Citrus Sinensis ID: 021760

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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-------31
Protein Sequence
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQQWALIVP
Secondary Structure (PSIPRED)
cEEEEEcccccEEEEEEcccccHHHHHHHHHHHccccccccccEEEEEEccccccccHHHHcccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHHHcHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEEEEccHHHHHHHHHHHHHHcccccccHHHcEEEEcccEccccccHHHcccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccHHHHHHHHHcccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHHHcHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MKVFVKTlkgthfeievkpedkvsdVKKNIetvqgsdvypasQQMLIHqgkvlkdvttleenkvaENSFVVVMLTKskvsssgastvsaapanqaqttssapptstqptttsqtpaptvappqsvpesapppaapapapapapapapapapvssvsdvYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYsgipeqtavppvarasaggqagnppaqtqaqqpaapaptsgpnanpldlfpqglpnmgsnagagtLDFLRNSQQFQALRTMVQANPQILQQWALIVP
Flexible Loop (DISEMBL)
mkvfvktlkgthfeievkpedkvsdvkKNIETvqgsdvypasqQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSssgastvsaapanqaqttssapptstqpTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQQWALIVP
Low Complexity Region (SEG)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLtkskvsssgastvsaAPANqaqttssapptstqptttsqtpaptvappqsvpesapppaapapapapapapapapapvssvsDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARasaggqagnppaqtqaqqpaapaptsgpNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQQWALIVP
Disordered region (IsUnstruct)
****VKTLKGTHFEI**********************VYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT*****************************************************************************************NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI**************************************************************LDFLRNSQQFQALRTMVQANPQILQQWALI**
Disordered Region (DISOPRED)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM*******************************************************************************************************************************NNPERAV************************************************************************LRNSQQFQALRTMVQANPQILQQWA****
Disordered Region (DISEMBL)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS******************************************************************************SDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVA***************************GPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQQWALIVP
Disordered Region (DISPRO)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS*****************************************************************************************VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE**********************************************************GTLDFLRNSQQFQALRTMVQANPQILQQWALIVP
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQQWALIVP
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	308	2.2.26 [Sep-21-2011]
Q84L31	419	Putative DNA repair prote	yes	no	0.922	0.677	0.661	1e-106
Q84L30	378	Putative DNA repair prote	no	no	0.896	0.730	0.645	1e-90
Q40742	392	Probable DNA repair prote	yes	no	0.918	0.721	0.601	3e-84
Q84L33	371	Putative DNA repair prote	no	no	0.860	0.714	0.549	2e-74
Q84L32	368	Putative DNA repair prote	no	no	0.860	0.720	0.491	3e-69
P54727	409	UV excision repair protei	yes	no	0.896	0.674	0.383	1e-36
Q4KMA2	415	UV excision repair protei	yes	no	0.899	0.667	0.360	2e-35
P54728	416	UV excision repair protei	yes	no	0.876	0.649	0.352	3e-35
Q29RK4	408	UV excision repair protei	yes	no	0.876	0.661	0.344	2e-34
P54725	363	UV excision repair protei	no	no	0.805	0.683	0.336	5e-30

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

 Score =  385 bits (989), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 219/331 (66%), Positives = 248/331 (74%), Gaps = 47/331 (14%)

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

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

Query: 117 ------------------------PTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPV 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 GIPEQTAVPPVAR--ASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGS 270
           GIPEQ  VPPVAR  ASA GQ  NPPAQT  QQPAA AP SGPNANPLDLFPQGLPN+G 
Sbjct: 228 GIPEQAEVPPVARPPASA-GQPANPPAQT--QQPAA-APASGPNANPLDLFPQGLPNVGG 283

Query: 271 NAGAGTLDFLRNSQQFQALRTMVQANPQILQ 301
           N GAGTLDFLRNSQQFQALR MVQANPQ+LQ
Sbjct: 284 NPGAGTLDFLRNSQQFQALRAMVQANPQVLQ 314

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 =  333 bits (854), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 195/302 (64%), Positives = 222/302 (73%), Gaps = 26/302 (8%)

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 LQ 301
           LQ
Sbjct: 276 LQ 277

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 =  312 bits (799), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 183/304 (60%), Positives = 216/304 (71%), Gaps = 21/304 (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 QAQQPAAPA-PTSGPNANPLDLFPQGLPNMGSN-AGAGTLDFLRNSQQFQALRTMVQANP 297
           QA QPAAP+  +SGPNA+PLDLFPQ LPN  ++ AG G LD LRN+ QF+ L ++VQANP
Sbjct: 223 QATQPAAPSILSSGPNASPLDLFPQALPNASTDAAGLGNLDALRNNAQFRTLLSLVQANP 282

Query: 298 QILQ 301
           QILQ
Sbjct: 283 QILQ 286

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 =  279 bits (713), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 167/304 (54%), Positives = 199/304 (65%), Gaps = 39/304 (12%)

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 QILQ 301
           QILQ
Sbjct: 265 QILQ 268

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 =  262 bits (669), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 148/301 (49%), Positives = 186/301 (61%), Gaps = 36/301 (11%)

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 +S      SA P+     ++    T+T   +++   AP+  
Sbjct: 61  ENKVTEEGFLVVMLSKSKTAS------SAGPS-----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 Q 301
           Q
Sbjct: 265 Q 265

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 =  153 bits (387), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 124/323 (38%), Positives = 168/323 (52%), Gaps = 47/323 (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 DFLRNSQQFQALRTMVQANPQIL 300
           +FLRN  QFQ +R ++Q NP +L
Sbjct: 277 EFLRNQPQFQQMRQIIQQNPSLL 299

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

 Score =  149 bits (376), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 116/322 (36%), Positives = 163/322 (50%), Gaps = 45/322 (13%)

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

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

Query: 108 PTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAP---APAPAPAP--VSSVSDVYGQA 162
            T  S TPA T A  +  P  A  P  PA  PA  P   +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------------PPQAVSTGTPQSPAVAAAAATTT--------ATTTTTSGGHPLE 277

Query: 279 FLRNSQQFQALRTMVQANPQIL 300
           FLRN  QFQ +R ++Q NP +L
Sbjct: 278 FLRNQPQFQQMRQIIQQNPSLL 299

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

 Score =  149 bits (375), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 116/329 (35%), Positives = 163/329 (49%), Gaps = 59/329 (17%)

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

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

Query: 109 --------TTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAP---APAPAPAP--VSSV 155
                   T  S  PA T A  +  P  A  P  PA  PA  P   +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 AGAGTLDFLRNSQQFQALRTMVQANPQIL 300
           +G   L+FLRN  QFQ +R ++Q NP +L
Sbjct: 271 SGGHPLEFLRNQPQFQQMRQIIQQNPSLL 299

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

 Score =  146 bits (368), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 113/328 (34%), Positives = 158/328 (48%), Gaps = 58/328 (17%)

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 GAGTLDFLRNSQQFQALRTMVQANPQIL 300
               L+FLRN  QFQ +R ++Q NP +L
Sbjct: 275 ----LEFLRNQPQFQQMRQIIQQNPSLL 298

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 =  131 bits (330), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 109/324 (33%), Positives = 157/324 (48%), Gaps = 76/324 (23%)

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-----PAPAPAPAPAPAPAPAPVSSVSDVYGQ--AASNLVAGSNLEAT 175
                S PPPAA     P+   AP  +P      V 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 PAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMV-- 293
                ++QPA  A                       AG   L+FLR+  QFQ +R ++  
Sbjct: 214 QESQVSEQPATEA-----------------------AGENPLEFLRDQPQFQNMRQVIQQ 250

Query: 294 -------------QANPQILQQWA 304
                        Q NPQ+LQQ +
Sbjct: 251 NPALLPALLQQLGQENPQLLQQIS 274

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	308
225452017	381	PREDICTED: putative DNA repair protein R	0.915	0.740	0.720	1e-113
255551362	381	uv excision repair protein rad23, putati	0.912	0.737	0.714	1e-111
15232924	419	putative DNA repair protein RAD23-3 [Ara	0.922	0.677	0.661	1e-104
225452019	361	PREDICTED: putative DNA repair protein R	0.899	0.767	0.677	1e-104
297832888	417	hypothetical protein ARALYDRAFT_477488 [	0.925	0.683	0.667	1e-104
334185033	418	putative DNA repair protein RAD23-3 [Ara	0.918	0.677	0.658	1e-103
5640111	389	RAD23 protein [Solanum lycopersicum var.	0.909	0.719	0.683	1e-102
224079274	385	predicted protein [Populus trichocarpa]	0.915	0.732	0.680	1e-102
224127650	384	predicted protein [Populus trichocarpa]	0.899	0.721	0.681	1e-100
77745475	384	RAD23-like [Solanum tuberosum]	0.922	0.739	0.717	1e-99

>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 =  415 bits (1067), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 217/301 (72%), Positives = 242/301 (80%), Gaps = 19/301 (6%)

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 Q 301
           Q
Sbjct: 282 Q 282

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 =  407 bits (1047), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 215/301 (71%), Positives = 236/301 (78%), Gaps = 20/301 (6%)

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 Q 301
           Q
Sbjct: 281 Q 281

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 219/331 (66%), Positives = 248/331 (74%), Gaps = 47/331 (14%)

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

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

Query: 117 ------------------------PTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPV 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 GIPEQTAVPPVAR--ASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGS 270
           GIPEQ  VPPVAR  ASA GQ  NPPAQT  QQPAA AP SGPNANPLDLFPQGLPN+G 
Sbjct: 228 GIPEQAEVPPVARPPASA-GQPANPPAQT--QQPAA-APASGPNANPLDLFPQGLPNVGG 283

Query: 271 NAGAGTLDFLRNSQQFQALRTMVQANPQILQ 301
           N GAGTLDFLRNSQQFQALR MVQANPQ+LQ
Sbjct: 284 NPGAGTLDFLRNSQQFQALRAMVQANPQVLQ 314

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225452019|ref|XP_002283661.1| PREDICTED: putative DNA repair protein RAD23-3 isoform 2 [Vitis vinifera]

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/301 (67%), Positives = 234/301 (77%), Gaps = 24/301 (7%)

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 Q      + + NP ++
Sbjct: 222 PQGPQTTVASSGPNANPLDLFPQGLPSMGSNASAGTLDFLRNSPQ-----ELGKQNPHLM 276

Query: 301 Q 301
           +
Sbjct: 277 R 277

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 219/328 (66%), Positives = 244/328 (74%), Gaps = 43/328 (13%)

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

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

Query: 117 ----------------------PTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSS 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 AQT  QQPAA AP SGPNANPLDLFPQGLPN+G N G
Sbjct: 228 PEQAEVPPVARAPASFGQPANPSAQT--QQPAA-APASGPNANPLDLFPQGLPNVGGNPG 284

Query: 274 AGTLDFLRNSQQFQALRTMVQANPQILQ 301
           AGTLDFLRNSQQFQALR MVQANPQ+LQ
Sbjct: 285 AGTLDFLRNSQQFQALRAMVQANPQVLQ 312

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185033|ref|NP_001189793.1| putative DNA repair protein RAD23-3 [Arabidopsis thaliana] gi|332640305|gb|AEE73826.1| putative DNA repair protein RAD23-3 [Arabidopsis thaliana]

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 218/331 (65%), Positives = 247/331 (74%), Gaps = 48/331 (14%)

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

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

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

Query: 153 SSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 212
               DVYGQAASNL AGSNLE+T+QQILDMGGG+WDRETV+ ALRAA+NNPERAVEYLY+
Sbjct: 168 GQ-GDVYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLYT 226

Query: 213 GIPEQTAVPPVAR--ASAGGQAGNPPAQTQAQQPAAPAPTSGPNANPLDLFPQGLPNMGS 270
           GIPEQ  VPPVAR  ASA GQ  NPPAQT  QQPAA AP SGPNANPLDLFPQGLPN+G 
Sbjct: 227 GIPEQAEVPPVARPPASA-GQPANPPAQT--QQPAA-APASGPNANPLDLFPQGLPNVGG 282

Query: 271 NAGAGTLDFLRNSQQFQALRTMVQANPQILQ 301
           N GAGTLDFLRNSQQFQALR MVQANPQ+LQ
Sbjct: 283 NPGAGTLDFLRNSQQFQALRAMVQANPQVLQ 313

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 212/310 (68%), Positives = 231/310 (74%), Gaps = 30/310 (9%)

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 +               +DVY QAASNLVAGSNLE TVQQI
Sbjct: 116 ALPQSASESAPTPAPVPAAASSV-------------TDVYDQAASNLVAGSNLETTVQQI 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 MVQANPQILQ 301
           MVQANPQILQ
Sbjct: 280 MVQANPQILQ 289

Source: Solanum lycopersicum var. cerasiforme

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 207/304 (68%), Positives = 233/304 (76%), Gaps = 22/304 (7%)

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 QILQ 301
           QILQ
Sbjct: 282 QILQ 285

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  369 bits (947), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 210/308 (68%), Positives = 238/308 (77%), Gaps = 31/308 (10%)

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     A  P+ GPNANPLDLFPQGLP+ GSNAGAG LDFLRNSQQFQALR MV
Sbjct: 220 NPPAQAQQ---PAAPPSGGPNANPLDLFPQGLPSTGSNAGAGNLDFLRNSQQFQALRAMV 276

Query: 294 QANPQILQ 301
           QANPQILQ
Sbjct: 277 QANPQILQ 284

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|77745475|gb|ABB02636.1| RAD23-like [Solanum tuberosum]

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 216/301 (71%), Positives = 240/301 (79%), Gaps = 17/301 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           MK+FVKTLKGTHFEIEVKPED V+DVKK+IETVQG DVYPA+QQMLIHQ KVLKD TTL+
Sbjct: 1   MKIFVKTLKGTHFEIEVKPEDTVADVKKSIETVQGQDVYPAAQQMLIHQVKVLKDPTTLD 60

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVA 120
           ENKVAENSFVV+ML+K+KVS+SG S    AP+N           S QP T++  P  TVA
Sbjct: 61  ENKVAENSFVVIMLSKNKVSTSGTSATQPAPSN-----------SAQPATSTGQPTQTVA 109

Query: 121 PPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQIL 180
           P  +    AP  +APAPAPAPAPAPAPAPA  + ++DVYGQAASNLVAGS LE TVQQIL
Sbjct: 110 PQATAASVAPAQSAPAPAPAPAPAPAPAPAAANPLTDVYGQAASNLVAGSTLETTVQQIL 169

Query: 181 DMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ 240
           DMGGGSW+R+TV+RALRAAYNNPERA+EYLYSGIPEQ  +PP A  S  GQA NPP   Q
Sbjct: 170 DMGGGSWERDTVVRALRAAYNNPERAIEYLYSGIPEQAEIPPAAPVS--GQAVNPP--VQ 225

Query: 241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQIL 300
           A  PA   P+ GPNANPLDLFPQGLPN+GSN GAG LDFL NS QFQALR MVQANPQIL
Sbjct: 226 ASPPA--VPSGGPNANPLDLFPQGLPNVGSNVGAGNLDFLSNSPQFQALRAMVQANPQIL 283

Query: 301 Q 301
           Q
Sbjct: 284 Q 284

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

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	308
TAIR|locus:2076944	419	RAD23C "RADIATION SENSITIVE23C	0.464	0.341	0.703	9.4e-82
TAIR|locus:2177376	378	RAD23D "RADIATION SENSITIVE23D	0.470	0.383	0.668	6.7e-75
TAIR|locus:2200522	368	RAD23A "RADIATION SENSITIVE23A	0.211	0.176	0.753	4.6e-60
ZFIN|ZDB-GENE-051113-160	404	zgc:123349 "rad23ab" [Danio re	0.188	0.143	0.540	1.5e-29
UNIPROTKB|K7ESE3	308	RAD23A "UV excision repair pro	0.165	0.165	0.574	4.4e-29
RGD|1309899	351	Rad23a "RAD23 homolog A (S. ce	0.165	0.145	0.574	9.4e-29
UNIPROTKB|A3KMV2	362	RAD23A "UV excision repair pro	0.165	0.140	0.574	1.2e-28
MGI|MGI:105126	363	Rad23a "RAD23a homolog (S. cer	0.165	0.140	0.574	1.2e-28
UNIPROTKB|P54725	363	RAD23A "UV excision repair pro	0.165	0.140	0.574	1.5e-28
UNIPROTKB|D4AD39	363	Rad23a "RAD23a homolog (S. cer	0.165	0.140	0.574	1.5e-28

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

 Score = 509 (184.2 bits), Expect = 9.4e-82, Sum P(2) = 9.4e-82
 Identities = 102/145 (70%), Positives = 110/145 (75%)

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 LDFLRNSQQFQALRTMVQANPQILQ 301
             LDFLRNSQQFQALR MVQANPQ+LQ
Sbjct:   290 LDFLRNSQQFQALRAMVQANPQVLQ 314

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 = 490 (177.5 bits), Expect = 6.7e-75, Sum P(2) = 6.7e-75
 Identities = 97/145 (66%), Positives = 107/145 (73%)

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 LDFLRNSQQFQALRTMVQANPQILQ 301
             LDFLRNSQQFQALR MVQANPQILQ
Sbjct:   253 LDFLRNSQQFQALRAMVQANPQILQ 277

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 = 267 (99.0 bits), Expect = 4.6e-60, Sum P(3) = 4.6e-60
 Identities = 49/65 (75%), Positives = 57/65 (87%)

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

Query:   217 QTAVP 221
                +P
Sbjct:   191 TVTIP 195

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

ZFIN|ZDB-GENE-051113-160 zgc:123349 "rad23ab" [Danio rerio (taxid:7955)]

 Score = 152 (58.6 bits), Expect = 1.5e-29, Sum P(3) = 1.5e-29
 Identities = 33/61 (54%), Positives = 43/61 (70%)

Query:   162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVP 221
             AAS LV G   E  V +I+ MG   ++RE VI ALRA++NNP+RAVEYL +GIP ++  P
Sbjct:   189 AASILVTGQAYENLVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLTGIPAESEQP 245

Query:   222 P 222
             P
Sbjct:   246 P 246

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|K7ESE3 RAD23A "UV excision repair protein RAD23 homolog A" [Homo sapiens (taxid:9606)]

 Score = 148 (57.2 bits), Expect = 4.4e-29, Sum P(3) = 4.4e-29
 Identities = 31/54 (57%), Positives = 39/54 (72%)

Query:   162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
             AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct:   153 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 203

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

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

 Score = 148 (57.2 bits), Expect = 9.4e-29, Sum P(3) = 9.4e-29
 Identities = 31/54 (57%), Positives = 39/54 (72%)

Query:   162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
             AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct:   153 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 203

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

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

 Score = 148 (57.2 bits), Expect = 1.2e-28, Sum P(3) = 1.2e-28
 Identities = 31/54 (57%), Positives = 39/54 (72%)

Query:   162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
             AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct:   153 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 203

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 = 148 (57.2 bits), Expect = 1.2e-28, Sum P(3) = 1.2e-28
 Identities = 31/54 (57%), Positives = 39/54 (72%)

Query:   162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
             AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct:   153 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 203

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 = 148 (57.2 bits), Expect = 1.5e-28, Sum P(3) = 1.5e-28
 Identities = 31/54 (57%), Positives = 39/54 (72%)

Query:   162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
             AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct:   153 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 203

GO:0003684 "damaged DNA binding" evidence=IEA

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

GO:0000502 "proteasome complex" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0031593 "polyubiquitin binding" evidence=IDA

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

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

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

GO:0005515 "protein binding" evidence=IPI

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

 Score = 148 (57.2 bits), Expect = 1.5e-28, Sum P(3) = 1.5e-28
 Identities = 31/54 (57%), Positives = 39/54 (72%)

Query:   162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
             AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct:   153 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 203

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

---

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	0.6019	0.9188	0.7219	yes	no
Q84L31	RD23C_ARATH	No assigned EC number	0.6616	0.9220	0.6778	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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	308
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	3e-63
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	2e-35
smart00213	72	smart00213, UBQ, Ubiquitin homologues	5e-21
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	8e-19
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	1e-18
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	6e-11
pfam00627	37	pfam00627, UBA, UBA/TS-N domain	1e-10
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	2e-10
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	5e-10
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	1e-09
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	3e-09
cd01803	76	cd01803, Ubiquitin, Ubiquitin	6e-09
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	1e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	1e-08
cd00194	38	cd00194, UBA, Ubiquitin Associated domain	2e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	1e-07
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-07
smart00165	37	smart00165, UBA, Ubiquitin associated domain	3e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-07
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	3e-07
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	5e-07
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	7e-07
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	9e-07
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	1e-06
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-06
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	5e-06
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	8e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	9e-06
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	1e-05
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	1e-05
PRK10672	361	PRK10672, PRK10672, rare lipoprotein A; Provisiona	1e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-05
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	2e-05
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-05
pfam09280	59	pfam09280, XPC-binding, XPC-binding domain	2e-05
PRK06302	155	PRK06302, PRK06302, acetyl-CoA carboxylase biotin	2e-05
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	2e-05
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	3e-05
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	3e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-05
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	5e-05
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	6e-05
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	7e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	8e-05
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	8e-05
cd01812	71	cd01812, BAG1_N, Ubiquitin-like domain of BAG1	9e-05
PRK07764	824	PRK07764, PRK07764, 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
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	1e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	2e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	2e-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
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	3e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	4e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	4e-04
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	4e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-04
PRK14960	702	PRK14960, PRK14960, DNA polymerase III subunits ga	4e-04
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	5e-04
PLN02983	274	PLN02983, PLN02983, biotin carboxyl carrier protei	5e-04
PRK05704	407	PRK05704, PRK05704, dihydrolipoamide succinyltrans	5e-04
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	6e-04
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	7e-04
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	7e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	8e-04
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	8e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.001
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.001
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	0.001
PRK11892	464	PRK11892, PRK11892, pyruvate dehydrogenase subunit	0.001
cd01793	74	cd01793, Fubi, Fubi ubiquitin-like protein	0.001
COG4982	866	COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein]	0.001
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	0.002
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	0.002
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	0.002
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	0.002
PRK05641	153	PRK05641, PRK05641, putative acetyl-CoA carboxylas	0.002
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.002
PRK11901	327	PRK11901, PRK11901, hypothetical protein; Reviewed	0.002
pfam04652	315	pfam04652, DUF605, Vta1 like	0.002
TIGR03593	366	TIGR03593, yidC_nterm, membrane protein insertase,	0.002
PRK14959	624	PRK14959, PRK14959, DNA polymerase III subunits ga	0.002
PRK10547	670	PRK10547, PRK10547, chemotaxis protein CheA; Provi	0.002
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.002
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	0.002
PRK11633	226	PRK11633, PRK11633, cell division protein DedD; Pr	0.002
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.003
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.003
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	0.003
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	0.003
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	0.003
PRK11892	464	PRK11892, PRK11892, pyruvate dehydrogenase subunit	0.003
PRK12438	991	PRK12438, PRK12438, hypothetical protein; Provisio	0.003
PRK09111	598	PRK09111, PRK09111, DNA polymerase III subunits ga	0.003
PRK12799	421	PRK12799, motB, flagellar motor protein MotB; Revi	0.003

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

 Score =  203 bits (519), Expect = 3e-63
 Identities = 109/302 (36%), Positives = 154/302 (50%), Gaps = 31/302 (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 LQ 301
           L 
Sbjct: 271 LP 272

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 =  122 bits (308), Expect = 2e-35
 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 = 84.6 bits (210), Expect = 5e-21
 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|176364 cd01769, UBL, Ubiquitin-like domain of UBL

 Score = 78.5 bits (194), Expect = 8e-19
 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 = 78.0 bits (193), Expect = 1e-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 = 57.2 bits (138), Expect = 6e-11
 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|201355 pfam00627, UBA, UBA/TS-N domain

 Score = 55.1 bits (134), Expect = 1e-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|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein

 Score = 55.7 bits (135), Expect = 2e-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|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein

 Score = 54.8 bits (132), Expect = 5e-10
 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 = 59.1 bits (144), Expect = 1e-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|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 57.6 bits (140), Expect = 3e-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 = 51.8 bits (124), Expect = 6e-09
 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 = 1e-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 = 1e-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 = 49.4 bits (119), Expect = 2e-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 = 1e-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|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 51.6 bits (124), 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|197551 smart00165, UBA, Ubiquitin associated domain

 Score = 45.9 bits (110), Expect = 3e-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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 51.5 bits (124), Expect = 3e-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|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like

 Score = 46.4 bits (111), Expect = 3e-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|176397 cd01802, AN1_N, ubiquitin-like domain of AN1

 Score = 47.2 bits (112), Expect = 5e-07
 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|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 50.3 bits (120), Expect = 7e-07
 Identities = 42/196 (21%), Positives = 58/196 (29%), Gaps = 17/196 (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 QAQQPAAPAPTSGPNA 255
            A           P A
Sbjct: 553 AAAATEPVVAPRPPRA 568

Length = 700

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

 Score = 49.9 bits (120), Expect = 9e-07
 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|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 49.4 bits (118), Expect = 1e-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|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 48.6 bits (116), 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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 48.8 bits (117), Expect = 2e-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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 48.8 bits (117), Expect = 2e-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|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.5 bits (113), 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|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 46.9 bits (112), Expect = 8e-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 = 46.9 bits (112), Expect = 9e-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|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 46.5 bits (111), 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|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 45.8 bits (109), Expect = 1e-05
 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|236733 PRK10672, PRK10672, rare lipoprotein A; Provisional

 Score = 45.8 bits (109), Expect = 1e-05
 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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.1 bits (110), Expect = 2e-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|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.6 bits (109), Expect = 2e-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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 46.1 bits (109), Expect = 2e-05
 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|192241 pfam09280, XPC-binding, XPC-binding domain

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 16/26 (61%), Positives = 19/26 (73%)

Query: 277 LDFLRNSQQFQALRTMVQANPQILQQ 302
           L FLRN+ QFQ LR MVQ NP++L  
Sbjct: 1   LAFLRNNPQFQQLRQMVQQNPELLPP 26

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|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|185411 PTZ00044, PTZ00044, ubiquitin; Provisional

 Score = 41.7 bits (98), Expect = 2e-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|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.3 bits (107), Expect = 3e-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|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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 44.6 bits (106), Expect = 4e-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|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 44.3 bits (105), 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|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 43.9 bits (104), 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|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 43.5 bits (103), Expect = 7e-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 = 43.8 bits (104), Expect = 8e-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|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 43.0 bits (101), Expect = 8e-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|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1

 Score = 39.6 bits (93), Expect = 9e-05
 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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 43.1 bits (102), Expect = 1e-04
 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|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 = 41.2 bits (97), 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|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.9 bits (101), Expect = 1e-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|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.8 bits (101), Expect = 2e-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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 42.3 bits (100), 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|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|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|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 41.7 bits (99), 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 = 41.7 bits (99), 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 = 41.7 bits (99), 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|176403 cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1 and hPLIC2

 Score = 38.2 bits (89), Expect = 3e-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|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.8 bits (98), Expect = 4e-04
 Identities = 35/175 (20%), Positives = 57/175 (32%), Gaps = 17/175 (9%)

Query: 75  TKSKVSSSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAA 134
            ++  ++    + +      A+  S+  P        +   AP  A   +     P  AA
Sbjct: 416 ARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAA 475

Query: 135 PAPAP---APAPAPAPAPAPVSSVSDVYGQAASNLVAGSNLEATVQQILDMGGGSWDRET 191
            A AP   APA APAPA        ++  + AS   A            D     W  E+
Sbjct: 476 AAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQP----------DAAPAGWVAES 525

Query: 192 VIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPAA 246
           +     A  ++    +    +  P     P  A A+    A  PP  + +  P  
Sbjct: 526 IPDPATADPDDAFETL----APAPAAAPAPRAAAATEPVVAPRPPRASASGLPDM 576

Length = 700

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

 Score = 41.7 bits (98), Expect = 4e-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|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 41.2 bits (97), Expect = 4e-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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.8 bits (98), Expect = 4e-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|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.6 bits (97), Expect = 4e-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|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.3 bits (97), Expect = 5e-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|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA carboxylase

 Score = 40.6 bits (95), Expect = 5e-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|235571 PRK05704, PRK05704, dihydrolipoamide succinyltransferase; Validated

 Score = 41.0 bits (97), Expect = 5e-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|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 40.8 bits (96), Expect = 6e-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 = 41.0 bits (96), Expect = 7e-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|176393 cd01798, parkin_N, amino-terminal ubiquitin-like of parkin protein

 Score = 37.0 bits (86), Expect = 7e-04
 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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.7 bits (96), Expect = 8e-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|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 = 39.7 bits (93), 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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 40.3 bits (94), Expect = 0.001
 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|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.6 bits (95), Expect = 0.001
 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|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta; Provisional

 Score = 39.9 bits (94), 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|176388 cd01793, Fubi, Fubi ubiquitin-like protein

 Score = 36.7 bits (85), Expect = 0.001
 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|227315 COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein]

 Score = 40.2 bits (94), 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|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional

 Score = 38.9 bits (91), 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 = 37.9 bits (88), Expect = 0.002
 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|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 37.9 bits (88), 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|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|235540 PRK05641, PRK05641, putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated

 Score = 37.9 bits (88), 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|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 39.0 bits (91), 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|237015 PRK11901, PRK11901, hypothetical protein; Reviewed

 Score = 38.9 bits (91), Expect = 0.002
 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|218191 pfam04652, DUF605, Vta1 like

 Score = 38.9 bits (91), 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 = 38.9 bits (91), 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|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.3 bits (91), 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|236712 PRK10547, PRK10547, chemotaxis protein CheA; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 39.3 bits (92), Expect = 0.002
 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|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 27/70 (38%), Positives = 27/70 (38%), Gaps = 6/70 (8%)

Query: 91  PANQAQTTSSAPPTSTQPTTTSQTPA-PTVAPPQSVPESAPPPAAPA-----PAPAPAPA 144
           PA  A      P    QP    Q P  P VAP      SAP PA  A     P  AP P 
Sbjct: 121 PAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPE 180

Query: 145 PAPAPAPVSS 154
           P   PAPV  
Sbjct: 181 PVAEPAPVMD 190

Length = 333

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

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 20/70 (28%), Positives = 22/70 (31%), Gaps = 7/70 (10%)

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 APAPAPAPAP 151
            P P      
Sbjct: 134 EPKPVVEEKA 143

Length = 226

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

 Score = 38.8 bits (90), Expect = 0.003
 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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 38.8 bits (90), 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|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional

 Score = 38.7 bits (90), Expect = 0.003
 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|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 39.0 bits (92), Expect = 0.003
 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|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 38.7 bits (91), 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 = 38.7 bits (91), 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|171499 PRK12438, PRK12438, hypothetical protein; Provisional

 Score = 39.1 bits (91), Expect = 0.003
 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|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated

 Score = 38.7 bits (91), 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|183756 PRK12799, motB, flagellar motor protein MotB; Reviewed

 Score = 38.5 bits (89), 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	308
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	100.0
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	100.0
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.8
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.78
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.77
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.76
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.75
PTZ00044	76	ubiquitin; Provisional	99.75
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.74
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.74
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.73
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.72
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.72
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.72
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.71
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.71
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.71
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.7
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.7
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.69
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.66
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.64
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.62
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.61
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.61
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.54
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.53
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.52
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.49
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.46
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.46
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.4
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.39
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.36
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.32
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.12
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	99.12
PF09280	59	XPC-binding: XPC-binding domain; InterPro: IPR0153	99.06
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	99.04
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	99.01
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	98.99
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.98
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	98.9
PLN02560	308	enoyl-CoA reductase	98.89
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	98.87
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	98.86
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.83
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.78
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.58
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.57
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.38
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.31
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.17
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	98.08
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	98.03
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.77
KOG4495	110	consensus RNA polymerase II transcription elongati	97.76
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	97.5
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	97.45
COG5417	81	Uncharacterized small protein [Function unknown]	97.27
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	97.25
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.2
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	97.18
KOG0944	763	consensus Ubiquitin-specific protease UBP14 [Postt	97.17
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.1
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	97.01
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	96.92
KOG1639	297	consensus Steroid reductase required for elongatio	96.91
KOG0013	231	consensus Uncharacterized conserved protein [Funct	96.89
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	96.87
KOG4583	391	consensus Membrane-associated ER protein involved	96.85
KOG0418	200	consensus Ubiquitin-protein ligase [Posttranslatio	96.71
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	96.61
smart00546	43	CUE Domain that may be involved in binding ubiquit	96.52
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	96.48
PF13019	162	Telomere_Sde2: Telomere stability and silencing	96.4
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	96.34
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	96.19
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	95.85
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	95.19
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	95.05
PF09288	55	UBA_3: Fungal ubiquitin-associated domain ; InterP	94.96
PF11626	87	Rap1_C: TRF2-interacting telomeric protein/Rap1 -	94.82
PRK06437	67	hypothetical protein; Provisional	94.71
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	94.41
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	94.17
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	94.13
KOG0012	380	consensus DNA damage inducible protein [Replicatio	94.03
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	93.83
PF14453	57	ThiS-like: ThiS-like ubiquitin	93.47
smart00727	41	STI1 Heat shock chaperonin-binding motif.	93.41
PRK08364	70	sulfur carrier protein ThiS; Provisional	93.29
PF07499	47	RuvA_C: RuvA, C-terminal domain; InterPro: IPR0111	93.08
PRK06488	65	sulfur carrier protein ThiS; Validated	93.05
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	92.97
PF06972	60	DUF1296: Protein of unknown function (DUF1296); In	92.84
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	92.6
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	91.91
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	91.6
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	90.77
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	90.71
PF12754	309	Blt1: Cell-cycle control medial ring component; In	90.42
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	89.99
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	89.57
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	89.53
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	89.3
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	89.27
PRK05863	65	sulfur carrier protein ThiS; Provisional	89.05
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	88.98
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	88.9
PRK05659	66	sulfur carrier protein ThiS; Validated	88.29
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	88.28
PRK08053	66	sulfur carrier protein ThiS; Provisional	87.6
PRK06944	65	sulfur carrier protein ThiS; Provisional	85.93
PF08938	79	HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This	85.71
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	85.25
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	84.9
KOG2982	418	consensus Uncharacterized conserved protein [Funct	84.86
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	84.01
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	83.51
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	83.42
PF11069	98	DUF2870: Protein of unknown function (DUF2870); In	82.92
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	82.86
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	82.73
COG2104	68	ThiS Sulfur transfer protein involved in thiamine	82.37
PRK06083	84	sulfur carrier protein ThiS; Provisional	81.81
PF07223	358	DUF1421: Protein of unknown function (DUF1421); In	81.35
PF14732	87	UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquiti	81.11
PRK07696	67	sulfur carrier protein ThiS; Provisional	80.75
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	80.54
smart00455	70	RBD Raf-like Ras-binding domain.	80.46

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=100.00  E-value=2.4e-63  Score=480.86  Aligned_cols=271  Identities=39%  Similarity=0.624  Sum_probs=180.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|++.+++++|||||+||+|+|+++|++|||+++++|+||++|+|..
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            89999999999999999999999999999999987555899999999999999999999999999999999999998875


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCccc
Q 021760           81 SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAP-APAPAPAPAPAPAPVSSVSDVY  159 (308)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  159 (308)
                      ....+.+...+.+++.++.+.+.    +.+....++++.++.    . .    .+.. .+ .++..  .+.+.+. ....
T Consensus        81 ~~~~~~~~~~~~~~p~~~~~~~~----~~~~~~~~~~~~~~~----~-~----~~~~~~~-~~~~~--~~~~~~~-~~~~  143 (378)
T TIGR00601        81 TGKSAPPAATPTSAPTPTPSPPA----SPASGMSAAPASAVE----E-K----SPSEESA-TATAP--ESPSTSV-PSSG  143 (378)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCc----c-c----cccCCCC-CCCCC--CCCCccc-cccC
Confidence            33222111011010111000000    000000000000000    0 0    0000 00 00000  0000000 0101


Q ss_pred             cccccccccCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCCCCCCCCccccCCCCCCCCCCCcc
Q 021760          160 GQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQT  239 (308)
Q Consensus       160 ~~~~s~l~~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~~~~~~~~~~~~~~~~~~~~~~~~  239 (308)
                      ..+.|+||+|++||++|++||+||   |+|+||+||||||||||||||||||+|||++++...+    ...    +... 
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   9999999999999999999999999999998762111    100    0000 


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCcCCCCCCCC------CCCCCCchHHhhChHHHHHHHHHHHhChhhHHHHHhcC
Q 021760          240 QAQQPAAPAPTSGPNANPLDLFPQGLPNMG------SNAGAGTLDFLRNSQQFQALRTMVQANPQILQQWALIV  307 (308)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~lf~~a~~~~~------~~~~~~~l~~Lr~~pqf~~lRq~vqqnP~~L~~~L~~~  307 (308)
                      .     + ....+.+..+ |||++++.++.      .+.|+++|+|||++|||++||++||+||+||++|||++
T Consensus       212 ~-----~-~~~~~~~~~~-~lf~~a~~~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLqql  278 (378)
T TIGR00601       212 T-----A-AATTETPQHG-SVFEQAAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQI  278 (378)
T ss_pred             c-----c-cccCCCCCCc-chhhhhhcccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHHHH
Confidence            0     0 0111112222 99999864321      11245699999999999999999999999999999986

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=1.7e-60  Score=443.32  Aligned_cols=246  Identities=53%  Similarity=0.801  Sum_probs=183.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|++|+|+|.+++||.+||++|+...|.+ +|+++|||||+||+|+|+.+|.+|+|+++++|+||++|+|..
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 021760           81 SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYG  160 (308)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (308)
                      ....     ++..  .+     +        ...+....+|.. ..+       ..    ..+++    ...++....++
T Consensus        80 ~t~~-----ap~s--~~-----~--------~~~p~~~~ap~~-s~a-------~~----~s~~~----~~~~~~~~~~~  123 (340)
T KOG0011|consen   80 STQV-----APQS--SA-----A--------THLPKAAEAPPS-SAA-------ED----ASPAT----PAQTSQEDTYE  123 (340)
T ss_pred             ccCC-----CCCC--cc-----c--------cCCCccCCCCCc-ccc-------cc----CCCCc----cccccccchhh
Confidence            1110     0000  00     0        000011111100 000       00    00000    00122234577


Q ss_pred             ccccccccCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCCCCCCCCccccCCCCCCCCCCCccc
Q 021760          161 QAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ  240 (308)
Q Consensus       161 ~~~s~l~~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~~~~~~~~~~~~~~~~~~~~~~~~~  240 (308)
                      .+.++|++|++||.+|.+||+||   |+||+|+|||||||||||||||||++|||+..........+++          .
T Consensus       124 ~aas~Lv~G~~~e~~V~~Im~MG---y~re~V~~AlRAafNNPeRAVEYLl~GIP~~~~~~~~~~~~~~----------~  190 (340)
T KOG0011|consen  124 IAASTLVVGSEYEQTVQQIMEMG---YDREEVERALRAAFNNPERAVEYLLNGIPEDAEVPEPEKSTAA----------A  190 (340)
T ss_pred             hhhhhhhccchhHHHHHHHHHhC---ccHHHHHHHHHHhhCChhhhHHHHhcCCcccccCCcccCCccc----------C
Confidence            88999999999999999999999   9999999999999999999999999999998665543211100          0


Q ss_pred             cCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCchHHhhChHHHHHHHHHHHhChhhHHHHHhcC
Q 021760          241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQQWALIV  307 (308)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~lf~~a~~~~~~~~~~~~l~~Lr~~pqf~~lRq~vqqnP~~L~~~L~~~  307 (308)
                      + .    .++   +.+|+++|++.+....   |+++|+|||++|||++||+||||||+||++|||.+
T Consensus       191 ~-~----~p~---~~~p~~~~~~~~~~~~---~~~~l~fLr~~~qf~~lR~~iqqNP~ll~~~Lqql  246 (340)
T KOG0011|consen  191 A-E----LPA---NAQPLDLFPQGAVEAS---GGDPLEFLRNQPQFQQLRQMIQQNPELLHPLLQQL  246 (340)
T ss_pred             C-C----CCC---CCChhhcCCccchhhh---cCCchhhhhccHHHHHHHHHHhhCHHHHHHHHHHH
Confidence            0 0    000   2356788988655432   44899999999999999999999999999999976

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.80  E-value=3e-19  Score=135.32  Aligned_cols=73  Identities=27%  Similarity=0.403  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+++|+++.++|++++||.+||++|+++.|   +++++|+|+|+||.|+|+.+|++|||+++++|+++++.
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   99999999999999999999999999999999999874

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=99.78  E-value=1.1e-18  Score=132.56  Aligned_cols=75  Identities=55%  Similarity=0.790  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCC--CCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVY--PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~i--p~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|++|.++|++++||.+||++|+...|   +  ++++|||+|+|++|+|+.+|++|||++|++|++++++++
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  999999999999999999999999999999999998874

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=99.77  E-value=1.5e-18  Score=133.33  Aligned_cols=74  Identities=22%  Similarity=0.354  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCcE-EEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTH-FEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~-~~le-V~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|++ +.|+ +++++||.+||++|++..|   +++++|||+|+||+|+|+.+|++|||+++++|+++++..
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   999999999999999999999999999999999999853

NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.76  E-value=2.8e-18  Score=130.35  Aligned_cols=71  Identities=18%  Similarity=0.328  Sum_probs=68.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+||++.|+.|.++|++++||.+||++|+...|   +++++|||||+||+|+|+++|++|||++|++||+..
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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.75  E-value=5.2e-18  Score=128.63  Aligned_cols=73  Identities=27%  Similarity=0.369  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+.  +++.++|++++||.+||.+|+...|   +|+++|+|+|+||+|+|+++|++|+|+++++||++++.+.
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.

>PTZ00044 ubiquitin; Provisional

Probab=99.75  E-value=7.4e-18  Score=127.84  Aligned_cols=74  Identities=28%  Similarity=0.446  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|+++.++|++++||.+||.+|+...|   +|+++|||+|+|+.|+|+.+|++|+|+++++||++++.+
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=99.74  E-value=1.1e-17  Score=135.25  Aligned_cols=75  Identities=33%  Similarity=0.546  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||++.|+++.|+|++++||.+||++|++..|   +++++|||+|+||+|+|+++|++|+|+++++|+++++.+.
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=99.74  E-value=9.9e-18  Score=128.66  Aligned_cols=73  Identities=23%  Similarity=0.407  Sum_probs=70.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+.+|+.+.|+|+++.||.+||++|+++.|   +++++|||+|+||+|+|+ +|++|||++|++|+||.+..
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~---~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~   74 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLK---VPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVE   74 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhC---CChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecc
Confidence            89999999999999999999999999999999999   999999999999999999 99999999999999998753

midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.73  E-value=2.4e-17  Score=124.38  Aligned_cols=74  Identities=36%  Similarity=0.557  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|+++.++|+++.||.+||++|+...|   +++++|||+|+|+.|+|+++|++|+|++|++|||+++.+
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   999999999999999999999999999999999999864

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

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

Probab=99.72  E-value=1.4e-17  Score=128.23  Aligned_cols=74  Identities=28%  Similarity=0.401  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEE--EeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkL--Iy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||++.|+++.++|+++.||.+||++|+...|   +++++|||  +|+|++|+|+++|++|||++|++|+|++++-
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.

