~v~~L~~MG---F~~~~a~~Al~~t~n~~ve~A~~Wl~~h~   42 (51)
T d2crna1           5 LLEPLLAMG---FPVHTALKALAATGRKTAEEALAWLHDHC   42 (51)
T ss_dssp             SHHHHHHTS---CCHHHHHHHHHHHTSCCHHHHHHHHHHHS
T ss_pred             HHHHHHHcC---CCHHHHHHHHHHHCCCCHHHHHHHHHHcC
Confidence            699999999   999999999999876 9999999999763

>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=98.41  E-value=2.5e-07  Score=71.50  Aligned_cols=71  Identities=20%  Similarity=0.169  Sum_probs=58.1

Q ss_pred             EEEEEeCCCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCeEEEeC--------------CeecCC-CCChhhhccC
Q 017906            2 KVFVKTLKGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQ--------------GKVLKD-VTTLEENKVA   65 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~-s~TV~dLK~kI~~~~g~~~ip~~~qkLif~--------------GkiL~D-~~tL~d~gIk   65 (364)
                      -|.||+.+| +..|+|+. +.||.+||.+|++..+   +|.++|.|..+              -..|.| ..+|++|||.
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 78899964 7899999999999999   99999999442              223554 5679999999


Q ss_pred             CCCEEEEEEec
Q 017906           66 ENSFVVVMLTK   76 (364)
Q Consensus        66 ~~s~I~v~v~k   76 (364)
                      +|++|++....
T Consensus        78 hGsivyL~y~~   88 (94)
T d1wf9a1          78 HGSMVYLAYEG   88 (94)
T ss_dssp             TTCEEECCCSS
T ss_pred             CceEEEEEeee
Confidence            99999987654

>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=98.29  E-value=5.1e-07  Score=64.81  Aligned_cols=41  Identities=20%  Similarity=0.407  Sum_probs=37.7

Q ss_pred             CcchHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       169 g~~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      -..|..-++.|.+||   | +++..++||+++.+|.++|||||+.
T Consensus        19 e~ry~~QL~qL~eMG---F~d~~~Nl~AL~~t~Gdv~~Aie~Ll~   60 (61)
T d1veja1          19 EGRYQQELEELKALG---FANRDANLQALVATDGDIHAAIEMLLG   60 (61)
T ss_dssp             TTTSHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcC---CCCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            346899999999999   9 8999999999999999999999983

>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=98.25  E-value=7e-07  Score=59.16  Aligned_cols=38  Identities=32%  Similarity=0.478  Sum_probs=35.8

Q ss_pred             hHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          172 LEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      |+.-++.|-+||   | +++..++||+++..|.++|||+|+.
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            677899999999   9 9999999999999999999999974

>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=98.24  E-value=6.8e-07  Score=61.58  Aligned_cols=40  Identities=20%  Similarity=0.291  Sum_probs=38.1

Q ss_pred             chHHHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHHhC
Q 017906          171 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (364)
Q Consensus       171 ~~e~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~~G  213 (364)
                      .|..-+++|-+||   | +++..++||+++..|.++|||+|+.+
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            5888999999999   9 99999999999999999999999976

>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=97.69  E-value=3.5e-05  Score=48.96  Aligned_cols=41  Identities=27%  Similarity=0.407  Sum_probs=38.0

Q ss_pred             CCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          168 AGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       168 ~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      +.++|-..|.+|+.||   |+|.-|+.||.--..+.+.|-|.|+
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            3467999999999999   9999999999999999999999886

>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=97.47  E-value=1.9e-05  Score=52.38  Aligned_cols=38  Identities=24%  Similarity=0.379  Sum_probs=35.9

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      -.++|.+|++||   |+|+.|+.|--|...|-+-|.+||+.
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            467999999999   99999999999999999999999985

>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=0.00033  Score=43.22  Aligned_cols=37  Identities=30%  Similarity=0.499  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       172 ~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      ++..|.+|++||   |+-=+...||.|+..+.|-|..||+
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   9999999999999999999999985