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

Probab=99.72  E-value=2e-17  Score=125.42  Aligned_cols=72  Identities=22%  Similarity=0.271  Sum_probs=69.5

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+||++.|+++.|+|++++||.+||++|+...|   +++++|+|+|+||+|+|+++|++|||+++++|+++++..
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---i~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~   72 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRER---VQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLR   72 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhC---CCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEcc
Confidence            689999999999999999999999999999999   999999999999999999999999999999999998864

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>cd01803 Ubiquitin Ubiquitin

Probab=99.72  E-value=3.7e-17  Score=123.38  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+.+|+.+.++|++++||.+||++|+...|   +++++|+|+|+|+.|+|+++|++|+|++|++|+++++.+
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=99.71  E-value=2.3e-17  Score=124.25  Aligned_cols=70  Identities=27%  Similarity=0.458  Sum_probs=66.9

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      ++||.++|+++.++|++++||.+||.+|++..|   +++++|||+|+||+|+|+.+|++|+|+++++|||++.
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~g---i~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~~   70 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEG---VDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIVN   70 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhC---CCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEeC
Confidence            468999999999999999999999999999999   9999999999999999999999999999999999873

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=99.71  E-value=4.7e-17  Score=121.58  Aligned_cols=72  Identities=36%  Similarity=0.459  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+||+++|+++.+++++++||.+||++|+...|   ++++.|+|+|+|++|+|+.+|++|||++|++||++.+
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=99.71  E-value=3.3e-17  Score=122.76  Aligned_cols=70  Identities=30%  Similarity=0.546  Sum_probs=67.5

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+||++.|+.+.++|++++||.+||++|+++.|   +++++|+|+|+||.|+|+.+|++|||+++++||++.|
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.

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

Probab=99.70  E-value=4.8e-17  Score=125.14  Aligned_cols=73  Identities=21%  Similarity=0.207  Sum_probs=64.6

Q ss_pred             CEEEEEeCCCcE--EEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhc--cCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTH--FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENK--VAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~--~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dyg--Ik~g~~I~v~v   74 (308)
                      |.|+||+.+|++  |.+++++++||.+||++|+...+.. +++++|||||+||+|+|+.+|++|+  |+++.+|||+.
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            579999999998  5556689999999999999987521 5689999999999999999999996  99999999986

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.

>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2

Probab=99.70  E-value=6.7e-17  Score=121.47  Aligned_cols=71  Identities=32%  Similarity=0.428  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+||+..|+ +.|+|++++||.+||++|++..|   ++.++|+|+|+||+|+|+++|++|||++|++||++++
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   9999999999999999999999999999999999875

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.

>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=99.69  E-value=8.8e-17  Score=119.49  Aligned_cols=69  Identities=38%  Similarity=0.603  Sum_probs=66.1

Q ss_pred             EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         6 ktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+++|+.|.|+|++++||.+||++|+...|   ++++.|+|+|+|++|+|+.+|++|||++|++|+++++++
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            678999999999999999999999999999   999999999999999999999999999999999998753

There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.66  E-value=2.4e-16  Score=119.89  Aligned_cols=70  Identities=29%  Similarity=0.414  Sum_probs=67.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe---CCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy---~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|| ++|++|.|+|++++||.+||++|++.+|   +|+++|||+|   +||+|+|+.+|++|+|++|++|+||.
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   9999999997   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=99.64  E-value=4.9e-16  Score=117.09  Aligned_cols=68  Identities=34%  Similarity=0.435  Sum_probs=64.4

Q ss_pred             EEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCC-CChhhhccCCCCEEEEE
Q 021760            3 VFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVM   73 (308)
Q Consensus         3 I~Vktl-~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~-~tL~dygIk~g~~I~v~   73 (308)
                      |+||+. .|+++.|+|++++||.+||.+|+...|   +|+++|||+|+||.|+|+ .+|++|||++|++||+.
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=99.62  E-value=1.5e-15  Score=113.27  Aligned_cols=70  Identities=29%  Similarity=0.421  Sum_probs=66.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+||+. |+.+.++|++++||.+||++|+..+|   +++++|||+|+|+.|+|+++|++|||++|++|+||.
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   999999999999999999999999999999999974

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).

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

Probab=99.61  E-value=2.5e-15  Score=114.62  Aligned_cols=68  Identities=26%  Similarity=0.396  Sum_probs=65.0

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         8 l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      ++|+++.|+|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+++|++|+|++|++|+|+++.+.
T Consensus         5 l~g~~~~l~v~~~~TV~~lK~~i~~~~g---ip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~g   72 (76)
T cd01800           5 LNGQMLNFTLQLSDPVSVLKVKIHEETG---MPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERG   72 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHC---CCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCC
Confidence            5799999999999999999999999999   9999999999999999999999999999999999998654

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.

>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.61  E-value=8.2e-16  Score=110.51  Aligned_cols=70  Identities=36%  Similarity=0.548  Sum_probs=68.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      |.|.||+++|+.+.|+++++++|..+|++|+++.|   ||+.+|||||.||.+.|+++-++|++.-|++||++
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            78999999999999999999999999999999999   99999999999999999999999999999999974

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

Probab=99.54  E-value=1.2e-14  Score=142.84  Aligned_cols=77  Identities=29%  Similarity=0.441  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      ++|+||+.++ ++.|.|..+.||++||++|...++   +++++++|||+||||+|++||..|||++|.+||||++....+
T Consensus        16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~---a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~~~~   91 (493)
T KOG0010|consen   16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFG---APPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQPRP   91 (493)
T ss_pred             eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcC---CChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccCCCC
Confidence            5799999888 899999999999999999999998   999999999999999999999999999999999998765544


Q ss_pred             C
Q 021760           81 S   81 (308)
Q Consensus        81 ~   81 (308)
                      .
T Consensus        92 ~   92 (493)
T KOG0010|consen   92 T   92 (493)
T ss_pred             C
Confidence            3

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.53  E-value=6.2e-14  Score=109.73  Aligned_cols=75  Identities=16%  Similarity=0.265  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |.|+|++.+|+.+.++|.++++|..||++++++.|   +++++|||+|+|+.|+|+.|+.+|+|+++++|+++++...
T Consensus        12 i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~g---i~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~G   86 (87)
T cd01763          12 INLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQG---LSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTG   86 (87)
T ss_pred             EEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhC---CCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEeccc
Confidence            67999999999999999999999999999999999   9999999999999999999999999999999999988653

Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.

>smart00213 UBQ Ubiquitin homologues

Probab=99.52  E-value=4.9e-14  Score=102.13  Aligned_cols=64  Identities=42%  Similarity=0.649  Sum_probs=61.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS   68 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~   68 (308)
                      |+|+||+.+ +.+.++|+++.||.+||.+|+..+|   +++++|+|+|+|+.|+|+++|++|||++|+
T Consensus         1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~---~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213        1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTG---IPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHC---CCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            899999998 7899999999999999999999999   999999999999999999999999999875

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

>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]

Probab=99.49  E-value=2.8e-15  Score=119.77  Aligned_cols=76  Identities=37%  Similarity=0.583  Sum_probs=73.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |.++++++.|+++.++|++++||..||.+|....|   +|++.|+|||+||+|+|..||++|||...++||++.+.+..
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

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.46  E-value=7e-14  Score=106.40  Aligned_cols=55  Identities=25%  Similarity=0.237  Sum_probs=49.0

Q ss_pred             CCCcHHHHHHHHHHHhCCCCC-CCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760           19 PEDKVSDVKKNIETVQGSDVY-PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus        19 ~~~TV~~LK~~I~~~~g~~~i-p~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      .++||.+||++|+++.+.. + ++++|||||+||+|+|+++|++|||++|++|||+.
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            4579999999999996322 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.

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

Probab=99.46  E-value=5.2e-14  Score=119.64  Aligned_cols=77  Identities=35%  Similarity=0.553  Sum_probs=73.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+|+++.++++.++|+.++||..+|.+|++..|   ||+++|||||.|+.|+|..+|+||+|+..++|+++++.+...
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   999999999999999999999999999999999999976544

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.40  E-value=6.4e-13  Score=107.93  Aligned_cols=78  Identities=17%  Similarity=0.244  Sum_probs=64.3

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCC--CCCC--CCCeEEEeCCEecCCCCChhhhc------cCCCCE
Q 021760            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGS--DVYP--ASQQMLIHQGKVLKDVTTLEENK------VAENSF   69 (308)
Q Consensus         1 M~I~Vktl~gk~~-~leV~~~~TV~~LK~~I~~~~g~--~~ip--~~~qkLIy~GKiL~D~~tL~dyg------Ik~g~~   69 (308)
                      +.|.||..+|..+ ...+++++||.+||++|+..++.  ..+|  +++|||||+||+|+|++||++|+      +....+
T Consensus         5 ~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~T   84 (113)
T cd01814           5 IEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVIT   84 (113)
T ss_pred             EEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceE
Confidence            3578888888654 46778999999999999977742  1244  89999999999999999999999      777789


Q ss_pred             EEEEEecCC
Q 021760           70 VVVMLTKSK   78 (308)
Q Consensus        70 I~v~v~k~k   78 (308)
                      +||+++.+.
T Consensus        85 mHvvlr~~~   93 (113)
T cd01814          85 MHVVVQPPL   93 (113)
T ss_pred             EEEEecCCC
Confidence            999987643

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

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.39  E-value=1.6e-12  Score=95.39  Aligned_cols=68  Identities=43%  Similarity=0.663  Sum_probs=64.3

Q ss_pred             EEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            4 FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         4 ~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      +||..+|+.+.++++++.||.+||++|+..+|   +++++|+|+|+|+.|+|+.+|.+|+|++++.|+++.
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            37778899999999999999999999999999   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=99.36  E-value=2.1e-12  Score=98.53  Aligned_cols=65  Identities=18%  Similarity=0.274  Sum_probs=59.0

Q ss_pred             EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecC-CCCChhhhccC-CCCEEEEEE
Q 021760            6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVA-ENSFVVVML   74 (308)
Q Consensus         6 ktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~-D~~tL~dygIk-~g~~I~v~v   74 (308)
                      |...|.++.|+|++++||.+||.+|+.+.|   +|++.||| |+|+.|. |+++|++|||+ +|+++++.+
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            344678999999999999999999999999   99999999 9999985 67999999999 889999875

HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.

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

Probab=99.32  E-value=7.3e-12  Score=93.86  Aligned_cols=71  Identities=24%  Similarity=0.391  Sum_probs=65.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~-~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|+..+|+.+.+.|.++++|..|++++++..|   ++. +.++|+|+|+.|++++|+++|||++|++|+|++
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~---i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKG---IPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHT---TTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhC---CCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            78999999999999999999999999999999999   889 999999999999999999999999999999875

SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.12  E-value=1.7e-10  Score=91.70  Aligned_cols=63  Identities=21%  Similarity=0.237  Sum_probs=57.4

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCC-CCChhhhccCCCCEEEEEEecC
Q 021760           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKD-VTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus        12 ~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D-~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      ...++|++++||.+||.+|...++   +++.+|||+|+|+.|.| .+||++|||..++.|++.+..+
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~---V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~LlideP   79 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFS---VAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADEP   79 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhc---CCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecCC
Confidence            467889999999999999999999   99999999999999965 5799999999999999987643

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=99.12  E-value=1.1e-10  Score=77.07  Aligned_cols=36  Identities=50%  Similarity=0.723  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHH
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL  210 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL  210 (308)
                      .++.|++|++||   |+|++|++||+++.||.|+||+||
T Consensus         2 ~~~~v~~L~~mG---f~~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    2 DEEKVQQLMEMG---FSREQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHHHHT---S-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHhC
Confidence            478999999999   999999999999999999999998

The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....

>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=99.06  E-value=7.6e-11  Score=85.89  Aligned_cols=31  Identities=52%  Similarity=0.789  Sum_probs=28.5

Q ss_pred             hHHhhChHHHHHHHHHHHhChhhHHHHHhcC
Q 021760          277 LDFLRNSQQFQALRTMVQANPQILQQWALIV  307 (308)
Q Consensus       277 l~~Lr~~pqf~~lRq~vqqnP~~L~~~L~~~  307 (308)
                      |+|||++|+|++||++||+||++|++|||++
T Consensus         1 L~~Lr~~Pqf~~lR~~vq~NP~lL~~lLqql   31 (59)
T PF09280_consen    1 LEFLRNNPQFQQLRQLVQQNPQLLPPLLQQL   31 (59)
T ss_dssp             CGGGTTSHHHHHHHHHHHC-GGGHHHHHHHH
T ss_pred             ChHHHcChHHHHHHHHHHHCHHHHHHHHHHH
Confidence            6899999999999999999999999999975

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 ....

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

Probab=99.04  E-value=1.8e-09  Score=88.35  Aligned_cols=76  Identities=20%  Similarity=0.292  Sum_probs=56.1

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCC----CCCCCCeEEEeCCEecCCCCChhhhccCCCC------E
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSD----VYPASQQMLIHQGKVLKDVTTLEENKVAENS------F   69 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~----~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~------~   69 (308)
                      +.|+|+..+|+ +..+.+++++||.+||+.|...+..+    ...++.+||||.||+|+|+++|++|++..++      +
T Consensus         3 i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~v   82 (111)
T PF13881_consen    3 IELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTV   82 (111)
T ss_dssp             EEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EE
T ss_pred             EEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEE
Confidence            35778888998 77889999999999999999877533    1234578999999999999999999998777      4


Q ss_pred             EEEEEec
Q 021760           70 VVVMLTK   76 (308)
Q Consensus        70 I~v~v~k   76 (308)
                      +||+++.
T Consensus        83 mHlvvrp   89 (111)
T PF13881_consen   83 MHLVVRP   89 (111)
T ss_dssp             EEEEE-S
T ss_pred             EEEEecC
Confidence            5555543

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

Probab=99.01  E-value=1.8e-09  Score=83.99  Aligned_cols=71  Identities=25%  Similarity=0.321  Sum_probs=59.5

Q ss_pred             EEEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEE-EeCCE-----ec-CCCCChhhhccCCCCEEEEE
Q 021760            2 KVFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQGK-----VL-KDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl-~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkL-Iy~GK-----iL-~D~~tL~dygIk~g~~I~v~   73 (308)
                      +|.|+.. ....++..+++++||.+||++|+..+|   +++..||| +|.|+     .| +|+++|++||+++|..|||+
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            5666653 334455669999999999999999999   99999999 58888     45 77889999999999999998


Q ss_pred             Ee
Q 021760           74 LT   75 (308)
Q Consensus        74 v~   75 (308)
                      -.
T Consensus        80 D~   81 (84)
T cd01789          80 DV   81 (84)
T ss_pred             eC
Confidence            64

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=98.99  E-value=6.1e-10  Score=117.34  Aligned_cols=70  Identities=26%  Similarity=0.400  Sum_probs=67.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      .|+||+++.++.++.|+..+||++||+.|..+.+   |+.+.|||||.|++|.|++++++|+| +|.+|||+-|
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 8999999987

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

Probab=98.98  E-value=5e-09  Score=76.25  Aligned_cols=72  Identities=39%  Similarity=0.585  Sum_probs=68.1

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      ++++++.|+.+.+++....+|..+|.+|....|   ++.+.|+|+|.|+.|.|+.+|.+|+|..+++++++.+.+
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            577889999999999999999999999999999   999999999999999999999999999999999988764

>cd00194 UBA Ubiquitin Associated domain

Probab=98.90  E-value=2.6e-09  Score=70.53  Aligned_cols=38  Identities=50%  Similarity=0.733  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      +++.|++|++||   |+|++|++||+++.||.++|++||+.
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            357899999999   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=98.89  E-value=5e-09  Score=99.93  Aligned_cols=70  Identities=33%  Similarity=0.440  Sum_probs=62.1

Q ss_pred             CEEEEEeCCCcEE---EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---C----EecCCCCChhhhccCCCCEE
Q 021760            1 MKVFVKTLKGTHF---EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G----KVLKDVTTLEENKVAENSFV   70 (308)
Q Consensus         1 M~I~Vktl~gk~~---~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~---G----KiL~D~~tL~dygIk~g~~I   70 (308)
                      |+|+|+..+|+.+   .|+++++.||++||++|++..+.  +++++|||+|.   |    +.|+|+++|++||+++|++|
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            8999998888887   79999999999999999999872  37899999972   3    48899999999999999988


Q ss_pred             EE
Q 021760           71 VV   72 (308)
Q Consensus        71 ~v   72 (308)
                      ++
T Consensus        79 y~   80 (308)
T PLN02560         79 VF   80 (308)
T ss_pred             EE
Confidence            76

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=98.87  E-value=7.3e-09  Score=84.21  Aligned_cols=73  Identities=21%  Similarity=0.276  Sum_probs=62.6

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhcc-------CCCCEEEE
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-------AENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygI-------k~g~~I~v   72 (308)
                      |-++++....| ++.+++.++.||.+||++|+....   .|++.|||+..+.+|+|++||++||+       +...+|-+
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            56666655544 677899999999999999999998   99999999988899999999999999       55777777


Q ss_pred             EEec
Q 021760           73 MLTK   76 (308)
Q Consensus        73 ~v~k   76 (308)
                      .+|+
T Consensus        78 a~r~   81 (119)
T cd01788          78 AFRS   81 (119)
T ss_pred             EEec
Confidence            7774

Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.

>smart00165 UBA Ubiquitin associated domain

Probab=98.86  E-value=3.3e-09  Score=69.72  Aligned_cols=37  Identities=51%  Similarity=0.791  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      +++.|++|++||   |++++|.+||+...||.++|++||+
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.

>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A

Probab=98.83  E-value=1.3e-08  Score=79.36  Aligned_cols=73  Identities=23%  Similarity=0.318  Sum_probs=57.8

Q ss_pred             EEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC----C---Eec-CCCCChhhhccCCCCEEE
Q 021760            2 KVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ----G---KVL-KDVTTLEENKVAENSFVV   71 (308)
Q Consensus         2 ~I~Vktl~g--k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~----G---KiL-~D~~tL~dygIk~g~~I~   71 (308)
                      +|+|.....  +.++..++.++||.+||.+|+..+|   ++++.|+|.|.    +   ..| +|+++|.+||+++|+.||
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            566765544  5889999999999999999999999   99999999765    2   224 567899999999999999


Q ss_pred             EEEecC
Q 021760           72 VMLTKS   77 (308)
Q Consensus        72 v~v~k~   77 (308)
                      |.-..+
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=98.78  E-value=1.9e-08  Score=76.84  Aligned_cols=69  Identities=23%  Similarity=0.253  Sum_probs=54.5

Q ss_pred             EEEEEeCC-CcEEEEEeC-CCCcHHHHHHHHHHHhCCCCCCCCCeEE--EeCCEecCCCCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLK-GTHFEIEVK-PEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~-gk~~~leV~-~~~TV~~LK~~I~~~~g~~~ip~~~qkL--Iy~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      .|.++... .....++++ ++.||.+||+.|+...+.  +++++|||  ++.|++|.|+.+|.+|||++|++|+|
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 333335554 788999999999988652  57899888  58999999999999999999999876

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=98.58  E-value=3.3e-07  Score=63.01  Aligned_cols=67  Identities=31%  Similarity=0.457  Sum_probs=60.7

Q ss_pred             EEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         5 Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+..++..+.+.+....||.+||++|..+.|   ++++.++|+++|+.+++...+.+|++.+++.|+++.
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   889999999999999999999999999999999864

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=98.57  E-value=9.9e-08  Score=73.73  Aligned_cols=69  Identities=28%  Similarity=0.359  Sum_probs=44.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---CEec--CCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---GKVL--KDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~---GKiL--~D~~tL~dygIk~g~~I~v~   73 (308)
                      |-|.|++.+| .+.|++++++|+.+||++|.+..+   ++.+.+.|..+   .+.|  .++++|+++||+.||.|+|.
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            6788998777 788999999999999999999999   88888888532   1334  56889999999999999873

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.

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

Probab=98.38  E-value=2.3e-06  Score=64.68  Aligned_cols=72  Identities=18%  Similarity=0.290  Sum_probs=62.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--EecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G--KVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~---G--KiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      ++|+|+-+.+..+.+.|+|..+|.+||++|....|   ++ ..|||.|.   |  ..|.+.++|.+|||-.+-.|.|+-.
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            58999999999999999999999999999999998   54 59999983   3  4579999999999998888877754


Q ss_pred             c
Q 021760           76 K   76 (308)
Q Consensus        76 k   76 (308)
                      -
T Consensus        77 ~   77 (80)
T cd01811          77 F   77 (80)
T ss_pred             C
Confidence            3

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.

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

Probab=98.31  E-value=9.9e-07  Score=83.23  Aligned_cols=72  Identities=28%  Similarity=0.391  Sum_probs=63.2

Q ss_pred             CEEEEEeC---CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTL---KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl---~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |.|.|+..   ....+.|+|+.+..|.+||+.++...|   +|+++.|+||.||.|.|+.++..+.+...+.+|+|.-
T Consensus         1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~g---vp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~l   75 (446)
T KOG0006|consen    1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQG---VPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIMLL   75 (446)
T ss_pred             CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhC---CChhheEEEEeccccccCceeecccccccchhhhhcc
Confidence            66777654   224588999999999999999999999   9999999999999999999999999988899998843

>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]

Probab=98.17  E-value=4.7e-06  Score=82.37  Aligned_cols=71  Identities=23%  Similarity=0.372  Sum_probs=66.0

Q ss_pred             EEEEeCCCcEEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            3 VFVKTLKGTHFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         3 I~Vktl~gk~~~le-V~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |.|| +.|+.|.++ ++.++|+..||.+|...+|   +++++||++++|+.|.|+-.+..++||+|.+|++|.+.-
T Consensus         6 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    6 VIVK-WGGKKYPVETLSTDETPSVLKAQLFALTG---VPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAE   77 (473)
T ss_pred             Eeee-ecCccccceeccCCCchHHHHHHHHHhcC---CCccceeEEEecccccccccccccccCCCCEEEeecccc
Confidence            5666 899999988 9999999999999999999   999999999999999999999999999999999998653

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

Probab=98.08  E-value=2.3e-05  Score=62.48  Aligned_cols=72  Identities=14%  Similarity=0.234  Sum_probs=64.8

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      +|.|+..++..+.+.|..+.....|++..++..|   +....+|++|+|+.+.+.+|-.++++++||.|.++...
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            4566665667778999999999999999999999   88999999999999999999999999999999998654

>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]

Probab=98.03  E-value=1.9e-06  Score=63.33  Aligned_cols=69  Identities=19%  Similarity=0.308  Sum_probs=60.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      .+.+...-|++..|.+.+++||+++|+.|+.+.|   ..++.+.|---+.+++|.-+|++|.|++|..+.+.
T Consensus         3 ev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtG---T~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely   71 (73)
T KOG3493|consen    3 EVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY   71 (73)
T ss_pred             eehhhhhcCceEEEEeCCcccccCHHHHHHHhhC---CChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence            4667777899999999999999999999999999   77888888766678899999999999999887765

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

Probab=97.77  E-value=6.8e-05  Score=60.04  Aligned_cols=61  Identities=16%  Similarity=0.213  Sum_probs=47.3

Q ss_pred             EEEEEeCCC-cEEEEEeC--CCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhc
Q 021760            2 KVFVKTLKG-THFEIEVK--PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENK   63 (308)
Q Consensus         2 ~I~Vktl~g-k~~~leV~--~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dyg   63 (308)
                      .|+||..++ ..+.|+|.  .+.||..||++|.+..+.+ ..-.++||||+||+|.|+..|...-
T Consensus         2 ~l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~-~s~~rLRlI~~Gr~L~d~t~l~~~l   65 (97)
T PF10302_consen    2 YLTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPE-PSRRRLRLIYAGRLLNDHTDLSSEL   65 (97)
T ss_pred             eEEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCC-CccccEEeeecCcccCccchhhhhh
Confidence            366665552 34677777  7789999999999998533 5667899999999999998877653

They contain a characteristic GFDRL sequence motif.

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

Probab=97.76  E-value=3.7e-05  Score=60.85  Aligned_cols=62  Identities=24%  Similarity=0.379  Sum_probs=50.5

Q ss_pred             CEEEEEeCC-CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe-CC-EecCCCCChhhhccC
Q 021760            1 MKVFVKTLK-GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-QG-KVLKDVTTLEENKVA   65 (308)
Q Consensus         1 M~I~Vktl~-gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy-~G-KiL~D~~tL~dygIk   65 (308)
                      |.++++... ..++.++.+++.||.+||.+++....   -|++.|||+. .- .+|+|.++|++||..
T Consensus         1 ~~~f~~VrR~kttif~da~es~tV~elK~~l~gi~~---~Pvn~qrL~kmd~eqlL~D~ktL~d~gft   65 (110)
T KOG4495|consen    1 MDVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILK---RPVNEQRLYKMDTEQLLDDGKTLGDCGFT   65 (110)
T ss_pred             CceeeeeeecceeEEeecCccccHHHHHHHHHHHHh---CCCcchheeecCHHHHhhccchhhhcccc
Confidence            345554433 34678899999999999999999998   8999999976 33 678999999999874

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

Probab=97.50  E-value=0.00021  Score=54.71  Aligned_cols=71  Identities=18%  Similarity=0.271  Sum_probs=50.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC---CeEEE-eCCEecCCCCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS---QQMLI-HQGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~---~qkLI-y~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      +|+|...+|+.+.+.+..+.+|.+|...|.+..+.......   ..+|. -+|..|+++++|.++||.+|+.|++
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            56777545689999999999999999999988773212222   35676 7899999999999999999999987

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.

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

Probab=97.45  E-value=0.00023  Score=48.04  Aligned_cols=39  Identities=33%  Similarity=0.401  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHh--cCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ++++|+.|.+|  .   |+++.++++|++.-+|.|+||++|+.|
T Consensus         1 ~~~~v~~L~~mFP~---~~~~~I~~~L~~~~~~ve~ai~~LL~~   41 (42)
T PF02845_consen    1 REEMVQQLQEMFPD---LDREVIEAVLQANNGDVEAAIDALLEM   41 (42)
T ss_dssp             CHHHHHHHHHHSSS---S-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            47899999999  7   999999999999999999999999975

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.

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.27  E-value=0.0011  Score=50.19  Aligned_cols=68  Identities=7%  Similarity=0.185  Sum_probs=56.7

Q ss_pred             EEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCC--CCCCCeEEEeCCEecCCCCChhhhccCCCCEEEE
Q 021760            5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDV--YPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         5 Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~--ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      ++.+.|++|.+.+....+|+.|-..+.+....+-  ..-..+|+.-++++|.++..|.+|+|.+||.+.+
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            4678899999999999999999998887765321  1224578899999999999999999999999875

>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=97.25  E-value=0.0021  Score=49.02  Aligned_cols=68  Identities=22%  Similarity=0.299  Sum_probs=57.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCC-eEEE--eCCEecCCC--CChhhhccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQ-QMLI--HQGKVLKDV--TTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~-qkLI--y~GKiL~D~--~tL~dygIk~g~~I~v   72 (308)
                      +|.||..+|+.+...+..++||.+|...|.....   .+... .+|+  |-.+.|.++  ++|+++|+..+.+|+|
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            6889999999999999999999999999988876   33443 7776  677888544  6999999999988876

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 ....

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.20  E-value=0.0027  Score=48.56  Aligned_cols=68  Identities=13%  Similarity=0.135  Sum_probs=55.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecCC---CCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~D---~~tL~dygIk~g~~I~v   72 (308)
                      +|.||..+|+.+...+..++||.+|.+.|....+   ......+|+  |-.|.|.+   +++|.++|+..+.+|+|
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            6889999999999999999999999999966555   445567775  67788854   47999999988877765

Present in FAF1 and Shp1p.

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

Probab=97.18  E-value=0.0014  Score=51.46  Aligned_cols=69  Identities=16%  Similarity=0.173  Sum_probs=60.3

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |.|...+|..+.+.|..+.+...|.+..+...|   -..+..|++|+|+.++-++|-.++++.+++.|.++.
T Consensus        27 Lkvv~qd~telfFkiKktT~f~klm~af~~rqG---K~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~   95 (103)
T COG5227          27 LKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQG---KNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVT   95 (103)
T ss_pred             eEEecCCCCEEEEEEeccchHHHHHHHHHHHhC---cCcceeEEEEcceecCCCCChhhcCCccchHHHHHH
Confidence            455556778888999999999999999999999   447899999999999999999999999999876543

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

Probab=97.17  E-value=0.00025  Score=73.03  Aligned_cols=43  Identities=40%  Similarity=0.652  Sum_probs=40.0

Q ss_pred             CcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 021760          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  215 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP  215 (308)
                      +.-|+.|..|++||   |.|.|++.||++..||.+|||||+++-+=
T Consensus       633 ~~~e~~v~si~smG---f~~~qa~~aL~~~n~nveravDWif~h~d  675 (763)
T KOG0944|consen  633 EVDEESVASIVSMG---FSRNQAIKALKATNNNVERAVDWIFSHMD  675 (763)
T ss_pred             CCChhHheeeeeec---CcHHHHHHHHHhcCccHHHHHHHHHhccc
Confidence            45688999999999   99999999999999999999999999854

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=97.10  E-value=0.0045  Score=46.92  Aligned_cols=67  Identities=27%  Similarity=0.339  Sum_probs=53.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecCC---CCChhhhccCCCCEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~D---~~tL~dygIk~g~~I~v~   73 (308)
                      +|.||..+|+.+...+..++||.+|.+-|.....   . ....+|+  |-.|.|.|   +.+|+++|+. .+.+++.
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 4556776  56788854   7899999999 4555543

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.

>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=97.01  E-value=0.0033  Score=46.71  Aligned_cols=63  Identities=17%  Similarity=0.210  Sum_probs=46.8

Q ss_pred             eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEE
Q 021760            7 TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         7 tl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      ..+++.+.|.|.++.++.++-+....++|   +..++-.|.|++|.|+-+.++.-.|+-+|..+.+
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            36789999999999999999999999999   8889999999999999999999999999998764

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.

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=96.92  E-value=0.007  Score=46.52  Aligned_cols=67  Identities=22%  Similarity=0.341  Sum_probs=53.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecCC-CCChhhhccCCCCEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENSFVV   71 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~D-~~tL~dygIk~g~~I~   71 (308)
                      +|.||..+|+.+...+..++||.+|.+.|....+.  .......|+  |-.|.|.| +.||+|.|+.+ +.|+
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  123456775  67888854 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.

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

Probab=96.91  E-value=0.0022  Score=59.22  Aligned_cols=70  Identities=17%  Similarity=0.212  Sum_probs=53.1

Q ss_pred             CEEEEEeCCCc-EEE-EEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEE----EeCCEecCCCCChhhhccCCCCEEEE
Q 021760            1 MKVFVKTLKGT-HFE-IEVKPEDKVSDVKKNIETVQGSDVYPASQQML----IHQGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~gk-~~~-leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkL----Iy~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      |+|++...++. ..+ .+++...||.|+++.|..+..+  +-+.++|+    --+||.|.|+.+|++|+..+|.+|+|
T Consensus         1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k--~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~v   76 (297)
T KOG1639|consen    1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLK--ITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIYV   76 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhc--cCccchhheeeccCCCccccchhHHHHhccCCCCEEEE
Confidence            78999877652 333 5677889999999888665542  55545544    35899999999999999999987776

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.89  E-value=0.0018  Score=58.34  Aligned_cols=61  Identities=26%  Similarity=0.380  Sum_probs=53.8

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEE
Q 021760            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         9 ~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      .++.|.+.+...+||.++|.+++...|   +.+-.|+++|+|++|.|...|.+|+|..|...+|
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg---~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvl  215 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEG---VDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVL  215 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhc---cchhhheeeccCCceeccccceeeeecCCCEEEE
Confidence            466788888889999999999999999   6688999999999999999999999999954433

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=96.87  E-value=0.009  Score=45.75  Aligned_cols=67  Identities=19%  Similarity=0.358  Sum_probs=55.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecCC---CCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~D---~~tL~dygIk~g~~I~v   72 (308)
                      +|.||..+|+.+...+..++||.+|++-|....+   . ....+|+  |-.|.+.+   ++||.++|+....+|+|
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            6889999999999999999999999999986654   2 2556776  77898854   47999999998877765

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.

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

Probab=96.85  E-value=0.00027  Score=67.45  Aligned_cols=76  Identities=20%  Similarity=0.213  Sum_probs=56.0

Q ss_pred             EEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCC--CCEEEEEEecC
Q 021760            2 KVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAE--NSFVVVMLTKS   77 (308)
Q Consensus         2 ~I~Vktl~g--k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~--g~~I~v~v~k~   77 (308)
                      .++||..+.  +...|..+.+.||++||..++...-.+ --..+|||||.||.|.|...|.|+-+|.  ..++||++..+
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            356665554  456677888899999999999887643 2346899999999999999999986654  34556665444


Q ss_pred             C
Q 021760           78 K   78 (308)
Q Consensus        78 k   78 (308)
                      .
T Consensus        90 ~   90 (391)
T KOG4583|consen   90 E   90 (391)
T ss_pred             C
Confidence            3

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

Probab=96.71  E-value=0.0022  Score=56.77  Aligned_cols=47  Identities=26%  Similarity=0.292  Sum_probs=44.0

Q ss_pred             cccccCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          164 SNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       164 s~l~~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ..+..+..+...|.+|.+||   |+|+.++.+|+-...|-.+|-|+|++|
T Consensus       154 ~~~~~~~~~~~~v~~l~~mG---f~~~~~i~~L~~~~w~~~~a~~~~~s~  200 (200)
T KOG0418|consen  154 GRLPDDPWDKKKVDSLIEMG---FSELEAILVLSGSDWNLADATEQLLSG  200 (200)
T ss_pred             CCCCCCchhHHHHHHHHHhc---ccHHHHHHHhhccccchhhhhHhhccC
Confidence            33778899999999999999   999999999999999999999999987

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=96.61  E-value=0.0024  Score=62.78  Aligned_cols=38  Identities=34%  Similarity=0.507  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      -.++|++|++||   |+|+.|+.|-.|+-.|=+.|+.||+.
T Consensus       337 E~~AIeRL~~LG---F~r~~viqaY~ACdKNEelAAn~Lf~  374 (378)
T TIGR00601       337 EKEAIERLCALG---FDRGLVIQAYFACDKNEELAANYLLS  374 (378)
T ss_pred             HHHHHHHHHHcC---CCHHHHHHHHHhcCCcHHHHHHHHHh
Confidence            357899999999   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).

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

Probab=96.52  E-value=0.0073  Score=40.78  Aligned_cols=39  Identities=26%  Similarity=0.406  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHh--cCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .++.|..|.+|  .   ++++.|++.|++.-||.|+|++.|+.|
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  6   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)

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=96.48  E-value=0.026  Score=43.82  Aligned_cols=69  Identities=19%  Similarity=0.338  Sum_probs=58.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecC---CCCChhhhccCCCCEEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~---D~~tL~dygIk~g~~I~v~v   74 (308)
                      +|.||..+|+.+.-.+..++++.+|...|.. .|   .+.+..+|+  |--|.|.   .+.||++.|+....+|+|--
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   677888887  6677773   35799999999999888743

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.

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=96.40  E-value=0.025  Score=49.27  Aligned_cols=75  Identities=19%  Similarity=0.258  Sum_probs=54.4

Q ss_pred             CEEEEEeCCC----cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCe-EEEe-CCEec--CCCCChhhhccCCCC----
Q 021760            1 MKVFVKTLKG----THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQ-MLIH-QGKVL--KDVTTLEENKVAENS----   68 (308)
Q Consensus         1 M~I~Vktl~g----k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~q-kLIy-~GKiL--~D~~tL~dygIk~g~----   68 (308)
                      |.|+|++++|    .++.+.+..+.||.+|+..|....+   ++...+ .|.+ .++.|  .++..+.++.-.+++    
T Consensus         1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~---~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~~~~   77 (162)
T PF13019_consen    1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLP---IPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDSDFI   77 (162)
T ss_pred             CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcC---CCccceeEEEEeCCCeeCCCccccHHhhccCcCCCCce
Confidence            7899999999    5889999999999999999999998   776663 4544 34444  566677777654443    


Q ss_pred             EEEEEEecCC
Q 021760           69 FVVVMLTKSK   78 (308)
Q Consensus        69 ~I~v~v~k~k   78 (308)
                      +|+|+++...
T Consensus        78 ~l~l~~rl~G   87 (162)
T PF13019_consen   78 TLRLSLRLRG   87 (162)
T ss_pred             EEEEEEeccC
Confidence            4455555443

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=96.34  E-value=0.031  Score=43.59  Aligned_cols=68  Identities=16%  Similarity=0.162  Sum_probs=55.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC--EecC--------CCCChhhhccCCCCEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG--KVLK--------DVTTLEENKVAENSFV   70 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G--KiL~--------D~~tL~dygIk~g~~I   70 (308)
                      .+|.||..+|+.+.-.+..++||.+|..-|.. .+   ..++...|+++=  |+|.        .+.||++.||....+|
T Consensus         5 ~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~---~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L   80 (85)
T cd01774           5 VKIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LK---ETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVL   80 (85)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CC---CCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEE
Confidence            36889999999999999999999999999964 34   446788888543  7885        3679999999987777


Q ss_pred             EE
Q 021760           71 VV   72 (308)
Q Consensus        71 ~v   72 (308)
                      +|
T Consensus        81 ~V   82 (85)
T cd01774          81 FV   82 (85)
T ss_pred             EE
Confidence            65

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.

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

Probab=96.19  E-value=0.012  Score=53.04  Aligned_cols=71  Identities=18%  Similarity=0.229  Sum_probs=55.3

Q ss_pred             EEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEE-EeCC-----Eec-CCCCChhhhccCCCCEEEEE
Q 021760            2 KVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQG-----KVL-KDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkL-Iy~G-----KiL-~D~~tL~dygIk~g~~I~v~   73 (308)
                      +|+|.+...+ .++.++..+.||.+||.+++..+|   .+++.++| +|.|     -.| +++..|..|+..+|..||++
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            4566543322 345667889999999999999999   88999998 5766     235 55779999999999999997


Q ss_pred             Ee
Q 021760           74 LT   75 (308)
Q Consensus        74 v~   75 (308)
                      -.
T Consensus        80 D~   81 (234)
T KOG3206|consen   80 DS   81 (234)
T ss_pred             ec
Confidence            53

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=95.85  E-value=0.075  Score=40.92  Aligned_cols=67  Identities=21%  Similarity=0.261  Sum_probs=56.6

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecC---CCCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~---D~~tL~dygIk~g~~I~v   72 (308)
                      +|.||..+|+.+.-.+..++++.+|..-|..+ |   ++.+..+|+  |--|.+.   .+.+|.+.|+....+|+|
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            68899999999999999999999999999764 6   667788886  6678774   357999999998888776

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.

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

Probab=95.19  E-value=0.033  Score=42.50  Aligned_cols=56  Identities=23%  Similarity=0.351  Sum_probs=45.8

Q ss_pred             eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhh-ccCCCCEEEEEE
Q 021760           17 VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN-KVAENSFVVVML   74 (308)
Q Consensus        17 V~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dy-gIk~g~~I~v~v   74 (308)
                      |.++++|.+||+.|......  .......|.|+|+.|+|...|+++ |+++|..|.++.
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            56789999999999876541  445677899999999999999988 588899888873

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

Probab=95.05  E-value=0.029  Score=53.82  Aligned_cols=39  Identities=31%  Similarity=0.432  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      -.++|.+|..||   |+|.-|+.|--|+..|=+-|.+||+..
T Consensus       298 e~eAIeRL~alG---F~ralViqayfACdKNEelAAN~Ll~~  336 (340)
T KOG0011|consen  298 EKEAIERLEALG---FPRALVIQAYFACDKNEELAANYLLSH  336 (340)
T ss_pred             HHHHHHHHHHhC---CcHHHHHHHHHhcCccHHHHHHHHHhh
Confidence            357899999999   999999999999999999999999964

>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=94.96  E-value=0.029  Score=40.27  Aligned_cols=23  Identities=35%  Similarity=0.679  Sum_probs=19.3

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHH
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRA  198 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrA  198 (308)
                      ...|+++++||   |+|+.|+.+||-
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            57899999999   999999999994

This domain is predominantly found in fungi []. ; PDB: 1TTE_A.

>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=94.82  E-value=0.057  Score=42.11  Aligned_cols=35  Identities=29%  Similarity=0.469  Sum_probs=31.4

Q ss_pred             HHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          176 VQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       176 v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      |+.+.+.|   |.++.|.+||++.-.++..|..|++++
T Consensus         1 i~~~~~~g---~~~~~v~~aL~~tSgd~~~a~~~vl~~   35 (87)
T PF11626_consen    1 IKHYEELG---YSREFVTHALYATSGDPELARRFVLNF   35 (87)
T ss_dssp             -HHHHHHT---B-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred             CchHHHhC---CCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            56788999   999999999999999999999999988

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.

>PRK06437 hypothetical protein; Provisional

Probab=94.71  E-value=0.23  Score=36.86  Aligned_cols=59  Identities=20%  Similarity=0.330  Sum_probs=45.2

Q ss_pred             EEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            4 FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         4 ~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      .|+--.++...++++...||.+|-+.    .|   ++.+...+..+|+++.     .++-|++||.|.++.
T Consensus         4 ~~~v~g~~~~~~~i~~~~tv~dLL~~----Lg---i~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv~   62 (67)
T PRK06437          4 MIRVKGHINKTIEIDHELTVNDIIKD----LG---LDEEEYVVIVNGSPVL-----EDHNVKKEDDVLILE   62 (67)
T ss_pred             eEEecCCcceEEEcCCCCcHHHHHHH----cC---CCCccEEEEECCEECC-----CceEcCCCCEEEEEe
Confidence            34433456677888888899988765    46   7788889999999997     566788999998863

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

Probab=94.41  E-value=0.25  Score=37.05  Aligned_cols=68  Identities=21%  Similarity=0.184  Sum_probs=50.7

Q ss_pred             EEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe----CC--EecCCCCChhhhccCCCCEEEEEE
Q 021760            5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH----QG--KVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         5 Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy----~G--KiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+.++|....++|+.+.|+.+|-++|+...|.  ...+..-|.|    +|  .-|+.+++|.++..+.+....+..
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            56789999999999999999999999999992  2344567777    33  447889999999877333333333

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 ....

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=94.17  E-value=0.24  Score=37.09  Aligned_cols=57  Identities=11%  Similarity=0.142  Sum_probs=41.7

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCC-CCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760           12 HFEIEVKPEDKVSDVKKNIETVQGS-DVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        12 ~~~leV~~~~TV~~LK~~I~~~~g~-~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      ...++++...||.+|.+.+...++. .........+..+|+...     .++-|++||.|.++
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~-----~~~~l~~gD~v~i~   74 (80)
T cd00754          17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVR-----LDTPLKDGDEVAII   74 (80)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcC-----CCcccCCCCEEEEe
Confidence            4667887789999999999887541 001234567778999987     34568999999987

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.

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

Probab=94.13  E-value=0.069  Score=53.73  Aligned_cols=42  Identities=36%  Similarity=0.522  Sum_probs=38.1

Q ss_pred             CCcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       169 g~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      -..|..-.+++-+||   | +|+.-++||||.+.+.++|||-|+.+
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            456778899999999   9 99999999999999999999999853

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

Probab=94.03  E-value=0.077  Score=51.54  Aligned_cols=69  Identities=14%  Similarity=0.135  Sum_probs=59.8

Q ss_pred             CEEEEEeC--CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCC--CChhhhccCCCCEEEE
Q 021760            1 MKVFVKTL--KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV--TTLEENKVAENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl--~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~--~tL~dygIk~g~~I~v   72 (308)
                      |.++|.+.  ..++|.++|..+.....|+..+....|   +..+..-|||+++.|.++  ..|..||++++++|.+
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            66777654  667889999999999999999999999   889999999999999654  6899999999988755

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=93.83  E-value=0.25  Score=37.57  Aligned_cols=66  Identities=11%  Similarity=0.166  Sum_probs=45.3

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC--CCeEEEeCCEecCCCCChhhhccCCCCEEE
Q 021760            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGSDVYPA--SQQMLIHQGKVLKDVTTLEENKVAENSFVV   71 (308)
Q Consensus         1 M~I~Vktl~------g-k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~--~~qkLIy~GKiL~D~~tL~dygIk~g~~I~   71 (308)
                      |+|+|+.+.      | ....+++....||.+|++.|......  +..  ....+..+|+...+     ++-|++||.|.
T Consensus         2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~--l~~~~~~~~vavN~~~v~~-----~~~l~dgDeVa   74 (82)
T PLN02799          2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPS--LEEVRSCCVLALNEEYTTE-----SAALKDGDELA   74 (82)
T ss_pred             eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChh--HHHHhhCcEEEECCEEcCC-----CcCcCCCCEEE
Confidence            678887542      4 45677888889999999999766420  111  22346678888753     34578899998


Q ss_pred             EE
Q 021760           72 VM   73 (308)
Q Consensus        72 v~   73 (308)
                      ++
T Consensus        75 i~   76 (82)
T PLN02799         75 II   76 (82)
T ss_pred             Ee
Confidence            86

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=93.47  E-value=0.45  Score=34.48  Aligned_cols=56  Identities=20%  Similarity=0.287  Sum_probs=40.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+|.   |+.  ++++.+.|+.+||+++..         +.=.+||+|-..+++     +-+++||.|+++-|
T Consensus         1 M~I~vN---~k~--~~~~~~~tl~~lr~~~k~---------~~DI~I~NGF~~~~d-----~~L~e~D~v~~Ikk   56 (57)
T PF14453_consen    1 MKIKVN---EKE--IETEENTTLFELRKESKP---------DADIVILNGFPTKED-----IELKEGDEVFLIKK   56 (57)
T ss_pred             CEEEEC---CEE--EEcCCCcCHHHHHHhhCC---------CCCEEEEcCcccCCc-----cccCCCCEEEEEeC
Confidence            666664   544  667778899999987543         223679999888775     45678999988743

>smart00727 STI1 Heat shock chaperonin-binding motif

Probab=93.41  E-value=0.11  Score=34.55  Aligned_cols=27  Identities=33%  Similarity=0.322  Sum_probs=23.6

Q ss_pred             HHhhChHHHHHHHHHHHhChhhHHHHHh
Q 021760          278 DFLRNSQQFQALRTMVQANPQILQQWAL  305 (308)
Q Consensus       278 ~~Lr~~pqf~~lRq~vqqnP~~L~~~L~  305 (308)
                      +.|+ +|+|+++.+-+++||+++..+++
T Consensus         6 ~~l~-~P~~~~~l~~~~~nP~~~~~~~~   32 (41)
T smart00727        6 LRLQ-NPQVQSLLQDMQQNPDMLAQMLQ   32 (41)
T ss_pred             HHHc-CHHHHHHHHHHHHCHHHHHHHHH
Confidence            3444 99999999999999999999886

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=93.29  E-value=0.62  Score=34.69  Aligned_cols=50  Identities=26%  Similarity=0.457  Sum_probs=39.4

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        12 ~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      ...++++...||.+|.+.+    +   ++.....+..+|+++..     ++-|++||.|.++
T Consensus        15 ~~~~~~~~~~tv~~ll~~l----~---~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii   64 (70)
T PRK08364         15 EKEIEWRKGMKVADILRAV----G---FNTESAIAKVNGKVALE-----DDPVKDGDYVEVI   64 (70)
T ss_pred             ceEEEcCCCCcHHHHHHHc----C---CCCccEEEEECCEECCC-----CcCcCCCCEEEEE
Confidence            5678888889999988765    5   66677788899999853     5568889998876

>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=93.08  E-value=0.12  Score=35.73  Aligned_cols=37  Identities=22%  Similarity=0.463  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      .++.+.-|+.+|   |.+.++.+|++....+++.-+|.++
T Consensus         3 ~~d~~~AL~~LG---y~~~e~~~av~~~~~~~~~~~e~~i   39 (47)
T PF07499_consen    3 LEDALEALISLG---YSKAEAQKAVSKLLEKPGMDVEELI   39 (47)
T ss_dssp             HHHHHHHHHHTT---S-HHHHHHHHHHHHHSTTS-HHHHH
T ss_pred             HHHHHHHHHHcC---CCHHHHHHHHHHhhcCCCCCHHHHH
Confidence            578899999999   9999999999998766666677665

The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=93.05  E-value=0.4  Score=34.97  Aligned_cols=60  Identities=13%  Similarity=0.258  Sum_probs=42.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|   +|+.+.+  + ..||.+|.+.+    +   +..+...+-++|+++. .....+.-+++||.|.++-
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   4777766  3 35899888754    5   5566677889999986 3345567789999998863

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

Probab=92.97  E-value=0.11  Score=51.94  Aligned_cols=59  Identities=20%  Similarity=0.148  Sum_probs=51.2

Q ss_pred             EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760           14 EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus        14 ~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      .++.+...|-.+|...|.++.|   ++-...|.|.+||+|.-.+||.+-|++.+-.+.|++.
T Consensus        53 l~k~sL~i~Gselqa~iakklg---i~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~~  111 (568)
T KOG2561|consen   53 LKKCSLHITGSELQALIAKKLG---IKENHVKCIINGKILSCRKTLAEQGLKINQELMVAVG  111 (568)
T ss_pred             hhhcccccccHHHHHHHHHHcC---CchhhhheeeccceeecccchhhhhhhhhhHHHHHhc
Confidence            4556667788999999999999   8888999999999999999999999998877666655

>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=92.84  E-value=0.3  Score=35.57  Aligned_cols=40  Identities=30%  Similarity=0.388  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      .-.+|++|-|.-|+ +..+++-+.|+-++++||.||+-||+
T Consensus         5 ~rk~VQ~iKEiv~~-hse~eIya~L~ecnMDpnea~qrLL~   44 (60)
T PF06972_consen    5 SRKTVQSIKEIVGC-HSEEEIYAMLKECNMDPNEAVQRLLS   44 (60)
T ss_pred             HHHHHHHHHHHhcC-CCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            45789999998655 89999999999999999999999996

>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=92.60  E-value=1.3  Score=34.78  Aligned_cols=74  Identities=18%  Similarity=0.201  Sum_probs=50.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe----CCEec-CCCCChhhh----ccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH----QGKVL-KDVTTLEEN----KVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy----~GKiL-~D~~tL~dy----gIk~g~~I~v   72 (308)
                      .+++|..+|+.+.+.+.++..+.+|+..|.++.|.++.......|.|    +-++| .-+.-|.+|    ......+|.+
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            46788899999999999999999999999999993311124677777    23443 333334443    2334456666


Q ss_pred             EEe
Q 021760           73 MLT   75 (308)
Q Consensus        73 ~v~   75 (308)
                      ++.
T Consensus        82 ~v~   84 (86)
T cd06409          82 HLH   84 (86)
T ss_pred             EEe
Confidence            554

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

>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=91.91  E-value=0.53  Score=36.42  Aligned_cols=36  Identities=17%  Similarity=0.162  Sum_probs=33.9

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 021760           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (308)
Q Consensus        12 ~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G   50 (308)
                      ++.|.|.+..+..+|+++|.++.+   ++.+..+|.|+.
T Consensus        12 tIaIrvp~~~~y~~L~~ki~~kLk---l~~e~i~LsYkd   47 (80)
T cd06406          12 TVAIQVARGLSYATLLQKISSKLE---LPAEHITLSYKS   47 (80)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhC---CCchhcEEEecc
Confidence            899999999999999999999999   999999999965

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

>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=91.60  E-value=0.58  Score=31.49  Aligned_cols=37  Identities=24%  Similarity=0.397  Sum_probs=30.5

Q ss_pred             HHHHHHHHHh-cCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          173 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       173 e~~v~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      ++.|.+.|++ |   -+++.++.-|+.+.+|.++||+.-+.
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            4678898886 6   69999999999999999999986653

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

Probab=90.77  E-value=0.32  Score=48.74  Aligned_cols=42  Identities=21%  Similarity=0.389  Sum_probs=38.6

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~~  217 (308)
                      ...|.+|+.||   |++-..+.||++.-||-|-|.++|+.-++..
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            35699999999   9999999999999999999999999988754

>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=90.71  E-value=1.7  Score=33.58  Aligned_cols=71  Identities=15%  Similarity=0.135  Sum_probs=48.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCeEEEeCC----Ee-cCCCCChhh----hccCCCCEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQG----KV-LKDVTTLEE----NKVAENSFV   70 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~-~~qkLIy~G----Ki-L~D~~tL~d----ygIk~g~~I   70 (308)
                      |+|++. .+|..+.+.+.++.+..+|+++|.++++   +.. ....|-|..    .+ |..+.-|.+    |.....++|
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            456665 4677889999999999999999999988   543 466776643    22 333334555    444556677


Q ss_pred             EEEEe
Q 021760           71 VVMLT   75 (308)
Q Consensus        71 ~v~v~   75 (308)
                      .+.+.
T Consensus        77 ~l~v~   81 (82)
T cd06407          77 RLLVH   81 (82)
T ss_pred             EEEee
Confidence            76653

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=90.42  E-value=0.08  Score=50.54  Aligned_cols=60  Identities=25%  Similarity=0.390  Sum_probs=0.0

Q ss_pred             EEEEEeCCCcEEEEEeC---C--CCcHHHHHHHHHH----------HhCCCCCCCCCeE-----EEeCCEecCCCCChhh
Q 021760            2 KVFVKTLKGTHFEIEVK---P--EDKVSDVKKNIET----------VQGSDVYPASQQM-----LIHQGKVLKDVTTLEE   61 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~---~--~~TV~~LK~~I~~----------~~g~~~ip~~~qk-----LIy~GKiL~D~~tL~d   61 (308)
                      .|++|.+.+-.+.|.+.   +  +.+|.+||..++.          +.+   +|.+.+|     |+|+.|.+.|.++|.+
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            46667666655554432   2  5789999999999          777   9999999     9999999999999888


Q ss_pred             hcc
Q 021760           62 NKV   64 (308)
Q Consensus        62 ygI   64 (308)
                      ..-
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.

>smart00295 B41 Band 4

Probab=89.99  E-value=3.3  Score=35.98  Aligned_cols=71  Identities=20%  Similarity=0.172  Sum_probs=50.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCeEEEe--C-C---EecCCCCChhhhccC-CCCEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIH--Q-G---KVLKDVTTLEENKVA-ENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~-~~qkLIy--~-G---KiL~D~~tL~dygIk-~g~~I~v~   73 (308)
                      .|.|...+|....+.++.+.||.+|.+.|..+.|   +.. ...-|.+  . +   ..|+...+|.+...+ ....+++.
T Consensus         5 ~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~---l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~l~fr   81 (207)
T smart00295        5 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLG---IRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVKSEPLTLYFR   81 (207)
T ss_pred             EEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhC---CCccceeEEEEEcCCCCcCeeCCCccCHHHhcCCCCCcEEEEE
Confidence            5778888999999999999999999999999999   632 2234433  1 2   356777888887665 23344444


Q ss_pred             Ee
Q 021760           74 LT   75 (308)
Q Consensus        74 v~   75 (308)
                      ++
T Consensus        82 ~r   83 (207)
T smart00295       82 VK   83 (207)
T ss_pred             EE
Confidence            33

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.

>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=89.57  E-value=0.99  Score=35.33  Aligned_cols=63  Identities=17%  Similarity=0.135  Sum_probs=44.6

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus        12 ~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      .+...++-...+..||+.++.+.+   +.-+...+...+..|+++++|-+-+|+-...+.+.+.-+
T Consensus         4 vI~q~mDI~epl~~Lk~lLe~Rl~---~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQi~   66 (88)
T PF11620_consen    4 VIMQHMDIREPLSTLKKLLERRLG---ISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQIK   66 (88)
T ss_dssp             EEEEEEESSSBGGGHHHHSHHHH----S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEEEE
T ss_pred             eEEEEEecCCcHHHHHHHHHHhhC---CCcCCCeEEeccceecCCccHHHhhccccCEEEEEEEEE
Confidence            345667778899999999999999   777888888888889999999999999888888877543

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.

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

Probab=89.53  E-value=1.5  Score=36.59  Aligned_cols=60  Identities=17%  Similarity=0.174  Sum_probs=43.9

Q ss_pred             EeCC-CCcHHHHHHHHHHHhCCC-------CCCCCCeEEEeC-----------------CEec---CCCCChhhhccCCC
Q 021760           16 EVKP-EDKVSDVKKNIETVQGSD-------VYPASQQMLIHQ-----------------GKVL---KDVTTLEENKVAEN   67 (308)
Q Consensus        16 eV~~-~~TV~~LK~~I~~~~g~~-------~ip~~~qkLIy~-----------------GKiL---~D~~tL~dygIk~g   67 (308)
                      .|+. +.||.+|++.|.+.....       .+..+.+||++.                 ..+|   +++++|.+|||.+.
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 889999999998765311       234456677652                 1467   77889999999999


Q ss_pred             CEEEEEEe
Q 021760           68 SFVVVMLT   75 (308)
Q Consensus        68 ~~I~v~v~   75 (308)
                      ..|-+..+
T Consensus       101 TEiSfF~~  108 (122)
T PF10209_consen  101 TEISFFNM  108 (122)
T ss_pred             ceeeeeCH
Confidence            88887654

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

Probab=89.30  E-value=1.2  Score=32.94  Aligned_cols=60  Identities=15%  Similarity=0.150  Sum_probs=47.1

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus        12 ~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      ...+++....||.+|.+.+....... .......+..||+++.+  ...++-+++||.|.++-
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            66788889999999999998886311 12367888899999988  36677789999999873

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 ....

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

Probab=89.27  E-value=2.4  Score=33.42  Aligned_cols=62  Identities=13%  Similarity=0.183  Sum_probs=42.7

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--e--CCE-ec-CCCCChhhhccCCCCEEEEEEec
Q 021760           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--H--QGK-VL-KDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y--~GK-iL-~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      ..+...++..+||..+++.+.+.+.   + ....||-  |  ++. .| +.+.||.+.+|.+|-.|++=.+.
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            3567788999999999999999998   8 6678884  3  232 35 45679999999999887776554

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=89.05  E-value=1.4  Score=32.23  Aligned_cols=60  Identities=17%  Similarity=0.240  Sum_probs=42.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|   +|+.+.+  ....||.+|-+.    .+   ++.....+.++|+++..+.- ..+ +++||.|.++.
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---FPEKGIAVAVDWSVLPRSDW-ATK-LRDGARLEVVT   60 (65)
T ss_pred             CEEEE---CCEEEEc--CCCCcHHHHHHH----cC---CCCCcEEEEECCcCcChhHh-hhh-cCCCCEEEEEe
Confidence            56665   4766555  467788877654    46   77889999999998854332 245 99999998864

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

Probab=88.98  E-value=2  Score=32.01  Aligned_cols=67  Identities=16%  Similarity=0.209  Sum_probs=52.6

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE-eCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-HQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         9 ~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI-y~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      +|+...++...+..+.-+..+--+..|...-|++...|- -+|.+|+-++.++|||+.++-++++.++
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            578888888888887777777766665333677776664 5789999999999999999988887654

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

Probab=88.90  E-value=2.4  Score=32.00  Aligned_cols=58  Identities=19%  Similarity=0.277  Sum_probs=42.0

Q ss_pred             CCc-EEEEEeCCC-CcHHHHHHHHHHHhCCCCCC--CCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760            9 KGT-HFEIEVKPE-DKVSDVKKNIETVQGSDVYP--ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         9 ~gk-~~~leV~~~-~TV~~LK~~I~~~~g~~~ip--~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      .|+ ...+++... .||.+|++.+....+.  +-  .....+..+|+.+.+     +.-|++||.|.++
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 357888866 8999999999887641  11  134566789988875     4578899999887

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

>PRK05659 sulfur carrier protein ThiS; Validated

Probab=88.29  E-value=2.2  Score=30.88  Aligned_cols=61  Identities=13%  Similarity=0.251  Sum_probs=42.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|   +|+.+  ++....||.+|-+.    .+   ++.+...+.++|+++..+. ..+.-+++||.|-++-
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---LAGRRVAVEVNGEIVPRSQ-HASTALREGDVVEIVH   61 (66)
T ss_pred             CEEEE---CCeEE--EcCCCCCHHHHHHh----cC---CCCCeEEEEECCeEeCHHH-cCcccCCCCCEEEEEE
Confidence            55555   47654  55667888887754    46   7778888899999886432 3344589999998764

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=88.28  E-value=3.4  Score=31.59  Aligned_cols=59  Identities=12%  Similarity=0.264  Sum_probs=40.8

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCC---CCC-----CCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760           11 THFEIEVKPEDKVSDVKKNIETVQGSD---VYP-----ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~~g~~---~ip-----~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      ....+++. ..||.+|.+.|...+...   .+.     .....+..+|+..+++..   .-|++||.|.++
T Consensus        16 ~~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~   82 (88)
T TIGR01687        16 KSEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIF   82 (88)
T ss_pred             ceEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEe
Confidence            35677886 889999999998775410   000     123566778988765532   568999999887

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.

>PRK08053 sulfur carrier protein ThiS; Provisional

Probab=87.60  E-value=3.2  Score=30.37  Aligned_cols=61  Identities=7%  Similarity=0.166  Sum_probs=42.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|.   |+.+.+  ....||.+|.+.    .+   +......+-.+|+++..+ ..+++-+++||.|.++-
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---QLQPGAALAINQQIIPRE-QWAQHIVQDGDQILLFQ   61 (66)
T ss_pred             CEEEEC---CeEEEc--CCCCCHHHHHHH----cC---CCCCcEEEEECCEEeChH-HcCccccCCCCEEEEEE
Confidence            566664   766555  567789988865    34   445667888999998522 23445689999998863

>PRK06944 sulfur carrier protein ThiS; Provisional

Probab=85.93  E-value=5.1  Score=28.82  Aligned_cols=60  Identities=10%  Similarity=0.130  Sum_probs=39.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|   +|+.+  ++....||.+|.+.+    +   +. ....+.++|+++..+. ..+.-+++||.|.++-
T Consensus         1 m~i~v---Ng~~~--~~~~~~tl~~ll~~l----~---~~-~~~~v~vN~~~v~~~~-~~~~~L~~gD~vei~~   60 (65)
T PRK06944          1 MDIQL---NQQTL--SLPDGATVADALAAY----G---AR-PPFAVAVNGDFVARTQ-HAARALAAGDRLDLVQ   60 (65)
T ss_pred             CEEEE---CCEEE--ECCCCCcHHHHHHhh----C---CC-CCeEEEECCEEcCchh-cccccCCCCCEEEEEe
Confidence            55555   46654  456677899888754    3   43 3467789999885432 2334488999998874

>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins

Probab=85.71  E-value=0.36  Score=36.99  Aligned_cols=26  Identities=35%  Similarity=0.484  Sum_probs=23.2

Q ss_pred             CHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          188 DRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       188 ~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .+.+++.||.-.|+|+++||.||++-
T Consensus        45 ~e~~i~eal~~~~fDvekAl~~Ll~~   70 (79)
T PF08938_consen   45 PEEQIKEALWHYYFDVEKALDYLLSK   70 (79)
T ss_dssp             -CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred             CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence            88999999999999999999999987

; PDB: 1UFZ_A 3IZQ_1.

>smart00666 PB1 PB1 domain

Probab=85.25  E-value=4.3  Score=30.34  Aligned_cols=45  Identities=16%  Similarity=0.178  Sum_probs=36.8

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G   50 (308)
                      +|+++. ++..+.+.+..+.|..+|+.+|...++   +.....+|-|..
T Consensus         3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~---~~~~~~~l~Y~D   47 (81)
T smart00666        3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFG---LDNQSFTLKYQD   47 (81)
T ss_pred             cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhC---CCCCCeEEEEEC
Confidence            455654 677888999999999999999999998   655678888864

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.

>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]

Probab=84.90  E-value=1.8  Score=42.59  Aligned_cols=65  Identities=23%  Similarity=0.354  Sum_probs=51.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecCC-CCChhhhccCCCC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENS   68 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~D-~~tL~dygIk~g~   68 (308)
                      .|.||.-+|+.+.+.+..+.||.+|+..|......  .....+.|+  |--|.|.| +.||++-||.+.-
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            47889889999999999999999999999988762  334456665  55688855 6799999998743

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.86  E-value=0.87  Score=44.00  Aligned_cols=55  Identities=16%  Similarity=0.122  Sum_probs=44.6

Q ss_pred             EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe---CCEec-----CCCCChhhhccCCCCEEEEE
Q 021760           16 EVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVL-----KDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        16 eV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy---~GKiL-----~D~~tL~dygIk~g~~I~v~   73 (308)
                      -|+-.-||.+||+++..+.|   +...++||+|   .||.-     +.++.|-.|+|++||.+.|-
T Consensus       353 ~I~~~~TV~D~~~~Ld~~VG---vk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~lvq  415 (418)
T KOG2982|consen  353 LICMTRTVLDFMKILDPKVG---VKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFLVQ  415 (418)
T ss_pred             EEEeehHHHHHHHHhccccc---cccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEeeee
Confidence            34556699999999999999   8899999987   45543     34578999999999988764

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

Probab=84.01  E-value=1.5  Score=44.91  Aligned_cols=39  Identities=31%  Similarity=0.601  Sum_probs=35.4

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGI  214 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GI  214 (308)
                      ...|.+|++||   |+.+.+.|||-+.-| +-+-|..||.-.+
T Consensus       559 qs~I~qL~~mG---fp~~~~~rAL~~tgNqDaEsAMNWLFqHM  598 (749)
T COG5207         559 QSLIRQLVDMG---FPEEDAARALGITGNQDAESAMNWLFQHM  598 (749)
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHhhccCcchHHHHHHHHhhc
Confidence            56899999999   999999999998877 7899999999875

>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases

Probab=83.51  E-value=3.5  Score=31.16  Aligned_cols=64  Identities=19%  Similarity=0.071  Sum_probs=45.9

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC--C--EecCCCCChhhhccCCCCEEEE
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--G--KVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~--G--KiL~D~~tL~dygIk~g~~I~v   72 (308)
                      +.|-..+|+.-.+.|.+..||.++-.++.++.|   +.++...|.+.  +  +.++.+.....   -.+..|.|
T Consensus         2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~---l~~~~~~v~~~~~~~~~~~~~~~d~~~---L~~~El~V   69 (72)
T cd01760           2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRG---LNPECCDVFLLGLDEKKPLDLDTDSSS---LAGEELEV   69 (72)
T ss_pred             EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcC---CCHHHEEEEEecCCCcCCcCchhhhhh---hcCCEEEE
Confidence            456667899999999999999999999999999   77777766554  4  45544443333   34444554

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.

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=83.42  E-value=4.2  Score=29.50  Aligned_cols=57  Identities=9%  Similarity=0.242  Sum_probs=40.5

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         8 l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      ++|+.+  +++...||.+|.+++    +   ++.+...+.++|+++..+ ...++-|++||.|.++-
T Consensus         4 iNg~~~--~~~~~~tv~~ll~~l----~---~~~~~i~V~vNg~~v~~~-~~~~~~L~~gD~V~ii~   60 (65)
T cd00565           4 VNGEPR--EVEEGATLAELLEEL----G---LDPRGVAVALNGEIVPRS-EWASTPLQDGDRIEIVT   60 (65)
T ss_pred             ECCeEE--EcCCCCCHHHHHHHc----C---CCCCcEEEEECCEEcCHH-HcCceecCCCCEEEEEE
Confidence            356554  446678999988764    4   567788889999998543 23345689999998863

ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.

>PF11069 DUF2870: Protein of unknown function (DUF2870); InterPro: IPR021298 This is a eukaryotic family of proteins with unknown function

Probab=82.92  E-value=2.1  Score=34.34  Aligned_cols=33  Identities=27%  Similarity=0.309  Sum_probs=22.9

Q ss_pred             EEEeCCEecCCCCChhhh-ccCCCCEEEEEEecC
Q 021760           45 MLIHQGKVLKDVTTLEEN-KVAENSFVVVMLTKS   77 (308)
Q Consensus        45 kLIy~GKiL~D~~tL~dy-gIk~g~~I~v~v~k~   77 (308)
                      .|-|.||.|.++++|++| |-.+...|+|-+.++
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 223344444444443

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

Probab=82.86  E-value=0.45  Score=48.48  Aligned_cols=38  Identities=18%  Similarity=0.282  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      -|..++.|++||   |.-.+|++||--..||-+|+|+|.++
T Consensus       621 dE~~~~Slle~G---ln~n~~Rkal~~~n~d~~r~V~w~~N  658 (749)
T COG5207         621 DESKARSLLENG---LNPNLCRKALMDMNTDSKRRVVWCIN  658 (749)
T ss_pred             cHHHHHHHHHcC---CCHHHHHHHHHHccCCchheEEEEEe
Confidence            478899999999   99999999999999999999999998

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=82.73  E-value=5.1  Score=39.88  Aligned_cols=73  Identities=15%  Similarity=0.233  Sum_probs=58.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe----CCEe--cCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH----QGKV--LKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy----~GKi--L~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |.+.||...| ...+++.++++..-|-.+|-.....+ +.++++.+.-    .|.+  +..++++.++|++.|+.|+|-.
T Consensus         1 Mi~rfRsk~G-~~Rve~qe~d~lg~l~~kll~~~~~n-~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~y   78 (571)
T COG5100           1 MIFRFRSKEG-QRRVEVQESDVLGMLSPKLLAFFEVN-YSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEY   78 (571)
T ss_pred             CeEEEecCCC-ceeeeccccchhhhhhHHHHhhhccC-CCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEe
Confidence            7788997776 57899999999999999887766544 7777877764    3443  3567899999999999999987


Q ss_pred             e
Q 021760           75 T   75 (308)
Q Consensus        75 ~   75 (308)
                      +
T Consensus        79 s   79 (571)
T COG5100          79 S   79 (571)
T ss_pred             c
Confidence            4

>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]

Probab=82.37  E-value=7.2  Score=29.14  Aligned_cols=63  Identities=16%  Similarity=0.298  Sum_probs=43.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |.++|. ++|+.  +++....|+.+|-+.    .+   +..+..-+.++|.++..+. ..++-+++||.|.++-
T Consensus         1 ~~m~i~-~ng~~--~e~~~~~tv~dLL~~----l~---~~~~~vav~vNg~iVpr~~-~~~~~l~~gD~ievv~   63 (68)
T COG2104           1 MPMTIQ-LNGKE--VEIAEGTTVADLLAQ----LG---LNPEGVAVAVNGEIVPRSQ-WADTILKEGDRIEVVR   63 (68)
T ss_pred             CcEEEE-ECCEE--EEcCCCCcHHHHHHH----hC---CCCceEEEEECCEEccchh-hhhccccCCCEEEEEE
Confidence            445555 34665  455656899987764    55   7788888899999986432 3455688889888763

>PRK06083 sulfur carrier protein ThiS; Provisional

Probab=81.81  E-value=6.4  Score=30.58  Aligned_cols=57  Identities=5%  Similarity=0.161  Sum_probs=40.6

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         8 l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      ++|+.+  +++...||.+|-+.    .+   ++....-+-++|.++. .....++-+++||.|.++.
T Consensus        23 VNG~~~--~~~~~~tl~~LL~~----l~---~~~~~vAVevNg~iVp-r~~w~~t~L~egD~IEIv~   79 (84)
T PRK06083         23 INDQSI--QVDISSSLAQIIAQ----LS---LPELGCVFAINNQVVP-RSEWQSTVLSSGDAISLFQ   79 (84)
T ss_pred             ECCeEE--EcCCCCcHHHHHHH----cC---CCCceEEEEECCEEeC-HHHcCcccCCCCCEEEEEE
Confidence            356554  44567788877664    35   7777778889999983 3446677799999998874

>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function

Probab=81.35  E-value=1.8  Score=42.47  Aligned_cols=30  Identities=17%  Similarity=0.360  Sum_probs=24.7

Q ss_pred             ccccCCcHHHHHHHHHHhcCCccCHHHHHHHHH
Q 021760          165 NLVAGSNLEATVQQILDMGGGSWDRETVIRALR  197 (308)
Q Consensus       165 ~l~~g~~~e~~v~~i~~MG~~~f~r~qv~~ALr  197 (308)
                      .++..--|+++|+.++.||   |.||+|+.-.|
T Consensus       314 ~~~~~~p~ddvidKv~~MG---f~rDqV~a~v~  343 (358)
T PF07223_consen  314 QSGNRHPYDDVIDKVASMG---FRRDQVRATVR  343 (358)
T ss_pred             cccccCcHHHHHHHHHHcC---CcHHHHHHHHH
Confidence            3555667999999999999   99999987444

>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B

Probab=81.11  E-value=3.2  Score=32.35  Aligned_cols=51  Identities=12%  Similarity=0.105  Sum_probs=27.4

Q ss_pred             CCcHHHHHHHHHH-HhCCCCCCCC----CeEEEeCCEe----cCCCCChhhhccCCCCEEEEE
Q 021760           20 EDKVSDVKKNIET-VQGSDVYPAS----QQMLIHQGKV----LKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        20 ~~TV~~LK~~I~~-~~g~~~ip~~----~qkLIy~GKi----L~D~~tL~dygIk~g~~I~v~   73 (308)
                      ..|+++|-++|-+ +.|   +-.-    .-++||..-.    -..+++|+++||++|++|.|.
T Consensus         8 ~~TL~~lv~~Vlk~~Lg---~~~P~v~~~~~ilyd~de~~~~~~l~k~L~elgi~~gs~L~v~   67 (87)
T PF14732_consen    8 KMTLGDLVEKVLKKKLG---MNEPDVSVGGTILYDSDEEEYDDNLPKKLSELGIVNGSILTVD   67 (87)
T ss_dssp             T-BHHHHHHHCCCCCS-----SSEEEEES-EEEE-SSSSSSTTCTTSBGGGGT--TT-EEEEE
T ss_pred             hCcHHHHHHHHHHhccC---CCCCEEEeCCCEEEcCCcchhhhcccCChhHcCCCCCCEEEEE
Confidence            5799999998744 555   2221    2234443321    123478999999999998864

>PRK07696 sulfur carrier protein ThiS; Provisional

Probab=80.75  E-value=8.1  Score=28.44  Aligned_cols=61  Identities=10%  Similarity=0.205  Sum_probs=41.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCC-CcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPE-DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~-~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|   +|+.+.+  ... .||.+|-+    ..+   +.....-+-++|+++.-+ ...++-|++||.|.++.
T Consensus         1 m~I~v---NG~~~~~--~~~~~tv~~lL~----~l~---~~~~~vav~vN~~iv~r~-~w~~~~L~~gD~iEIv~   62 (67)
T PRK07696          1 MNLKI---NGNQIEV--PESVKTVAELLT----HLE---LDNKIVVVERNKDILQKD-DHTDTSVFDGDQIEIVT   62 (67)
T ss_pred             CEEEE---CCEEEEc--CCCcccHHHHHH----HcC---CCCCeEEEEECCEEeCHH-HcCceecCCCCEEEEEE
Confidence            55665   4776544  444 57877665    345   667777788999998533 34556689999998864

>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA

Probab=80.54  E-value=7.4  Score=30.52  Aligned_cols=45  Identities=16%  Similarity=0.244  Sum_probs=35.0

Q ss_pred             EEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCE
Q 021760            3 VFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK   51 (308)
Q Consensus         3 I~Vktl-~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GK   51 (308)
                      |+||.. .|..+.+.|.++.+..+|.++|.++++   +. ..++|-|...
T Consensus         3 ikVKv~~~~Dv~~i~v~~~i~f~dL~~kIrdkf~---~~-~~~~iKykDE   48 (86)
T cd06408           3 IRVKVHAQDDTRYIMIGPDTGFADFEDKIRDKFG---FK-RRLKIKMKDD   48 (86)
T ss_pred             EEEEEEecCcEEEEEcCCCCCHHHHHHHHHHHhC---CC-CceEEEEEcC
Confidence            445543 677899999999999999999999999   63 5666666543

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

>smart00455 RBD Raf-like Ras-binding domain

Probab=80.46  E-value=6.4  Score=29.42  Aligned_cols=50  Identities=18%  Similarity=0.157  Sum_probs=41.2

Q ss_pred             EEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC--EecCCC
Q 021760            4 FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG--KVLKDV   56 (308)
Q Consensus         4 ~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G--KiL~D~   56 (308)
                      .|-..+|+...+.+.+..||.++-.+|.++.|   +.++...|+..|  |.|+=+
T Consensus         3 ~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~---l~~~~~~v~~~g~~k~ldl~   54 (70)
T smart00455        3 KVHLPDNQRTVVKVRPGKTVRDALAKALKKRG---LNPECCVVRLRGEKKPLDLN   54 (70)
T ss_pred             EEECCCCCEEEEEECCCCCHHHHHHHHHHHcC---CCHHHEEEEEcCCCcceecC
Confidence            45556899999999999999999999999999   888888888755  455433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	308
1uel_A	95	Solution Structure Of Ubiquitin-Like Domain Of Hhr2		7e-12
1p1a_A	85	Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Le		1e-11
1oqy_A	368	Structure Of The Dna Repair Protein Hhr23a Length =		4e-11
1ify_A	49	Solution Structure Of The Internal Uba Domain Of Hh		6e-09
2wyq_A	85	The Crystal Structure Of The Ubiquitin-Like (Ubl) D		4e-08
1p98_A	78	High-Resolution Nmr Structure Of The Ubl-Domain Of		5e-08
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		1e-07
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		5e-07
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		7e-07
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		2e-06
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-06
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		2e-06
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		2e-06
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		2e-06
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		2e-06
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		2e-06
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		2e-06
3jvz_X	81	E2~ubiquitin-Hect Length = 81		2e-06
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-06
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		3e-06
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		3e-06
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		3e-06
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		3e-06
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		3e-06
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		3e-06
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		3e-06
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		3e-06
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		3e-06
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		4e-06
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		4e-06
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		5e-06
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		5e-06
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		5e-06
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		5e-06
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		5e-06
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		5e-06
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		5e-06
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		6e-06
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		6e-06
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		6e-06
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		6e-06
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		6e-06
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		6e-06
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		7e-06
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		7e-06
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		7e-06
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		8e-06
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		8e-06
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		8e-06
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		8e-06
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		9e-06
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		9e-06
1ndd_B	76	Structure Of Nedd8 Length = 76		9e-06
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		9e-06
3h7s_A	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		9e-06
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		1e-05
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		1e-05
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		1e-05
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		1e-05
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		1e-05
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		1e-05
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-05
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		2e-05
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		2e-05
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-05
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-05
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		2e-05
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		2e-05
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		2e-05
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		3e-05
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		3e-05
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		3e-05
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		4e-05
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		5e-05
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		7e-05
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		7e-05
4hk2_A	78	U7ub25.2540 Length = 78		7e-05
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		8e-05
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		1e-04
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		2e-04
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		2e-04
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		3e-04
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		4e-04
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		5e-04

>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 = 7e-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 = 67.4 bits (163), 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|1OQY|A Chain A, Structure Of The Dna Repair Protein Hhr23a Length = 368

Iteration: 1
 Score = 65.5 bits (158), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 31/54 (57%), Positives = 39/54 (72%), Gaps = 3/54 (5%)
Query: 162 AASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 215
           AAS LV GS  E  + +I+ MG   ++RE V+ ALRA+YNNP RAVEYL +GIP
Sbjct: 158 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 208

>pdb|1IFY|A Chain A, Solution Structure Of The Internal Uba Domain Of Hhr23a Length = 49

Iteration: 1
 Score = 58.2 bits (139), Expect = 6e-09,   Method: Composition-based stats.
 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

>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 = 4e-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 = 55.1 bits (131), 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: 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 = 53.5 bits (127), Expect = 1e-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 = 51.6 bits (122), Expect = 5e-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 = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 9  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 65
Query: 61 ENKVAENSFVVVML 74
          E  + + S + ++L
Sbjct: 66 EYNIQKESTLHLVL 79

>pdb|2K6D|B Chain B, Cin85 Sh3-C Domain In Complex With Ubiquitin Length = 76

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: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3DVG|X Chain X, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 80

Iteration: 1
 Score = 49.7 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: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|2OJR|A Chain A, Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag Length = 111

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-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: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92
Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

>pdb|2KHW|B Chain B, Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex Length = 79

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: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>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: 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: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92
Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

>pdb|1YX5|B Chain B, Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Length = 98

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-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 = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ L+   K L+D  TL 
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQKLLFARKQLEDGRTLS 59
Query: 61 ENKVAENSFVVVML 74
          +  + + SF+ ++L
Sbjct: 60 DYNIHKESFLYLVL 73

>pdb|3NOB|A Chain A, Structure Of K11-Linked Di-Ubiquitin Length = 78

Iteration: 1
 Score = 49.3 bits (116), 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: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 59
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 60 DYNIQKESTLHLVL 73

>pdb|3JVZ|X Chain X, E2~ubiquitin-Hect Length = 81

Iteration: 1
 Score = 49.3 bits (116), 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: 6  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 62
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 63 DYNIQKESTLHLVL 76

>pdb|3DVG|Y Chain Y, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 79

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 61 DYNIQRESTLHLVL 74

>pdb|2ZNV|C Chain C, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 77

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: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>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 = 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: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 59 DYNIQKESTLHLVL 72

>pdb|3K9O|B Chain B, The Crystal Structure Of E2-25k And Ubb+1 Complex Length = 96

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: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 59 DYNIQKESTLHLVL 72

>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 = 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: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|4AP4|C Chain C, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 80

Iteration: 1
 Score = 49.3 bits (116), 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: 5  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 61
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 62 DYNIQKESTLHLVL 75

>pdb|3RUL|A Chain A, New Strategy To Analyze Structures Of Glycopeptide-Target Complexes Length = 79

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: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1XD3|B Chain B, Crystal Structure Of Uchl3-Ubvme Complex Length = 75

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: 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 = 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: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>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 = 48.9 bits (115), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

>pdb|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 = 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: 21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 77
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 78 DYNIQKESTLHLVL 91

>pdb|2ZVN|A Chain A, Nemo Cozi Domain Incomplex With Diubiquitin In P212121 Space Group Length = 154

Iteration: 1
 Score = 48.5 bits (114), Expect = 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: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 59
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 60 DYNIQKESTLHLVL 73

>pdb|2W9N|A Chain A, Crystal Structure Of Linear Di-Ubiquitin Length = 152

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: 77  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 133
Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 134 DYNIQKESTLHLVL 147

>pdb|3B08|A Chain A, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With Linear Di- Ubiquitin Length = 152

Iteration: 1
 Score = 48.5 bits (114), Expect = 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: 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 = 48.5 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: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPQQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|2GBR|A Chain A, Crystal Structure Of The 35-36 Moad Insertion Mutant Of Ubiquitin Length = 81

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-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|3AI5|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein Length = 307

Iteration: 1
 Score = 48.5 bits (114), Expect = 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: 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 = 48.5 bits (114), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  G+ L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGRQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|2ZCB|A Chain A, Crystal Structure Of Ubiquitin P37aP38A Length = 76

Iteration: 1
 Score = 48.1 bits (113), 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     A QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IAADQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3DBH|I Chain I, Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1- Uba3arg190ala-Nedd8ala72arg) Length = 88

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   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|4HJK|A Chain A, U7ub7 Disulfide Variant Length = 77

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   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|2Y5B|B Chain B, Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde Length = 152

Iteration: 1
 Score = 48.1 bits (113), 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: 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 = 48.1 bits (113), 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: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3ONS|A Chain A, Crystal Structure Of Human Ubiquitin In A New Crystal Form Length = 72

Iteration: 1
 Score = 48.1 bits (113), 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: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 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 = 48.1 bits (113), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  G+ L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGRQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

>pdb|1YIW|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin Length = 76

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|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 = 47.8 bits (112), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 6  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 62
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 63 DYKILGGSVLHLVL 76

>pdb|1UD7|A Chain A, Solution Structure Of The Designed Hydrophobic Core Mutant Of Ubiquitin, 1d7 Length = 76

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   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|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 = 47.8 bits (112), Expect = 8e-06,   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|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant Of Ubiquitin Length = 88

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++F+KTL G  F +E++P D + ++K  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 66
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 67 DYNIQKESTLHLVL 80

>pdb|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 = 47.8 bits (112), Expect = 8e-06,   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|3MTN|B Chain B, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 85

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 61 DYNIQKWS 68

>pdb|4F8C|B Chain B, Structure Of The Cif:nedd8 Complex - Yersinia Pseudotuberculosis Cycle Inhibiting Factor In Complex With Human Nedd8 Length = 88

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 58 DYKILGGSVLHLVL 71

>pdb|2BKR|B Chain B, Nedd8 Nedp1 Complex Length = 77

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 2  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 58
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 59 DYKILGGSVLHLVL 72

>pdb|1NDD|B Chain B, Structure Of Nedd8 Length = 76

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 58 DYKILGGSVLHLVL 71

>pdb|3GZN|I Chain I, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8 And Mln4924 Length = 82

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 7  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 63
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 64 DYKILGGSVLHLVL 77

>pdb|3H7S|A Chain A, Crystal Structures Of K63-Linked Di- And Tri-Ubiquitin Reveal A Highly Extended Chain Architecture Length = 76

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKV 64
          +  +
Sbjct: 58 DYNI 61

>pdb|4HCP|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Nedd8 Length = 78

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M + VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK + D  T  
Sbjct: 3  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 59
Query: 61 ENKVAENSFVVVML 74
          + K+   S + ++L
Sbjct: 60 DYKILGGSVLHLVL 73

>pdb|1YJ1|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin Length = 76

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++FVKTL G    +EV+P D + +VK  I   Q  +  P  QQ LI  GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKI---QDKEXIPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1S1Q|B Chain B, Tsg101(Uev) Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 2  KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
          ++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL +
Sbjct: 2  QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSD 58
Query: 62 NKVAENSFVVVML 74
            + + S + ++L
Sbjct: 59 YNIQKESTLHLVL 71

>pdb|4II3|B Chain B, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme 1 (uba1) In Complex With Ubiquitin And Atp/mg Length = 96

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  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|2O6V|B Chain B, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  G  L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGXQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

>pdb|1C3T|A Chain A, Rotamer Strain As A Determinant Of Protein Structural Specificity Length = 76

Iteration: 1
 Score = 47.0 bits (110), 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    +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|4HCN|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Ubiquitin Length = 98

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++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|1OTR|B Chain B, Solution Structure Of A Cue-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|1OGW|A Chain A, Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Length = 76

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK  +D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQXEDGRTLS 57
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 58 DYNIQKES 65

>pdb|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 = 2e-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|2FCS|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [l-Gln35]ubiquitin With A Cubic Space Group Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +++FVKTL G    +EV+P D + +VK  I   Q  +  P  QQ LI  GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKI---QDKEQIPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3OLM|D Chain D, Structure And Function Of A Ubiquitin Binding Site Within The Catalytic Domain Of A Hect Ubiquitin Ligase Length = 79

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|2JWZ|A Chain A, Mutations In The Hydrophobic Core Of Ubiquitin Differentially Affect Its Recognition By Receptor Proteins Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-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|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-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 = 45.8 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: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 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 = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+   G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGATITLEVESSDTIDNVKSKIQAAPG---IPPDQQELIFAGKQLEDGRTLS 57
Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3DQV|A Chain A, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 81

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 5  VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV 64
          VKTL G   EI+++P DKV  +K+ +E  +G    P  QQ LI+ GK   D  T  + K+
Sbjct: 10 VKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQXNDEKTAADYKI 66
Query: 65 AENSFVVVML 74
             S + ++L
Sbjct: 67 XGGSVLHLVL 76

>pdb|4GSW|A Chain A, Crystal Structure Of Ubiquitin From Entamoeba Histolytica To 2.15 Angstrom Length = 80

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-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|3N3K|B Chain B, The Catalytic Domain Of Usp8 In Complex With A Usp8 Specific Inhibitor Length = 85

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++ VKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 61 ENKVAENS 68
          +  +  +S
Sbjct: 61 DYNIHNHS 68

>pdb|3U5C|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome A Length = 152