>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=97.13  E-value=0.0011  Score=48.96  Aligned_cols=72  Identities=18%  Similarity=0.161  Sum_probs=66.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCChhhhccCCCCEEEEEEec
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~GkiL~D~~tL~d~gIk~~s~I~v~v~k   76 (364)
                      .|+|-+.+|+..+|.|.++.|+.++-+..+.++|   +.+++..|.|.+|.|+-+..+.-.|+-+|..+.++-..
T Consensus         2 ~V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~---~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~~s   73 (76)
T d2al3a1           2 AVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQD---FNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVS   73 (76)
T ss_dssp             CEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTT---CCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSS
T ss_pred             cEEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhC---CChhHceeeeCCEEcCccceeeecCCCCCCEEEEEEcc
Confidence            3678888999999999999999999999999999   88999999999999999999999999999999987543

>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=97.13  E-value=0.0012  Score=49.27  Aligned_cols=67  Identities=18%  Similarity=0.242  Sum_probs=56.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC---CCCChhhhccCCCCEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~---D~~tL~d~gIk~~s~I~v   72 (364)
                      +|.||..+|+.+.-....++||.+|...|... +   .......|+  |-.|.|.   ++++|+++|+....+|+|
T Consensus         7 ~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~-~---~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~v   78 (82)
T d1h8ca_           7 KLRIRTPSGEFLERRFLASNKLQIVFDFVASK-G---FPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFL   78 (82)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-T---CCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCCCcHHHHHHHHHhc-C---CCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEE
Confidence            68999999999999999999999999999874 5   556778886  6788883   468999999998888775

>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=96.80  E-value=0.002  Score=48.82  Aligned_cols=66  Identities=18%  Similarity=0.328  Sum_probs=53.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHh-CCCCCCCCCeEEEeC--CeecC-CCCChhhhccCCCCEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQ-GSDVYPASQQMLIHQ--GKVLK-DVTTLEENKVAENSFVV   71 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~-g~~~ip~~~qkLif~--GkiL~-D~~tL~d~gIk~~s~I~   71 (364)
                      +|.||..+|+.+...+..++||.+|+..|.... +   .......|+..  -|.|. ++.+|.++|+.+ +.|+
T Consensus        16 ~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~---~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~-s~vl   85 (89)
T d1i42a_          16 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPA---MAATSFVLMTTFPNKELADENQTLKEANLLN-AVIV   85 (89)
T ss_dssp             EEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTT---TSSCCEEEEETTTTEECCCCSSCSGGGTTCC-SEEE
T ss_pred             EEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCcc---CCCCCEEEecCCCCcccCCCcCcHHHCCCcC-ceEE
Confidence            588999999999999999999999999998764 3   45667888854  67785 478999999985 5543

>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=96.55  E-value=0.0036  Score=47.69  Aligned_cols=67  Identities=16%  Similarity=0.157  Sum_probs=53.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC--CCCChhhhccCCCCEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--DVTTLEENKVAENSFVVV   72 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL~--D~~tL~d~gIk~~s~I~v   72 (364)
                      +|.||..+|+.+.-....++||.+|...|... +   ......+|+  |-.+.|.  ++++|.++||....+|+|
T Consensus        18 ~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~-~---~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v   88 (96)
T d2cr5a1          18 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-G---YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNV   88 (96)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-T---CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcccHHHHHHHHHHh-c---cCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEE
Confidence            68999999999998999999999999999765 3   345677776  4446663  368999999998777655

>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=96.46  E-value=0.0033  Score=50.51  Aligned_cols=68  Identities=21%  Similarity=0.339  Sum_probs=55.8

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeec---CCCCChhhhccCCCCEEEEE
Q 017906            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVL---KDVTTLEENKVAENSFVVVM   73 (364)
Q Consensus         2 kI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f~GkiL---~D~~tL~d~gIk~~s~I~v~   73 (364)
                      +|.||..+|+.+...+..++||.+|...|... +   +.....+|+  |--|.|   +.+++|+++||....+|+|-
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  566777   34789999999988888654