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+  D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 58 DYNIQKES 65

>pdb|2GBM|A Chain A, Crystal Structure Of The 35-36 8 Glycine Insertion Mutant Of Ubiquitin Length = 84

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQ-----GSDVYPASQQMLIHQGKVLKD 55
          M++FVKTL G    +EV+P D + +VK  I+  +     G    P  QQ LI  GK L+D
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGGGGGGGGGIPPDQQRLIFAGKQLED 60
Query: 56 VTTLEENKVAENSFVVVML 74
            TL +  + + S + ++L
Sbjct: 61 GRTLSDYNIQKESTLHLVL 79

>pdb|4HK2|A Chain A, U7ub25.2540 Length = 78

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVK   G  + +EV+P D + +VK  I+   G    P  QQ LI  GK L+D  TL 
Sbjct: 3  MQIFVKFRTGKTYTLEVEPSDTIENVKAKIQDKLG---IPPDQQWLIFAGKRLEDGRTLS 59
Query: 61 ENKVAENS 68
          +  + + S
Sbjct: 60 DYNIQKES 67

>pdb|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 = 8e-05,   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|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1 Length = 76

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-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|3ZF7|SS Chain s, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 128

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-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|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 = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FV+TL G    +EV+  D + +V+  I+  +G    P  QQ LI  G+ L+D  TL 
Sbjct: 8  MQIFVRTLTGRTITLEVESSDTIDNVRARIQDREG---IPPDQQRLIFAGRQLEDGRTLA 64
Query: 61 ENKVAENSFVVVML 74
          +  +   S + ++L
Sbjct: 65 DYNIQRESTLHLVL 78

>pdb|2KDI|A Chain A, Solution Structure Of A UbiquitinUIM FUSION PROTEIN Length = 114

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 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

>pdb|1GJZ|A Chain A, Solution Structure Of A Dimeric N-Terminal Fragment Of Human Ubiquitin Length = 53

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK 54
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLE 53

>pdb|2GBK|A Chain A, Crystal Structure Of The 9-10 Moad Insertion Mutant Of Ubiquitin Length = 83

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-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	308
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	4e-46
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	2e-38
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	2e-38
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	2e-32
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	4e-32
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	2e-26
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	1e-25
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	6e-25
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	7e-23
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	7e-23
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-22
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	2e-22
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	8e-22
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	1e-21
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	2e-21
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	3e-21
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	4e-21
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	7e-21
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	7e-21
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	1e-20
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	3e-20
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	4e-20
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	7e-20
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	4e-19
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	4e-19
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	4e-19
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	4e-19
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	2e-18
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	1e-17
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	1e-17
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	2e-17
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	9e-17
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	3e-16
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	3e-16
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	1e-15
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	2e-15
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	2e-15
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	2e-15
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	3e-15
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	2e-08
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	5e-15
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	3e-14
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	7e-14
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	1e-07
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	1e-13
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	3e-13
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	1e-09
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	1e-11
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	8e-10
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	2e-09
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	3e-09
1we6_A	111	Splicing factor, putative; structural genomics, ub	5e-09
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	8e-09
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	8e-09
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	9e-08
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	2e-07
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	2e-07
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	5e-07
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	1e-06
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	2e-06
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	2e-06
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	2e-06
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	2e-06
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	5e-06
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	7e-06
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	1e-05
2uv9_A	1878	Fatty acid synthase alpha subunits; fungal, dehydr	2e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	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	6e-04
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	4e-05
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	8e-05
3nwa_A	703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	1e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	2e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	2e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	7e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	4e-04
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	4e-04
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	5e-04
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	6e-04
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	7e-04
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	8e-04

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A Length = 368

 Score =  158 bits (401), Expect = 4e-46
 Identities = 89/302 (29%), Positives = 138/302 (45%), Gaps = 47/302 (15%)

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 QQ 302
             
Sbjct: 261 PA 262

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 95

 Score =  130 bits (328), Expect = 2e-38
 Identities = 38/93 (40%), Positives = 59/93 (63%)

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

Query: 61 ENKVAENSFVVVMLTKSKVSSSGASTVSAAPAN 93
          E K+ E +FVVVM+TK K  S+ A        +
Sbjct: 61 EYKIDEKNFVVVMVTKPKAVSTPAPATLEHHHH 93

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A Length = 85

 Score =  129 bits (327), Expect = 2e-38
 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

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score =  114 bits (287), Expect = 2e-32
 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

>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 (286), Expect = 4e-32
 Identities = 19/101 (18%), Positives = 45/101 (44%), Gaps = 3/101 (2%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           + +  K  K     ++++P + + + K  +           SQ  LI+ GKVL+D  T+ 
Sbjct: 2   VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSIS---CEESQIKLIYSGKVLQDSKTVS 58

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSA 101
           E  + +   VV M+++ K + +  +      ++  +  ++ 
Sbjct: 59  ECGLKDGDQVVFMVSQKKSTKTKVTERDPNSSSVDKLAAAL 99

>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 = 98.1 bits (245), Expect = 2e-26
 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 = 96.6 bits (241), Expect = 1e-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

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 95.2 bits (237), Expect = 6e-25
 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

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Length = 85

 Score = 89.3 bits (222), Expect = 7e-23
 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 = 91.4 bits (227), Expect = 7e-23
 Identities = 7/74 (9%), Positives = 16/74 (21%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M      ++       V+    V       E VQ         ++         +V    
Sbjct: 1  MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQ---AQTEIKLFNKWSFEEVEVKDAS 57

Query: 61 ENKVAENSFVVVML 74
               +    + + 
Sbjct: 58 LVDYVQVRQPIFVA 71

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ... Length = 76

 Score = 87.7 bits (218), Expect = 2e-22
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

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

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

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p Length = 128

 Score = 89.3 bits (221), Expect = 2e-22
 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

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Length = 88

 Score = 86.6 bits (215), Expect = 8e-22
 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

>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 = 86.3 bits (214), Expect = 1e-21
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60

Query: 61 ENKVAENSFVVVML 74
          +  + + S + ++L
Sbjct: 61 DYNIQKWSTLFLLL 74

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: k.45.1.1 PDB: 3dbr_I 3dbl_I Length = 88

 Score = 85.9 bits (213), Expect = 2e-21
 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

>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 = 83.7 bits (207), Expect = 3e-21
 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

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 81

 Score = 84.3 bits (209), Expect = 4e-21
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++ VK L+G    ++V  ++ VS +K+ +         P  QQ L+ +GK L D   L 
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLN---VPVRQQRLLFKGKALADGKRLS 64

Query: 61 ENKVAENSFVVVML 74
          +  +  NS + +++
Sbjct: 65 DYSIGPNSKLNLVV 78

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Length = 98

 Score = 84.5 bits (209), Expect = 7e-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: 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 = 84.9 bits (210), Expect = 7e-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: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92

Query: 61  ENKVAENSFVVVML 74
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

>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 = 83.9 bits (208), Expect = 1e-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

>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 = 82.0 bits (203), Expect = 3e-20
 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

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S Length = 77

 Score = 81.9 bits (203), Expect = 4e-20
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 1  MKVFVKTLKGTH-FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTL 59
          M + +    G   +E+ V PE  V   K+ I    G    P + Q LI+ GK+LKD  T+
Sbjct: 3  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTV 59

Query: 60 EENKVAENSFVVVMLTK 76
          E   + +   V ++ ++
Sbjct: 60 ESYHIQDGHSVHLVKSQ 76

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 87

 Score = 81.3 bits (201), Expect = 7e-20
 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 = 80.2 bits (198), Expect = 4e-19
 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 = 79.3 bits (196), Expect = 4e-19
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V VKTL        V  +  V + K++I         P+ +Q LI+QG+VL+D   L+
Sbjct: 18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQ 74

Query: 61 ENKVAEN 67
          E  V   
Sbjct: 75 EYNVGGK 81

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A Length = 96

 Score = 79.8 bits (197), Expect = 4e-19
 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 = 80.2 bits (198), Expect = 4e-19
 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 = 77.8 bits (192), Expect = 2e-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

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score = 75.1 bits (185), Expect = 1e-17
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + V+  KG     EV+    V+ +K+ +    G +        L  +GK L+D   L 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPLG 61

Query: 61 ENKVAENSFVVVML 74
          E  +   S V + L
Sbjct: 62 EYGLKPLSTVFMNL 75

>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 = 75.5 bits (186), Expect = 1e-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

>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 = 75.1 bits (185), Expect = 2e-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

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 75.9 bits (186), Expect = 9e-17
 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 = 72.4 bits (178), 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 = 71.2 bits (175), Expect = 3e-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: 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 = 70.1 bits (172), Expect = 1e-15
 Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          ++V VKT +  H E  +     V   KK I          A + +LI  GK+L+D   L 
Sbjct: 18 IRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDILS 73

Query: 61 ENKVAENSFVVVMLTKSKVSSSG 83
          +  + + S V V++      SSG
Sbjct: 74 QRGILDGSTVHVVVRSHSGPSSG 96

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 70.1 bits (172), Expect = 2e-15
 Identities = 24/70 (34%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          MKV VKT K    E  V     V   K+ I     S      Q +LI  GK+LKD  TL 
Sbjct: 26 MKVTVKTPKEKE-EFAVPENSSVQQFKEEISKRFKS---HTDQLVLIFAGKILKDQDTLS 81

Query: 61 ENKVAENSFV 70
          ++ + +   V
Sbjct: 82 QHGIHDGLTV 91

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 70.3 bits (172), Expect = 2e-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

>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 = 69.3 bits (170), Expect = 2e-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 = 70.8 bits (173), Expect = 3e-15
 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 = 51.6 bits (123), Expect = 2e-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 = 70.8 bits (173), Expect = 5e-15
 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 = 66.2 bits (162), Expect = 3e-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 = 67.4 bits (164), Expect = 7e-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: 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 = 49.7 bits (118), Expect = 1e-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 = 64.8 bits (158), Expect = 1e-13
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FV+  +  H   EV  ++ V+ +K ++ +++G        Q+++  G  L+D  TL 
Sbjct: 20 MQLFVRAQE-LH-TFEVTGQETVAQIKAHVASLEG---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 = 65.7 bits (160), Expect = 3e-13
 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 = 55.3 bits (133), Expect = 1e-09
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
           + + V+  KG     EV+    V+ +K+ +    G +        L  +GK L+D   L 
Sbjct: 82  LSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPLG 138

Query: 61  ENKVAENSFVVVML 74
           E  +   S V + L
Sbjct: 139 EYGLKPLSTVFMNL 152

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A Length = 115

 Score = 59.8 bits (145), Expect = 1e-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 = 56.5 bits (136), Expect = 8e-10
 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

>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 = 53.1 bits (127), Expect = 2e-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

>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 = 52.3 bits (125), 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

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 111

 Score = 52.5 bits (126), Expect = 5e-09
 Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 1   MKVFVKT-LKGTHFEIEVKPE-DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
           ++V       G   EI V+   + V  +K+ I         PA++Q L  +   LKD  +
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMS 86

Query: 59  LEENKVAENSFVVVML 74
           L    V     + + L
Sbjct: 87  LAHYNVGAGEILTLSL 102

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 51.3 bits (123), Expect = 8e-09
 Identities = 18/83 (21%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +     T  +++V  +   S++K+ I ++ G    P + Q ++++G  + +  TL 
Sbjct: 18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMYKGL-VPEDKTLR 72

Query: 61 ENKVAENSFVVVMLTKSKVSSSG 83
          E KV   + ++V+ +     SSG
Sbjct: 73 EIKVTSGAKIMVVGSTISGPSSG 95

>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 = 8e-09
 Identities = 24/91 (26%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTL 59
          + V +K L  T      +PED V  +K      Q       SQ  LI+QG++L+    TL
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ------ESQMKLIYQGRLLQDPARTL 61

Query: 60 EENKVAENSFVVVMLTKSKVSSSGASTVSAA 90
              +  N  +    +    + SG S  S  
Sbjct: 62 SSLNITNNCVIHCHRSPPGAAVSGPSASSGP 92

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 48.4 bits (115), Expect = 9e-08
 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

>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 = 47.6 bits (113), 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

>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

>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 = 47.9 bits (113), Expect = 1e-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

>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 = 44.0 bits (104), Expect = 2e-06
 Identities = 13/29 (44%), Positives = 18/29 (62%)

Query: 274 AGTLDFLRNSQQFQALRTMVQANPQILQQ 302
              L+FLRN  QFQ +R ++Q NP +L  
Sbjct: 1   GHPLEFLRNQPQFQQMRQIIQQNPSLLPA 29

>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 = 44.2 bits (104), Expect = 2e-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

>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 = 2e-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

>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 = 43.7 bits (103), Expect = 2e-06
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 273 GAGTLDFLRNSQQFQALRTMVQANPQILQQ 302
               L+FLRN  QFQ +R ++Q NP +L  
Sbjct: 2   SHMPLEFLRNQPQFQQMRQIIQQNPSLLPA 31

>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 = 5e-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

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 43.9 bits (103), Expect = 7e-06
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 3  VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-----ASQQMLIHQGKVLKDVT 57
          + +  + G   E    P D  SD+ K++      D         +   LI+QG+ L    
Sbjct: 20 LRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNV 79

Query: 58 TLEENKVAENSFVVVMLT 75
          TL   K+      V+ L 
Sbjct: 80 TLGALKLPFGKTTVMHLV 97

>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 = 42.8 bits (100), Expect = 1e-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

>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 = 44.9 bits (106), Expect = 2e-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

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 44.8 bits (105), Expect = 3e-05
 Identities = 14/72 (19%), Positives = 20/72 (27%)

Query: 94  QAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVS 153
           QAQ       T  Q       P    A   S  +   PP    P+        PA   + 
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70

Query: 154 SVSDVYGQAASN 165
              D    + ++
Sbjct: 71  QQIDQATTSMND 82

>2uv8_A Fatty acid synthase subunit alpha (FAS2); fatty acid biosynthesis, malonyl/palmitoyl transferase, phosphopantetheine, transferase; HET: GVL FMN; 3.10A {Saccharomyces cerevisiae} PDB: 2vkz_A* 3hmj_A* Length = 1887

 Score = 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 = 42.3 bits (99), 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 = 41.5 bits (97), 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 = 6e-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 = 40.8 bits (95), Expect = 4e-05
 Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 3/71 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + V    +      + V+P+  V+ +K  +    G   +P   Q  +   ++ +D  TL 
Sbjct: 27 VSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYG---FPPVLQQWVIGQRLARDQETLH 83

Query: 61 ENKVAENSFVV 71
           + V +N    
Sbjct: 84 SHGVRQNGDSA 94

>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 = 40.2 bits (93), 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

>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 = 42.3 bits (99), 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

>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 = 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 = 41.3 bits (96), 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 = 40.1 bits (93), Expect = 7e-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

>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 = 40.7 bits (95), Expect = 4e-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

>2lbc_A Ubiquitin carboxyl-terminal hydrolase 13; tandem UBA of USP13; NMR {Homo sapiens} Length = 126

 Score = 38.7 bits (89), Expect = 4e-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 = 38.1 bits (88), Expect = 5e-04
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 1  MKVFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTL 59
          M VF+   +  T    + K    V ++K+ +E +      P  +Q L    ++L D  TL
Sbjct: 1  MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKR---PPEEQRLYKDDQLLDDGKTL 57

Query: 60 EENKVAENS 68
           E      +
Sbjct: 58 GECGFTSQT 66

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 40.2 bits (93), 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

>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 83

 Score = 37.1 bits (86), Expect = 7e-04
 Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAG 229
           EA ++Q+ +MG   +      +AL+  + +  +A+E+L     + T   P++  S+G
Sbjct: 30  EAALRQLTEMG---FPENRATKALQLNHMSVPQAMEWLIEHAEDPTIDTPLSGPSSG 83

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} Length = 854

 Score = 39.9 bits (92), Expect = 8e-04
 Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 160 GQAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTA 219
           G  +++  A    E  V  I+ MG     R+  ++ALRA  N+ ERAV++++S I +  A
Sbjct: 708 GPGSTSAAADPPPEDCVTTIVSMGF---SRDQALKALRATNNSLERAVDWIFSHIDDLDA 764

Query: 220 VPPVARASAGGQAGNPPAQTQAQQPAAPAPT 250
              +  +     A +              P 
Sbjct: 765 EAAMDISEGRSAADSISESVPVGPKVRDGPG 795

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	308
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	100.0
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.82
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.8
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.8
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.8
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.79
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.79
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.78
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.78
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.77
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.77
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.77
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.77
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.77
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.76
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.76
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.76
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.76
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.75
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.75
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.75
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.75
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.75
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.75
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.75
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.75
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.75
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.75
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.75
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.74
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.74
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	99.74
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.74
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.74
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.74
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.73
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.73
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.72
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.72
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.72
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.72
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.72
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.72
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.72
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.71
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.55
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.71
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.7
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.69
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.69
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.69
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.68
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.68
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.68
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.67
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.67
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.67
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.67
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.67
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.67
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.67
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.67
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.66
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.66
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.65
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.64
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.64
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.64
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.64
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.63
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.62
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.62
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.61
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.6
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.6
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.58
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.58
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.55
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.54
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.53
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.5
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.48
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.46
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	99.45
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.44
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.44
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	99.44
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.43
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	99.43
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	99.41
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.41
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.39
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	99.38
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.37
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.36
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.36
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	99.36
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	99.35
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.34
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.32
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	99.31
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.3
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	99.3
2dna_A	67	Unnamed protein product; ubiquitin associated doma	99.3
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.27
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.26
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.24
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	99.23
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	99.21
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	99.21
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.21
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	99.21
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	99.2
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	99.19
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	99.18
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	99.18
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	99.14
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	99.1
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	99.09
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	99.05
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	99.03
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	99.02
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	99.01
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	99.01
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	98.93
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	98.81
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.77
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	98.74
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	98.7
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	98.65
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	98.64
2pjh_A	80	Protein NPL4, nuclear protein localization protein	98.62
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	98.62
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	98.54
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	98.54
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	98.48
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	98.46
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	98.44
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	98.39
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	98.35
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.35
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	98.25
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	98.23
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	98.18
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	98.13
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	98.07
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.05
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	98.0
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	97.99
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	97.93
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	97.88
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	97.81
2cos_A	54	Serine/threonine protein kinase LATS2; UBA domain,	97.8
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	97.8
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	97.54
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	97.45
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.37
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	96.87
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	96.57
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	96.5
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	96.41
2pwq_A	216	Ubiquitin conjugating enzyme; structural genomics	96.38
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	96.35
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	96.27
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	96.01
2dhy_A	67	CUE domain-containing protein 1; structural genomi	95.96
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	95.88
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	95.76
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	95.74
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	95.49
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	95.48
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	95.41
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	94.88
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	94.82
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	94.58
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	94.5
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	94.31
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	93.89
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	93.55
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	91.57
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	91.43
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	91.0
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	90.52
1ip9_A	85	BEM1 protein; ubiquitin alpha/beta roll, signaling	90.49
4dbg_B	162	Ring finger protein 31; ubiquitin fold, ubiquitina	90.43
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	90.18
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	90.18
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	89.94
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	89.91
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	89.33
1q02_A	52	Sequestosome 1; helical bundle, protein binding; N	88.83
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	88.65
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	88.39
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	88.36
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	88.36
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	87.87
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	87.67
2k5p_A	78	THis protein, thiamine-biosynthesis protein; NESG,	87.6
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	86.81
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	86.62
3qij_A	296	Protein 4.1; cytoskeleton, structural genomics, st	86.33
1tte_A	215	Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiq	84.87
2k9x_A	110	Tburm1, uncharacterized protein; unknown function;	84.68
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	84.24
2l52_A	99	Methanosarcina acetivorans SAMP1 homolog; beta-grA	83.63
2qjl_A	99	URM1, ubiquitin-related modifier 1; ubiquitin-like	83.56
1ixs_A	62	Holliday junction DNA helicase RUVA; heterodimeric	82.86
3onh_A	127	Ubiquitin-activating enzyme E1-like; ligase, SUMO	82.59
1wgr_A	100	Growth factor receptor-bound protein 7; RA domain,	81.76
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	81.71
1ufz_A	83	Hypothetical protein BAB28515; HBS1-like domain, s	80.78
1y8x_B	98	Ubiquitin-activating enzyme E1C; ubiquitin-conjuga	80.45

>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=1e-53  Score=412.28  Aligned_cols=260  Identities=32%  Similarity=0.561  Sum_probs=169.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+.++|+..+++++|||||+||+|+|+++|++|||++|++|++|+++.+..
T Consensus         8 M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~~~   87 (368)
T 1oqy_A            8 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKAG   87 (368)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCCSS
T ss_pred             EEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCCCC
Confidence            89999999999999999999999999999999532222999999999999999999999999999999997777776654


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q 021760           81 SSGASTVSAAPANQAQTTSSAPPTSTQPTTTSQTPAPTVAPPQSVPESAPPPAAPAPAPAPAPAPAPAPAPVSSVSDVYG  160 (308)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (308)
                      +.....++..+.+++++   .++.+   ......+++...+...  ..++   .....+..+|.......+..+....++
T Consensus        88 ~~~~~~~~~~~~~~~~~---~~~~~---~~~~~~~~~~~~~~~~--~~~~---~~~~~~~~~p~~~~~~~~~~~~~~~~~  156 (368)
T 1oqy_A           88 QGTSAPPEASPTAAPES---STSFP---PAPTSGMSHPPPAARE--DKSP---SEESAPTTSPESVSGSVPSSGSSGREE  156 (368)
T ss_dssp             SCCCCCSSCCCCCSSSC---CCSCC---CSSSCCCCCCCSSSSC--CCCC---SCSCCCCSSTTCSCCCSCSCCCSCCCC
T ss_pred             CCCCCCcccCCCCCccc---cCCCC---CCCCCCCCCCCccccc--cCCc---cccCCCCCCCCcccccccccccccccc
Confidence            33111111011110100   00000   0000000000000000  0000   000000001111001111111223456


Q ss_pred             ccccccccCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCCCCCCCCccccCCCCCCCCCCCccc
Q 021760          161 QAASNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQ  240 (308)
Q Consensus       161 ~~~s~l~~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~~~~~~~~~~~~~~~~~~~~~~~~~  240 (308)
                      .+.|+||+|+++|++|++||+||   |+|++|++|||++|||+|||||||++|||++.+....          .+. ...
T Consensus       157 ~~~s~l~~g~~~~~~i~~l~~MG---f~~~~~~~AL~a~~nn~~~A~e~L~~gip~~~~~~~~----------~~~-~~~  222 (368)
T 1oqy_A          157 DAASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIPGSPEPEHG----------SVQ-ESQ  222 (368)
T ss_dssp             CCCTTTCCTTTHHHHHHHHHTTT---CCSHHHHHHHHHSCSSTTHHHHTTTTSSTTCSSCCCC----------CCC-CCC
T ss_pred             cccccccCCcchHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCcccccccC----------Ccc-ccc
Confidence            77899999999999999999999   9999999999999999999999999999987442210          000 000


Q ss_pred             cCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCchHHhhChHHHHHHHHHHHhChhhHHHHHhcC
Q 021760          241 AQQPAAPAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQQWALIV  307 (308)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~lf~~a~~~~~~~~~~~~l~~Lr~~pqf~~lRq~vqqnP~~L~~~L~~~  307 (308)
                        .    ....                +.++++.++|+|||++|||++||++||+||++|++|||+|
T Consensus       223 --~----~~~~----------------~~~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~l~~~lq~l  267 (368)
T 1oqy_A          223 --V----SEQP----------------ATEAAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQL  267 (368)
T ss_dssp             --S----SCCC----------------CSSCCSCCTTHHHHHSHHHHHHHHSTTTCTTHHHHHHTTT
T ss_pred             --c----cccc----------------CccccccchHHHHhcChHHHHHHHHHHhChHHHHHHHHHH
Confidence              0    0000                1122356799999999999999999999999999999986

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.82  E-value=2.3e-20  Score=149.89  Aligned_cols=77  Identities=25%  Similarity=0.402  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|+.|.|+|++++||.+||++|+...|   +++++|||||+||+|+|+++|++|||++|++|+|++++++..
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   999999999999999999999999999999999999977644

>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=99.80  E-value=4.4e-19  Score=139.37  Aligned_cols=77  Identities=44%  Similarity=0.705  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHH---hCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETV---QGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~---~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|+.|.++|++++||.+||++|+..   .|   +++++|||+|+||.|+|+++|++|||++|++|+|+++++
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             CCC
Q 021760           78 KVS   80 (308)
Q Consensus        78 k~~   80 (308)
                      +..
T Consensus        78 ~~~   80 (95)
T 1uel_A           78 KAV   80 (95)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            544

>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=99.80  E-value=1.9e-19  Score=139.42  Aligned_cols=75  Identities=28%  Similarity=0.380  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+.++|   +++++|||||+||.|+|+++|++|+| +|++|||+++.+..
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            78999999999999999999999999999999999   99999999999999999999999999 89999999986543

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.80  E-value=2.8e-19  Score=135.02  Aligned_cols=74  Identities=24%  Similarity=0.320  Sum_probs=71.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|++|.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|||++|++|+++++.+
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

>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=99.79  E-value=2.7e-19  Score=138.63  Aligned_cols=78  Identities=35%  Similarity=0.518  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++.+...
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   999999999999999999999999999999999999987654


Q ss_pred             C
Q 021760           81 S   81 (308)
Q Consensus        81 ~   81 (308)
                      .
T Consensus        78 ~   78 (88)
T 4fbj_B           78 G   78 (88)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.79  E-value=4.8e-19  Score=135.25  Aligned_cols=76  Identities=36%  Similarity=0.640  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHH---hCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETV---QGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~---~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|+.|.++|++++||.+||++|+..   .|   +++++|||+|+||.|+|+++|++|||++|++|||+++++
T Consensus         6 m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~~   82 (85)
T 2wyq_A            6 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDA---FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKT   82 (85)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTT---CCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC--
T ss_pred             EEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccC---CCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcCC
Confidence            789999999999999999999999999999998   67   999999999999999999999999999999999999876


Q ss_pred             CC
Q 021760           78 KV   79 (308)
Q Consensus        78 k~   79 (308)
                      ++
T Consensus        83 ~~   84 (85)
T 2wyq_A           83 KA   84 (85)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.78  E-value=5e-19  Score=137.67  Aligned_cols=74  Identities=39%  Similarity=0.646  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.+
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   999999999999999999999999999999999998864

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.78  E-value=5.3e-19  Score=136.26  Aligned_cols=72  Identities=36%  Similarity=0.517  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEe-cCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV-LKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKi-L~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+||++.|+.|.|+|++++||.+||++|+...|   +|+++|||+|+||. |+|+++|++|||++|++|+|+++
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

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.77  E-value=5e-19  Score=140.60  Aligned_cols=74  Identities=27%  Similarity=0.459  Sum_probs=69.0

Q ss_pred             CEEEEEeCCCcEEEE--EeCCCCcHHHHHHHH-HHHhCCCCCCCCCeEEEeCCEecCCCCChhhhcc-CCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEI--EVKPEDKVSDVKKNI-ETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~l--eV~~~~TV~~LK~~I-~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygI-k~g~~I~v~v~k   76 (308)
                      |+|+||+++|++|.+  +|++++||.+||++| +...|   +++++|||||+||+|+|+.+|++|+| ++|++|+||+++
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 021760           77 S   77 (308)
Q Consensus        77 ~   77 (308)
                      +
T Consensus        97 p   97 (98)
T 4a20_A           97 N   97 (98)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.77  E-value=1.9e-18  Score=138.34  Aligned_cols=76  Identities=26%  Similarity=0.324  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+.+|+ |.|+|++++||.+||++|+..+|   +++++|||+|+||+|+|+++|++|+|++|++|||+++++..+
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

>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=99.77  E-value=8.5e-19  Score=137.53  Aligned_cols=71  Identities=27%  Similarity=0.379  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+||++.|+++.|+|++++||.+||++|+++.|   +|+++|||+|+||+|+|+.+|++|+|++|++|+++.
T Consensus        22 IqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~G---ip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~~   92 (93)
T 3plu_A           22 IEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIG---TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   92 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhC---CCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEEe
Confidence            68999999999999999999999999999999999   999999999999999999999999999999999863

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A

Probab=99.77  E-value=1.9e-18  Score=135.07  Aligned_cols=77  Identities=36%  Similarity=0.589  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|+.|.|+|++++||.+||++|+..+|   +++++|||+|+||.|+|+++|++|+|++|++|+|+++.+...
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   999999999999999999999999999999999999877543

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.77  E-value=5.1e-19  Score=137.58  Aligned_cols=74  Identities=28%  Similarity=0.455  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCcEEEEEeC--CCCcHHHHHHHH-HHHhCCCCCCCCCeEEEeCCEecCCCCChhhhcc-CCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVK--PEDKVSDVKKNI-ETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~--~~~TV~~LK~~I-~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygI-k~g~~I~v~v~k   76 (308)
                      |+|+||+++|++|.|+|+  +++||.+||++| +...|   +|+++|||||+||+|+|+.+|++|+| .+|++|+|++++
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKA---SHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSC---SSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcC---CChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            899999999999988755  999999999999 88889   99999999999999999999999999 699999999875


Q ss_pred             C
Q 021760           77 S   77 (308)
Q Consensus        77 ~   77 (308)
                      .
T Consensus        79 ~   79 (87)
T 2lxa_A           79 N   79 (87)
T ss_dssp             C
T ss_pred             C
Confidence            3

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.76  E-value=1.8e-18  Score=136.59  Aligned_cols=75  Identities=36%  Similarity=0.577  Sum_probs=72.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|||+|+||+|+|+++|++|+|++|++|+|+++.+.
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   9999999999999999999999999999999999998753

>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=99.76  E-value=3e-18  Score=127.38  Aligned_cols=74  Identities=36%  Similarity=0.562  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+.+|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+++++.+
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   999999999999999999999999999999999998865

>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=99.76  E-value=1.4e-18  Score=133.36  Aligned_cols=75  Identities=36%  Similarity=0.546  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|+.|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
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=99.76  E-value=2.5e-18  Score=129.31  Aligned_cols=73  Identities=22%  Similarity=0.349  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCcEE-EEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHF-EIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~-~le-V~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+++|+.+ .++ |++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+++++.
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            7999999999985 999 9999999999999999999   99999999999999999999999999999999999875

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...

Probab=99.75  E-value=5.4e-18  Score=125.94  Aligned_cols=74  Identities=38%  Similarity=0.614  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+.+|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|++|++|+++++.+
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~---i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~   74 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLR   74 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999998865

>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=99.75  E-value=2.6e-18  Score=130.87  Aligned_cols=76  Identities=36%  Similarity=0.546  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++|+++.|+|++++||.+||++|+...+   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+..
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

>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=99.75  E-value=1.4e-18  Score=138.30  Aligned_cols=71  Identities=17%  Similarity=0.281  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+||++.|+++.|+|++++||.+||++|+++.|   +++++|||||.||+|+|+.+|++|||+++++|+|+.
T Consensus        29 m~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~G---ip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHC---CCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhC---CCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEe
Confidence            78999999999999999999999999999999999   999999999999999999999999999999999864

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=3.3e-18  Score=129.16  Aligned_cols=73  Identities=27%  Similarity=0.424  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.
T Consensus         8 m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~---i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A            8 MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLN---VPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             EEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTC---CCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            78999999999999999999999999999999999   99999999999999999999999999999999999875

>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=99.75  E-value=2.8e-18  Score=137.56  Aligned_cols=76  Identities=20%  Similarity=0.364  Sum_probs=72.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++|+.|.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|||++++++.
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

>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=99.75  E-value=2.9e-18  Score=129.47  Aligned_cols=74  Identities=19%  Similarity=0.276  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|+++.++|++++||.+||++|+++.|   +++++|||+|+|+.|+|+++|++|+|++|++|+++++.+
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~g---i~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~   77 (79)
T 2uyz_B            4 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQT   77 (79)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHC---CCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEecc
Confidence            78999999999999999999999999999999999   999999999999999999999999999999999999865

>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=99.75  E-value=7.9e-18  Score=129.83  Aligned_cols=76  Identities=20%  Similarity=0.295  Sum_probs=72.1

Q ss_pred             CEEEEEeCCC-cEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKG-THFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~g-k~~~l-eV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++| ++|.| +|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|+++++|||+++.+.
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            7899999999 79999 59999999999999999999   9999999999999999999999999999999999998765


Q ss_pred             C
Q 021760           79 V   79 (308)
Q Consensus        79 ~   79 (308)
                      .
T Consensus        85 G   85 (89)
T 1wy8_A           85 G   85 (89)
T ss_dssp             S
T ss_pred             C
Confidence            4

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.75  E-value=3.6e-18  Score=131.62  Aligned_cols=71  Identities=30%  Similarity=0.411  Sum_probs=68.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+++|++||| +|++||+++|
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

>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=99.75  E-value=4.7e-18  Score=129.27  Aligned_cols=76  Identities=37%  Similarity=0.577  Sum_probs=72.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...+   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+..
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

>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=99.75  E-value=6.3e-18  Score=129.70  Aligned_cols=75  Identities=29%  Similarity=0.467  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|+.|.++|++++||.+||++|++..|   +++++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999998764

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.75  E-value=3.5e-18  Score=132.24  Aligned_cols=75  Identities=24%  Similarity=0.310  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++.+.
T Consensus         5 m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~g   79 (88)
T 2hj8_A            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG   79 (88)
T ss_dssp             EEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTC---SCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC---
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhC---CChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCC
Confidence            78999999999999999999999999999999999   9999999999999999999999999999999999998654

>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=99.74  E-value=7e-18  Score=131.75  Aligned_cols=76  Identities=20%  Similarity=0.215  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHh--CCCCCCCCCeEEEeCCEecCCCCChhhh--ccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQ--GSDVYPASQQMLIHQGKVLKDVTTLEEN--KVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk--~~~leV~~~~TV~~LK~~I~~~~--g~~~ip~~~qkLIy~GKiL~D~~tL~dy--gIk~g~~I~v~v   74 (308)
                      |+|+||+.+++  .+.|+|++++||.+||++|+..+  +   +++++|||||+||+|+|+++|++|  +|+++++|||++
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            78999999988  67788889999999999999998  8   999999999999999999999999  999999999998


Q ss_pred             ecCCC
Q 021760           75 TKSKV   79 (308)
Q Consensus        75 ~k~k~   79 (308)
                      +.+..
T Consensus        85 ~~~gg   89 (93)
T 1wgd_A           85 NVKSG   89 (93)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=99.74  E-value=7.2e-18  Score=130.59  Aligned_cols=75  Identities=33%  Similarity=0.604  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|+++.++|++++||.+||++|++..|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++.+.
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

>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=99.74  E-value=1.5e-18  Score=120.93  Aligned_cols=49  Identities=57%  Similarity=1.000  Sum_probs=47.3

Q ss_pred             ccccCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 021760          165 NLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  216 (308)
Q Consensus       165 ~l~~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~  216 (308)
                      +|++|+.+++.|++|++||   |+|++|++|||+++||+|||||||++|||+
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

>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=99.74  E-value=7.7e-18  Score=131.90  Aligned_cols=74  Identities=27%  Similarity=0.300  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCC-CChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~-~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++|+.|.|+|++++||.+||++|+..     . +++|||||+||+|+|+ ++|++|+|++|++|||++++++.
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~-----~-~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~~~   81 (95)
T 1wia_A            8 INVRLKFLNDTEELAVARPEDTVGTLKSKYFPG-----Q-ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGA   81 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHSSS-----T-TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhh-----C-cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCCC
Confidence            789999999999999999999999999999876     3 7899999999999999 99999999999999999987654


Q ss_pred             C
Q 021760           80 S   80 (308)
Q Consensus        80 ~   80 (308)
                      .
T Consensus        82 ~   82 (95)
T 1wia_A           82 A   82 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.74  E-value=3.9e-18  Score=137.03  Aligned_cols=76  Identities=21%  Similarity=0.228  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC---------------CCeEEEeCCEecC-CCCChhhhcc
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA---------------SQQMLIHQGKVLK-DVTTLEENKV   64 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~---------------~~qkLIy~GKiL~-D~~tL~dygI   64 (308)
                      |+|+||+++|++|.|+|++++||.+||++|++..+   +++               ++|+|||+||+|. |+++|++|||
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 6699999999


Q ss_pred             CCCCEEEEEEecCCC
Q 021760           65 AENSFVVVMLTKSKV   79 (308)
Q Consensus        65 k~g~~I~v~v~k~k~   79 (308)
                      ++|++|||+.+.+..
T Consensus        85 ~~g~~l~lv~~lr~~   99 (105)
T 1v2y_A           85 RNRDEVSFIKKLGQK   99 (105)
T ss_dssp             CSSEEEEEEECSCSC
T ss_pred             CCCCEEEEEehhccC
Confidence            999999999998765

>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=99.74  E-value=6.3e-18  Score=133.37  Aligned_cols=75  Identities=19%  Similarity=0.268  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +++++|||||+|+.|+|+++|++|+|+++++|+|+++.+.
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=99.73  E-value=1.2e-17  Score=131.17  Aligned_cols=75  Identities=31%  Similarity=0.370  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCC-CChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~-~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++| ++.|+|++++||.+||++|+...|   +|+++|||+|+||+|+|+ ++|++|||++|++|+|+++.+..
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

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.73  E-value=1.6e-17  Score=124.20  Aligned_cols=71  Identities=30%  Similarity=0.517  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+||+ +|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+.+
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            6899998 999999999999999999999999999   9999999999999999999999999999999999865

>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=99.72  E-value=1.5e-17  Score=132.33  Aligned_cols=72  Identities=19%  Similarity=0.146  Sum_probs=64.5

Q ss_pred             EEEEeCC----CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            3 VFVKTLK----GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         3 I~Vktl~----gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |.|+..+    +++|.|+|++++||.+||++|+++.|   +|+++|||||+||+|+|++||++|+|++|++|+|| +.+.
T Consensus        18 i~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~g---ip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti~vl-~lrg   93 (100)
T 1wju_A           18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG---LQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVL-ELKQ   93 (100)
T ss_dssp             EEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTT---CCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEE-CCCC
T ss_pred             EEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHC---cCHHHeEEEeCCeECCCCCcHHHcCCCCCCEEEEE-EECC
Confidence            5666655    77999999999999999999999999   99999999999999999999999999999999555 4443

>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=99.72  E-value=8e-18  Score=131.95  Aligned_cols=75  Identities=27%  Similarity=0.322  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+. |+.|.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|++|++|||+++.+..
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            78999988 89999999999999999999999999   99999999999999999999999999999999999887654

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.72  E-value=2.7e-17  Score=129.49  Aligned_cols=76  Identities=37%  Similarity=0.583  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+.+|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.+..
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~g---i~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~gG   76 (98)
T 1yx5_B            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (98)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCCC
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999987643

>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=99.72  E-value=2e-17  Score=131.59  Aligned_cols=76  Identities=20%  Similarity=0.334  Sum_probs=69.8

Q ss_pred             CEEEEEeCCC----cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCC-CChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKG----THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~g----k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~-~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+||+..+    ++|.|+|++++||.+||++|+.+.|   +++++|||+|+||.|+|+ ++|++|+|++|++|||+.+
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            7899998754    7999999999999999999999999   999999999999999988 7999999999999999987


Q ss_pred             cCCC
Q 021760           76 KSKV   79 (308)
Q Consensus        76 k~k~   79 (308)
                      .+..
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=99.72  E-value=2e-17  Score=133.76  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|+.|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++.+.
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

>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=99.72  E-value=1.8e-17  Score=131.70  Aligned_cols=76  Identities=26%  Similarity=0.324  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+.+|+ |.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.+..+
T Consensus        23 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~~p   98 (100)
T 1yqb_A           23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRA   98 (100)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCSC
T ss_pred             EEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHC---cChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCCCC
Confidence            78999999886 79999999999999999999999   999999999999999999999999999999999999876543

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.72  E-value=2.4e-17  Score=131.09  Aligned_cols=74  Identities=30%  Similarity=0.353  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+. |+.|.|+|++++||.+||++|+...|   +++++|||+|+||+|+|+++|++|||++|++|+|+++++.
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            78999988 88999999999999999999999999   9999999999999999999999999999999999988654

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.71  E-value=2.6e-17  Score=136.02  Aligned_cols=76  Identities=29%  Similarity=0.329  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||++ |+.|.|+|++++||.+||++|+...|   +++++|||||+||+|+|+++|++|+|++|++|+|+++++...
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=99.55  E-value=6.4e-19  Score=131.80  Aligned_cols=74  Identities=27%  Similarity=0.402  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+.+|++|.++|++++||.+||++|+...|   +++++|+|+|+||.|+|+++|++|||++|++|+++++.+
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlr   74 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQG---VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPR   74 (76)
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999865

>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=99.71  E-value=5.1e-17  Score=132.75  Aligned_cols=77  Identities=21%  Similarity=0.226  Sum_probs=65.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCC---CC--CCCCeEEEeCCEecCCCCChhhhccCCCCE--EEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSD---VY--PASQQMLIHQGKVLKDVTTLEENKVAENSF--VVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~---~i--p~~~qkLIy~GKiL~D~~tL~dygIk~g~~--I~v~   73 (308)
                      |+|+||+++|+++.|+|++++||.+||++|+..++.+   .+  ++++|||||.||+|+|+++|++|+|+.+++  |||+
T Consensus        17 m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlhLv   96 (116)
T 1wgh_A           17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   96 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEE
Confidence            7899999999999999999999999999999954321   14  699999999999999999999999988764  5555


Q ss_pred             EecC
Q 021760           74 LTKS   77 (308)
Q Consensus        74 v~k~   77 (308)
                      ++..
T Consensus        97 lr~~  100 (116)
T 1wgh_A           97 ARET  100 (116)
T ss_dssp             ECSS
T ss_pred             ccCC
Confidence            5543

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.70  E-value=3.7e-17  Score=128.01  Aligned_cols=72  Identities=22%  Similarity=0.352  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+  |+.+.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|++|++|+|+++.+
T Consensus        20 m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~   91 (93)
T 2l7r_A           20 MQLFVRA--QELHTFEVTGQETVAQIKAHVASLEG---IAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRML   91 (93)
T ss_dssp             CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHT---CCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCC
T ss_pred             EEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhC---cChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            7899997  89999999999999999999999999   999999999999999999999999999999999998865

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.69  E-value=1e-16  Score=138.89  Aligned_cols=77  Identities=35%  Similarity=0.549  Sum_probs=73.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|||+++.+...
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   999999999999999999999999999999999999977543

>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=99.69  E-value=8.5e-17  Score=129.13  Aligned_cols=75  Identities=23%  Similarity=0.151  Sum_probs=68.8

Q ss_pred             CEEEEEeCCC---cEEEEEeC--------C-CCcHHHHHHHHHHHh--CCCCCCCCC-eEEEeCCEecCCCCChhhhccC
Q 021760            1 MKVFVKTLKG---THFEIEVK--------P-EDKVSDVKKNIETVQ--GSDVYPASQ-QMLIHQGKVLKDVTTLEENKVA   65 (308)
Q Consensus         1 M~I~Vktl~g---k~~~leV~--------~-~~TV~~LK~~I~~~~--g~~~ip~~~-qkLIy~GKiL~D~~tL~dygIk   65 (308)
                      |+|+||+.++   ++|.|+|+        + ++||.+||++|+...  |   +++++ |||||+||+|+|+++|++|+|+
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             CCCEEEEEEecCC
Q 021760           66 ENSFVVVMLTKSK   78 (308)
Q Consensus        66 ~g~~I~v~v~k~k   78 (308)
                      +|++|||+++.+.
T Consensus        90 ~g~~i~lv~~~~~  102 (107)
T 1x1m_A           90 PGSTVHVLRKSWS  102 (107)
T ss_dssp             TTCEEEEEESSCC
T ss_pred             CCCEEEEEeCCCC
Confidence            9999999987643

>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=99.69  E-value=5.3e-17  Score=128.10  Aligned_cols=72  Identities=21%  Similarity=0.276  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~-~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+|| +.|+.| .|+|++++||.+||++|+..+|   +++++|||+|+||+|+|+ +|++|+|++|++|+||.+..
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 99999999999999987654

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.68  E-value=1.7e-16  Score=128.15  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=71.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|++|++|+|+++.+.
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=99.68  E-value=7.2e-17  Score=132.03  Aligned_cols=72  Identities=22%  Similarity=0.290  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccC-------CCCEEEE
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVA-------ENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk-------~g~~I~v   72 (308)
                      |.|+|+...++ ++.|+|++++||.+||++|+.+.|   +|+++|||||+||+|+|+++|++|||+       ++++||+
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 021760           73 MLT   75 (308)
Q Consensus        73 ~v~   75 (308)
                      ++|
T Consensus        78 ~lr   80 (118)
T 2fnj_B           78 AFR   80 (118)
T ss_dssp             EEB
T ss_pred             Eec
Confidence            998

>4ajy_B Transcription elongation factor B polypeptide 2; E3 ubiquitin ligase, transcription factor, hypoxic signaling transcription; 1.73A {Homo sapiens} PDB: 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A 3ztc_A* 3ztd_A* 3zun_A* 1lm8_B 4b95_A* 2fnj_B 4b9k_A* 4awj_A*

Probab=99.68  E-value=7.2e-17  Score=131.78  Aligned_cols=73  Identities=22%  Similarity=0.286  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCC-------CCEEEE
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAE-------NSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~-------g~~I~v   72 (308)
                      |.|+|+...++ ++.++|++++||.+||++|+.+.|   +|+++|||||+||+|+|++||++|||++       +++||+
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            78898888777 788999999999999999999999   9999999999999999999999999999       999999


Q ss_pred             EEec
Q 021760           73 MLTK   76 (308)
Q Consensus        73 ~v~k   76 (308)
                      ++|.
T Consensus        78 vlr~   81 (118)
T 4ajy_B           78 AFRA   81 (118)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.67  E-value=2.4e-16  Score=122.62  Aligned_cols=73  Identities=29%  Similarity=0.408  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCC-----CcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCC-CCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPE-----DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKD-VTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~-----~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D-~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+||+ .|+.|.|+|+++     +||.+||++|+...|   +|+++|||+|+||.|+| +++|++|+|++|++|||+.
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   99999999999999998 6689999999999999987


Q ss_pred             ecC
Q 021760           75 TKS   77 (308)
Q Consensus        75 ~k~   77 (308)
                      +..
T Consensus        84 ~~~   86 (92)
T 1wxv_A           84 KKN   86 (92)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            654

>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=99.67  E-value=1.5e-16  Score=131.55  Aligned_cols=79  Identities=16%  Similarity=0.262  Sum_probs=67.7

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhC--CCCCCC--CCeEEEeCCEecCCCCChhhhccCCC------CE
Q 021760            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQG--SDVYPA--SQQMLIHQGKVLKDVTTLEENKVAEN------SF   69 (308)
Q Consensus         1 M~I~Vktl~gk~~-~leV~~~~TV~~LK~~I~~~~g--~~~ip~--~~qkLIy~GKiL~D~~tL~dygIk~g------~~   69 (308)
                      |+|+||+++|+.| .+++++++||.+||++|+..++  ++.+|+  ++|||||+||+|+|++||++|+|.+|      .+
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 6999999999999999976543  122776  79999999999999999999999998      56


Q ss_pred             EEEEEecCCC
Q 021760           70 VVVMLTKSKV   79 (308)
Q Consensus        70 I~v~v~k~k~   79 (308)
                      |||+++.+..
T Consensus        97 mhlVlrl~g~  106 (126)
T 1se9_A           97 MHVIIQAPVT  106 (126)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEeccCCc
Confidence            8888876643

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.67  E-value=7.8e-17  Score=128.11  Aligned_cols=71  Identities=20%  Similarity=0.239  Sum_probs=64.1

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHh-CCCCCCCCCeEEEeCCEecCCCCChhhh--ccCCCCEEEEE
Q 021760            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQ-GSDVYPASQQMLIHQGKVLKDVTTLEEN--KVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk--~~~leV~~~~TV~~LK~~I~~~~-g~~~ip~~~qkLIy~GKiL~D~~tL~dy--gIk~g~~I~v~   73 (308)
                      |+|+||+++|+  .+.|+|++++||.+||++|+.+. |.  .++++|||||+||+|+|+++|++|  +|+++++|+|+
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  67899999999999999999864 51  446999999999999999999999  99999999974

>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=99.67  E-value=1.9e-16  Score=134.61  Aligned_cols=75  Identities=24%  Similarity=0.310  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|+++.++|++++||.+||++|+...|   +|+++|||+|+|+.|+|+++|++|+|++|++||++++.+.
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~G  156 (159)
T 3rt3_B           82 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG  156 (159)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC-
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHC---CCHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            78999999999999999999999999999999999   9999999999999999999999999999999999998765

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.67  E-value=4.1e-17  Score=129.93  Aligned_cols=72  Identities=29%  Similarity=0.517  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+ .|+.|.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.
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            5688886 899999999999999999999999999   99999999999999999999999999999999998764

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.67  E-value=1.1e-16  Score=132.44  Aligned_cols=77  Identities=21%  Similarity=0.226  Sum_probs=65.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCC---CC--CCCCeEEEeCCEecCCCCChhhhccCCCCE--EEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSD---VY--PASQQMLIHQGKVLKDVTTLEENKVAENSF--VVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~---~i--p~~~qkLIy~GKiL~D~~tL~dygIk~g~~--I~v~   73 (308)
                      |+|+||+++|+++.|+|++++||.+||++|+..++.+   .+  ++++|||||+||+|+|+++|++|+|+++++  |||+
T Consensus        18 m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tlhlv   97 (125)
T 2gow_A           18 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   97 (125)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEE
Confidence            6899999999999999999999999999999843211   15  489999999999999999999999998885  5555


Q ss_pred             EecC
Q 021760           74 LTKS   77 (308)
Q Consensus        74 v~k~   77 (308)
                      ++.+
T Consensus        98 ~r~~  101 (125)
T 2gow_A           98 ARET  101 (125)
T ss_dssp             ECSC
T ss_pred             ecCC
Confidence            5543

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.67  E-value=3.1e-16  Score=127.40  Aligned_cols=76  Identities=33%  Similarity=0.522  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      ++|+||+++|+.+.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++.+..
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            47999999999999999999999999999999999   99999999999999999999999999999999999987654

>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=99.67  E-value=2.3e-16  Score=122.70  Aligned_cols=72  Identities=25%  Similarity=0.409  Sum_probs=68.2

Q ss_pred             CEEEEEeCCCcEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE---eCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~l-eV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI---y~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||. .|+.|.| +|++++||.+||++|++.+|   +|+++|||+   |+||+|+|+.+|++|+|++|++|+||.+.
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

>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=99.66  E-value=1.9e-16  Score=127.74  Aligned_cols=76  Identities=24%  Similarity=0.324  Sum_probs=71.8

Q ss_pred             CEEEEEeC---CCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTL---KGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl---~gk~~~leV~~-~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+|++.   +|+.+.++|++ ++||.+||++|+...|   +|+++|||+|+||+|+|+++|++|+|++|++|+|+++.
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 021760           77 SKV   79 (308)
Q Consensus        77 ~k~   79 (308)
                      +..
T Consensus       105 ~GG  107 (111)
T 1we6_A          105 RSG  107 (111)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.66  E-value=3.8e-16  Score=120.31  Aligned_cols=70  Identities=24%  Similarity=0.436  Sum_probs=66.2

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      +++++++|+.|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|||++|++|+|+++
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            456778999999999999999999999999999   9999999999999999999999999999999999864

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.65  E-value=4.2e-16  Score=134.47  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|+++++|+|+++.+
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

>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=99.64  E-value=2e-16  Score=124.43  Aligned_cols=71  Identities=23%  Similarity=0.365  Sum_probs=65.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+|| +.+++|.|+|++++||.+||++|+..+|   +|+++|||+|+||+| |+.+|++|+|+++++||||.++
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            678898 6789999999999999999999999999   999999999999999 5569999999999999998654

>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=99.64  E-value=5.4e-16  Score=131.78  Aligned_cols=73  Identities=30%  Similarity=0.420  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE-e-CCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-H-QGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI-y-~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+++|++|.++|++++||.+||++|+...|   +|+++|||+ | +|+.|+|+++|++|+|++|++|+++++.
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=99.64  E-value=3.7e-16  Score=137.77  Aligned_cols=77  Identities=35%  Similarity=0.543  Sum_probs=73.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+...
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            79999999999999999999999999999999999   999999999999999999999999999999999999876543

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.64  E-value=6.8e-16  Score=123.84  Aligned_cols=73  Identities=19%  Similarity=0.250  Sum_probs=68.5

Q ss_pred             CEEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhcc-CCCCEEEEEEec
Q 021760            1 MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-AENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~g--k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygI-k~g~~I~v~v~k   76 (308)
                      |+|+|++..+  .++.|+|++++||.+||++|++++|   +|+++|||||+|+.|+|+++|.+||| ++|++||+++-.
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            6899999874  6899999999999999999999999   99999999999999999999999999 599999999864

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=8.9e-16  Score=124.91  Aligned_cols=73  Identities=25%  Similarity=0.282  Sum_probs=67.1

Q ss_pred             EEEEE-eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            2 KVFVK-TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         2 ~I~Vk-tl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      .|+|+ ...++.|.++++++.||.+||++|+...+   +|.++|+|||+||+|+|+.||++|||++|.+|||+++..
T Consensus        17 tvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~---iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~   90 (118)
T 2daf_A           17 TVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLG---IPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFST   90 (118)
T ss_dssp             EEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHT---CCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEES
T ss_pred             EEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhC---CChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecC
Confidence            45555 45688999999999999999999999999   999999999999999999999999999999999998864

>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=99.62  E-value=2.7e-17  Score=136.08  Aligned_cols=76  Identities=36%  Similarity=0.555  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+.+|++|||++|++|+|+++.+..
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=99.62  E-value=2.3e-15  Score=125.98  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|+.+.++|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+++|++|||++|++|+|+.+.+
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

>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=99.61  E-value=2.6e-15  Score=125.63  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=71.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|+.|.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++.+.
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=99.60  E-value=1.4e-15  Score=131.18  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |.|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|||+|+|+.|+|+++|.+|+|++|++|||+++.+.
T Consensus        97 ~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~q~L~~~g~~L~D~~tL~~y~i~~g~tl~l~~rlrg  171 (172)
T 3u30_A           97 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  171 (172)
T ss_dssp             EEEEEEESSCCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCCEEETTEECCTTSBSGGGTCCTTCEEEECC----
T ss_pred             ccceeecccCcceeEEecCCCCHHHHHHHHHHHhC---CCceeEEEEECCccCCCCCcHHHhCCCCCCEEEEEEecCC
Confidence            57899999999999999999999999999999999   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=99.60  E-value=3.2e-15  Score=121.28  Aligned_cols=76  Identities=24%  Similarity=0.338  Sum_probs=69.2

Q ss_pred             CEEEEEeC----------CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEE
Q 021760            1 MKVFVKTL----------KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFV   70 (308)
Q Consensus         1 M~I~Vktl----------~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I   70 (308)
                      |.|+|+..          +|+++.|+|++++||.+||++|+...|   +++++|||+|+|+.|+|+++|++|+|++|++|
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            35667654          578999999999999999999999999   99999999999999999999999999999999


Q ss_pred             EEEEecCCC
Q 021760           71 VVMLTKSKV   79 (308)
Q Consensus        71 ~v~v~k~k~   79 (308)
                      ||+++.+..
T Consensus       103 ~lv~rl~GG  111 (115)
T 1we7_A          103 HLALKERSG  111 (115)
T ss_dssp             EEEECCCSC
T ss_pred             EEEEEcCCC
Confidence            999987653

>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=99.58  E-value=1.6e-16  Score=135.53  Aligned_cols=76  Identities=36%  Similarity=0.555  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+|++++|++|.|+|++++||.+||.+|+...|   +|+++|+|+|+|++|+|+.+|++|+|++|++|+|+++.+..
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=99.58  E-value=1.7e-15  Score=117.78  Aligned_cols=69  Identities=20%  Similarity=0.265  Sum_probs=63.4

Q ss_pred             CEEEEEeCCCcEE--EE-EeCCCCcHHHHHHHHHHH-hCCCCCCCCCeEEEeC--CEecCCCCChhhhccCCCCEEEE
Q 021760            1 MKVFVKTLKGTHF--EI-EVKPEDKVSDVKKNIETV-QGSDVYPASQQMLIHQ--GKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~gk~~--~l-eV~~~~TV~~LK~~I~~~-~g~~~ip~~~qkLIy~--GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      |+|+||+++|+++  .| +|++++||.+||++|++. .|   +++++|||+|.  ||+|+|+++|++|+|+++++|||
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=99.55  E-value=6.7e-15  Score=117.16  Aligned_cols=71  Identities=20%  Similarity=0.314  Sum_probs=65.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe--CCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy--~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |.++++.+.|++|.|+|++++||.+||++|++++|   +|+++|||+|  .|+ |+|+.+|++|+|+.|++|||++.
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            56777789999999999999999999999999999   9999999996  566 99999999999999999998764

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.54  E-value=5.9e-15  Score=114.26  Aligned_cols=73  Identities=15%  Similarity=0.070  Sum_probs=64.3

Q ss_pred             EEEEE--eCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe-------CCEecCCCCChhhhccCCCCEEEE
Q 021760            2 KVFVK--TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-------QGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vk--tl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy-------~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      +|.|.  ..+.+.+++.+++++||.+||++|+..+|   +|+++|||||       .|+.|+|+++|++|||++|++|||
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            34443  44667789999999999999999999999   9999999997       488999999999999999999999


Q ss_pred             EEecC
Q 021760           73 MLTKS   77 (308)
Q Consensus        73 ~v~k~   77 (308)
                      +-+.+
T Consensus        81 vd~~P   85 (86)
T 4b6w_A           81 VDLQP   85 (86)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            97654

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.53  E-value=1.8e-14  Score=135.53  Aligned_cols=74  Identities=38%  Similarity=0.618  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|+.+.|+|++++||.+||++|+...|   +++++|||+|+||+|+|+++|++|+|+++++|+|++|.+
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

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.50  E-value=8.2e-14  Score=109.77  Aligned_cols=70  Identities=17%  Similarity=0.195  Sum_probs=62.2

Q ss_pred             CEEEEEeCCC--cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC--CE---ec-CCCCChhhhccCCCCEEEE
Q 021760            1 MKVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GK---VL-KDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~g--k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~--GK---iL-~D~~tL~dygIk~g~~I~v   72 (308)
                      ++|+|+...+  +.++++|++++||.+||++|+..+|   +|+++|||+|.  |+   .| +|+++|++|||++|++|+|
T Consensus        16 v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~G---iP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihl   92 (95)
T 2kjr_A           16 IKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTG---GCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHV   92 (95)
T ss_dssp             EEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHC---SCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEE
T ss_pred             EEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHC---cCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEE
Confidence            3677887655  4889999999999999999999999   99999999997  55   34 8999999999999999998


Q ss_pred             E
Q 021760           73 M   73 (308)
Q Consensus        73 ~   73 (308)
                      +
T Consensus        93 v   93 (95)
T 2kjr_A           93 V   93 (95)
T ss_dssp             E
T ss_pred             E
Confidence            7

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.48  E-value=4.4e-14  Score=113.33  Aligned_cols=71  Identities=20%  Similarity=0.234  Sum_probs=65.5

Q ss_pred             CEEEEEeCCCcEEEEEeC-CCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCE-----------e----cCCCCChhhhcc
Q 021760            1 MKVFVKTLKGTHFEIEVK-PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-----------V----LKDVTTLEENKV   64 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~-~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GK-----------i----L~D~~tL~dygI   64 (308)
                      |+|+||+.+|+. .|+|+ +++||.+||++|+.++|   +++++|+|+|.|+           .    ++|+++|++|||
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           3    589999999999


Q ss_pred             CCCCEEEEEEe
Q 021760           65 AENSFVVVMLT   75 (308)
Q Consensus        65 k~g~~I~v~v~   75 (308)
                      ++|++|||+..
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

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.46  E-value=1.4e-13  Score=108.89  Aligned_cols=71  Identities=11%  Similarity=0.040  Sum_probs=62.3

Q ss_pred             EEEEEeCC--CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC---Ee----cCCCCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLK--GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~--gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G---Ki----L~D~~tL~dygIk~g~~I~v   72 (308)
                      +|+|+...  ++.++++|++++||.+||++|+..+|   +|+++|||+|.|   +.    ++|+++|++|+|++|++|+|
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            56677543  35799999999999999999999999   999999999988   43    58999999999999999999


Q ss_pred             EEe
Q 021760           73 MLT   75 (308)
Q Consensus        73 ~v~   75 (308)
                      +-.
T Consensus        93 vd~   95 (97)
T 2kj6_A           93 IDL   95 (97)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            864

>1vej_A Riken cDNA 4931431F19; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.45  E-value=1.2e-13  Score=103.90  Aligned_cols=47  Identities=17%  Similarity=0.337  Sum_probs=43.5

Q ss_pred             cCCcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhCCCCC
Q 021760          168 AGSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (308)
Q Consensus       168 ~g~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~GIP~~  217 (308)
                      ..+.|+..|++|++||   | +|+.+++|||++++|++||||||++|||+.
T Consensus        25 pe~~ye~qi~qL~eMG---F~dr~~~~~AL~~t~Gnve~Ave~L~~~~~~~   72 (74)
T 1vej_A           25 TEGRYQQELEELKALG---FANRDANLQALVATDGDIHAAIEMLLGASGPS   72 (74)
T ss_dssp             TTTTSHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHTCCCCC
T ss_pred             chHHHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHhCCCCC
Confidence            3567899999999999   9 899999999999999999999999999864

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.44  E-value=8e-15  Score=128.97  Aligned_cols=70  Identities=21%  Similarity=0.276  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|++|.|+|++++||.+||.+|+...|   +|+++|||||+|++|+|+.+|+     ++++|||+++.+.
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keG---IP~~qQRLIf~GK~LeD~~TLs-----~~STLhLvlRLrG   70 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMG---FEIDMMTLVNNGFIAPNTELVT-----DDVTYYLSLKLLG   70 (189)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhC---cChhHEEEEecCeECCCCCccc-----CCCEEEEEEecCC
Confidence            89999999999999999999999999999999999   9999999999999999999999     8899999998764

>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=99.44  E-value=2.1e-13  Score=106.89  Aligned_cols=73  Identities=22%  Similarity=0.209  Sum_probs=63.5

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC---Ee----cCCCCChhhhccCCCCEEEE
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G---Ki----L~D~~tL~dygIk~g~~I~v   72 (308)
                      |+|+|+..... .++++|++++||.+||++|+...|   +|+++|||+|.|   +.    |+|+++|++|||++|++|||
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            36778765543 689999999999999999999999   999999999986   54    58999999999999999999


Q ss_pred             EEec
Q 021760           73 MLTK   76 (308)
Q Consensus        73 ~v~k   76 (308)
                      +...
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=99.44  E-value=1.2e-13  Score=93.37  Aligned_cols=40  Identities=23%  Similarity=0.327  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  214 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GI  214 (308)
                      .++.|++|++||   |+|++|++|||+++||++||+|||++||
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            368899999999   9999999999999999999999999987

>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=99.43  E-value=3.1e-13  Score=106.22  Aligned_cols=76  Identities=14%  Similarity=0.206  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+|++.+|+.+.++|.+++++..||++++++.|   ++++++||+|+|+.|++++|+++|+|++||+|+|+++....
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            67899999999999999999999999999999999   99999999999999999999999999999999999987653

>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=99.43  E-value=1.5e-13  Score=103.09  Aligned_cols=44  Identities=36%  Similarity=0.389  Sum_probs=40.9

Q ss_pred             CCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 021760          169 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  215 (308)
Q Consensus       169 g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP  215 (308)
                      ...+++.|++||+||   |+|++|++|||+++||+|||||||++|+.
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            456799999999999   99999999999999999999999999943

>2bwb_A Ubiquitin-like protein DSK2; UBA, signaling protein; 2.3A {Saccharomyces cerevisiae} SCOP: a.5.2.1 PDB: 2bwe_A

Probab=99.41  E-value=1.7e-13  Score=94.02  Aligned_cols=41  Identities=29%  Similarity=0.464  Sum_probs=38.4

Q ss_pred             CcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          170 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      +.|+..|++|++||   | +|+.+++||+++++|++||||||++|
T Consensus         5 ~~~~~~i~~L~~MG---F~d~~~~~~AL~~~~gnv~~Ave~L~~~   46 (46)
T 2bwb_A            5 ERYEHQLRQLNDMG---FFDFDRNVAALRRSGGSVQGALDSLLNG   46 (46)
T ss_dssp             HHTHHHHHHHHHTT---CCCHHHHHHHHHHHTTCHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHcc
Confidence            45889999999999   9 78999999999999999999999987

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.41  E-value=3.1e-13  Score=104.00  Aligned_cols=71  Identities=17%  Similarity=0.304  Sum_probs=63.5

Q ss_pred             CEEEEEeCCCcEEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC--CEecC---CCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GKVLK---DVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~le-V~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~--GKiL~---D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+||+.+|+. .++ |++++||.+||.+|+++.|   +++++|+|+|+  +|.|+   |+++|++|||++|++|||..
T Consensus         1 m~i~vr~~~G~~-~v~~l~~~~Tv~~Lk~~I~~~~g---i~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~   76 (86)
T 2kzr_A            1 WRVRCKAKGGTH-LLQGLSSRTRLRELQGQIAAITG---IAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEE   76 (86)
T ss_dssp             CCEEEEETTEEE-EECSCCTTCBHHHHHHHHHHHTC---CCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCC
T ss_pred             CEEEEEcCCCCE-EeeecCCCCCHHHHHHHHHHHhC---CCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEe
Confidence            899999999964 477 9999999999999999999   99999999987  48874   68899999999999998865


Q ss_pred             e
Q 021760           75 T   75 (308)
Q Consensus        75 ~   75 (308)
                      .
T Consensus        77 ~   77 (86)
T 2kzr_A           77 D   77 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.39  E-value=1.4e-12  Score=97.33  Aligned_cols=71  Identities=15%  Similarity=0.227  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|++.+|+.+.+.|.+++++..|++.++++.|   ++++.+||+|.|+.|.++.|+++|++++||+|+|++
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            67999999999999999999999999999999999   999999999999999999999999999999999873

>2knz_A Ubiquilin-4; cytoplasm, endoplasmic reticulum, nucleus, phosphoprotein, protein binding; NMR {Mus musculus}

Probab=99.38  E-value=4.3e-13  Score=94.73  Aligned_cols=43  Identities=26%  Similarity=0.375  Sum_probs=41.0

Q ss_pred             CcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 021760          170 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIP  215 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~GIP  215 (308)
                      +.|+..|++|++||   | +|+.|++||++++||.+||||||++|++
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            56899999999999   9 9999999999999999999999999975

>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=99.37  E-value=2.1e-12  Score=100.92  Aligned_cols=75  Identities=15%  Similarity=0.224  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+|++.+|+.+.+.|.+++++..||+.++++.|   ++++.+||+|+|+.|.+++|+++|++++||+|+|++....
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            57889999999999999999999999999999999   9999999999999999999999999999999999987654

>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=99.36  E-value=1.7e-12  Score=106.45  Aligned_cols=74  Identities=14%  Similarity=0.130  Sum_probs=64.1

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC---Ee----cCCCCChhhhccCCCCEEEE
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KV----LKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G---Ki----L~D~~tL~dygIk~g~~I~v   72 (308)
                      |.|+|+...+. .++++|++++||.+||.+|+...|   +|+++|||+|.|   +.    ++|+++|++|||++|++|||
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            46778765543 688999999999999999999999   999999999987   43    48999999999999999999


Q ss_pred             EEecC
Q 021760           73 MLTKS   77 (308)
Q Consensus        73 ~v~k~   77 (308)
                      +...+
T Consensus        84 vd~~p   88 (122)
T 1t0y_A           84 VDVTG   88 (122)
T ss_dssp             EECTT
T ss_pred             EeCCC
Confidence            87543

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.36  E-value=4.4e-12  Score=96.40  Aligned_cols=70  Identities=13%  Similarity=0.236  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      |+|+|++.+|+ .+.+.|..++++..||+.++++.|   ++++++||+|.|+.|.+++|+++|++++||+|+|+
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            57899999996 899999999999999999999999   99999999999999999999999999999999986

>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=99.36  E-value=8.3e-13  Score=101.23  Aligned_cols=45  Identities=27%  Similarity=0.371  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh--C-CCCCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS--G-IPEQTA  219 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~--G-IP~~~~  219 (308)
                      .++.|++||+||   |+|++|++|||+++||++||+|||++  | ||+.++
T Consensus        29 ~ee~I~~Lv~MG---F~~~~A~~AL~~t~gdve~A~e~L~sh~~~ip~~~~   76 (83)
T 1veg_A           29 SQESINQLVYMG---FDTVVAEAALRVFGGNVQLAAQTLAHHGGSLPPDLQ   76 (83)
T ss_dssp             CHHHHHHHHHHS---CCHHHHHHHHHHTTTCHHHHHHHHHHHTSSCCTTSS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCCCchhhh
Confidence            578999999999   99999999999999999999999999  7 886543

>2jy5_A Ubiquilin-1; UBA, alternative splicing, cytoplasm, nucleus, phosphoprotein, proteasome, signaling protein; NMR {Homo sapiens} PDB: 2jy6_B

Probab=99.35  E-value=1.2e-12  Score=92.00  Aligned_cols=42  Identities=26%  Similarity=0.411  Sum_probs=39.9

Q ss_pred             CCcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       169 g~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .+.|+..|++|++||   | +|+.|++||++++||.+||||||++|
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            467899999999999   9 99999999999999999999999986

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.34  E-value=7.6e-13  Score=125.34  Aligned_cols=72  Identities=18%  Similarity=0.285  Sum_probs=65.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE---eCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI---y~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+|| ++|++|.|+|++++||.+||++|++.+|   +|+++||||   |+||+|+|+.+|++|||++|++|+||.+.
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            578899 6899999999999999999999999999   999999999   89999999999999999999999999653

>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=99.32  E-value=4.8e-12  Score=99.15  Aligned_cols=74  Identities=15%  Similarity=0.231  Sum_probs=69.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |.|+|++.+|+.+.+.|..++++..|++.++++.|   ++++.+||+|.|+.|.++.|+++|+|.+||+|+|+++..
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            57888988999999999999999999999999999   999999999999999999999999999999999998754

>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=99.31  E-value=3.2e-12  Score=93.32  Aligned_cols=42  Identities=29%  Similarity=0.369  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  216 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~  216 (308)
                      .++.|++|++||   |+|++|++|||+++||++||+|||+++..+
T Consensus         9 ~~~~I~~L~~MG---F~~~~a~~AL~~~~~nve~A~e~L~~~~~~   50 (63)
T 1wji_A            9 DEKALKHITEMG---FSKEASRQALMDNGNNLEAALNVLLTSNKQ   50 (63)
T ss_dssp             CHHHHHHHHTTT---CCHHHHHHHHHHTTSCHHHHHHHHHHHSSC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHHCCCC
Confidence            478999999999   999999999999999999999999999543

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.30  E-value=5.7e-12  Score=100.84  Aligned_cols=75  Identities=15%  Similarity=0.229  Sum_probs=70.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+|++.+|+.+.+.|..++++..||+.++++.|   ++++.+||+|.|+.|.+++|+.+|+|++||+|+|++....
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            57899999999999999999999999999999999   9999999999999999999999999999999999987654

>1wr1_B Ubiquitin-like protein DSK2; UBA domain, UBA-ubiquitin complex, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.30  E-value=1.9e-12  Score=92.95  Aligned_cols=42  Identities=29%  Similarity=0.446  Sum_probs=39.8

Q ss_pred             CCcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       169 g~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .+.|+..|++|++||   | +|+.+++||+++++|++||||||++|
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            467899999999999   9 79999999999999999999999998

>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.30  E-value=2.8e-12  Score=94.41  Aligned_cols=46  Identities=17%  Similarity=0.188  Sum_probs=42.1

Q ss_pred             CCcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhCCCCC
Q 021760          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (308)
Q Consensus       169 g~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~GIP~~  217 (308)
                      .+.|+..|++|++||   | +|+.+++|||+++||++||||||++++++.
T Consensus        16 e~~y~~ql~qL~~MG---F~d~~an~~AL~at~Gnve~Ave~L~~~~~~~   62 (67)
T 2dna_A           16 EVRFSKEMECLQAMG---FVNYNANLQALIATDGDTNAAIYKLKSSQGFS   62 (67)
T ss_dssp             HHHTHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHHCCSSS
T ss_pred             HHHHHHHHHHHHHcC---CCcHHHHHHHHHHcCCCHHHHHHHHHhCCCcc
Confidence            456889999999999   9 788889999999999999999999998864

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.27  E-value=2.6e-12  Score=93.83  Aligned_cols=43  Identities=40%  Similarity=0.677  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~~  217 (308)
                      .++.|++||+||   |+|++|++|||+++||++||+|||+.++++.
T Consensus         9 ~~~~v~~L~~MG---F~~~~a~~AL~~t~~nve~A~e~L~~~~~d~   51 (63)
T 2dak_A            9 PEDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSHIDDL   51 (63)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTSCSHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCCc
Confidence            578999999999   9999999999999999999999999998753

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.26  E-value=9.6e-12  Score=100.51  Aligned_cols=75  Identities=15%  Similarity=0.248  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |.|+|++.+|+.+.+.|..++++..||+.++++.|   ++++.+||+|.|+.|.+++|+++|+|++||+|+|++....
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            57899999999999999999999999999999999   9999999999999999999999999999999999987543

>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=99.24  E-value=1.7e-11  Score=98.36  Aligned_cols=73  Identities=11%  Similarity=0.157  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+|++ +|+.+.+.|..++++..||++++++.|   ++++.+||+|.|+.|.+++|.++|++++||+|+|+++..
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            5788998 999999999999999999999999999   899999999999999999999999999999999998754

>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=99.23  E-value=1.1e-11  Score=93.14  Aligned_cols=41  Identities=20%  Similarity=0.455  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  215 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP  215 (308)
                      .++.|++|++||   |+|++|++|||+++||++||||||+++.-
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            478999999999   99999999999999999999999999843

>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=99.21  E-value=5.8e-12  Score=91.15  Aligned_cols=33  Identities=39%  Similarity=0.691  Sum_probs=31.2

Q ss_pred             CchHHhhChHHHHHHHHHHHhChhhHHHHHhcC
Q 021760          275 GTLDFLRNSQQFQALRTMVQANPQILQQWALIV  307 (308)
Q Consensus       275 ~~l~~Lr~~pqf~~lRq~vqqnP~~L~~~L~~~  307 (308)
                      ++|+|||++|||++||++||+||++|++|||++
T Consensus         2 ~~l~~Lr~~Pqf~~lR~~vq~NP~~L~~lLqql   34 (61)
T 2f4m_B            2 HPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQI   34 (61)
T ss_dssp             CGGGGGTTCHHHHHHHHHHHHCGGGHHHHHHHH
T ss_pred             chHHHHHcChHHHHHHHHHHHCHHHHHHHHHHH
Confidence            479999999999999999999999999999975

>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} SCOP: a.5.2.1

Probab=99.21  E-value=1.3e-11  Score=81.64  Aligned_cols=39  Identities=28%  Similarity=0.480  Sum_probs=36.4

Q ss_pred             CcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      +++++.|++|++||   |+|++|++||+++.||+++|++||+
T Consensus         2 ~~~~~~i~~L~~mG---f~~~~a~~AL~~~~~n~e~A~~~L~   40 (40)
T 1z96_A            2 PGLNSKIAQLVSMG---FDPLEAAQALDAANGDLDVAASFLL   40 (40)
T ss_dssp             -CHHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             chHHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHC
Confidence            35789999999999   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=99.21  E-value=1.5e-11  Score=92.52  Aligned_cols=43  Identities=21%  Similarity=0.370  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCCCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  217 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GIP~~  217 (308)
                      .++.|++||+||   |+|++|++|||+++| |.+||+|||+.++++.
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            378999999999   999999999999997 7999999999998864

>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=99.21  E-value=7.5e-12  Score=91.65  Aligned_cols=45  Identities=22%  Similarity=0.358  Sum_probs=40.7

Q ss_pred             CcHHHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCCCCC
Q 021760          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  217 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GIP~~  217 (308)
                      ...+..|++|++||   |+|++|++||++++| |+++|+|||+.++.+.
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            34467899999999   999999999999999 9999999999998753

>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=99.20  E-value=9.7e-12  Score=91.06  Aligned_cols=42  Identities=19%  Similarity=0.344  Sum_probs=38.8

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhc-CChHHHHHHHHhCCCCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAY-NNPERAVEYLYSGIPEQ  217 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAaf-nNpdRAvEYL~~GIP~~  217 (308)
                      ++.|++||+||   |+|++|++|||+++ +|++||+|||+.++++.
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            46899999999   99999999999995 89999999999998764

>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=99.19  E-value=2.7e-12  Score=95.74  Aligned_cols=34  Identities=38%  Similarity=0.642  Sum_probs=31.9

Q ss_pred             CCchHHhhChHHHHHHHHHHHhChhhHHHHHhcC
Q 021760          274 AGTLDFLRNSQQFQALRTMVQANPQILQQWALIV  307 (308)
Q Consensus       274 ~~~l~~Lr~~pqf~~lRq~vqqnP~~L~~~L~~~  307 (308)
                      +++|+|||++|||++||++||+||++|++|||++
T Consensus         3 ~~~l~~Lr~~Pqf~qlR~~vqqNP~lL~~lLqqL   36 (72)
T 1pve_A            3 HMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQI   36 (72)
T ss_dssp             TCTTGGGTTCTTTTTHHHHHTTCGGGHHHHHHHH
T ss_pred             CchHHHHHcChHHHHHHHHHHHCHHHHHHHHHHH
Confidence            4679999999999999999999999999999975

>2ekk_A UBA domain from E3 ubiquitin-protein ligase HUWE1; ubiquitin associated domain, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.18  E-value=1.9e-11  Score=84.03  Aligned_cols=38  Identities=37%  Similarity=0.597  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      +++.|++|++||   |+|++|++|||++ ||++||+|||+..
T Consensus         9 ~~~~v~~L~~MG---F~~~~a~~AL~~~-~n~e~A~~~L~~h   46 (47)
T 2ekk_A            9 NQQQLQQLMDMG---FTREHAMEALLNT-STMEQATEYLLTH   46 (47)
T ss_dssp             CHHHHHHHHHHH---CCHHHHHHHHHHS-CSHHHHHHHHHTC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHc-CCHHHHHHHHHcC
Confidence            478999999999   9999999999999 7999999999864

>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=99.18  E-value=1.5e-11  Score=90.12  Aligned_cols=40  Identities=23%  Similarity=0.408  Sum_probs=37.6

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIP  215 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GIP  215 (308)
                      ++.|++||+||   |+|++|++|||+++| |++||||||+.++-
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   999999999999999 99999999999864

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.14  E-value=1.2e-10  Score=91.41  Aligned_cols=72  Identities=18%  Similarity=0.238  Sum_probs=62.1

Q ss_pred             EEEEEe---CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC------Ee-c-CCCCChhhhccCCCCEE
Q 021760            2 KVFVKT---LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG------KV-L-KDVTTLEENKVAENSFV   70 (308)
Q Consensus         2 ~I~Vkt---l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G------Ki-L-~D~~tL~dygIk~g~~I   70 (308)
                      +|+|+.   .+|+.+++.+..++||.+||.+|+..+|   +|+..|||+|.+      .+ | +|+++|.+|+|.+|++|
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            566664   5678899999999999999999999999   999999999863      23 5 67789999999999999


Q ss_pred             EEEEec
Q 021760           71 VVMLTK   76 (308)
Q Consensus        71 ~v~v~k   76 (308)
                      ||....
T Consensus        88 ~V~d~~   93 (97)
T 1wjn_A           88 LVRWSG   93 (97)
T ss_dssp             EEECCS
T ss_pred             EEEecC
Confidence            998754

>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.10  E-value=8.2e-11  Score=90.37  Aligned_cols=43  Identities=23%  Similarity=0.366  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~~  217 (308)
                      .++.|++||+||   |+|++|++|||+++||.++|+|||+.++.+.
T Consensus        29 ~e~~i~~L~~MG---F~~~~a~~AL~~t~~nve~A~ewL~~~~~d~   71 (83)
T 2dai_A           29 DEAALRQLTEMG---FPENRATKALQLNHMSVPQAMEWLIEHAEDP   71 (83)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHHGGGCS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHHHCCCCc
Confidence            578999999999   9999999999999999999999999997654

>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=99.09  E-value=1.1e-10  Score=89.98  Aligned_cols=43  Identities=26%  Similarity=0.365  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCCCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPEQ  217 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GIP~~  217 (308)
                      .+..|++||+||   |+|++|++|||+++| |.+||+|||+.++.+.
T Consensus        29 ~e~~v~~L~~MG---F~~~~a~~AL~~t~n~n~e~A~ewL~~h~~d~   72 (84)
T 1vek_A           29 NEEIVAQLVSMG---FSQLHCQKAAINTSNAGVEEAMNWLLSHMDDP   72 (84)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTTCCHHHHHHHHHHHTTCS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHHcCCCHHHHHHHHHhCCCcc
Confidence            478999999999   999999999999985 9999999999998764

>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.05  E-value=1.7e-10  Score=82.68  Aligned_cols=38  Identities=29%  Similarity=0.616  Sum_probs=36.4

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ++.|..|++||   |.++|+.+||++.-||.|||+|||++.
T Consensus        20 ~e~V~~LvsMG---Fs~~qA~kALKat~~NvErAaDWLFSH   57 (63)
T 1wgn_A           20 RQCVETVVNMG---YSYECVLRAMKKKGENIEQILDYLFAH   57 (63)
T ss_dssp             HHHHHHHHHHH---CCHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            67799999999   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=99.03  E-value=2.1e-10  Score=81.20  Aligned_cols=41  Identities=29%  Similarity=0.442  Sum_probs=37.3

Q ss_pred             cHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhCC
Q 021760          171 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGI  214 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~GI  214 (308)
                      .|+..|++|++||   | +|+.+++||+++.+|.+||||||+++.
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            5789999999999   9 556689999999999999999999884

>2lbc_A Ubiquitin carboxyl-terminal hydrolase 13; tandem UBA of USP13; NMR {Homo sapiens}

Probab=99.02  E-value=2.6e-10  Score=93.99  Aligned_cols=41  Identities=41%  Similarity=0.608  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP  215 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP  215 (308)
                      .+..|++|++||   |+|++|++|||+++||++||+|||++|++
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            578999999999   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=99.01  E-value=3.4e-10  Score=90.82  Aligned_cols=43  Identities=35%  Similarity=0.514  Sum_probs=39.9

Q ss_pred             CcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 021760          170 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSGIP  215 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~GIP  215 (308)
                      ..|+..|++|++||   | +|+++++||+++++|++||||||++|.+
T Consensus        64 ~~~~~qL~qL~eMG---F~d~~~ni~AL~~t~Gdve~AVe~L~~~~~  107 (108)
T 2cwb_A           64 SQWQPQLQQLRDMG---IQDDELSLRALQATGGDIQAALELIFAGGA  107 (108)
T ss_dssp             CTTHHHHHHHHTTT---CCCHHHHHHHHHHHTSCHHHHHHHHHHTSC
T ss_pred             cchHHHHHHHHHcC---CCCHHHHHHHHHHhCCCHHHHHHHHHhcCC
Confidence            45789999999999   9 7899999999999999999999999854

>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=99.01  E-value=1.4e-09  Score=88.27  Aligned_cols=73  Identities=19%  Similarity=0.273  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+|+..+|+.+.+.|..++++..|++.++++.|   ++...+||+|.|+.|.++.|.++|++++||+|.|++..
T Consensus        41 I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~G---l~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~Q  113 (115)
T 3kyd_D           41 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ  113 (115)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHT---CCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhC---CChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEeec
Confidence            46788888899999999999999999999999999   99999999999999999999999999999999998753

>2dkl_A Trinucleotide repeat containing 6C protein; TNRC6C, KIAA1582 protein, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.93  E-value=9.6e-10  Score=84.76  Aligned_cols=38  Identities=29%  Similarity=0.430  Sum_probs=36.9

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ++.|++|++||   |+|++|++||++.++|.+||+|||+..
T Consensus        22 ~~~I~qL~~MG---F~~~~a~~AL~~~n~n~e~A~ewL~~h   59 (85)
T 2dkl_A           22 SRLIKQLTDMG---FPREPAEEALKSNNMNLDQAMSALLEK   59 (85)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHTT
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHHC
Confidence            78999999999   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=98.81  E-value=8.8e-10  Score=75.76  Aligned_cols=41  Identities=22%  Similarity=0.327  Sum_probs=38.3

Q ss_pred             cHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCC
Q 021760          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  214 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GI  214 (308)
                      +-++.|++|++||   |+|.+|++||.+.-+|.++|++||+++.
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            3478899999999   9999999999999999999999999875

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.77  E-value=2.3e-08  Score=88.53  Aligned_cols=76  Identities=11%  Similarity=0.116  Sum_probs=70.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+|+ .+|+.+.+.|..++++..||+.++++.|   ++..++||+|.|+.|.++.|.++|++++||+|+|++......
T Consensus        30 I~LkV~-~~g~~v~fkIk~~t~l~kL~~ay~er~G---i~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q~gg~  105 (200)
T 3pge_A           30 INLKVS-DGSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGG  105 (200)
T ss_dssp             EEEEEE-CSSCEEEEEECTTSCTHHHHHHHHHHHS---SCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCSCCC
T ss_pred             EEEEEe-cCCCEEEEEEecCCHHHHHHHHHHHHhC---CChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCcCc
Confidence            467787 5889999999999999999999999999   999999999999999999999999999999999999876544

>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=98.74  E-value=1.3e-08  Score=89.17  Aligned_cols=74  Identities=11%  Similarity=0.138  Sum_probs=68.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |.|+|+ .+|+.+.+.|..++++..|++.++++.|   ++...+||+|+|+.|.+++|.++|+|++||+|.|++....
T Consensus        58 InLKVk-~dG~eV~FKIKrtTpL~KLmeAYcERqG---L~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~G  131 (207)
T 3tix_A           58 INLKVS-DGSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIG  131 (207)
T ss_dssp             EEEEEE-CSSCEEEEEEETTSCTHHHHHHHHHHTT---CCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCT
T ss_pred             EEEEEe-cCCCEEEEEEccCChHHHHHHHHHHHhC---CCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            457776 4888999999999999999999999999   9999999999999999999999999999999999987654

>2ooa_A E3 ubiquitin-protein ligase CBL-B; alpha-helical domain; 1.56A {Homo sapiens} PDB: 2oob_A 2jnh_A 2do6_A

Probab=98.70  E-value=1.9e-08  Score=69.73  Aligned_cols=38  Identities=34%  Similarity=0.424  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      .+..|+.||+||   |+|++|++||+.+-||.|-|-.+|+.
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            467899999999   99999999999999999999999974

>2d9s_A CBL E3 ubiquitin protein ligase; UBA domain, dimer, protein binding, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.65  E-value=3.4e-08  Score=68.72  Aligned_cols=38  Identities=26%  Similarity=0.401  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      .|..|..||+||   |+|++|++||+.+-||.|-|..+|+.
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            456799999999   99999999999999999999999984