>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=96.46  E-value=0.0021  Score=48.73  Aligned_cols=45  Identities=27%  Similarity=0.559  Sum_probs=40.8

Q ss_pred             CcchHHHHHHHHHc-CCCCCCHHHHHHHHHHHcCChHHHHHHHHhCCCC
Q 017906          169 GSNLEATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  216 (364)
Q Consensus       169 g~~~e~~V~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEyL~~GIP~  216 (364)
                      -++++..|..||+| |   -..++|.-||-=+.|+.+|||+|||-|-+.
T Consensus        29 D~~i~~kVkql~e~T~---rsede~~~ALhDcn~D~~~AIn~lLEg~~~   74 (91)
T d1wj7a1          29 DADFEEKVKQLIDITG---KNQDECVIALHDCNGDVNRAINVLLEGNPD   74 (91)
T ss_dssp             CHHHHHHHHHHHHHTC---CCHHHHHHHHHHHTSCHHHHHHHHHTCSSS
T ss_pred             cHHHHHHHHHHHHHhC---CCHHHHHHHHhcCCccHHHHHHHHHhcCCC
Confidence            45689999999999 6   799999999999999999999999998553

>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=95.92  E-value=0.0062  Score=38.37  Aligned_cols=36  Identities=31%  Similarity=0.475  Sum_probs=31.9

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcC-ChHHHHHHHH
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLY  211 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEyL~  211 (364)
                      .++++.|+.-|   |+.+.|+||||-..| |-+-|+||+.
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   999999999998765 7899999985

>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=95.14  E-value=0.016  Score=42.33  Aligned_cols=44  Identities=27%  Similarity=0.395  Sum_probs=38.7

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh-C--CCCCCC
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS-G--IPEQTA  219 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~-G--IP~~~~  219 (364)
                      .+.|++|+-||   |+|+-++.|||.--.|..-|..-|.. |  +|..+.
T Consensus        30 QesidqLvYMG---F~~~~Ae~ALRvfrGnVQlAaQtLahngG~LP~dLq   76 (83)
T d1vega_          30 QESINQLVYMG---FDTVVAEAALRVFGGNVQLAAQTLAHHGGSLPPDLQ   76 (83)
T ss_dssp             HHHHHHHHHHS---CCHHHHHHHHHHTTTCHHHHHHHHHHHTSSCCTTSS
T ss_pred             HHHHHHHHHhc---ccHHHHHHHHHHhcccHHHHHHHHHHcCCcCCcccc
Confidence            56899999999   99999999999999999999988863 3  887654

>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=94.98  E-value=0.072  Score=39.18  Aligned_cols=68  Identities=21%  Similarity=0.224  Sum_probs=48.9

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCCC--------CCCCCCeEEEeCCeecCCCCChhhhccC
Q 017906            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGSD--------VYPASQQMLIHQGKVLKDVTTLEENKVA   65 (364)
Q Consensus         1 MkI~VKtl~------g-k~~~ieV~~s~TV~dLK~kI~~~~g~~--------~ip~~~qkLif~GkiL~D~~tL~d~gIk   65 (364)
                      |+|+||.+.      | ....|++....||.+|++.+..+++.-        .......++..+|+...++     +-|+
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 467889999999999999999876410        0012345666788777554     4578


Q ss_pred             CCCEEEEE
Q 017906           66 ENSFVVVM   73 (364)
Q Consensus        66 ~~s~I~v~   73 (364)
                      +|+.|.++
T Consensus        77 ~gDevai~   84 (88)
T d1vjka_          77 DGDVVGVF   84 (88)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEe
Confidence            89998876

>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=93.96  E-value=0.029  Score=39.13  Aligned_cols=38  Identities=29%  Similarity=0.396  Sum_probs=35.2

Q ss_pred             hHHHHHHHHHc--CCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          172 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       172 ~e~~V~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      .|+.|+.|.+|  .   ++++-|+.-|++.-+|.|+||+-||.
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  6   89999999999999999999999983