>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=98.64  E-value=2.1e-08  Score=81.81  Aligned_cols=39  Identities=18%  Similarity=0.313  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      +.+.|.+|++||   |++++|+.||+...||.|||||||+++
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=98.62  E-value=2.1e-08  Score=76.27  Aligned_cols=69  Identities=10%  Similarity=0.181  Sum_probs=57.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEe---c--CCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV---L--KDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKi---L--~D~~tL~dygIk~g~~I~v~   73 (308)
                      |.|.||+.+| .+.|+|++++||.+||++|.+.++   ++.+.+.|.++-..   |  .++.+|+++||++||.|+|.
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 788999999999999999999999   88888777654432   3  47889999999999999874

>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=98.62  E-value=2.2e-07  Score=69.93  Aligned_cols=70  Identities=16%  Similarity=0.224  Sum_probs=64.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~-~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      .+.++..+...+.+.|.++.+|.+|-+..+.+.|   |+.+ .++|.|.|..|+.+.++.+|++.+||.|.+|+
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            4556777777899999999999999999999999   9999 99999999999999999999999999999985

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=98.54  E-value=4.2e-07  Score=71.63  Aligned_cols=70  Identities=10%  Similarity=0.202  Sum_probs=63.9

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      +.|+|+..+|+ .+.+.|..++++..|.+..+++.|   ++....||+|.|..|..+.|..++++++||+|.|+
T Consensus        26 I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g---~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           26 LQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMG---LSGRKLSFFFDGTKLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             EEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTT---CSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHC---CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            35677777784 788999999999999999999999   88999999999999999999999999999999886

>2oo9_A E3 ubiquitin-protein ligase CBL; alpha-helical domain, homodimer; 2.10A {Homo sapiens}

Probab=98.54  E-value=1.3e-07  Score=63.56  Aligned_cols=41  Identities=29%  Similarity=0.447  Sum_probs=38.7

Q ss_pred             CCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          169 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       169 g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      |..+|..|..||+||   |+|+.|++||-.+-||.+-|-+.|+.
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            577899999999999   99999999999999999999999874

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=98.48  E-value=1.7e-08  Score=89.67  Aligned_cols=74  Identities=11%  Similarity=0.139  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |.|+| ..+|+.+.+.|..++++..||+.++++.|   ++.+.+||+|+|+.|.+++|.+++++++||+|.|+.....
T Consensus        22 InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqG---Ls~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~G   95 (227)
T 3v7o_A           22 INLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (227)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             EEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhC---CCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccC
Confidence            56777 66888899999999999999999999999   9999999999999999999999999999999999987654

>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=98.46  E-value=1.2e-07  Score=83.75  Aligned_cols=43  Identities=33%  Similarity=0.470  Sum_probs=40.3

Q ss_pred             ccCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          167 VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       167 ~~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      ..+..|++.|++|++||   |+|++|+.||+...+|.++|+|||++
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            34678999999999999   99999999999999999999999985

>2juj_A E3 ubiquitin-protein ligase CBL; alpha helix, UBA domain, calcium, cytoplasm, metal- binding, phosphorylation, proto-oncogene, SH2 domain; NMR {Homo sapiens}

Probab=98.44  E-value=2.4e-07  Score=64.66  Aligned_cols=40  Identities=25%  Similarity=0.341  Sum_probs=37.1

Q ss_pred             cHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ..|..|..||+||   |+|+.|++||+.+-||.+-|-..|+.=
T Consensus         6 p~e~~Ia~L~smG---fsr~da~~AL~ia~Ndv~~AtNiLlEf   45 (56)
T 2juj_A            6 QLSSEIENLMSQG---YSYQDIQKALVIAQNNIEMAKNILREF   45 (56)
T ss_dssp             HHHHHHHHHHTTT---CCHHHHHHHHHHTTTCSHHHHHHHHHS
T ss_pred             CChHHHHHHHHcC---CCHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            3578999999999   999999999999999999999999854

>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=98.35  E-value=6.2e-07  Score=71.10  Aligned_cols=44  Identities=27%  Similarity=0.571  Sum_probs=41.5

Q ss_pred             CcHHHHHHHHHHh-cCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 021760          170 SNLEATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  216 (308)
Q Consensus       170 ~~~e~~v~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~  216 (308)
                      .++++.|..||+| |   |++++|+.||.-+.++.++|++||+.|.++
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   999999999999999999999999999884

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.35  E-value=2.6e-06  Score=66.56  Aligned_cols=72  Identities=11%  Similarity=0.197  Sum_probs=66.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      +.|+|+ .+|..+.+.|..++....|.+..+++.|   +.++.+|++|.|..+.++.|-.++++.++|+|.+++.+
T Consensus        22 IniKV~-~~g~ev~FkIK~tt~l~KL~~aYc~r~g---v~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~~~   93 (95)
T 2l76_A           22 FPLKIR-CRADLVRLPLRMSEPLQSVVDHMATHLG---VSPSRILLLFGETELSPTATPRTLKLGVADIIDCVVLT   93 (95)
T ss_dssp             EEEEEE-CSSSEEEEEECSSSCTHHHHHHHHHHHT---SCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEECC
T ss_pred             EEEEEE-cCCcEEEEEEecCChHHHHHHHHHhhcC---CChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEEec
Confidence            357788 4788999999999999999999999999   88999999999999999999999999999999999865

>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=98.25  E-value=9.6e-07  Score=71.95  Aligned_cols=40  Identities=33%  Similarity=0.606  Sum_probs=36.9

Q ss_pred             cHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .-.+.|+.|++||   |+++.|++||++..||+++|+|||+.-
T Consensus         7 ~e~~~v~~l~~MG---Fp~~~~~kAl~~~g~~~e~amewL~~h   46 (118)
T 4ae4_A            7 SERQCVETVVNMG---YSYECVLRAMKAAGANIEQILDYLFAH   46 (118)
T ss_dssp             HHHHHHHHHHHTT---CCHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC---CCHHHHHHHHHHHCcCHHHHHHHHHHh
Confidence            3468899999999   999999999999999999999999863

>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=98.23  E-value=1.2e-06  Score=61.60  Aligned_cols=43  Identities=23%  Similarity=0.343  Sum_probs=39.7

Q ss_pred             cCCcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          168 AGSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       168 ~g~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ..+.|...+++|.+||   | +++..++|||...+|.+|||++|+.+
T Consensus         5 ~ee~~a~~L~~L~eMG---F~D~~~N~~aL~~~~gnv~~aI~~Ll~~   48 (54)
T 2cp8_A            5 SSGQTAALMAHLFEMG---FCDRQLNLRLLKKHNYNILQVVTELLQL   48 (54)
T ss_dssp             SCTTHHHHHHHHHHHT---CCCHHHHHHHHTTTTTCHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHcC---CCcHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            3466888999999999   9 99999999999999999999999975

>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=98.18  E-value=3.8e-06  Score=74.62  Aligned_cols=73  Identities=11%  Similarity=0.141  Sum_probs=66.8

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      .|+|++ +++.+.+.|..++++..||+..+++.|   ++.+++||+|.|+.+.+++|..++.++++|+|.++..+..
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            566776 677888999999999999999999999   9999999999999999999999999999999999876654

>2lbc_A Ubiquitin carboxyl-terminal hydrolase 13; tandem UBA of USP13; NMR {Homo sapiens}

Probab=98.13  E-value=1.4e-06  Score=71.44  Aligned_cols=41  Identities=27%  Similarity=0.386  Sum_probs=37.8

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCCCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPE  216 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GIP~  216 (308)
                      +..|+.|++||   |+++.|++|||+..| |.++|++||+....+
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            46899999999   999999999999988 899999999998664

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.05  E-value=1.5e-05  Score=62.31  Aligned_cols=63  Identities=16%  Similarity=0.109  Sum_probs=50.0

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEec--CCCCChhhhccC-CCCEEEEEE
Q 021760            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVL--KDVTTLEENKVA-ENSFVVVML   74 (308)
Q Consensus         9 ~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL--~D~~tL~dygIk-~g~~I~v~v   74 (308)
                      .+..+.+.|.+++||..||++|++++|   |++++|+|||.||.|  +.++.-..|--. ..+-|+++-
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            567889999999999999999999999   999999999999875  556666666443 334454443

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=98.00  E-value=1.1e-05  Score=61.50  Aligned_cols=70  Identities=13%  Similarity=0.226  Sum_probs=59.2

Q ss_pred             EEEEEe--CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC---CCeEEEeCCEecCCCCChhhhccCCCCEEEE
Q 021760            2 KVFVKT--LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA---SQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vkt--l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~---~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      +|+|..  +.++.|.|++....||+.|++.+.+.++.+ .+.   .++|+.-+|.+|.+++.|.+|+|.+||.|.+
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  588999999999999999999999998843 221   2468888999999999999999999999976

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=97.99  E-value=8.2e-07  Score=84.89  Aligned_cols=74  Identities=11%  Similarity=0.150  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      +.|+|++ +|+.+.+.|..++++..|++.++++.|   ++.+.+||+|+|+.|.++.|.+++++++||+|.|+.....
T Consensus        22 I~LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G---~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q~g   95 (360)
T 3ix6_A           22 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (360)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             EEEEEec-CCcEEEEEEecCChHHHHHHHHHHHhC---CCcceEEEEECCeECCCCCChHHcCCCccchhhhhhccCc
Confidence            3566776 677888999999999999999999999   8999999999999999999999999999999999987543

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=97.93  E-value=2e-05  Score=64.89  Aligned_cols=69  Identities=25%  Similarity=0.243  Sum_probs=57.4

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-------------------------------------Ce
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-------------------------------------QQ   44 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~-------------------------------------~q   44 (308)
                      .|+|+.++|...++.|+.+.+|.+++..|+.+.|   +...                                     ++
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            3889999999999999999999999999999999   5533                                     34


Q ss_pred             EEEe--CCEecCCCCChhhhccCCCCEEEEE
Q 021760           45 MLIH--QGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        45 kLIy--~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      ||..  .+..|+++++|.++||.++++|.+-
T Consensus        90 kL~~dd~~~WLD~srtL~EQGI~e~~tllLR  120 (128)
T 2kc2_A           90 KLHTDDELNWLDHGRTLREQGVEEHETLLLR  120 (128)
T ss_dssp             SCCCSSSEEEECSSSCHHHHTCCTTSEEEEE
T ss_pred             HhcccCCCCcccCCCcHHHcCCCCCCEEEEE
Confidence            4422  2367889999999999999997653

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=97.88  E-value=5.7e-05  Score=58.43  Aligned_cols=74  Identities=18%  Similarity=0.149  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |.|+|-..+++.+.|.|.++.++.++-+..+.++|   +..++..|.|++|.|+-+..+.-.||-+|..|.++.+.+
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            67899989999999999999999999999999999   888899999999999999999999999999999986544

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=97.81  E-value=2.7e-06  Score=81.91  Aligned_cols=73  Identities=10%  Similarity=0.132  Sum_probs=0.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      .|+|+. +++.+.+.|..++++..||+..+++.|   ++..+++|+|+|+.|.+++|.+++++++||+|.+++....
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            456665 667788999999999999999999999   9999999999999999999999999999999999987654

>2cos_A Serine/threonine protein kinase LATS2; UBA domain, structure genomics, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=97.80  E-value=2.7e-05  Score=54.22  Aligned_cols=37  Identities=30%  Similarity=0.435  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHH
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLY  211 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~  211 (308)
                      .-++++.|++||   |+++-|++||+..-| +.+-|+|||.
T Consensus         9 n~qmlq~L~eMG---Fd~erae~Alk~Tg~~Gle~AmewL~   46 (54)
T 2cos_A            9 NRQMLQELVNAG---CDQEMAGRALKQTGSRSIEAALEYIS   46 (54)
T ss_dssp             CHHHHHHHHHHH---CCHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcC---CCHHHHHHHHHHhCcccHHHHHHHHH
Confidence            457899999999   999999999999987 7999999997

>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=97.80  E-value=4.6e-06  Score=80.20  Aligned_cols=41  Identities=22%  Similarity=0.353  Sum_probs=38.4

Q ss_pred             CcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ++-++.|++|++||   |+|++|++||+++-+|.+||++||+++
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            45678999999999   999999999999999999999999986

>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=97.54  E-value=7.6e-05  Score=68.23  Aligned_cols=43  Identities=30%  Similarity=0.431  Sum_probs=40.3

Q ss_pred             ccCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          167 VAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       167 ~~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      +.+.+|++.|++|++||   |+|++|+.||+-.-+|-++|+|||+.
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=97.45  E-value=0.00048  Score=52.11  Aligned_cols=68  Identities=18%  Similarity=0.246  Sum_probs=57.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEec---CCCCChhhhccCCCCEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVL---KDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL---~D~~tL~dygIk~g~~I~v~   73 (308)
                      +|.||..+|+.+.-.+..++||.+|...|.. .+   +.....+|+  |-.|.|   +.+++|+++|+.++.+|+|-
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            5889999999988899999999999999987 56   567788887  557888   45789999999988888774

>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=97.37  E-value=0.0018  Score=51.62  Aligned_cols=71  Identities=13%  Similarity=0.209  Sum_probs=59.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecC--C-CCChhhhccCCCCEEEEEEe
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--D-VTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~--D-~~tL~dygIk~g~~I~v~v~   75 (308)
                      +|.||..+|+.+.-.+..++||.+|.+.|....+   .+.....|+  |-.|.|.  | +++|+++|+.+..+|+|...
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            6889999999999999999999999999998877   556677786  5678886  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=96.87  E-value=0.0025  Score=51.91  Aligned_cols=69  Identities=22%  Similarity=0.344  Sum_probs=58.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEec--CC-CCChhhhccCCCCEEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVL--KD-VTTLEENKVAENSFVVVML   74 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL--~D-~~tL~dygIk~g~~I~v~v   74 (308)
                      +|.||..+|+.+.-.+..++||.+|...|... +   +.....+|+  |-.|.|  .| +++|.++|+.....|+|..
T Consensus        45 ~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~---~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~~  118 (124)
T 1wj4_A           45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-G---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE  118 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-H---CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C---CCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEEE
Confidence            68899999999999999999999999999876 6   666778887  568888  34 7899999999988777653

>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=96.57  E-value=0.017  Score=45.81  Aligned_cols=68  Identities=16%  Similarity=0.145  Sum_probs=56.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecC--CCCChhhhccCCCCEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--DVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~--D~~tL~dygIk~g~~I~v~   73 (308)
                      +|.||..+|+.+.-.+..++||.+|..-|... +   +.....+|+  |-.|.|.  .++||+++||.+..+|+|-
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            68899999999888999999999999999855 4   445678886  5678885  4689999999988777664

>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=96.50  E-value=0.01  Score=48.48  Aligned_cols=65  Identities=18%  Similarity=0.285  Sum_probs=53.1

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecCC-CCChhhhccCCCC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENS   68 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~D-~~tL~dygIk~g~   68 (308)
                      +|.||..+|+.+.-.+..++||.+|+..|..... + +......|+  |-.|.|.| +++|+++|+.+..
T Consensus        54 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~-~-~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psa  121 (127)
T 1s3s_G           54 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARP-A-MAATSFVLMTTFPNKELADENQTLKEANLLNAV  121 (127)
T ss_dssp             CEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCS-G-GGTSCEEEEETTTTEECCSTTCBHHHHTCSSCE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCc-C-CCCCCeEEecCCCCCCCCCCCCcHHHCCCcCce
Confidence            5889999999999999999999999999988632 1 445667776  56899965 6899999999743

>1wgl_A TOLL-interacting protein; CUE domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, immune system; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=96.41  E-value=0.0034  Score=44.72  Aligned_cols=40  Identities=28%  Similarity=0.332  Sum_probs=37.2

Q ss_pred             cHHHHHHHHHHh--cCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          171 NLEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       171 ~~e~~v~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ..|+.|+.|.+|  .   ++++.|+..|++.-||.|+|++.|+.-
T Consensus         8 ~~ee~l~~L~emFP~---ld~~~I~~vL~a~~gdvd~aI~~LL~m   49 (59)
T 1wgl_A            8 CSEEDLKAIQDMFPN---MDQEVIRSVLEAQRGNKDAAINSLLQM   49 (59)
T ss_dssp             SCHHHHHHHHHHCSS---SCHHHHHHHHTTTTTCHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            358999999999  6   899999999999999999999999976

>2pwq_A Ubiquitin conjugating enzyme; structural genomics consortium, SGC, ligase; 1.90A {Plasmodium yoelii}

Probab=96.38  E-value=0.00054  Score=61.11  Aligned_cols=41  Identities=24%  Similarity=0.293  Sum_probs=0.0

Q ss_pred             cHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCC
Q 021760          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGI  214 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GI  214 (308)
                      ++++.|+++++||   |+|+++++||+-.-.+-++|+|.|+.|+
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            4689999999999   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=96.35  E-value=0.02  Score=43.65  Aligned_cols=70  Identities=14%  Similarity=0.208  Sum_probs=59.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe---CCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy---~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      ++.|.....+++.+.|++..++.+|--.|+++..   +.++...|..   .+..|+-+++|.||||++   ++.+-.++
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            5677777888899999999999999999999987   8888888864   456789999999999998   77776655

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=96.27  E-value=0.029  Score=44.85  Aligned_cols=64  Identities=20%  Similarity=0.252  Sum_probs=46.1

Q ss_pred             CcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCeEEEe----CCEecCCC-------------CChhhhccCC
Q 021760           10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGKVLKDV-------------TTLEENKVAE   66 (308)
Q Consensus        10 gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~------~~qkLIy----~GKiL~D~-------------~tL~dygIk~   66 (308)
                      +..+.+.|-.++||.++|+||-+..-+. +|.      +.+.|-|    .|++|.|.             .||..|+|.+
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            4568888889999999999997665332 443      4556765    35777652             3799999999


Q ss_pred             CCEEEEEE
Q 021760           67 NSFVVVML   74 (308)
Q Consensus        67 g~~I~v~v   74 (308)
                      |.+|.++-
T Consensus       102 gatl~l~~  109 (111)
T 4e71_A          102 GATLILSK  109 (111)
T ss_dssp             TCEEEEEE
T ss_pred             CCEEEEEe
Confidence            99998764

>2di0_A Activating signal cointegrator 1 complex subunit 2; ASCC2, CUE domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=96.01  E-value=0.022  Score=41.97  Aligned_cols=51  Identities=14%  Similarity=0.305  Sum_probs=44.5

Q ss_pred             cccCCcHHHHHHHHHHh--cCCccCHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCC
Q 021760          166 LVAGSNLEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG-IPEQTA  219 (308)
Q Consensus       166 l~~g~~~e~~v~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEYL~~G-IP~~~~  219 (308)
                      -+.+.+.+..|.+|.++  -   |....|.++|..--+|+|+.|.+|+.| +|.++.
T Consensus         7 ~~~~~~l~s~I~qV~DLfPd---LG~gfi~~~L~~y~~nvE~vin~LLE~~LPp~L~   60 (71)
T 2di0_A            7 GMCGVELDSLISQVKDLLPD---LGEGFILACLEYYHYDPEQVINNILEERLAPTLS   60 (71)
T ss_dssp             CCSSHHHHHHHHHHHHHCCS---SCHHHHHHHHHHTTTCHHHHHHHHHTTCCCTTTT
T ss_pred             CCcHHHHHHHHHHHHHHccc---CCHHHHHHHHHHhCCCHHHHHHHHHccCCCHHHH
Confidence            34678899999999998  5   679999999999889999999999999 787654

>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.96  E-value=0.014  Score=42.52  Aligned_cols=45  Identities=13%  Similarity=0.137  Sum_probs=39.4

Q ss_pred             cCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          168 AGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       168 ~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .+.+++..|+.|.+|= -.++++-|+..|++.-+|.|+||+-||.-
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            5678899999999991 12799999999999999999999999864

>1otr_A Protein CUE2; protein-protein complex, cell cycle; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.4

Probab=95.88  E-value=0.012  Score=40.24  Aligned_cols=39  Identities=15%  Similarity=0.236  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHh--cCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .+.-|+.|+||  .   -++++|.++|+++-+|-|||+.-||++
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  5   589999999999999999999999987

>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=95.76  E-value=0.041  Score=45.51  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=47.9

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCeEEEe----CCE-ecCCC-------------CChhhhccCC
Q 021760           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGK-VLKDV-------------TTLEENKVAE   66 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~------~~qkLIy----~GK-iL~D~-------------~tL~dygIk~   66 (308)
                      ..+.+.|-.++||.++|+||-+..-++ +|.      +++-|-+    .|+ +|.|.             .||..|+|.+
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            468889989999999999998776544 544      3445554    344 46553             2899999999


Q ss_pred             CCEEEEEEec
Q 021760           67 NSFVVVMLTK   76 (308)
Q Consensus        67 g~~I~v~v~k   76 (308)
                      |.+|.++-+.
T Consensus       120 ga~l~l~~~~  129 (138)
T 2r2o_A          120 GATVALVPCL  129 (138)
T ss_dssp             TCEEEEEEC-
T ss_pred             CCEEEEEECC
Confidence            9999887554

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=95.74  E-value=0.028  Score=41.50  Aligned_cols=60  Identities=17%  Similarity=0.248  Sum_probs=47.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      |+|+||....+...+++....||.+|-+    ..|   ++++...+..||+++..+.      +.+||.|.++
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 MNVTVEVVGEETSEVAVDDDGTYADLVR----AVD---LSPHEVTVLVDGRPVPEDQ------SVEVDRVKVL   60 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHH----TTC---CCSSCCCEECCCCCCCTTS------SSCCCCEEEC
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHH----HcC---CCcceEEEEECCEECCHHH------CCCCCEEEEE
Confidence            8999997755556689999999999776    466   8888888889999986665      2348888775

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=95.49  E-value=0.088  Score=38.10  Aligned_cols=61  Identities=18%  Similarity=0.270  Sum_probs=45.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|.... ....+++....||.+|.+.+    +   ++.....+..+|+++..+.     -+++||.|.++-
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            567776332 24567777778999998865    5   5567777889999997665     688999998863

>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=95.48  E-value=0.011  Score=62.32  Aligned_cols=41  Identities=39%  Similarity=0.670  Sum_probs=37.7

Q ss_pred             CcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ..-++.|..|++||   |++++.++||++.-||.+||||||.+.
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            34578899999999   999999999999999999999999986

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=95.41  E-value=0.082  Score=46.70  Aligned_cols=62  Identities=13%  Similarity=0.240  Sum_probs=50.7

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CeEEE--e-CC--EecCC-CCChhhhccCCCCEEEEEEec
Q 021760           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLI--H-QG--KVLKD-VTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus        12 ~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~-~qkLI--y-~G--KiL~D-~~tL~dygIk~g~~I~v~v~k   76 (308)
                      .+.+.++..+||.+|++++...++   ++.+ ..||-  | .+  ..|+| +++|.+++|.++..|+|=++.
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            356788999999999999999999   8886 68883  4 33  34665 579999999999999987764

>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=94.88  E-value=0.15  Score=45.39  Aligned_cols=62  Identities=13%  Similarity=0.246  Sum_probs=50.6

Q ss_pred             EEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CeEEEe-C----CEecCC-CCChhhhccCCCCEEEEEEecC
Q 021760           13 FEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIH-Q----GKVLKD-VTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus        13 ~~leV~~~~TV~~LK~~I~~~~g~~~ip~~-~qkLIy-~----GKiL~D-~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      +.+.++..+||.+|++++...++   ++.+ ..||-. .    ...|.| +.+|.+++|.++..|.|=++.+
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~---i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE~r~~  222 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFN---IPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQNE  222 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTT---CCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEEECCT
T ss_pred             EEEEecccCcHHHHHHHHHHHhC---CCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEEEecC
Confidence            55778999999999999999999   8887 688842 2    245665 6899999999999998877653

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=94.82  E-value=0.15  Score=41.58  Aligned_cols=66  Identities=20%  Similarity=0.267  Sum_probs=48.1

Q ss_pred             CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCeEEEe----CCE-ecCCC-------------CChhhhcc
Q 021760            9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGK-VLKDV-------------TTLEENKV   64 (308)
Q Consensus         9 ~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~------~~qkLIy----~GK-iL~D~-------------~tL~dygI   64 (308)
                      .+..+.+.|-.++||.++|+||-+..-+. +|.      +.+.|-|    .|+ +|.|.             .||..|+|
T Consensus        15 ~~~~i~VkVLdCDTItQvKeKiLd~vyk~-~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~~krLNTL~HY~V   93 (127)
T 3h6n_A           15 GMDSLSVRAMDTDTLTQVKEKILEAFCKN-VPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDGRKKLNTLAHYKI   93 (127)
T ss_dssp             CCCCEEEEEETTSBHHHHHHHHHHHHSTT-SCGGGSCCGGGEEEEEECSSSCEEECCSSSTTSCEETTEECCCBTTTTTC
T ss_pred             CCCceeeeeeccCchhhhhHHHHHHHhcc-CCcccCCCCcccceEEecCCCCceEeecCCCcceecCceeEeccccccCC
Confidence            34568888889999999999998765433 443      4567765    344 36552             36899999


Q ss_pred             CCCCEEEEEEe
Q 021760           65 AENSFVVVMLT   75 (308)
Q Consensus        65 k~g~~I~v~v~   75 (308)
                      .+|.+|.+..+
T Consensus        94 ~dgatv~l~~~  104 (127)
T 3h6n_A           94 PEGASLAMSLI  104 (127)
T ss_dssp             CTTCEEEEEEC
T ss_pred             CCCCEEEEEEc
Confidence            99999988754

>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.2

Probab=94.58  E-value=0.059  Score=38.91  Aligned_cols=35  Identities=14%  Similarity=0.170  Sum_probs=32.8

Q ss_pred             HHHHHHHHh-cCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          174 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       174 ~~v~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      +.|..|.++ |   +...+|..||..+-+|.+.|++||-
T Consensus        11 ~~Vk~LRe~TG---ag~~dcKkAL~e~~GDi~~Ai~~Lr   46 (64)
T 2cp9_A           11 ELLMKLRRKTG---YSFVNCKKALETCGGDLKQAEIWLH   46 (64)
T ss_dssp             HHHHHHHHHHC---CCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            679999997 8   8999999999999999999999995

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=94.50  E-value=0.12  Score=41.55  Aligned_cols=65  Identities=25%  Similarity=0.360  Sum_probs=46.0

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC------CeEEEe-CC---E-ecCCC-------------CChhhhccCC
Q 021760           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPAS------QQMLIH-QG---K-VLKDV-------------TTLEENKVAE   66 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~------~qkLIy-~G---K-iL~D~-------------~tL~dygIk~   66 (308)
                      ..+.+.|-.++||.++|+||-+..-+. +|..      .+.|-| .|   + +|.|.             .||..|+|.+
T Consensus        27 ~~i~VkVLdCDTItQvKeKiLd~vyk~-~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~d  105 (117)
T 4e74_A           27 PEVPVKILNCDTITQVKEKILDAIFKN-VPCSHRPKAADMDLEWRQGSGARMILQDEDITTKIENDWKRLNTLAHYQVPD  105 (117)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTT-SCGGGSCCGGGEEEEEECTTSCEEEECSSSTTCCC---CCCCCBHHHHTCCT
T ss_pred             CceEeeeecCCchHHHHHHHHHHHhcC-CCcccCCCCCceeEEEecCCCCceEeecCCCccEecCcceEeccccccCCCC
Confidence            347788889999999999997665332 4443      456655 23   3 35441             3699999999


Q ss_pred             CCEEEEEEec
Q 021760           67 NSFVVVMLTK   76 (308)
Q Consensus        67 g~~I~v~v~k   76 (308)
                      |.+|.++-+.
T Consensus       106 gatl~l~~~~  115 (117)
T 4e74_A          106 GSVVALVSKQ  115 (117)
T ss_dssp             TCEEEEEECC
T ss_pred             CCEEEEEeCC
Confidence            9999887543

>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=94.31  E-value=0.28  Score=37.62  Aligned_cols=68  Identities=21%  Similarity=0.291  Sum_probs=47.6

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCC--CCC------CCCCeEEEeCCEecCCCCChhhhccC
Q 021760            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGS--DVY------PASQQMLIHQGKVLKDVTTLEENKVA   65 (308)
Q Consensus         1 M~I~Vktl~------g-k~~~leV~~~~TV~~LK~~I~~~~g~--~~i------p~~~qkLIy~GKiL~D~~tL~dygIk   65 (308)
                      |+|+||.+.      | ....+++....||.+|.+.+......  ..+      ......+..||+.+..     ++-|+
T Consensus        10 ~~v~V~~FA~lre~~g~~~~~~e~~~~~Tv~~Ll~~L~~~~p~l~~~l~~~~g~~~~~v~v~VNg~~v~~-----~~~L~   84 (98)
T 1vjk_A           10 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSW-----DEELK   84 (98)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCT-----TCBCC
T ss_pred             EEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHhHChhHHHHhhccccccCCcEEEEECCEECCC-----CCCCC
Confidence            678888653      3 46778887788999999999876320  000      0234567789988763     56789


Q ss_pred             CCCEEEEE
Q 021760           66 ENSFVVVM   73 (308)
Q Consensus        66 ~g~~I~v~   73 (308)
                      +||.|.++
T Consensus        85 dGDeV~i~   92 (98)
T 1vjk_A           85 DGDVVGVF   92 (98)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEE
Confidence            99998886

>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=93.89  E-value=0.18  Score=47.55  Aligned_cols=71  Identities=13%  Similarity=0.067  Sum_probs=54.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCC-CCCCCCeEEEe------CCEecCCCCChhhhccCCCCEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSD-VYPASQQMLIH------QGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~-~ip~~~qkLIy------~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      .++|... +.+-++.++++.||.++..+|.++.... ..+.++--|..      +|+-|++.++|+.|++.+|+.|...
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            3455543 6677899999999999999998876410 12455666765      5677999999999999999988875

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=93.55  E-value=0.19  Score=36.48  Aligned_cols=65  Identities=6%  Similarity=0.183  Sum_probs=44.8

Q ss_pred             CEEEEEeCCCc-EEEEEeCCCCcHHHHHHHHHHHhCCCCCCC--CCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPA--SQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk-~~~leV~~~~TV~~LK~~I~~~~g~~~ip~--~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      |+|+||.+..- .-.+++ ...||.+|++.+....+   +..  ....+..||+.+.+    .+.-+++||.|.++
T Consensus         1 M~v~V~~fa~l~~~~~e~-~~~tv~~ll~~L~~~~~---l~~~l~~~~vavN~~~v~~----~~~~l~~gDeV~i~   68 (74)
T 3rpf_C            1 MMVEVRFFGPIKEENFFI-KANDLKELRAILQEKEG---LKEWLGVCAIALNDHLIDN----LNTPLKDGDVISLL   68 (74)
T ss_dssp             CEEEEEECTTCCCCCEEE-ECSSHHHHHHHHHTCTT---TTTTTTTCEEEESSSEECC----TTCCCCTTCEEEEE
T ss_pred             CEEEEEEEeecceeEEee-CCCcHHHHHHHHHHCcC---HHHHhhccEEEECCEEcCC----CCcCCCCCCEEEEE
Confidence            88999976431 134666 56799999999986533   221  45667778888543    24568999999886

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=91.57  E-value=1.8  Score=32.11  Aligned_cols=56  Identities=9%  Similarity=0.147  Sum_probs=41.3

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCC-----C-----CCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760           11 THFEIEVKPEDKVSDVKKNIETVQGSDVY-----P-----ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~~g~~~i-----p-----~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      +...+++....||.+|++.+...+..  +     .     .....+..||+....     ++-|++||.|.++
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~--~~~~~l~~~g~l~~~~~v~VN~~~v~~-----~~~l~~gDeV~i~   83 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPA--LESRVFGDDGELYDHINVLRNGEAAAL-----GEATAAGDELALF   83 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGG--GHHHHBCTTSCBCTTSEEEETTEECCT-----TSBCCTTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcH--HHHHHhccCCcccccEEEEECCEECCC-----CcccCCCCEEEEE
Confidence            56788888788999999999876430  1     0     023577789988865     4568899999886

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=91.43  E-value=0.55  Score=35.57  Aligned_cols=62  Identities=13%  Similarity=0.115  Sum_probs=53.3

Q ss_pred             EEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760           13 FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus        13 ~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      +...+|-..++..||+.++.+.|   +.-+...+...+..|+++++|-+-+|+-...|.+.+.-+
T Consensus         5 i~qhmDI~epL~~Lk~LLe~Rl~---i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqik   66 (89)
T 2juo_A            5 VSQAIDINEPIGNLKKLLEPRLQ---CSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQVI   66 (89)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHHC---SCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEEE
T ss_pred             hhhhccccCcHHHHHHHHHHHhc---CCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEEE
Confidence            34466778899999999999999   778888998899889999999999999888888877543

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=91.00  E-value=0.31  Score=37.04  Aligned_cols=57  Identities=9%  Similarity=0.239  Sum_probs=41.1

Q ss_pred             CCCcEEEEEeCCC-CcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            8 LKGTHFEIEVKPE-DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         8 l~gk~~~leV~~~-~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      ++|+.  +++... .||.+|.+.+    +   ++.....+..||+++..+ ...+.-|++||.|.|+-
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            35654  445665 7999998865    5   666777888999998543 34456799999998873

>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=90.52  E-value=1.1  Score=40.39  Aligned_cols=74  Identities=16%  Similarity=0.167  Sum_probs=55.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC-CCeEEEe---CC--EecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIH---QG--KVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~-~~qkLIy---~G--KiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |.|.|..++| ++.+.|+.+.|+.+|-+.|....|   +.. +..-|.|   +|  ..|+.++.|.+.+++.+..+.+..
T Consensus         2 i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~---L~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l~f   77 (294)
T 1ef1_A            2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIG---LREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKF   77 (294)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHT---CCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEE
T ss_pred             EEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcC---CCCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEEEE
Confidence            4678888888 788999999999999999999999   432 3345554   34  347888999988777666666666


Q ss_pred             ecCC
Q 021760           75 TKSK   78 (308)
Q Consensus        75 ~k~k   78 (308)
                      +++-
T Consensus        78 r~kf   81 (294)
T 1ef1_A           78 RAKF   81 (294)
T ss_dssp             EESS
T ss_pred             EEEE
Confidence            6554

>1ip9_A BEM1 protein; ubiquitin alpha/beta roll, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 1ipg_A 2kfk_A

Probab=90.49  E-value=0.41  Score=36.30  Aligned_cols=43  Identities=14%  Similarity=0.116  Sum_probs=32.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE-eCC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-HQG   50 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI-y~G   50 (308)
                      ||+|- .++..|.|.|..+.+..+||.+|..+..   +  +.+.|+ |++
T Consensus        14 KVK~y-y~DDIiAIrvP~di~~~~L~dKi~~RLk---~--~~~~l~~ykd   57 (85)
T 1ip9_A           14 KIKFY-YKDDIFALMLKGDTTYKELRSKIAPRID---T--DNFKLQTKLF   57 (85)
T ss_dssp             EEEEC-BTTCCEEEEECSCCCHHHHHHHHHHHHT---S--SCEEEEECCS
T ss_pred             EEEEE-ecCcEEEEECCCCCCHHHHHHHHHHHhc---c--cceEEEEecC
Confidence            44443 3567899999999999999999999987   4  455554 443

>4dbg_B Ring finger protein 31; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens}

Probab=90.43  E-value=0.22  Score=42.01  Aligned_cols=38  Identities=24%  Similarity=0.222  Sum_probs=32.0

Q ss_pred             cHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHH
Q 021760          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL  210 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL  210 (308)
                      .+...|.+|++.|  -|+|++|+.||+.+-.|.++|+--|
T Consensus       101 ~R~~K~~eL~s~G--~~~~~~~~~aL~~~~Gdv~~Al~eL  138 (162)
T 4dbg_B          101 TRRRKVQELQSLG--FGPEEGSLQALFQHGGDVSRALTEL  138 (162)
T ss_dssp             HHHHHHHHHHHTT--CCGGGTHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhcC--CchHHHHHHHHHHcCCcHHHHHHHH
Confidence            3456778899988  3499999999999999999998655

>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=90.18  E-value=0.21  Score=52.70  Aligned_cols=41  Identities=22%  Similarity=0.426  Sum_probs=37.3

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcCC-hHHHHHHHHhCCCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYNN-PERAVEYLYSGIPE  216 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafnN-pdRAvEYL~~GIP~  216 (308)
                      +..|+.|++||   |++..+++||.+.-|+ .++|.+||+..+-+
T Consensus       653 ~~~l~~L~~mG---f~~~~~~kal~~t~n~~~e~a~~wl~~hmdd  694 (854)
T 3ihp_A          653 ESVIIQLVEMG---FPMDACRKAVYYTGNSGAEAAMNWVMSHMDD  694 (854)
T ss_dssp             CHHHHHHHHHT---CCHHHHHHHHHHTTSCCHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHhcC---CCHHHHHHHHhhcCCCchHHHhHHHhhccCc
Confidence            57899999999   9999999999999886 99999999988653

>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=90.18  E-value=1.3  Score=40.54  Aligned_cols=74  Identities=15%  Similarity=0.054  Sum_probs=55.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCC-CCCeEEEe--CCE--ecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-ASQQMLIH--QGK--VLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip-~~~qkLIy--~GK--iL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |.+.|..++| ++.++|+.+.|+.+|-+.|....|   +. .+..-|.|  +|.  -|+.++.|.+.+++.+..+.+..+
T Consensus        23 ~~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~---L~e~~~FgL~~~~~~~~~wL~~~~~i~~q~~~~~~~~~l~fr   98 (314)
T 1h4r_A           23 FTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLG---LRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   98 (314)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHT---CCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             eEEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhC---CCCCccceEEEEeCCcCeeCCCccCHHHcCCCCCCCEEEEEE
Confidence            3577888898 788999999999999999999999   43 33345544  453  378889999987766666656655


Q ss_pred             cCC
Q 021760           76 KSK   78 (308)
Q Consensus        76 k~k   78 (308)
                      ++-
T Consensus        99 ~kf  101 (314)
T 1h4r_A           99 AKF  101 (314)
T ss_dssp             ESS
T ss_pred             EEE
Confidence            543

>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=89.94  E-value=0.55  Score=35.48  Aligned_cols=44  Identities=11%  Similarity=0.052  Sum_probs=37.6

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G   50 (308)
                      +|+|..  .-++.|+|....+..+|+++|.++.+   ++.+..+|.|+.
T Consensus         7 ~VKV~~--~~tvairvp~~~~y~~L~~~l~~kL~---l~~~~~~LsYk~   50 (83)
T 1oey_A            7 TLKVHY--KYTVVMKTQPGLPYSQVRDMVSKKLE---LRLEHTKLSYRP   50 (83)
T ss_dssp             EEEEES--SSEEEEEECTTCCHHHHHHHHHHHTT---CCGGGCCEEECC
T ss_pred             EEEEEE--EEEEEEECCCCCCHHHHHHHHHHHhC---CCcceeEEEeeC
Confidence            445553  36899999999999999999999999   888999999965

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=89.91  E-value=0.95  Score=36.76  Aligned_cols=60  Identities=22%  Similarity=0.255  Sum_probs=41.1

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHH----hCCCCCCC----CCeEEEe-C---CEecCC----------C----CChhhhcc
Q 021760           11 THFEIEVKPEDKVSDVKKNIETV----QGSDVYPA----SQQMLIH-Q---GKVLKD----------V----TTLEENKV   64 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~----~g~~~ip~----~~qkLIy-~---GKiL~D----------~----~tL~dygI   64 (308)
                      ..+.+.|-.++||.++|+||-+.    .|   +|.    +.+.|-| .   |++|.|          .    .||..|+|
T Consensus        39 ~~v~VkVLdCDTItQVKEKILdavYk~k~---~pys~r~~d~dLEwr~g~~~~~L~D~D~tS~~~e~~wkrLNTL~HY~V  115 (126)
T 3kuz_A           39 RNISVNVLDCDTIGQAKEKIFQAFLSKNG---SPYGLQLNEIGLELQMGTRQKELLDIDSSSVILEDGITKLNTIGHYEI  115 (126)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHHHHHS---SCCSSCGGGEEEEEEETTEEEEECSSCTTCCBCTTSCBCCCBTGGGTC
T ss_pred             CceEeeeecCCcHHHHHHHHHHHHhccCC---CcCCCCccccceEEecCCCcceeeccCCcceEecCCeeEeccccccCC
Confidence            46888888999999999999544    35   544    3344544 1   233322          1    36788999


Q ss_pred             CCCCEEEEE
Q 021760           65 AENSFVVVM   73 (308)
Q Consensus        65 k~g~~I~v~   73 (308)
                      .+|.+|-++
T Consensus       116 ~Dgatlal~  124 (126)
T 3kuz_A          116 SNGSTIKVF  124 (126)
T ss_dssp             CTTCEEEEE
T ss_pred             CCCCEEEEe
Confidence            999999765

>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=89.33  E-value=1.1  Score=45.39  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=45.6

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC------CCeEEEe----CCE-ecCCC-------------CChhhhccCC
Q 021760           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPA------SQQMLIH----QGK-VLKDV-------------TTLEENKVAE   66 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~------~~qkLIy----~GK-iL~D~-------------~tL~dygIk~   66 (308)
                      ..+.+.|-.++||.++|+||-+..-++ +|.      +.+.|-|    .|+ +|.|.             .||..|+|.+
T Consensus       274 ~~i~VkVLdCDTItQVKeKiLDavYk~-~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~d  352 (644)
T 3hm6_X          274 QGVPVKVLDCDTISQAKEKMLDQLYKG-VPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPD  352 (644)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTT-SCGGGSCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBTTTTTCCT
T ss_pred             CceeeEeeccCcHHHHHHHHHHHHHcC-CCcccCCCCCCcceEEeeCCCCceeecccCccceecCcceeecchhhcCCCC
Confidence            357788889999999999998654322 443      3455655    244 46553             3799999999


Q ss_pred             CCEEEEEEec
Q 021760           67 NSFVVVMLTK   76 (308)
Q Consensus        67 g~~I~v~v~k   76 (308)
                      |.+|.++-+.
T Consensus       353 ga~v~L~p~~  362 (644)
T 3hm6_X          353 GATVALVPCL  362 (644)
T ss_dssp             TCEEEEEEC-
T ss_pred             CcEEEEEecc
Confidence            9999876543

>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=88.83  E-value=0.3  Score=33.59  Aligned_cols=38  Identities=24%  Similarity=0.360  Sum_probs=32.8

Q ss_pred             CcHHHHHHHHHHhcCCccCHHHH--HHHHHHhcCChHHHHHHH
Q 021760          170 SNLEATVQQILDMGGGSWDRETV--IRALRAAYNNPERAVEYL  210 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f~r~qv--~~ALrAafnNpdRAvEYL  210 (308)
                      +..++.|.+|++||   |+-|--  .+.|.+.-+|-.+|++-|
T Consensus         8 ~rl~~al~qMl~MG---F~negGWLt~LL~~k~gDI~~aLD~l   47 (52)
T 1q02_A            8 PRLIESLSQMLSMG---FSDEGGWLTRLLQTKNYDIGAALDTI   47 (52)
T ss_dssp             HHHHHHHHHHHTTT---CCCTTSHHHHHHHHTTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHcC---CCccccHHHHHHHHccCCHHHHHHHh
Confidence            34789999999999   976654  699999999999999987

>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=88.65  E-value=1.3  Score=33.19  Aligned_cols=72  Identities=13%  Similarity=0.087  Sum_probs=44.4

Q ss_pred             CEEEEEeCC------CcEEEEEeCCCCcHHHHHHHHHHHhCC----------CCCCCCCeEEEeCCEecCCCCChhhhcc
Q 021760            1 MKVFVKTLK------GTHFEIEVKPEDKVSDVKKNIETVQGS----------DVYPASQQMLIHQGKVLKDVTTLEENKV   64 (308)
Q Consensus         1 M~I~Vktl~------gk~~~leV~~~~TV~~LK~~I~~~~g~----------~~ip~~~qkLIy~GKiL~D~~tL~dygI   64 (308)
                      |+|+|+.+.      |+...++++ ..||.+|++.+...+..          +.-......+..||+...+..- .++-|
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      333346654 57999999999877420          0000113566778887754322 24568


Q ss_pred             CCCCEEEEEE
Q 021760           65 AENSFVVVML   74 (308)
Q Consensus        65 k~g~~I~v~v   74 (308)
                      ++||.|.++-
T Consensus        79 ~~gDeV~i~P   88 (93)
T 3dwg_C           79 ADGDSVTILP   88 (93)
T ss_dssp             CTTCEEEEEE
T ss_pred             CCCCEEEEEC
Confidence            9999998873

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=88.39  E-value=1.1  Score=31.82  Aligned_cols=63  Identities=17%  Similarity=0.084  Sum_probs=42.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |.|+|...+|+.  +++....|+.+|-+.|....+     ....-...+|++.+-+     +-|++|+.|.++-.
T Consensus         1 m~i~i~~p~g~~--~~~~~g~T~~dla~~i~~~l~-----~~~vaa~vNg~lvdl~-----~~L~~~~~Veivt~   63 (73)
T 2kmm_A            1 MEVMVFTPKGEI--KRLPQGATALDFAYSLHSDLG-----DHCIGAKVNHKLVPLS-----YVLNSGDQVEVLSS   63 (73)
T ss_dssp             CCEEEECTTCCE--EEECTTCBHHHHHHHHCSHHH-----HTEEEEEETTEECCTT-----CBCCSSSBEEEEEC
T ss_pred             CeEEEEcCCCCE--EEcCCCCcHHHHHHHHhhccc-----cceEEEEECCEEeCCC-----cCcCCCCEEEEEEC
Confidence            788888768876  456678899999888754332     1223334689877654     45667888877653

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=88.36  E-value=0.63  Score=32.90  Aligned_cols=61  Identities=7%  Similarity=0.202  Sum_probs=42.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|   +|+.+  ++....||.+|.+.+    +   ++.....+..+|+++..+ ...+.-+++||.|.++-
T Consensus         1 m~i~v---Ng~~~--~~~~~~tv~~ll~~l----~---~~~~~v~vavN~~~v~~~-~~~~~~L~~gD~v~i~~   61 (66)
T 1f0z_A            1 MQILF---NDQAM--QCAAGQTVHELLEQL----D---QRQAGAALAINQQIVPRE-QWAQHIVQDGDQILLFQ   61 (66)
T ss_dssp             CCEEE---SSCEE--CCCTTCCHHHHHHHH----T---CCCSSEEEEETTEEECHH-HHTTCCCCTTEEECEEE
T ss_pred             CEEEE---CCEEE--EcCCCCcHHHHHHHc----C---CCCCCEEEEECCEECCch-hcCCcCCCCCCEEEEEe
Confidence            55554   46654  556678999998876    4   556777888999988532 23345688999998763

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=88.36  E-value=1.8  Score=43.81  Aligned_cols=65  Identities=18%  Similarity=0.295  Sum_probs=46.0

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCC------CCCeEEEe----CCE-ecCCC-------------CChhhhccCC
Q 021760           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYP------ASQQMLIH----QGK-VLKDV-------------TTLEENKVAE   66 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~~g~~~ip------~~~qkLIy----~GK-iL~D~-------------~tL~dygIk~   66 (308)
                      ..+.+.|-.++||.++|+||-+..-++ +|      ++++.|-|    .|+ +|.|.             .||.+|+|.+
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            468888989999999999997665322 43      34556654    233 35442             3689999999


Q ss_pred             CCEEEEEEec
Q 021760           67 NSFVVVMLTK   76 (308)
Q Consensus        67 g~~I~v~v~k   76 (308)
                      |.+|.++-+.
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            9999987543

>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=87.87  E-value=1.5  Score=44.06  Aligned_cols=75  Identities=13%  Similarity=0.105  Sum_probs=56.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCC-CCCeEEEeC---C--EecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-ASQQMLIHQ---G--KVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip-~~~qkLIy~---G--KiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |.|.|..++| ++.|.|+.+.|+.+|-..|+...|   +. .+..-|.|.   |  ..|+.++.|.+.+++.+..+.|.+
T Consensus         5 i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~Lg---L~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L~F   80 (575)
T 2i1j_A            5 MNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIG---LREVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQFKF   80 (575)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHT---CCCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEEEE
T ss_pred             EEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcC---CCCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEEEE
Confidence            3577888888 788999999999999999999999   43 334566552   2  457888999988877777666666


Q ss_pred             ecCCC
Q 021760           75 TKSKV   79 (308)
Q Consensus        75 ~k~k~   79 (308)
                      +++--
T Consensus        81 Rvkfy   85 (575)
T 2i1j_A           81 RAKFY   85 (575)
T ss_dssp             EESSC
T ss_pred             EEEEc
Confidence            65543

>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=87.67  E-value=0.61  Score=37.09  Aligned_cols=69  Identities=10%  Similarity=0.060  Sum_probs=41.7

Q ss_pred             CEEEEEeCC------C--cEEEEEeCC---CCcHHHHHHHHHHHhCCCCCCCCCeEEEe-CCE------ecCCCCC---h
Q 021760            1 MKVFVKTLK------G--THFEIEVKP---EDKVSDVKKNIETVQGSDVYPASQQMLIH-QGK------VLKDVTT---L   59 (308)
Q Consensus         1 M~I~Vktl~------g--k~~~leV~~---~~TV~~LK~~I~~~~g~~~ip~~~qkLIy-~GK------iL~D~~t---L   59 (308)
                      |+|+|+...      |  +.++|++..   ..||.+|.+.|.+.+.     ..+-+|+. +|+      +|-++..   |
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            678887542      3  366788873   3699999999987742     22333322 121      2322322   2


Q ss_pred             --hhhccCCCCEEEEEE
Q 021760           60 --EENKVAENSFVVVML   74 (308)
Q Consensus        60 --~dygIk~g~~I~v~v   74 (308)
                        .++-+++||.|.++-
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              357799999988864

>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=87.60  E-value=0.65  Score=34.39  Aligned_cols=63  Identities=16%  Similarity=0.210  Sum_probs=44.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCC-CCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip-~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|   +|+.+.+......||.+|.+.    .+   ++ ....-+.+||.++..+ ...++-+++||.|.++-
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---VAQAEYVTVELNGEVLERE-AFDATTVKDGDAVEFLY   64 (78)
T ss_dssp             CEEEE---TTEEEECSSCSCEEHHHHHHH----HT---CSCTTTCCEEETTEECCTT-HHHHCEECSSBCEEECC
T ss_pred             CEEEE---CCEEEEcCCCCCCcHHHHHHH----cC---CCCCCcEEEEECCEECChH-HcCcccCCCCCEEEEEe
Confidence            66665   476554421156799998775    45   66 6777788999998543 46677899999998863

>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=86.81  E-value=2.4  Score=39.70  Aligned_cols=72  Identities=22%  Similarity=0.215  Sum_probs=54.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC---------EecCCCCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---------KVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G---------KiL~D~~tL~dygIk~g~~I~v   72 (308)
                      .+.|..++|....+.|+.+.|+.+|-+.|+...|.  ...+..-|.+..         +-|+.+++|.+.++.....+++
T Consensus        87 ~~~V~l~dg~~~~~~vd~~tt~~el~~~v~~~l~L--~e~~~FgL~~~~~~~~~~~~~~wL~~~k~l~~q~~~~~~~l~f  164 (371)
T 3ivf_A           87 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGI--TNHDEYSLVRELMEEKKDDELNWLDHGRTLREQGVEEHETLLL  164 (371)
T ss_dssp             EEEEECTTSCEEEEEEETTSBHHHHHHHHHHHTTC--SCGGGEEEECCC----------CCCTTSBTGGGTCCTTCEEEE
T ss_pred             EEEEECcCCCEEEEEECCCCCHHHHHHHHHHHcCC--CCccccEEEEEecccccchHHHHHhcCchhHhhCCCCCceEEE
Confidence            57788899999999999999999999999999983  234456666532         3467778888877766666665


Q ss_pred             EEe
Q 021760           73 MLT   75 (308)
Q Consensus        73 ~v~   75 (308)
                      .++
T Consensus       165 rvK  167 (371)
T 3ivf_A          165 RRK  167 (371)
T ss_dssp             EEC
T ss_pred             EEE
Confidence            443

>3qij_A Protein 4.1; cytoskeleton, structural genomics, structural genomics conso SGC; 1.80A {Homo sapiens} PDB: 1gg3_A 3bin_A 2he7_A 2rq1_A

Probab=86.33  E-value=2.8  Score=38.19  Aligned_cols=71  Identities=14%  Similarity=-0.011  Sum_probs=50.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--EecCCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G--KVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~---G--KiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      |.+.|..++|....++|+...|+.+|-+.|....|.  ...+..-|.|.   |  ..|+.++.|.+........+++.
T Consensus        18 ~~~~V~lldgt~~~~~vd~~tt~~el~~~v~~~l~L--~e~~~FgL~~~~~~~~~~wLd~~k~i~~q~~~~~~~l~fr   93 (296)
T 3qij_A           18 GHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNL--LEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTFN   93 (296)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHTC--SSGGGEEEEEEEETTEEEECCTTSBHHHHC---CCEEEEE
T ss_pred             EEEEEEccCCCEEEEEECCCCCHHHHHHHHHHHcCC--CCcceeEEEEEcCCCccchhccchhHHHhcCCCCcEEEEE
Confidence            568899999999999999999999999999999992  22333555542   3  34788888888754333344443

>1tte_A Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiquitin-dependent degradation, ligase; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1 d.20.1.1

Probab=84.87  E-value=0.6  Score=41.26  Aligned_cols=23  Identities=13%  Similarity=0.514  Sum_probs=21.2

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHH
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRA  198 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrA  198 (308)
                      +..|+++++||   |+|++|+.||+-
T Consensus       170 ~~~v~~~~~mg---~~~~~~~~al~~  192 (215)
T 1tte_A          170 HDLIDEFESQG---FEKDKIVEVLRR  192 (215)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHH
Confidence            67999999999   999999999964

>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei}

Probab=84.68  E-value=0.26  Score=39.11  Aligned_cols=69  Identities=10%  Similarity=0.099  Sum_probs=41.3

Q ss_pred             CEEEEEeCC------CcEEEEEeCC----CCcHHHHHHHHHHHhCCCCCCCCCeEEE-eCC--E------ecCCCCCh--
Q 021760            1 MKVFVKTLK------GTHFEIEVKP----EDKVSDVKKNIETVQGSDVYPASQQMLI-HQG--K------VLKDVTTL--   59 (308)
Q Consensus         1 M~I~Vktl~------gk~~~leV~~----~~TV~~LK~~I~~~~g~~~ip~~~qkLI-y~G--K------iL~D~~tL--   59 (308)
                      |+|+||...      |+...+++..    ..||.+|-+.|.+.+.     ..+-+|+ -+|  +      +|-++..+  
T Consensus         5 m~v~V~f~g~l~~l~g~~~~v~l~~~~g~~~TV~dLl~~L~~~~~-----~~r~~lf~~~g~~~lrpgIlVLVNg~d~e~   79 (110)
T 2k9x_A            5 NHITVQFAGGCELLFAKQTSLQLDGVVPTGTNLNGLVQLLKTNYV-----KERPDLLVDQTGQTLRPGILVLVNSCDAEV   79 (110)
T ss_dssp             SCCEEEEESSCGGGTTSCSEECCCCSCGGGCCHHHHHHHHTTTTC-----CSCHHHHBCSSSSSBCTTEEEEESSSBHHH
T ss_pred             cEEEEEEEecHHHHhCCeEEEEeCCcCCCCccHHHHHHHHHHHcc-----ccchhhEecCCCcccCCCeEEEECCeeeec
Confidence            567777543      4555677763    2499999888887643     2333333 223  1      34344433  


Q ss_pred             ---hhhccCCCCEEEEEE
Q 021760           60 ---EENKVAENSFVVVML   74 (308)
Q Consensus        60 ---~dygIk~g~~I~v~v   74 (308)
                         .+|-+++||.|.++-
T Consensus        80 l~gldt~L~dgD~V~fis   97 (110)
T 2k9x_A           80 VGGMDYVLNDGDTVEFIS   97 (110)
T ss_dssp             HTSSCCCCCSSCEEEEEE
T ss_pred             cCCcccCCCCcCEEEEeC
Confidence               346799999987753

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=84.24  E-value=2.2  Score=30.58  Aligned_cols=54  Identities=7%  Similarity=0.089  Sum_probs=39.7

Q ss_pred             cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCe--EEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760           11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQ--MLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        11 k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~q--kLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      +...+++....||.+|.+.+...+..    ....  .+..||++...+     .-+++||.|.++
T Consensus        16 ~~~~~~~~~~~tv~~ll~~l~~~~p~----~~~v~~~v~vNg~~v~~~-----~~L~~gD~V~i~   71 (77)
T 2q5w_D           16 AQEDIVLEQALTVQQFEDLLFERYPQ----INNKKFQVAVNEEFVQKS-----DFIQPNDTVALI   71 (77)
T ss_dssp             SEEECCCSSCEEHHHHHHHHHHHCGG----GTTCCCEEEETTEEECTT-----SEECTTCEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCcc----hhcceEEEEECCEECCCC-----CCcCCCCEEEEE
Confidence            35667777778999999998776320    1233  778899998753     578999998886

>2l52_A Methanosarcina acetivorans SAMP1 homolog; beta-grAsp fold, protein binding, E1-like, SAMP activator, ELSA, adenylation, ubiquitin; NMR {Methanosarcina acetivorans}

Probab=83.63  E-value=4.1  Score=31.05  Aligned_cols=67  Identities=16%  Similarity=0.228  Sum_probs=41.9

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCC---------CCe-------EEEeCCEecCCCC
Q 021760            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGSDVYPA---------SQQ-------MLIHQGKVLKDVT   57 (308)
Q Consensus         1 M~I~Vktl~------g-k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~---------~~q-------kLIy~GKiL~D~~   57 (308)
                      |+|+|+.+.      | +.+.++   ..||.+|.+.+......  +..         ...       .+..||+......
T Consensus         4 m~v~V~~fa~lr~~~g~~~~~l~---~~tv~~ll~~L~~~~p~--l~~~l~~~g~l~~~v~~~~~~~~v~VNg~~v~~~~   78 (99)
T 2l52_A            4 AEVKVKLFANLREAAGTPELPLS---GEKVIDVLLSLTDKYPA--LKYVIFEKGDEKSEILILCGSINILINGNNIRHLE   78 (99)
T ss_dssp             CEEEEEECTHHHHHHSSSEEEEE---CSSHHHHHHHHHHHCGG--GTTTSBCSCCTTSSCCCBCSSCEEEETTSCGGGTT
T ss_pred             eEEEEEEeHHHHHHhCCCeEEEe---CCcHHHHHHHHHHHChh--HHHHHhcccccccceeccccccEEEECCEEccccC
Confidence            688888653      3 344444   57999999999877420  111         123       5677887663221


Q ss_pred             ChhhhccCCCCEEEEE
Q 021760           58 TLEENKVAENSFVVVM   73 (308)
Q Consensus        58 tL~dygIk~g~~I~v~   73 (308)
                       -.++-+++||.|.++
T Consensus        79 -~~~~~L~~gD~V~i~   93 (99)
T 2l52_A           79 -GLETLLKDSDEIGIL   93 (99)
T ss_dssp             -STTSCCCTTEEEEEE
T ss_pred             -CCCCCCCCCCEEEEE
Confidence             124468999998886

>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A

Probab=83.56  E-value=1.7  Score=33.23  Aligned_cols=68  Identities=12%  Similarity=0.118  Sum_probs=40.5

Q ss_pred             CEEEEEeC------C-C-cEEEEEeC--CCCcHHHHHHHHHHHhCCCCCCC--------C----CeEEEeCCEecCCCCC
Q 021760            1 MKVFVKTL------K-G-THFEIEVK--PEDKVSDVKKNIETVQGSDVYPA--------S----QQMLIHQGKVLKDVTT   58 (308)
Q Consensus         1 M~I~Vktl------~-g-k~~~leV~--~~~TV~~LK~~I~~~~g~~~ip~--------~----~qkLIy~GKiL~D~~t   58 (308)
                      |+|+|+.+      . | +.+++++.  ...||.+|.+.+.++...  ...        .    ...+..||+..+   .
T Consensus         2 M~i~V~~fa~lre~~~g~~~~~~~l~~~~~~Tv~~L~~~L~~~~~~--~~~~l~~~~~~~~lr~~~~v~VN~~~~~---~   76 (99)
T 2qjl_A            2 VNVKVEFLGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMIN--NPNDVSIFIEDDSIRPGIITLINDTDWE---L   76 (99)
T ss_dssp             EEEEEEEETTGGGGTTTCCEEEEEECSCSCCBHHHHHHHHHHHTCS--SGGGHHHHEETTEECTTEEEEETTEEGG---G
T ss_pred             cEEEEEEchHHHHHhCCCcEEEEecCCCCCCcHHHHHHHHHHHCch--hhHHHhhhccCCccccCeEEEECCEEcc---c
Confidence            57787743      2 2 45677776  678999999999887531  100        0    011233443211   1


Q ss_pred             h--hhhccCCCCEEEEE
Q 021760           59 L--EENKVAENSFVVVM   73 (308)
Q Consensus        59 L--~dygIk~g~~I~v~   73 (308)
                      +  .++-|++||.|.++
T Consensus        77 ~~~~d~~L~dgDeVa~~   93 (99)
T 2qjl_A           77 EGEKDYILEDGDIISFT   93 (99)
T ss_dssp             GTGGGCBCCTTCEEEEE
T ss_pred             cCCCCcCcCCCCEEEEE
Confidence            2  35679999998876

>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=82.86  E-value=1.1  Score=31.82  Aligned_cols=29  Identities=10%  Similarity=0.186  Sum_probs=25.2

Q ss_pred             cCCcHHHHHHHHHHhcCCccCHHHHHHHHHHh
Q 021760          168 AGSNLEATVQQILDMGGGSWDRETVIRALRAA  199 (308)
Q Consensus       168 ~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAa  199 (308)
                      .+...++.|.-|+.+|   |.+.++.+|++..
T Consensus        13 ~~~~~~ea~~AL~aLG---Y~~~ea~kav~~v   41 (62)
T 1ixs_A           13 ESEAAEEAVMALAALG---FKEAQARAVVLDL   41 (62)
T ss_dssp             CCHHHHHHHHHHHHTT---CCHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHcC---CCHHHHHHHHHHH
Confidence            3445688999999999   9999999999876

>3onh_A Ubiquitin-activating enzyme E1-like; ligase, SUMO conjugation, UBC9; 1.60A {Saccharomyces cerevisiae} PDB: 3ong_A

Probab=82.59  E-value=3.8  Score=33.25  Aligned_cols=58  Identities=24%  Similarity=0.327  Sum_probs=40.8

Q ss_pred             EEEeCC----CCcHHHHHHHHHHHhCCCCCCCCCeEEEe--CCEec-----CC--CCChhhhccCCCCEEEEEEe
Q 021760           14 EIEVKP----EDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVL-----KD--VTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus        14 ~leV~~----~~TV~~LK~~I~~~~g~~~ip~~~qkLIy--~GKiL-----~D--~~tL~dygIk~g~~I~v~v~   75 (308)
                      .|.|+.    ..|+.+|-+.|..++|   +. +.+-++-  ..+.|     +|  +++|+++||++|++|.|+--
T Consensus         9 vl~v~~~dl~~~TL~dLV~~l~~~~g---y~-~eiSV~~~~~~rLLyD~DfDDnl~k~L~dLgv~~gsfLtv~DE   79 (127)
T 3onh_A            9 VIKLSSDCLNKMKLSDFVVLIREKYS---YP-QDISLLDASNQRLLFDYDFEDLNDRTLSEINLGNGSIILFSDE   79 (127)
T ss_dssp             EEEECHHHHHHCBHHHHHHHHHHHHT---CC-SSEEEEETTTTEEEEETTBCTTTTSBTTTTTCCTTCEEEEEES
T ss_pred             EEEeCcccccccCHHHHHHHHHHhcC---CC-CcEEEEecCCCCeEeCCCccccccCcHHHcCcCCCcEEEEEcc
Confidence            355553    4699999888988888   54 3454442  33444     33  47999999999999988753

>1wgr_A Growth factor receptor-bound protein 7; RA domain, GRB7, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=81.76  E-value=5.3  Score=31.03  Aligned_cols=74  Identities=19%  Similarity=0.098  Sum_probs=50.3

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--e----CCEecCCCCChhhh----ccCCCCEEEE
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--H----QGKVLKDVTTLEEN----KVAENSFVVV   72 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y----~GKiL~D~~tL~dy----gIk~g~~I~v   72 (308)
                      |+|-..+|....|.|+..+|+.++-+++..+.++. . ...--|+  +    --+.|+|+..|-+.    .+..+..|++
T Consensus        12 vkvf~~Dgssksi~V~~~~Ta~dv~~~L~~K~~~~-~-~~~WaLvE~~P~L~~ER~~EDHE~vvevl~~W~~~s~nr~~F   89 (100)
T 1wgr_A           12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHAL-S-DETWGLVECHPHLALERGLEDHESVVEVQAAWPVGGDSRFVF   89 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCC-C-CCCCCEEEEETTTTEEEEECSSSCHHHHHTTSCSSSCCEEEE
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCC-C-CCCeEEEEecCCCCcEEeccCchhHHHHHhhCccCCCcEEEE
Confidence            45556789999999999999999999999998742 1 2222232  1    23778998876554    4555666666


Q ss_pred             EEecCC
Q 021760           73 MLTKSK   78 (308)
Q Consensus        73 ~v~k~k   78 (308)
                      .-+..|
T Consensus        90 ~kr~~K   95 (100)
T 1wgr_A           90 RKNFAS   95 (100)
T ss_dssp             CSCCSS
T ss_pred             ecchhc
Confidence            444333

>1vd2_A Protein kinase C, IOTA type; PB1 domain, OPCA motif, APKC, ZIP/P62, MEK5, molecular recognition, transferase; NMR {Homo sapiens} SCOP: d.15.2.2 PDB: 1wmh_A

Probab=81.71  E-value=4  Score=31.08  Aligned_cols=45  Identities=7%  Similarity=0.105  Sum_probs=35.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCC-CeEEEeCC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS-QQMLIHQG   50 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~-~qkLIy~G   50 (308)
                      +|++. .+|..+.+.|+++.+..+|.++|.+.++   +..+ ...|-|..
T Consensus         8 kvK~~-~~gdi~~~~v~~~i~~~~L~~kv~~~~~---~~~~~~f~lky~D   53 (89)
T 1vd2_A            8 RVKAY-YRGDIMITHFEPSISFEGLCNEVRDMCS---FDNEQLFTMKWID   53 (89)
T ss_dssp             EEEEE-SSSCEEEEEECTTCCHHHHHHHHHHHTT---CCSSCCEEEEECC
T ss_pred             EEEEE-eCCeEEEEECCCCCCHHHHHHHHHHHhC---CCCCCeEEEEEEC
Confidence            44444 4678889999999999999999999988   6544 46777765

>1ufz_A Hypothetical protein BAB28515; HBS1-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, translatio; NMR {Mus musculus} SCOP: a.5.9.1

Probab=80.78  E-value=3.8  Score=30.82  Aligned_cols=42  Identities=10%  Similarity=0.158  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      +..-+.+|-+.=|.++++.+.+.|.-..-+|++||+.|+|+.
T Consensus        34 L~SCLd~iR~VlGdsV~e~~Lv~ailk~dfD~ekALd~vL~~   75 (83)
T 1ufz_A           34 LYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQ   75 (83)
T ss_dssp             HHHHHHHHHHHTTTTSCHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccCCHHHHHHHHHHhcCCHHHHHHHHHhc
Confidence            445567777765678899999888888999999999999964

>1y8x_B Ubiquitin-activating enzyme E1C; ubiquitin-conjugating enzyme E2 M, ligase; 2.40A {Homo sapiens} SCOP: c.111.1.2 PDB: 3fn1_A

Probab=80.45  E-value=1.3  Score=34.46  Aligned_cols=59  Identities=17%  Similarity=0.217  Sum_probs=40.0

Q ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCC-----------eEEEeCC-EecC------CCCChhhhccCCCCEEEEE
Q 021760           12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQ-----------QMLIHQG-KVLK------DVTTLEENKVAENSFVVVM   73 (308)
Q Consensus        12 ~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~-----------qkLIy~G-KiL~------D~~tL~dygIk~g~~I~v~   73 (308)
                      ...|+|+++.|+.+|-+.|.+.-.   +....           ..|++.+ ..|+      =+++|.++|+.+|+.|+|.
T Consensus         6 ~~~l~v~~~~TL~~lid~L~~~p~---~qlk~PSltt~~~~~~k~LYmq~pp~Lee~Tr~NL~k~l~eLgl~~g~ei~Vt   82 (98)
T 1y8x_B            6 PQNIQFSPSAKLQEVLDYLTNSAS---LQMKSPAITATLEGKNRTLYMQSVTSIEERTRPNLSKTLKELGLVDGQELAVA   82 (98)
T ss_dssp             CCCEECCTTCBHHHHHHHHHHCTT---CCCSSCEEEEEETTEEEEEECSSCHHHHHHHHHHHHSBSGGGTCCTTCEEEEE
T ss_pred             cEEEEECCchhHHHHHHHHHhChH---hhccCCeeeeecCCCCCeEEEeCcHHHHHHhHhhhhCCHHHhCCCCCCEEEEE
Confidence            346899999999999999988533   22222           2333333 2332      2577999999999998883

---

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	308
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	3e-27
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	8e-24
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	6e-21
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	8e-20
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	6e-19
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	3e-18
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	5e-18
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	9e-18
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	1e-17
d1oqya1	41	a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Hum	4e-17
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	6e-17
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	8e-17
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	2e-16
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	2e-16
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	6e-16
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	7e-16
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	9e-16
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	2e-15
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	2e-13
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	2e-13
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	3e-13
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	3e-13
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	5e-13
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	7e-13
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	1e-12
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	1e-12
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	6e-11
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	1e-10
d1wjia_	63	a.5.2.1 (A:) Tudor domain containing protein 3, TD	3e-10
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	8e-10
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	9e-10
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	1e-09
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	5e-09
d1wiva_	73	a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress	6e-09
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	8e-09
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	2e-08
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	3e-08
d1wgna_	63	a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1	1e-07
d2f4mb1	58	a.189.1.1 (B:275-332) XPC-binding domain of Rad23	9e-07
d1vg5a_	73	a.5.2.1 (A:) Rhomboid family protein At3g58460 {Th	2e-06
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	1e-05
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	1e-05
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	1e-05
d1whca_	64	a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus	1e-04
d2bwba1	44	a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharom	8e-04
d2gqba1	130	a.282.1.1 (A:1-130) Hypothetical protein RPA2825 {	0.003

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 99.6 bits (248), Expect = 3e-27
 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 = 90.9 bits (225), Expect = 8e-24
 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

>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 = 82.6 bits (204), Expect = 6e-21
 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 = 80.0 bits (197), Expect = 8e-20
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          M++FVKTL G    +EV+P D + +VK  I+  +G    P  QQ LI  GK L+D  TL 
Sbjct: 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 = 77.2 bits (190), Expect = 6e-19
 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 = 75.7 bits (186), Expect = 3e-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

>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 = 74.8 bits (184), Expect = 5e-18
 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

>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 = 74.9 bits (184), 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

>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 = 73.7 bits (181), Expect = 1e-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 = 71.5 bits (176), Expect = 4e-17
 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 = 71.8 bits (176), Expect = 6e-17
 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 = 71.5 bits (175), Expect = 8e-17
 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

>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 = 70.7 bits (173), Expect = 2e-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

>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 = 70.7 bits (173), Expect = 2e-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

>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 = 69.6 bits (170), Expect = 6e-16
 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

>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 = 69.5 bits (170), Expect = 7e-16
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 1  MKVFVKTLKGTH--FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTT 58
          + + VK+    H   E+       V  +K ++  V          Q LI+ GK+L D   
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERP-RPEDQRLIYSGKLLLDHQC 66

Query: 59 LEENKVAENSFVVVMLTKS--KVSSSG 83
          L +    +    V+ L  +     SSG
Sbjct: 67 LRDLLPKQEKRHVLHLVCNVKSGPSSG 93

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 116

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.0 bits (171), Expect = 9e-16
 Identities = 19/90 (21%), Positives = 33/90 (36%), Gaps = 5/90 (5%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNI-----ETVQGSDVYPASQQMLIHQGKVLKD 55
           + + +  + G   E    P D  SD+ K++        +   V   +   LI+QG+ L  
Sbjct: 17  INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHG 76

Query: 56  VTTLEENKVAENSFVVVMLTKSKVSSSGAS 85
             TL   K+      V+ L   +      S
Sbjct: 77  NVTLGALKLPFGKTTVMHLVARETLPEPNS 106

>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

>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 = 63.5 bits (154), Expect = 2e-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

>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 = 63.1 bits (153), Expect = 2e-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

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.7 bits (152), Expect = 3e-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

>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 = 62.3 bits (151), Expect = 3e-13
 Identities = 18/101 (17%), Positives = 36/101 (35%), Gaps = 12/101 (11%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
             V VK  K     +E+  ++     K  +  + G      ++Q ++ +G  LKD     
Sbjct: 8   YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTG---VQPARQKVMVKGGTLKD-DDWG 63

Query: 61  ENKVAENSFVVVMLTKSKVSSSGASTVSAAPANQAQTTSSA 101
             K+     V++M +   +           P+ +    SS 
Sbjct: 64  NIKMKNGMTVLMMGSADALPE--------EPSAKTSGPSSG 96

>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 = 61.5 bits (149), Expect = 5e-13
 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

>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 = 60.8 bits (147), Expect = 7e-13
 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

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 105

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.2 bits (148), Expect = 1e-12
 Identities = 19/102 (18%), Positives = 30/102 (29%), Gaps = 21/102 (20%)

Query: 1   MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM--------------- 45
           M V V  + G    + V     V D+KK I+           ++                
Sbjct: 8   MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ---LKQEREGGVQHISWSYVWRTYH 64

Query: 46  LIHQGKVLKDVT-TLEENKVAENSFVVVMLTKSKVSSSGAST 86
           L   G+ L +    L +  +       V   K     SG S+
Sbjct: 65  LTSAGEKLTEDRKKLRDYGIRNRD--EVSFIKKLGQKSGPSS 104

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.7 bits (147), Expect = 1e-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

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 6e-11
 Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 3  VFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
          VF+   +  T    + K    V ++K+ +E +      P  +Q L    ++L D  TL E
Sbjct: 2  VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK---RPPDEQRLYKDDQLLDDGKTLGE 58

Query: 62 NKVAENS 68
                +
Sbjct: 59 CGFTSQT 65

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.9 bits (132), Expect = 1e-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

>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 = 52.7 bits (126), Expect = 8e-10
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +KV VKT K    +  V     +  +K+ I            Q +LI  GK+LKD  +L 
Sbjct: 8  IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLA 63

Query: 61 ENKVAENSFVVVMLTKSK 78
          +  V +   V +++ +  
Sbjct: 64 QCGVRDGLTVHLVIKRQH 81

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.6 bits (126), Expect = 9e-10
 Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          + + +     T  +++V  +   S++K+ I ++ G    P + Q +++   ++ +  TL 
Sbjct: 18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMY-KGLVPEDKTLR 72

Query: 61 ENKVAENSFVVVMLTKSKVSSSG 83
          E KV   + ++V+ +     SSG
Sbjct: 73 EIKVTSGAKIMVVGSTISGPSSG 95

>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 = 52.3 bits (125), 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

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 50.7 bits (121), Expect = 5e-09
 Identities = 12/80 (15%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 1  MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGSD----VYPASQQMLIHQGKVLKD 55
          +++  +   G+            VS +K+ + +    +         +  LI  GKVL++
Sbjct: 8  LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLEN 67

Query: 56 VTTLEENKVAENSFVVVMLT 75
            T+++ +   ++    + T
Sbjct: 68 SKTVKDYRSPVSNLAGAVTT 87

>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 = 6e-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

>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 = 49.3 bits (118), Expect = 8e-09
 Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 1  MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLE 60
          +K+ V     +    +VK    +  +K++    QG    P +    + +G+ + D  T +
Sbjct: 3  IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPK 59

Query: 61 ENKVAENSFVVVML 74
          E  + E   + V  
Sbjct: 60 ELGMEEEDVIEVYQ 73

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]} Length = 79

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

 Score = 48.3 bits (115), Expect = 2e-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

>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 = 3e-08
 Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 2  KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEE 61
          K  ++ L  T           +S +K+ I       V       LI+ G+ LKD  TL+ 
Sbjct: 20 KSILQ-LPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDF 78

Query: 62 NKVAENSFVVVML 74
            +   S V V+ 
Sbjct: 79 YGIQPGSTVHVLR 91

>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 = 45.9 bits (109), 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

>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 = 43.1 bits (102), Expect = 9e-07
 Identities = 13/26 (50%), Positives = 18/26 (69%)

Query: 277 LDFLRNSQQFQALRTMVQANPQILQQ 302
           L+FLRN  QFQ +R ++Q NP +L  
Sbjct: 2   LEFLRNQPQFQQMRQIIQQNPSLLPA 27

>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 = 42.6 bits (100), Expect = 2e-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

>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 = 41.0 bits (96), Expect = 1e-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 = 41.5 bits (97), Expect = 1e-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

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 11/79 (13%), Positives = 26/79 (32%), Gaps = 11/79 (13%)

Query: 6  KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK--------DVT 57
             +    E ++     V  VK  +  +      P S+ +L ++   +         D+ 
Sbjct: 18 NQPERQILEKQLPDSMTVQKVKGLLSRLLK---VPVSELLLSYESSKMPGREIELENDLQ 74

Query: 58 TLEENKVAENSFVVVMLTK 76
           L+   V     ++V  + 
Sbjct: 75 PLQFYSVENGDCLLVRWSG 93

>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 = 37.1 bits (86), Expect = 1e-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 = 34.6 bits (80), Expect = 8e-04
 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	308
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.86
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.84
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.84
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.83
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.82
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.82
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.82
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.82
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.81
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.81
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.8
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.78
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.78
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.78
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.78
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.77
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.77
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.75
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.74
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.74
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.74
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.73
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.73
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.72
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.71
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.71
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.69
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	99.67
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.66
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.66
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.66
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.65
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.58
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.51
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.44
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.42
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.38
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.37
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	99.36
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	99.35
d2f4mb1	58	XPC-binding domain of Rad23 homolog B (Hhr23b) {Hu	99.35
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	99.32
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	99.23
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.22
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	99.04
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	98.93
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	98.81
d2bwba1	44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.64
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	98.64
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	98.63
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	98.59
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.51
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	98.46
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	98.4
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	98.39
d3e46a1	42	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal	97.77
d1oqya2	44	DNA repair protein Hhr23a {Human (Homo sapiens) [T	97.57
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	97.49
d1z96a1	38	UBA-domain protein mud1 {Schizosaccharomyces pombe	97.32
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.29
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.87
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	96.76
d1wj7a1	91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	96.67
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	96.65
d2cosa1	41	Serine/threonine protein kinase LATS2 {Mouse (Mus	96.49
d1vega_	83	NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculu	96.13
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	95.54
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	95.01
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	94.0
d1ttea1	55	Ubiquitin-protein ligase ubc1 {Baker's yeast (Sacc	93.91
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	93.88
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	93.23
d1x3zb1	57	Rad23 STI1 domain {Baker's yeast (Saccharomyces ce	92.98
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	92.95
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	91.98
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	91.25
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	91.21
d2dkla1	72	Trinucleotide repeat containing 6c protein, TNRC6C	89.96
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	89.36
d2cp8a1	41	Migration-inducing protein 19 NBR1 {Human (Homo sa	88.32
d2di0a1	63	Activating signal cointegrator 1 complex subunit 2	88.29
d1h4ra3	84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	87.02
d1ip9a_	85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	83.89
d1v92a_	46	NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {	83.28
d1cuka1	48	DNA helicase RuvA subunit, C-terminal domain {Esch	82.57
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	80.49

>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=99.86  E-value=1.4e-21  Score=152.22  Aligned_cols=80  Identities=45%  Similarity=0.727  Sum_probs=74.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKVS   80 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~~   80 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|.+.+++++|||||+||+|+|+++|++|||++|++|+|++++++..
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            99999999999999999999999999999999987555899999999999999999999999999999999999876543

>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=99.84  E-value=3e-21  Score=143.21  Aligned_cols=73  Identities=34%  Similarity=0.545  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+++|++|.++|++++||.+||++|+.+.|   +++++|||+|+||+|+|+.+|++|||++|++||+++|.
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=99.84  E-value=6.6e-21  Score=146.14  Aligned_cols=76  Identities=29%  Similarity=0.446  Sum_probs=73.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||||+||+|+|+++|++|+|+++++|||+.+++..
T Consensus         8 mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~g   83 (87)
T d1wh3a_           8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSG   83 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTC---CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCC
T ss_pred             EEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHC---cChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCCC
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999887653

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=8.9e-21  Score=141.71  Aligned_cols=75  Identities=37%  Similarity=0.605  Sum_probs=72.9

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|++|.++|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++|||++|++|+++++.+.
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=99.82  E-value=1.1e-20  Score=142.20  Aligned_cols=75  Identities=27%  Similarity=0.406  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+.+|++|.|+|++++||.+||++|+++.|   +|+++|||+|+||.|+|+++|++|+|+++++||++.|.+.
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~g---ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~rg   77 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQG---VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   77 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHT---CCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESSCC
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHC---cChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998764

>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=99.82  E-value=9.2e-21  Score=142.06  Aligned_cols=75  Identities=36%  Similarity=0.663  Sum_probs=71.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+...|.+.+|+++|||||+||+|+|+++|++|||++|++|+||++
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            789999999999999999999999999999999885558999999999999999999999999999999999985

>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=99.82  E-value=2.8e-20  Score=138.88  Aligned_cols=73  Identities=25%  Similarity=0.325  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+++|+++.++|++++||.+||.+|+.+.|   +++++|||+|+||.|+|+++|++|||++|++||+++|.
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=99.82  E-value=2e-20  Score=141.26  Aligned_cols=75  Identities=20%  Similarity=0.376  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+++|++|.|+|++++||.+||.+|+.+.|   +|+++|||+|+||.|+|+++|++|||++|++|||+++++.
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   9999999999999999999999999999999999998754

>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=99.81  E-value=3.9e-20  Score=138.57  Aligned_cols=73  Identities=22%  Similarity=0.352  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCc-EEEEE-eCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGT-HFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk-~~~le-V~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+++|+ ++.++ +++++||.+||.+|+.+.|   +|+++|||+|+||.|+|+.+|++|||++|++||+++|+
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 8999999999999999999   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=99.81  E-value=1.5e-20  Score=139.58  Aligned_cols=73  Identities=29%  Similarity=0.400  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||||+||.|+|+++|++|+| +|++||++.|.|
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 579999887653

>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=99.80  E-value=1.6e-19  Score=135.10  Aligned_cols=73  Identities=21%  Similarity=0.319  Sum_probs=69.3

Q ss_pred             CEEEEEeCCC-cEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKG-THFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~g-k~~~l-eV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+++| +++.+ +|++++||.+||.+|+.+.|   +|+++|||+|+||.|+|+++|++|||++|++||+++|.
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~rp   75 (76)
T d1wy8a1           1 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD---VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   75 (76)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSC---CCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHC---CCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEcc
Confidence            8999999998 57887 59999999999999999999   99999999999999999999999999999999999873

>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=99.78  E-value=1.9e-19  Score=142.14  Aligned_cols=75  Identities=21%  Similarity=0.380  Sum_probs=68.8

Q ss_pred             CEEEE----EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecC-CCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFV----KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~V----ktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~-D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+|    |++++++|.|+|++++||.+||++|+.+.|   +|+++|||||+||.|. |+++|++|||++|++|+|+.+
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            78999    788899999999999999999999999999   9999999999999995 567999999999999998866


Q ss_pred             cCC
Q 021760           76 KSK   78 (308)
Q Consensus        76 k~k   78 (308)
                      +..
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=99.78  E-value=2.7e-19  Score=133.81  Aligned_cols=72  Identities=29%  Similarity=0.393  Sum_probs=70.0

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe--CCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy--~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      +|+||+++|+.|.|+|++++||.+||.+|+.+.|   +|+++|||+|  +||+|+|+.+|++|||++|++|||++++
T Consensus         2 ~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           2 DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG---VHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             EEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHC---CCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhc---cCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            6999999999999999999999999999999999   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=99.78  E-value=2.5e-19  Score=132.98  Aligned_cols=71  Identities=27%  Similarity=0.388  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+||+..|+++.|+|++++||.+||++|+.+.|   +++++|||+|+||.|+|+.+|++|||++|++|++..
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   999999999999999999999999999999999863

>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=99.78  E-value=4.7e-19  Score=138.12  Aligned_cols=75  Identities=25%  Similarity=0.272  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecC-CCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~-D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+++|+.|.|+|++++||.+||++|+   .   ++.++|||||+||+|. |.++|++|+|++|++|||++++++.
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 5689999999999999999987765


Q ss_pred             CC
Q 021760           80 SS   81 (308)
Q Consensus        80 ~~   81 (308)
                      +.
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=99.77  E-value=3.8e-19  Score=135.35  Aligned_cols=75  Identities=27%  Similarity=0.326  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      |+|+||+.++ +|.|+|++++||.+||++|+.+.|   +++++|||+|+||.|+|+++|++|||++|++|||+++++..
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            7899998765 689999999999999999999999   99999999999999999999999999999999999887653

>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=99.77  E-value=5.5e-19  Score=130.97  Aligned_cols=72  Identities=29%  Similarity=0.501  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+. +++|.|+|++++||.+||++|+...|   +|+++|||||+||.|+|+++|++|||++|++|||+.++
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   99999999999999999999999999999999999864

>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=99.75  E-value=8.5e-19  Score=136.75  Aligned_cols=74  Identities=20%  Similarity=0.204  Sum_probs=68.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+||+.+++.+.|+|++++||.+||++|+..+|   +|+++|||||+||.|+|+ +|++|||++|++|+||.++..
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 799999999999999876544

>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=99.74  E-value=2.4e-18  Score=135.70  Aligned_cols=71  Identities=31%  Similarity=0.356  Sum_probs=67.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|+||+.++ ++.|+|++++||.+||++|+.++|   +++++|||+|+||+|+|+++|++|||++|++|||++|
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            6899998766 589999999999999999999999   9999999999999999999999999999999999985

>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=99.74  E-value=1.4e-18  Score=136.64  Aligned_cols=71  Identities=17%  Similarity=0.281  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+||+..|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||+|+|+.+|++|||++|++|+|+.
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

>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=99.74  E-value=4.6e-18  Score=136.98  Aligned_cols=76  Identities=24%  Similarity=0.257  Sum_probs=67.1

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHH--------HhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIET--------VQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~--------~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v   72 (308)
                      |+|+|++++|+++.|+|++++||.+||++|..        +.+   +++++|||||.||+|+|+.+|++|+|.+|++++|
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            57999999999999999999999999999964        445   8999999999999999999999999999998666


Q ss_pred             EEecCCC
Q 021760           73 MLTKSKV   79 (308)
Q Consensus        73 ~v~k~k~   79 (308)
                      ++..++.
T Consensus        94 hlv~r~~  100 (116)
T d1wgha_          94 HLVARET  100 (116)
T ss_dssp             EEEECSS
T ss_pred             EEEeCCC
Confidence            5554443