>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=93.19  E-value=0.064  Score=36.94  Aligned_cols=36  Identities=14%  Similarity=0.196  Sum_probs=32.1

Q ss_pred             HHHHHHHHHc-CCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          173 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       173 e~~V~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      -++|.+|-+. |   +.--+|..||..+.+|.|.|+|||-
T Consensus         5 ~~lvk~LRe~Tg---a~~~dcKkAL~e~~gD~ekA~e~Lr   41 (56)
T d1xb2b1           5 KELLMKLRRKTG---YSFINCKKALETCGGDLKQAESWLH   41 (56)
T ss_dssp             HHHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            3578888886 7   8889999999999999999999995

>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=93.18  E-value=0.066  Score=36.31  Aligned_cols=35  Identities=29%  Similarity=0.304  Sum_probs=31.0

Q ss_pred             HHHHHHHHc-CCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          174 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       174 ~~V~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      +.|.+|-++ |   +.--+|..||..+.+|.|+|+|||-
T Consensus         4 elvK~LR~~Tg---a~~~dcKkAL~e~~gD~ekA~e~Lr   39 (52)
T d1aipc1           4 ELIKKLREATG---AGMMDVKRALEDAGWDEEKAVQLLR   39 (52)
T ss_dssp             HHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            467777775 7   8899999999999999999999995

>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=92.56  E-value=0.047  Score=37.27  Aligned_cols=23  Identities=13%  Similarity=0.514  Sum_probs=21.7

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHH
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRA  198 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrA  198 (364)
                      ...|.++.+||   |+|+.|+.+||-
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            67899999999   999999999996

>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=91.83  E-value=0.12  Score=35.17  Aligned_cols=35  Identities=23%  Similarity=0.243  Sum_probs=31.1

Q ss_pred             HHHHHHHHc-CCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          174 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       174 ~~V~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      +.|.+|-++ |   +.--+|..||..+.+|.|+|+|||-
T Consensus         6 ~~iK~LR~~Tg---ag~~dCKkAL~e~~gD~ekA~e~Lr   41 (54)
T d1efub3           6 SLVKELRERTG---AGMMDCKKALTEANGDIELAIENMR   41 (54)
T ss_dssp             HHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            467888776 7   8889999999999999999999995

>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=91.25  E-value=0.083  Score=36.07  Aligned_cols=39  Identities=18%  Similarity=0.181  Sum_probs=36.3

Q ss_pred             cchHHHHHHHHHc--CCCCCCHHHHHHHHHHHcCChHHHHHHHH
Q 017906          170 SNLEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       170 ~~~e~~V~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      .++++.++.|.+|  .   +|++=+..-|++.-+|.|+||+.||
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  6   8999999999999999999999998

>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=88.80  E-value=0.75  Score=33.64  Aligned_cols=72  Identities=18%  Similarity=0.163  Sum_probs=53.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---Ce--ecCCCCChhhhccCCCCEEEEEEe
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---GK--VLKDVTTLEENKVAENSFVVVMLT   75 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~---Gk--iL~D~~tL~d~gIk~~s~I~v~v~   75 (364)
                      |+|.|..+++ .+.+.|+...+..+|-.+|+...+.  ...+-.-|-|-   |.  =|+.++.|....++.+..+.+..+
T Consensus         2 ~~v~V~~LD~-~~~~~v~~~a~G~~l~~~Vc~~l~L--~E~dYFGL~y~d~~~~~~WLd~~k~l~kq~~~~~~~~~l~F~   78 (84)
T d1ef1a3           2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGL--REVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFR   78 (84)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTC--CCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEEcCC-EEEEEEcCCChHHHHHHHHHHHcCC--cccccceEEEECCCCCeEeccCCCchhhhccCCCCCEEEEEE
Confidence            6789999997 5899999999999999999999992  33444556553   32  278889998887766665555443