>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=99.73  E-value=2.2e-18  Score=130.75  Aligned_cols=72  Identities=28%  Similarity=0.363  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||+.++ .+.|+|++++||.+||++|+...|   +++++|||+|+||+|+|+++|++|||++|++|||++|.
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            6899998765 578999999999999999999999   99999999999999999999999999999999998874

>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=99.73  E-value=8.8e-18  Score=128.44  Aligned_cols=67  Identities=27%  Similarity=0.399  Sum_probs=65.1

Q ss_pred             CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         8 l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      ++|++|.|+|++++||.+||++|+.+.|   +|+++|+|+|+||.|+|+++|++|||++|++||++++++
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~---ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~R   85 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATG---MPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKER   85 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTC---CCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhc---CChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecC
Confidence            6899999999999999999999999999   999999999999999999999999999999999999876

>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=99.72  E-value=1.8e-18  Score=137.01  Aligned_cols=77  Identities=21%  Similarity=0.235  Sum_probs=71.5

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeE---------------EEeCCEecCCC-CChhhhcc
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM---------------LIHQGKVLKDV-TTLEENKV   64 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qk---------------LIy~GKiL~D~-~tL~dygI   64 (308)
                      |+|+||+++|++|.|+|+++.||.+||.+|+...+   +|+++||               |+|+||.|.|+ .+|.+|||
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               99999999766 58999999


Q ss_pred             CCCCEEEEEEecCCCC
Q 021760           65 AENSFVVVMLTKSKVS   80 (308)
Q Consensus        65 k~g~~I~v~v~k~k~~   80 (308)
                      ++|++|||+.+.++..
T Consensus        85 ~~g~~l~lv~r~~~~~  100 (105)
T d1v2ya_          85 RNRDEVSFIKKLGQKS  100 (105)
T ss_dssp             CSSEEEEEEECSCSCC
T ss_pred             CCCCEEEEEEecCCCC
Confidence            9999999998876544

>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=99.71  E-value=1.9e-17  Score=130.04  Aligned_cols=78  Identities=17%  Similarity=0.264  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCcEE-EEEeCCCCcHHHHHHHHHHHhCC--CCCC--CCCeEEEeCCEecCCCCChhhhccCCCC------E
Q 021760            1 MKVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGS--DVYP--ASQQMLIHQGKVLKDVTTLEENKVAENS------F   69 (308)
Q Consensus         1 M~I~Vktl~gk~~-~leV~~~~TV~~LK~~I~~~~g~--~~ip--~~~qkLIy~GKiL~D~~tL~dygIk~g~------~   69 (308)
                      |.|+||+++|+.+ .+.|++++||.+||++|+..+.+  ..+|  +++|||||+||+|+|+++|++|+|..|+      +
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 69999999999999999987431  1276  7799999999999999999999999998      9


Q ss_pred             EEEEEecCC
Q 021760           70 VVVMLTKSK   78 (308)
Q Consensus        70 I~v~v~k~k   78 (308)
                      +||++|.+.
T Consensus        88 mHlVvrpp~   96 (101)
T d1se9a_          88 MHVIIQAPV   96 (101)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999998643

>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=99.71  E-value=5.1e-18  Score=133.31  Aligned_cols=75  Identities=23%  Similarity=0.243  Sum_probs=68.2

Q ss_pred             CEEEE--EeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCC
Q 021760            1 MKVFV--KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSK   78 (308)
Q Consensus         1 M~I~V--ktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k   78 (308)
                      |+|+|  |...|++|.|+|+.++||.+||++|+.+.|   +++++|||||+||+|+|+++|++|||+++++|+||..+..
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            35565  556799999999999999999999999999   9999999999999999999999999999999998876543

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.2e-17  Score=125.39  Aligned_cols=76  Identities=18%  Similarity=0.205  Sum_probs=65.1

Q ss_pred             CEEEEEeCCCc--EEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCC--EEEEEEec
Q 021760            1 MKVFVKTLKGT--HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS--FVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk--~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~--~I~v~v~k   76 (308)
                      |+|+||+.+++  .|.|+|++++||.+||++|++..+.+ +++++|||||+||+|+|+.+|++|+++.++  +|||+++.
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            78999998775  48899999999999999999997633 899999999999999999999999776544  77777544


Q ss_pred             C
Q 021760           77 S   77 (308)
Q Consensus        77 ~   77 (308)
                      +
T Consensus        87 ~   87 (93)
T d1wgda_          87 K   87 (93)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.67  E-value=6.2e-18  Score=111.70  Aligned_cols=41  Identities=56%  Similarity=0.985  Sum_probs=39.8

Q ss_pred             CCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          169 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       169 g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      |+++|++|++||+||   |+|++|++|||+++||+|||+|||++
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            789999999999999   99999999999999999999999985

>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=99.66  E-value=4.9e-17  Score=126.38  Aligned_cols=71  Identities=21%  Similarity=0.366  Sum_probs=66.4

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+|+ +++++|.|+|++++||.+||++|+..+|   +|+++|||+|+|+ |+|+++|++|+|++|++|+||.+.
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 999999999999999999998654

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=1.1e-16  Score=123.01  Aligned_cols=73  Identities=25%  Similarity=0.404  Sum_probs=66.8

Q ss_pred             CEEEEEeCCCcEEEE-EeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE---eCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEI-EVKPEDKVSDVKKNIETVQGSDVYPASQQMLI---HQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~l-eV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI---y~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+||. .|+.|.+ +|++++||.+||++|+.++|   +|+++||||   |+||+|+|+.+|.+|+|++|++|+|+.++
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 6667777 79999999999999999999   999999999   58999999999999999999999998765


Q ss_pred             C
Q 021760           77 S   77 (308)
Q Consensus        77 ~   77 (308)
                      .
T Consensus        84 ~   84 (90)
T d1v5ta_          84 E   84 (90)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.66  E-value=4.7e-17  Score=130.07  Aligned_cols=76  Identities=24%  Similarity=0.318  Sum_probs=68.4

Q ss_pred             EEEEEeC-CCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecCCC
Q 021760            2 KVFVKTL-KGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKSKV   79 (308)
Q Consensus         2 ~I~Vktl-~gk~~~leV~~-~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~k~   79 (308)
                      +|+|++. +|+++.|+|.+ ++||.+||.+|+++.|   +|+++|||+|+||.|+|+.+|++|||++|++|||++|.+..
T Consensus        31 ~V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rGG  107 (111)
T d1we6a_          31 RVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG  107 (111)
T ss_dssp             EECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTT---CCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCS
T ss_pred             EEEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHC---CCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCCC
Confidence            3444443 58999999986 8999999999999999   99999999999999999999999999999999999998864


Q ss_pred             C
Q 021760           80 S   80 (308)
Q Consensus        80 ~   80 (308)
                      +
T Consensus       108 ~  108 (111)
T d1we6a_         108 P  108 (111)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.9e-16  Score=119.46  Aligned_cols=73  Identities=30%  Similarity=0.383  Sum_probs=65.8

Q ss_pred             CEEEEEeCCCcEEEEEe-----CCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecC-CCCChhhhccCCCCEEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEV-----KPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVAENSFVVVML   74 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV-----~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~-D~~tL~dygIk~g~~I~v~v   74 (308)
                      |+|+|+ ..++.|.|+|     ++++||.+||++|+..+|   +|+++|||+|+||.|. |+++|++|||++|++|+|+.
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            678887 5778899888     568899999999999999   9999999999999995 56899999999999999998


Q ss_pred             ecC
Q 021760           75 TKS   77 (308)
Q Consensus        75 ~k~   77 (308)
                      ++.
T Consensus        78 ~~~   80 (81)
T d1wxva1          78 KKN   80 (81)
T ss_dssp             CCS
T ss_pred             ecC
Confidence            764

>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=99.58  E-value=3.5e-15  Score=117.41  Aligned_cols=72  Identities=22%  Similarity=0.290  Sum_probs=61.8

Q ss_pred             EEEEeCCC-cEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCC-------EEEEEE
Q 021760            3 VFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS-------FVVVML   74 (308)
Q Consensus         3 I~Vktl~g-k~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~-------~I~v~v   74 (308)
                      |+|+...+ ++|.|+|++++||.+||++|+.+.|   +++++|||||+||.|+|+++|++|||.+++       ++++.+
T Consensus         2 ifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~~~~~~~~~~~l~~   78 (103)
T d2c9wb1           2 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK---RPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAF   78 (103)
T ss_dssp             EEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEE
T ss_pred             EEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhC---CCcccEEEEECCEEcCCCCCHHHcCCCcccccccCCcEEEEEE
Confidence            56665555 4788999999999999999999999   999999999999999999999999996544       677766


Q ss_pred             ecC
Q 021760           75 TKS   77 (308)
Q Consensus        75 ~k~   77 (308)
                      +..
T Consensus        79 ~~~   81 (103)
T d2c9wb1          79 RAD   81 (103)
T ss_dssp             EET
T ss_pred             ecC
Confidence            543

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=1.1e-14  Score=112.99  Aligned_cols=75  Identities=21%  Similarity=0.220  Sum_probs=67.5

Q ss_pred             CEEEEEe-CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCE-------ecCCCCChhhhccCCCCEEEE
Q 021760            1 MKVFVKT-LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-------VLKDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         1 M~I~Vkt-l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GK-------iL~D~~tL~dygIk~g~~I~v   72 (308)
                      |.|+|++ +++..++..+++++||.+||++|+..+|   +|++.|||+|.|+       +++|+++|++|+|.+|++|||
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            5788887 4666789999999999999999999999   9999999999887       578999999999999999999


Q ss_pred             EEecCC
Q 021760           73 MLTKSK   78 (308)
Q Consensus        73 ~v~k~k   78 (308)
                      +.+.+.
T Consensus        85 vd~~p~   90 (95)
T d1v6ea_          85 IDHSGS   90 (95)
T ss_dssp             BCCSCC
T ss_pred             EeCCCC
Confidence            977643

>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=99.44  E-value=1.4e-13  Score=102.84  Aligned_cols=72  Identities=11%  Similarity=0.148  Sum_probs=66.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEecC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKS   77 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k~   77 (308)
                      .|+|+. +|+.+.+.|..++++..||+.++++.|   ++.++++|+|+|+.|++++|+++|+|++||+|+++++..
T Consensus         6 ~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~---i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~   77 (79)
T d1euvb_           6 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQI   77 (79)
T ss_dssp             EEEEES-SSCEEEEEEETTSCTHHHHHHHHHHTT---CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCB
T ss_pred             EEEECC-CCeEEEEEECCCCcHHHHHHHHHHHhC---CChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEecc
Confidence            455553 678888999999999999999999999   999999999999999999999999999999999999865

>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=99.42  E-value=1.5e-13  Score=106.74  Aligned_cols=74  Identities=18%  Similarity=0.207  Sum_probs=63.8

Q ss_pred             EEEEEe---CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEe-------c-CCCCChhhhccCCCCEE
Q 021760            2 KVFVKT---LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV-------L-KDVTTLEENKVAENSFV   70 (308)
Q Consensus         2 ~I~Vkt---l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKi-------L-~D~~tL~dygIk~g~~I   70 (308)
                      .|+|+.   .+++.++++|+.++||.+||.+|+..+|   +|++.|||+|.|+.       | +|+++|.+|||++|++|
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            456664   4577899999999999999999999999   99999999998872       4 47899999999999999


Q ss_pred             EEEEecCC
Q 021760           71 VVMLTKSK   78 (308)
Q Consensus        71 ~v~v~k~k   78 (308)
                      +|....++
T Consensus        88 ~V~~~~P~   95 (97)
T d1wjna_          88 LVRWSGPS   95 (97)
T ss_dssp             EEECCSSC
T ss_pred             EEEeCCCC
Confidence            99875544

>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=99.38  E-value=7.5e-13  Score=98.33  Aligned_cols=73  Identities=19%  Similarity=0.273  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      |+|+|++.+|+.+.+.|..+.++..||+.++++.|   ++.++++|+|+|+.|.++.|+++|+|++|++|+|+++.
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

>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=99.37  E-value=2.4e-13  Score=104.93  Aligned_cols=56  Identities=25%  Similarity=0.132  Sum_probs=49.9

Q ss_pred             CCCcHHHHHHHHHHHhCCCCC-CCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEe
Q 021760           19 PEDKVSDVKKNIETVQGSDVY-PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus        19 ~~~TV~~LK~~I~~~~g~~~i-p~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      .+.||.+||++|+.+.... . .+++|||||+||.|+|+++|++|||++|++||++.|
T Consensus        36 ~~~tV~~lK~~i~~~~~~~-~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r   92 (94)
T d1x1ma1          36 GGYSISFLKQLIAGKLQES-VPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK   92 (94)
T ss_dssp             CCCBHHHHHHHHHHHCTTT-CCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEES
T ss_pred             CccCHHHHHHHHHHHcccC-CCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEe
Confidence            3679999999999987633 4 368999999999999999999999999999999976

>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=99.36  E-value=3.2e-13  Score=99.62  Aligned_cols=40  Identities=40%  Similarity=0.474  Sum_probs=38.1

Q ss_pred             cHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      ..|+.|++||+||   |+|++|++|||+++||.|||||||+..
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            3589999999999   999999999999999999999999987

>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=99.35  E-value=3.1e-13  Score=96.95  Aligned_cols=43  Identities=28%  Similarity=0.557  Sum_probs=39.8

Q ss_pred             CcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC-CC
Q 021760          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG-IP  215 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G-IP  215 (308)
                      ...+++|++||+||   |+|++|++|||+++||.+||||||++. +|
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

>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=99.35  E-value=1.7e-13  Score=96.07  Aligned_cols=32  Identities=41%  Similarity=0.727  Sum_probs=30.7

Q ss_pred             chHHhhChHHHHHHHHHHHhChhhHHHHHhcC
Q 021760          276 TLDFLRNSQQFQALRTMVQANPQILQQWALIV  307 (308)
Q Consensus       276 ~l~~Lr~~pqf~~lRq~vqqnP~~L~~~L~~~  307 (308)
                      ||+|||++|||++||++||+||++|++|||++
T Consensus         1 pL~~Lr~~PqFq~lR~~vq~nP~~L~~lLqql   32 (58)
T d2f4mb1           1 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQI   32 (58)
T ss_dssp             GGGGGTTCHHHHHHHHHHHHCGGGHHHHHHHH
T ss_pred             CcHHHhcChHHHHHHHHHHHCHHHHHHHHHHH
Confidence            69999999999999999999999999999975

>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=99.32  E-value=1.1e-12  Score=94.00  Aligned_cols=43  Identities=28%  Similarity=0.372  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCCC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ  217 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~~  217 (308)
                      .+++|++||+||   |+|++|++||++..||+++||+||+.+..+.
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            389999999999   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=99.23  E-value=4.1e-12  Score=93.57  Aligned_cols=39  Identities=21%  Similarity=0.507  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .++.|++||+||   |+|++|++|||++.||.+||||||+++
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            378999999999   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=99.22  E-value=1.7e-11  Score=93.61  Aligned_cols=73  Identities=14%  Similarity=0.127  Sum_probs=61.7

Q ss_pred             EEEEEe-CCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCE-------ecCCCCChhhhccCCCCEEEEE
Q 021760            2 KVFVKT-LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-------VLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vkt-l~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GK-------iL~D~~tL~dygIk~g~~I~v~   73 (308)
                      .|.|.+ ..+..++..++.++||.+||.+|+..+|   +|++.|||+|.|+       .++|+++|.+|||++|++|||+
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            455554 3344578889999999999999999999   9999999999886       4578899999999999999998


Q ss_pred             EecC
Q 021760           74 LTKS   77 (308)
Q Consensus        74 v~k~   77 (308)
                      -...
T Consensus        83 d~~~   86 (90)
T d1t0ya_          83 DVTG   86 (90)
T ss_dssp             ECTT
T ss_pred             eCCC
Confidence            6543

>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=99.04  E-value=9.5e-11  Score=84.01  Aligned_cols=41  Identities=22%  Similarity=0.379  Sum_probs=37.9

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCCCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIPE  216 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GIP~  216 (308)
                      +++|++|++||   |+|++|++||++..| |+++|||||+...-+
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            57899999999   999999999999999 799999999998643

>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=98.93  E-value=2.8e-10  Score=77.81  Aligned_cols=37  Identities=24%  Similarity=0.484  Sum_probs=34.5

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHh
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYS  212 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~  212 (308)
                      ++.|++|++||   |++++|++||++.-| |.++|||||+.
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            35799999999   999999999999998 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=98.81  E-value=1.1e-08  Score=74.35  Aligned_cols=70  Identities=16%  Similarity=0.238  Sum_probs=66.0

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEE
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~   73 (308)
                      ++|+|+..+|+.+.+.|..+.++..|+...++..|   ++...++|+|+|+.|..+.|.+++++++||.|.|.
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            46888888999999999999999999999999999   88999999999999999999999999999999875

>d2bwba1 a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.64  E-value=2e-08  Score=66.12  Aligned_cols=40  Identities=30%  Similarity=0.473  Sum_probs=37.9

Q ss_pred             cHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          171 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .|..-+++|-+||   | +++..++||+++..|.++|||+|++|
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            4778899999999   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=98.64  E-value=1.4e-08  Score=76.23  Aligned_cols=40  Identities=28%  Similarity=0.396  Sum_probs=37.4

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGIP  215 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GIP  215 (308)
                      +++|++|++||   |+|++|++||++..| |.++|++||+...-
T Consensus        30 ~~~v~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~   70 (84)
T d1veka_          30 EEIVAQLVSMG---FSQLHCQKAAINTSNAGVEEAMNWLLSHMD   70 (84)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHHcCCCHHHHHHHHHHcCC
Confidence            78999999999   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=98.63  E-value=1.7e-08  Score=68.84  Aligned_cols=38  Identities=26%  Similarity=0.421  Sum_probs=34.8

Q ss_pred             HHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHHhCC
Q 021760          174 ATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGI  214 (308)
Q Consensus       174 ~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~~GI  214 (308)
                      +.|++|++||   |+|+++++||++.-| |.++|||||+...
T Consensus         4 ~~v~~L~~MG---F~~~~a~~Al~~t~n~~ve~A~~Wl~~h~   42 (51)
T d2crna1           4 SLLEPLLAMG---FPVHTALKALAATGRKTAEEALAWLHDHC   42 (51)
T ss_dssp             SSHHHHHHTS---CCHHHHHHHHHHHTSCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHcC---CCHHHHHHHHHHHCCCCHHHHHHHHHHcC
Confidence            3599999999   999999999999977 9999999999763

>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=98.59  E-value=3.9e-08  Score=63.44  Aligned_cols=39  Identities=23%  Similarity=0.342  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      .+..|++|++||   |+++++++||+-...|-+-|+.||+-|
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            467899999999   999999999999999999999999976

>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=98.51  E-value=9.7e-08  Score=72.08  Aligned_cols=71  Identities=20%  Similarity=0.169  Sum_probs=57.8

Q ss_pred             EEEEEeCCCcEEEEEeCC-CCcHHHHHHHHHHHhCCCCCCCCCeEEEeC--------------CEecCC-CCChhhhccC
Q 021760            2 KVFVKTLKGTHFEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQ--------------GKVLKD-VTTLEENKVA   65 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~-~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~--------------GKiL~D-~~tL~dygIk   65 (308)
                      .|.||+.+| +..|+|+. +.||.+||.+|+++.+   +|.+.|.|..+              -..|.| ..+|++|||.
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 67889964 6899999999999999   99999999442              223544 4679999999


Q ss_pred             CCCEEEEEEec
Q 021760           66 ENSFVVVMLTK   76 (308)
Q Consensus        66 ~g~~I~v~v~k   76 (308)
                      +|++|++...-
T Consensus        78 hGsivyL~y~~   88 (94)
T d1wf9a1          78 HGSMVYLAYEG   88 (94)
T ss_dssp             TTCEEECCCSS
T ss_pred             CceEEEEEeee
Confidence            99999987653

>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=98.46  E-value=1.2e-07  Score=66.44  Aligned_cols=41  Identities=20%  Similarity=0.407  Sum_probs=37.8

Q ss_pred             CCcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          169 GSNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       169 g~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      -+.|..-++.|.+||   | +++..++||+++.+|.++|||||+.
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            456899999999999   9 7888899999999999999999983

>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=98.40  E-value=2.1e-07  Score=60.29  Aligned_cols=38  Identities=32%  Similarity=0.478  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          172 LEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      |+.-++.|-+||   | +++..++||+++..|.++|||+|+.
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=98.39  E-value=2.1e-07  Score=62.65  Aligned_cols=41  Identities=20%  Similarity=0.276  Sum_probs=38.3

Q ss_pred             CcHHHHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 021760          170 SNLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG  213 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~~G  213 (308)
                      +.|..-+++|-+||   | +++.+++||+++..|.++|||+|+.+
T Consensus         6 ~ry~~QL~qL~~MG---F~d~~~Ni~AL~~t~GdV~~Aie~Ll~~   47 (50)
T d2dnaa1           6 VRFSKEMECLQAMG---FVNYNANLQALIATDGDTNAAIYKLKSS   47 (50)
T ss_dssp             HHTHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcC---CCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            35788899999999   9 99999999999999999999999986

>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=97.77  E-value=2.2e-05  Score=48.75  Aligned_cols=41  Identities=27%  Similarity=0.407  Sum_probs=38.2

Q ss_pred             cCCcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          168 AGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       168 ~g~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      ...+|-..|.+|+.||   |+|.-|+.||.--..+.+.|-|.|+
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            3568999999999999   9999999999999999999999986

>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=97.57  E-value=1.2e-05  Score=52.08  Aligned_cols=37  Identities=24%  Similarity=0.415  Sum_probs=35.4

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      .++|.+|++||   |+|++|+.|--|.-.|-+-|..||+.
T Consensus         5 ~~aIeRL~~LG---F~r~~viqay~ACdKNEelAaN~L~~   41 (44)
T d1oqya2           5 KEAIERLKALG---FPESLVIQAYFACEKNENLAANFLLS   41 (44)
T ss_dssp             HHHHHHHHHHT---CCSHHHHHHTSSSSSCSSHHHHHHHH
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhCcCHHHHHHHHHH
Confidence            57899999999   99999999999999999999999985

>d2al3a1 d.15.1.2 (A:10-85) Tether containing UBX domain for GLUT4 (Tug) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Tether containing UBX domain for GLUT4 (Tug)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.49  E-value=0.00027  Score=51.11  Aligned_cols=72  Identities=18%  Similarity=0.161  Sum_probs=66.9

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCCEecCCCCChhhhccCCCCEEEEEEec
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK   76 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~GKiL~D~~tL~dygIk~g~~I~v~v~k   76 (308)
                      .|+|-+.+|+...|.|.++.|+.++-+..+.++|   +.+++..|.|++|.|+-+..+.-.|+-+|..+.++-..
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            3778888999999999999999999999999999   88999999999999999999999999999999988543

>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=97.32  E-value=0.00019  Score=43.28  Aligned_cols=37  Identities=30%  Similarity=0.499  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          172 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       172 ~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      ++..|.+|++||   |+-=+...||.|+..+-|-|..||+
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            567899999999   9999999999999999999999985

>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=97.29  E-value=0.0007  Score=49.18  Aligned_cols=67  Identities=18%  Similarity=0.244  Sum_probs=56.7

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEec---CCCCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVL---KDVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL---~D~~tL~dygIk~g~~I~v   72 (308)
                      +|.||..+|+.+.-.+..++||.+|.+.|... +   ......+|+  |-.|.|   ++++||.++|+....+|+|
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            58899999999999999999999999999875 5   556777776  678888   3467999999998888776

>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=96.87  E-value=0.0021  Score=47.37  Aligned_cols=66  Identities=18%  Similarity=0.333  Sum_probs=53.6

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHh-CCCCCCCCCeEEEeC--CEec-CCCCChhhhccCCCCEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQ-GSDVYPASQQMLIHQ--GKVL-KDVTTLEENKVAENSFVV   71 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~-g~~~ip~~~qkLIy~--GKiL-~D~~tL~dygIk~g~~I~   71 (308)
                      +|.||..+|+.+...+..++||.+|.+.|.... +   .......|+..  -|.| +++.||.++|+.+ +.|+
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   45567888754  6778 4578999999985 4443

>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=96.76  E-value=0.0022  Score=47.69  Aligned_cols=67  Identities=15%  Similarity=0.120  Sum_probs=53.4

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEecC--CCCChhhhccCCCCEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--DVTTLEENKVAENSFVVV   72 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL~--D~~tL~dygIk~g~~I~v   72 (308)
                      +|.||..+|+.+...+..++||.+|..-|....    ......+|+  |-.+.|.  +++||.++||....+|+|
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 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVG----YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNV   88 (96)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHHT----CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcccHHHHHHHHHHhc----cCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEE
Confidence            688999999999999999999999999997653    345677776  3446663  468999999998777665

>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=96.67  E-value=0.0012  Score=48.94  Aligned_cols=45  Identities=27%  Similarity=0.559  Sum_probs=40.8

Q ss_pred             CCcHHHHHHHHHHh-cCCccCHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 021760          169 GSNLEATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE  216 (308)
Q Consensus       169 g~~~e~~v~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEYL~~GIP~  216 (308)
                      -.+++..|..||+| |   -..++|.-||-=+.|+.+|||+|||-|-++
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            45789999999999 6   789999999999999999999999998553

>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=96.65  E-value=0.0022  Score=50.19  Aligned_cols=68  Identities=19%  Similarity=0.302  Sum_probs=55.5

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--eCCEec---CCCCChhhhccCCCCEEEEE
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVL---KDVTTLEENKVAENSFVVVM   73 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y~GKiL---~D~~tL~dygIk~g~~I~v~   73 (308)
                      +|.||..+|+.+...+..++||.+|...|....    +.....+|+  |--|.|   +.+++|.++||....+|+|-
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 QLMLRYPDGKREQITLPEQAKLLALVKHVQSKG----YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHHH----CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcc----cCCcceEEeecccccccccccccCcHHHcCCCCCCEEEEE
Confidence            688999999999999999999999999997653    445677776  456777   34689999999988888664

>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=96.49  E-value=0.0022  Score=39.56  Aligned_cols=36  Identities=31%  Similarity=0.475  Sum_probs=32.1

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcC-ChHHHHHHHH
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLY  211 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafn-NpdRAvEYL~  211 (308)
                      .+|++.|+.-|   |+.|.|+||||-..| |-+-|+||+.
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            36899999999   999999999998765 7899999984

>d1vega_ a.5.2.1 (A:) NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: NEDD8 ultimate buster-1 (Nub1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.13  E-value=0.0047  Score=44.20  Aligned_cols=45  Identities=27%  Similarity=0.387  Sum_probs=39.5

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHHh-C--CCCCCCC
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS-G--IPEQTAV  220 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~~-G--IP~~~~~  220 (308)
                      .+.|++|+-||   |+|+-++.|||---.|..-|..-|.. |  ||..++-
T Consensus        30 QesidqLvYMG---F~~~~Ae~ALRvfrGnVQlAaQtLahngG~LP~dLq~   77 (83)
T d1vega_          30 QESINQLVYMG---FDTVVAEAALRVFGGNVQLAAQTLAHHGGSLPPDLQF   77 (83)
T ss_dssp             HHHHHHHHHHS---CCHHHHHHHHHHTTTCHHHHHHHHHHHTSSCCTTSSS
T ss_pred             HHHHHHHHHhc---ccHHHHHHHHHHhcccHHHHHHHHHHcCCcCCccccc
Confidence            57899999999   99999999999999999999988864 3  8877653

>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=95.54  E-value=0.045  Score=39.26  Aligned_cols=68  Identities=21%  Similarity=0.224  Sum_probs=48.8

Q ss_pred             CEEEEEeCC------C-cEEEEEeCCCCcHHHHHHHHHHHhCCC--------CCCCCCeEEEeCCEecCCCCChhhhccC
Q 021760            1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGSD--------VYPASQQMLIHQGKVLKDVTTLEENKVA   65 (308)
Q Consensus         1 M~I~Vktl~------g-k~~~leV~~~~TV~~LK~~I~~~~g~~--------~ip~~~qkLIy~GKiL~D~~tL~dygIk   65 (308)
                      |+|+|+.+.      | ....+++....||.+|++.+..+++.-        .......++..+|+...++     +-|+
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            899998763      3 467889998999999999998875410        0012345666788777554     5688


Q ss_pred             CCCEEEEE
Q 021760           66 ENSFVVVM   73 (308)
Q Consensus        66 ~g~~I~v~   73 (308)
                      +||.|.++
T Consensus        77 ~gDevai~   84 (88)
T d1vjka_          77 DGDVVGVF   84 (88)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEe
Confidence            99999886

>d1wgla_ a.5.2.4 (A:) Toll-interacting protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Toll-interacting protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.01  E-value=0.013  Score=39.89  Aligned_cols=37  Identities=30%  Similarity=0.425  Sum_probs=34.8

Q ss_pred             HHHHHHHHHh--cCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          173 EATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       173 e~~v~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      |+.|+.|.+|  .   +|++-|+.-|++.-+|.|+||+-||.
T Consensus        10 Ee~i~~LkeMFP~---~D~~vI~~VL~a~~G~vd~aid~LL~   48 (59)
T d1wgla_          10 EEDLKAIQDMFPN---MDQEVIRSVLEAQRGNKDAAINSLLQ   48 (59)
T ss_dssp             HHHHHHHHHHCSS---SCHHHHHHHHTTTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            6789999999  7   89999999999999999999999984

>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=94.00  E-value=0.045  Score=36.24  Aligned_cols=35  Identities=29%  Similarity=0.304  Sum_probs=31.0

Q ss_pred             HHHHHHHHh-cCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          174 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       174 ~~v~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      ++|.+|-++ |   +.=-+|..||..+-+|.|+|+|||-
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            567777775 8   8889999999999999999999994

>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=93.91  E-value=0.023  Score=37.92  Aligned_cols=23  Identities=13%  Similarity=0.514  Sum_probs=21.5

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHH
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRA  198 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrA  198 (308)
                      ...|.++++||   |+|+.|+..||-
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   999999999995

>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=93.88  E-value=0.047  Score=36.66  Aligned_cols=35  Identities=14%  Similarity=0.190  Sum_probs=31.6

Q ss_pred             HHHHHHHHh-cCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          174 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       174 ~~v~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      ++|.+|-++ |   +.=-+|..||..+-||.|.|+|||-
T Consensus         6 ~lvk~LRe~Tg---a~~~dcKkAL~e~~gD~ekA~e~Lr   41 (56)
T d1xb2b1           6 ELLMKLRRKTG---YSFINCKKALETCGGDLKQAESWLH   41 (56)
T ss_dssp             HHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            578888886 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=93.23  E-value=0.039  Score=36.82  Aligned_cols=40  Identities=20%  Similarity=0.194  Sum_probs=36.9

Q ss_pred             CcHHHHHHHHHHh--cCCccCHHHHHHHHHHhcCChHHHHHHHHh
Q 021760          170 SNLEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYS  212 (308)
Q Consensus       170 ~~~e~~v~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEYL~~  212 (308)
                      .++++.++.|.+|  +   +|++=++.-|++.-+|.|+||+.||.
T Consensus        10 ~e~~e~~~~Lk~MFP~---~D~~VI~~VL~a~~G~vd~aidaLL~   51 (54)
T d1mn3a_          10 NERKDTLNTLQNMFPD---MDPSLIEDVCIAKKSRIEPCVDALLS   51 (54)
T ss_dssp             HHHHHHHHHHHHHCTT---SCHHHHHHHHSCSSCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4678999999999  7   89999999999999999999999983

>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=92.98  E-value=0.037  Score=36.18  Aligned_cols=23  Identities=26%  Similarity=0.391  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHhChhhHHHHHhc
Q 021760          284 QQFQALRTMVQANPQILQQWALI  306 (308)
Q Consensus       284 pqf~~lRq~vqqnP~~L~~~L~~  306 (308)
                      .++-+||++|..||+.|.+||+-
T Consensus         8 edl~~lr~vvsg~peal~plle~   30 (57)
T d1x3zb1           8 EDLLSLRQVVSGNPEALAPLLEN   30 (57)
T ss_dssp             THHHHHHHHHHHCGGGHHHHHHH
T ss_pred             HHHHHHHHHhcCChHHHHHHHHH
Confidence            36789999999999999999974

>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=92.95  E-value=0.084  Score=35.13  Aligned_cols=35  Identities=23%  Similarity=0.243  Sum_probs=31.1

Q ss_pred             HHHHHHHHh-cCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          174 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       174 ~~v~~i~~M-G~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      +.|.+|-++ |   +.=-+|..||..+-+|.|+|+|||-
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   8889999999999999999999994

>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=91.98  E-value=0.27  Score=35.20  Aligned_cols=72  Identities=18%  Similarity=0.178  Sum_probs=54.6

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--EecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G--KVLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~---G--KiL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |+|.|..+++ .+++.|+...+..+|-++|....+.  ...+-.-|-|-   |  .-|+.++.|..+.++.+..+.+..+
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  23444556553   3  2378899999987776665555444

>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=91.25  E-value=0.15  Score=37.66  Aligned_cols=71  Identities=6%  Similarity=-0.008  Sum_probs=41.8

Q ss_pred             CEEEEEeCC--------CcEEEEEeCC---CCcHHHHHHHHHHHhCCC--CCCCC------CeEEEeCCEecCCCCCh--
Q 021760            1 MKVFVKTLK--------GTHFEIEVKP---EDKVSDVKKNIETVQGSD--VYPAS------QQMLIHQGKVLKDVTTL--   59 (308)
Q Consensus         1 M~I~Vktl~--------gk~~~leV~~---~~TV~~LK~~I~~~~g~~--~ip~~------~qkLIy~GKiL~D~~tL--   59 (308)
                      |+|+|+...        .+.+.++++.   ..||.+|-+.+.+++...  .+-.+      ...++.+|+...   .+  
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            889998743        2445666643   469999999999887621  00000      012223333211   12  


Q ss_pred             hhhccCCCCEEEEEE
Q 021760           60 EENKVAENSFVVVML   74 (308)
Q Consensus        60 ~dygIk~g~~I~v~v   74 (308)
                      -++.|++||.|.++-
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            256899999999874

>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=91.21  E-value=0.52  Score=33.41  Aligned_cols=60  Identities=18%  Similarity=0.123  Sum_probs=46.8

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe---CC--EecCCCCChhhh
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QG--KVLKDVTTLEEN   62 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy---~G--KiL~D~~tL~dy   62 (308)
                      |+.+|..++|..+.+.|+...+..+|-++|....+.  ...+-.-|-|   +|  .-|+.++.|...
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  2333334433   23  247888888776

>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=89.96  E-value=0.29  Score=33.92  Aligned_cols=36  Identities=31%  Similarity=0.462  Sum_probs=33.4

Q ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHHH
Q 021760          173 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       173 e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      +..|.++.+||   |.|+..+.+|+..-+|-|-|+--|+
T Consensus        15 np~~KQfsnMG---f~re~~e~~l~sN~m~L~~a~~~l~   50 (72)
T d2dkla1          15 SRLIKQLTDMG---FPREPAEEALKSNNMNLDQAMSALL   50 (72)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHH
T ss_pred             hHHHHHHhhcC---CcCCChHHhhhccCcchhhcccchh
Confidence            56789999999   9999999999999999999998776

>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=89.36  E-value=0.9  Score=33.17  Aligned_cols=71  Identities=18%  Similarity=0.108  Sum_probs=46.1

Q ss_pred             EEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEE--e--CC--EecCCCCChhhh----ccCCCCEEEE
Q 021760            3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--H--QG--KVLKDVTTLEEN----KVAENSFVVV   72 (308)
Q Consensus         3 I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLI--y--~G--KiL~D~~tL~dy----gIk~g~~I~v   72 (308)
                      |.|-..+|.+..|.|+.++|+.+|-+.+.++.+.. ..+ ..-|+  +  .|  +.|+|+..+-+.    ....  .-.+
T Consensus        12 vkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~-~~~-~f~L~E~~~~~~leR~L~d~E~vl~v~~~W~~~~--~~r~   87 (100)
T d1wgra_          12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHAL-SDE-TWGLVECHPHLALERGLEDHESVVEVQAAWPVGG--DSRF   87 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCC-CCC-CCCEEEEETTTTEEEEECSSSCHHHHHTTSCSSS--CCEE
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCC-CCC-CeEEEEecCCCcceeecCchHhHHHHHHcCCCCC--CCEE
Confidence            45556789889999999999999999999998843 111 22222  2  24  778887654443    3333  3345


Q ss_pred             EEecC
Q 021760           73 MLTKS   77 (308)
Q Consensus        73 ~v~k~   77 (308)
                      ++||.
T Consensus        88 v~rkn   92 (100)
T d1wgra_          88 VFRKN   92 (100)
T ss_dssp             EECSC
T ss_pred             EEeec
Confidence            55554

>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=88.32  E-value=0.33  Score=30.01  Aligned_cols=35  Identities=29%  Similarity=0.448  Sum_probs=31.3

Q ss_pred             HHHHHHHHhcCCcc-CHHHHHHHHHHhcCChHHHHHHHH
Q 021760          174 ATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLY  211 (308)
Q Consensus       174 ~~v~~i~~MG~~~f-~r~qv~~ALrAafnNpdRAvEYL~  211 (308)
                      .+...|+|||   | +|.-=.+=|+---||...+|.-|+
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            5688999999   9 898888999999999999997775

>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=88.29  E-value=0.7  Score=31.35  Aligned_cols=49  Identities=14%  Similarity=0.337  Sum_probs=37.8

Q ss_pred             cCCcHHHHHHHHHHh--cCCccCHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCC
Q 021760          168 AGSNLEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG-IPEQTA  219 (308)
Q Consensus       168 ~g~~~e~~v~~i~~M--G~~~f~r~qv~~ALrAafnNpdRAvEYL~~G-IP~~~~  219 (308)
                      .|-+.+..|.++.++  -   +...=|.++|..--+|+|+.|..|+.| +|.++.
T Consensus         2 ~~vel~s~I~qV~Dl~Pd---LG~GFi~~~L~~Y~~n~E~vI~~lLe~~Lpp~L~   53 (63)
T d2di0a1           2 CGVELDSLISQVKDLLPD---LGEGFILACLEYYHYDPEQVINNILEERLAPTLS   53 (63)
T ss_dssp             SSHHHHHHHHHHHHHCCS---SCHHHHHHHHHHTTTCHHHHHHHHHTTCCCTTTT
T ss_pred             chhHHHHHHHHHHHHcCC---CcHHHHHHHHHHhCCCHHHHHHHHHccCCCHHHH
Confidence            577889999999886  1   234557777876556999999999999 787654

>d1h4ra3 d.15.1.4 (A:20-103) Merlin {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: Merlin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.02  E-value=1.5  Score=31.06  Aligned_cols=72  Identities=15%  Similarity=0.056  Sum_probs=53.3

Q ss_pred             CEEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEe--CCE--ecCCCCChhhhccCCCCEEEEEEe
Q 021760            1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGK--VLKDVTTLEENKVAENSFVVVMLT   75 (308)
Q Consensus         1 M~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy--~GK--iL~D~~tL~dygIk~g~~I~v~v~   75 (308)
                      |.|.|..+++ ++++.|+...+..+|-++|....+.  ...+-.-|.|  +|.  -|+.++.|..+.++.+..+++..+
T Consensus         3 ~~v~V~lLD~-~le~~v~~~a~G~~L~d~Vc~~L~L--~E~~YFGL~y~~~~~~~WLd~~k~l~kq~~~~~~~~~~~F~   78 (84)
T d1h4ra3           3 FTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGL--RETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   78 (84)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTC--CCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             EEEEEEEcCC-cEEEEEcCCChHHHHHHHHHHHcCC--cccccceEEEecCCceEEccCCCchhhhccCCCCCEEEEEE
Confidence            4688999998 4799999999999999999999992  2233334433  443  378889999887777666555544

>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=83.89  E-value=0.98  Score=32.11  Aligned_cols=43  Identities=14%  Similarity=0.157  Sum_probs=34.3

Q ss_pred             EEEEeC-CCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 021760            3 VFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG   50 (308)
Q Consensus         3 I~Vktl-~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~G   50 (308)
                      |+||.. ++..+.+.|.++.+..+|+++|..+++     .+..+|-|..
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            555644 567888999999999999999999987     3567887753

>d1v92a_ a.5.2.3 (A:) NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TAP-C domain-like
domain: NSFL1 (p97 ATPase) cofactor p47, UBA-like domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=83.28  E-value=1.4  Score=27.71  Aligned_cols=38  Identities=11%  Similarity=0.103  Sum_probs=32.5

Q ss_pred             CcHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHH
Q 021760          170 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEY  209 (308)
Q Consensus       170 ~~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEY  209 (308)
                      ++.++.|++.+++- | =++++.+.=|.++-+|-++||.-
T Consensus         3 ~~~~~lI~qF~~iT-g-~~~~~A~~~Le~~~w~Le~Ai~~   40 (46)
T d1v92a_           3 EERQDALREFVAVT-G-AEEDRARFFLESAGWDLQIALAS   40 (46)
T ss_dssp             THHHHHHHHHHHHT-C-CCHHHHHHHHHHTTSCSHHHHHH
T ss_pred             ccHHHHHHHHHHHH-C-cCHHHHHHHHHHcCCcHHHHHHH
Confidence            45678999999983 2 59999999999999999999953

>d1cuka1 a.5.1.1 (A:156-203) DNA helicase RuvA subunit, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: DNA helicase RuvA subunit, C-terminal domain
family: DNA helicase RuvA subunit, C-terminal domain
domain: DNA helicase RuvA subunit, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=82.57  E-value=0.36  Score=31.05  Aligned_cols=36  Identities=17%  Similarity=0.364  Sum_probs=28.5

Q ss_pred             cHHHHHHHHHHhcCCccCHHHHHHHHHHhcCChHHHHHHH
Q 021760          171 NLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL  210 (308)
Q Consensus       171 ~~e~~v~~i~~MG~~~f~r~qv~~ALrAafnNpdRAvEYL  210 (308)
                      ..+++|.-|+.+|   |.|.++.+|++...+ ++.-+|=|
T Consensus         4 ~~~eAi~AL~~LG---Y~~~ea~~av~~i~~-~~~s~E~l   39 (48)
T d1cuka1           4 AEQEAVARLVALG---YKPQEASRMVSKIAR-PDASSETL   39 (48)
T ss_dssp             HHHHHHHHHHHHT---CCHHHHHHHHHHSCC-SSCCHHHH
T ss_pred             hHHHHHHHHHHcC---CCHHHHHHHHHHhcC-CCCCHHHH
Confidence            4688999999999   999999999988754 44444444

>d1oeya_ d.15.2.2 (A:) Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.49  E-value=1.5  Score=31.17  Aligned_cols=45  Identities=11%  Similarity=0.037  Sum_probs=38.2

Q ss_pred             EEEEEeCCCcEEEEEeCCCCcHHHHHHHHHHHhCCCCCCCCCeEEEeC
Q 021760            2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ   49 (308)
Q Consensus         2 ~I~Vktl~gk~~~leV~~~~TV~~LK~~I~~~~g~~~ip~~~qkLIy~   49 (308)
                      ..+||-.-.-++.|++.+.....+|..+|.++..   .+++..+|-|+
T Consensus         5 ~~~vkVh~~fTVal~v~~G~~y~~L~~lvs~KL~---l~~~~~~LSY~   49 (82)
T d1oeya_           5 AYTLKVHYKYTVVMKTQPGLPYSQVRDMVSKKLE---LRLEHTKLSYR   49 (82)
T ss_dssp             CEEEEEESSSEEEEEECTTCCHHHHHHHHHHHTT---CCGGGCCEEEC
T ss_pred             CEEEEEEEEEEEEEEccCCCCHHHHHHHHHHHhC---CChhheEEEec
Confidence            3445544456888999999999999999999999   99999999995