>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=88.16  E-value=0.41  Score=33.99  Aligned_cols=37  Identities=30%  Similarity=0.452  Sum_probs=34.0

Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHh
Q 017906          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (364)
Q Consensus       173 e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~  212 (364)
                      ...|.++..||   |.|+..+.||+..-+|.+-|+--|+-
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            66899999999   99999999999999999999988863

>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=87.91  E-value=0.33  Score=36.70  Aligned_cols=71  Identities=6%  Similarity=-0.003  Sum_probs=41.7

Q ss_pred             CEEEEEeCC--------CcEEEEEeC---CCCcHHHHHHHHHHHhCCC--CCCCC------CeEEEeCCeecCCCCCh--
Q 017906            1 MKVFVKTLK--------GTHFEIEVK---PEDKVSDVKKNIETVQGSD--VYPAS------QQMLIHQGKVLKDVTTL--   59 (364)
Q Consensus         1 MkI~VKtl~--------gk~~~ieV~---~s~TV~dLK~kI~~~~g~~--~ip~~------~qkLif~GkiL~D~~tL--   59 (364)
                      |+|+|+...        .+...++++   ...||.+|-+.+.+.+...  .+-.+      ...++.+|+-..   .+  
T Consensus         5 m~V~V~F~g~L~~lf~~~r~~~v~l~~~~~~~TV~dll~~L~~~~p~~~~~l~~~~~~lr~~v~v~vN~~di~---~l~g   81 (101)
T d1xo3a_           5 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWE---LLGE   81 (101)
T ss_dssp             CEEEEEECSSGGGGGTTCCCEEEECCSSSCCCCHHHHHHHHHHHHCCSCGGGSCCTTSCCSSEEEEETTEEHH---HHTT
T ss_pred             eEEEEEEechHHHHhCCcceEEEEcCCCCCCcCHHHHHHHHHHhCCcchhhhhccCcCeeeeEEEEEcCccee---ccCC
Confidence            899999743        244566665   3479999999999987621  00000      012223333211   11  


Q ss_pred             hhhccCCCCEEEEEE
Q 017906           60 EENKVAENSFVVVML   74 (364)
Q Consensus        60 ~d~gIk~~s~I~v~v   74 (364)
                      -++.|++|+.|.++-
T Consensus        82 l~t~l~dgDeV~~~p   96 (101)
T d1xo3a_          82 LDYQLQDQDSILFIS   96 (101)
T ss_dssp             TSCCCCTTCEEEEEE
T ss_pred             CccCcCCCCEEEEeC
Confidence            256799999998873

>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=87.32  E-value=1.3  Score=33.24  Aligned_cols=58  Identities=19%  Similarity=0.117  Sum_probs=40.7

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--e--CC--eecCCCCChhhh
Q 017906            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--H--QG--KVLKDVTTLEEN   62 (364)
Q Consensus         3 I~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLi--f--~G--kiL~D~~tL~d~   62 (364)
                      |.|-..+|.+..|.|+.++|+.+|-+.+.++.+.. ..+ ..-|+  +  .|  +.|.|+..+-+.
T Consensus        12 vkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~-~~~-~f~L~E~~~~~~leR~L~d~E~vl~v   75 (100)
T d1wgra_          12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHAL-SDE-TWGLVECHPHLALERGLEDHESVVEV   75 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCC-CCC-CCCEEEEETTTTEEEEECSSSCHHHH
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCC-CCC-CeEEEEecCCCcceeecCchHhHHHH
Confidence            45556789899999999999999999999998843 111 22332  2  23  778886654444

>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=87.11  E-value=0.38  Score=30.48  Aligned_cols=35  Identities=29%  Similarity=0.448  Sum_probs=31.5

Q ss_pred             HHHHHHHHcCCCCC-CHHHHHHHHHHHcCChHHHHHHHH
Q 017906          174 ATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLY  211 (364)
Q Consensus       174 ~~V~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEyL~  211 (364)
                      .+...|+|||   | +|.-=.+=|+.-.||...+|.-|+
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            4678999999   9 999999999999999999998775

>d1gg3a3 d.15.1.4 (A:1-81) Erythroid membrane protein 4.1R {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: Erythroid membrane protein 4.1R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.17  E-value=1.8  Score=31.20  Aligned_cols=60  Identities=18%  Similarity=0.109  Sum_probs=45.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---Ce--ecCCCCChhhh
Q 017906            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---GK--VLKDVTTLEEN   62 (364)
Q Consensus         1 MkI~VKtl~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~---Gk--iL~D~~tL~d~   62 (364)
                      |..+|..++|..+.+.|+...+..+|=.+|....+.  ...+-.-|-|-   |.  =|+.++.|...
T Consensus         1 ~~C~V~lLD~~~~~~~v~~~~~G~~l~~~Vc~~l~l--~E~~YFGL~y~d~~~~~~WLd~~K~i~kq   65 (81)
T d1gg3a3           1 MHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNL--LEEDYFGLAIWDNATSKTWLDSAKEIKKQ   65 (81)
T ss_dssp             CEEEEECTTSCEEEEECCTTCCHHHHHHHHHHHHTT--CSCCSSSCEEECCSSSCCBCCTTSCHHHH
T ss_pred             CEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCC--cccccceEEEECCCCceEecccccchhhh
Confidence            788999999999999999999999999999999982  23333333332   32  25667777665

>d1ip9a_ d.15.2.2 (A:) Bud emergence mediator Bemp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Bud emergence mediator Bemp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.17  E-value=2  Score=31.22  Aligned_cols=43  Identities=14%  Similarity=0.157  Sum_probs=34.9

Q ss_pred             EEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 017906            3 VFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (364)
Q Consensus         3 I~VKtl-~gk~~~ieV~~s~TV~dLK~kI~~~~g~~~ip~~~qkLif~G   50 (364)
                      |+||.. ++..+.|.|.++.+..+|+++|..+++     ....+|-|..
T Consensus        13 ikVKv~~~~D~~~~~l~~~it~~dL~~kI~~rf~-----~~~~~lkY~D   56 (85)
T d1ip9a_          13 TKIKFYYKDDIFALMLKGDTTYKELRSKIAPRID-----TDNFKLQTKL   56 (85)
T ss_dssp             EEEEECBTTCCEEEEECSCCCHHHHHHHHHHHHT-----SSCEEEEECC
T ss_pred             EEEEEEECCcEEEEEeCCCCCHHHHHHHHHHHhC-----CCceEEEEEc
Confidence            566655 567899999999999999999999987     3567887753

>d2di0a1 a.5.2.4 (A:8-70) Activating signal cointegrator 1 complex subunit 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Activating signal cointegrator 1 complex subunit 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.75  E-value=2.3  Score=29.42  Aligned_cols=51  Identities=14%  Similarity=0.287  Sum_probs=36.4

Q ss_pred             CCcchHHHHHHHHHcCCCCCCHHHHHHHHHHHcCChHHHHHHHHhC-CCCCCC
Q 017906          168 AGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG-IPEQTA  219 (364)
Q Consensus       168 ~g~~~e~~V~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEyL~~G-IP~~~~  219 (364)
                      .|-+.+..|.++.++== -+...=|.++|..-.+|+++.|..|+.| +|.++.
T Consensus         2 ~~vel~s~I~qV~Dl~P-dLG~GFi~~~L~~Y~~n~E~vI~~lLe~~Lpp~L~   53 (63)
T d2di0a1           2 CGVELDSLISQVKDLLP-DLGEGFILACLEYYHYDPEQVINNILEERLAPTLS   53 (63)
T ss_dssp             SSHHHHHHHHHHHHHCC-SSCHHHHHHHHHHTTTCHHHHHHHHHTTCCCTTTT
T ss_pred             chhHHHHHHHHHHHHcC-CCcHHHHHHHHHHhCCCHHHHHHHHHccCCCHHHH
Confidence            57788999999987500 0123337778876445999999999999 787653