Citrus Sinensis ID: 022228

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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
Protein Sequence
MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWGNKILS
Secondary Structure (PSIPRED)
ccEEEEEcccccEEEEEccccccHHHHHHHHHHHHcccccccccEEEEEccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHHHcccHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEccccEEEEEcccccEHHHHHHHHHHHHccccccHHHcEEEEcccEEcccccHHHcccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHHHcHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MMKIFVKTLkgtsfdvevkpedtvFDVKMKIetvqgsdvypAAQQMLIYQgkvlkddttleenkvaENSFVVIMLTknkrptgegstrstaptkapqssaptpaatpatapqtavpisteptpaptpapasasvssvsatsesgvyghaasnlvagnnLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYsgipeqaevqpvarapgngqaansptqmpqptqpapvtssgpnanpldlfpqglpdvgsgaagagsldflrnspQFQVLRAMVQanpqlfpcfkswgnkils
Flexible Loop (DISEMBL)
mmkifvktlkgtsfdvevkpedtvfdVKMKIEtvqgsdvypaAQQMLIYQGKVLKDDTTLeenkvaensfvVIMLtknkrptgegstrstaptkapqssaptpaatpaTAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPqlfpcfkswgnkils
Low Complexity Region (SEG)
MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRPTGEGSTRstaptkapqssaptpaatpatapqtaVPIsteptpaptpapasasvssvsatsesGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSptqmpqptqpapvtSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWGNKILS
Disordered region (IsUnstruct)
***IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT*********************************************************************YGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGI***************************************************************LDFLRNSPQFQVLRAMVQANPQLFPCFKSWGN****
Disordered Region (DISOPRED)
MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM***********************************************************************************************************ALRAAYNNPERAVEYL**********************************************************************LRNSPQFQVLRAMVQANPQLFPCFKSW******
Disordered Region (DISEMBL)
MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK***********************************VPIS**************************VYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVAR*************************SGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWGNKILS
Disordered Region (DISPRO)
MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN***************************************************************************VAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPE***********************************************************GSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWGNKIL*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWGNKILS
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	300	2.2.26 [Sep-21-2011]
Q84L31	419	Putative DNA repair prote	yes	no	0.966	0.692	0.589	4e-93
Q84L30	378	Putative DNA repair prote	no	no	0.943	0.748	0.595	2e-84
Q40742	392	Probable DNA repair prote	yes	no	0.943	0.721	0.561	2e-80
Q84L33	371	Putative DNA repair prote	no	no	0.906	0.733	0.481	4e-67
Q84L32	368	Putative DNA repair prote	no	no	0.903	0.736	0.458	1e-61
P54727	409	UV excision repair protei	yes	no	0.9	0.660	0.357	2e-39
P54728	416	UV excision repair protei	yes	no	0.88	0.634	0.332	2e-38
Q4KMA2	415	UV excision repair protei	yes	no	0.89	0.643	0.335	8e-37
Q29RK4	408	UV excision repair protei	yes	no	0.89	0.654	0.327	1e-35
P54725	363	UV excision repair protei	no	no	0.796	0.658	0.356	3e-33

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

 Score =  341 bits (875), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 194/329 (58%), Positives = 227/329 (68%), Gaps = 39/329 (11%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MKIFVKTLKGT F++EVKPED+V DVK  IE+VQG+DVYPAA+QMLI+QGKVLKD+TT+E
Sbjct: 1   MKIFVKTLKGTHFEIEVKPEDSVVDVKKNIESVQGADVYPAAKQMLIHQGKVLKDETTIE 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPIS--- 118
           ENKVAENSF+VIM+ K+K  +   S+ S   ++A   S P   + P+ +PQT   +S   
Sbjct: 61  ENKVAENSFIVIMMNKSKPASAAASSASAGTSQA--KSIPPSTSQPSISPQTPASVSAPV 118

Query: 119 -----------------------TEPTPAPTPAPASASVS-----SVSATSESGVYGHAA 150
                                  T  TP P P PA+ S S     S    S+  VYG AA
Sbjct: 119 APAPTRPPPPAPTPTPAPVAATETVTTPIPEPVPATISSSTPAPDSAPVGSQGDVYGQAA 178

Query: 151 SNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPV 210
           SNL AG+NLE  IQQILDMGGGTWDR+TVV ALRAA+NNPERAVEYLY+GIPEQAEV PV
Sbjct: 179 SNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLYTGIPEQAEVPPV 238

Query: 211 ARAPGN-GQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLR 269
           AR P + GQ AN P Q     QPA   +SGPNANPLDLFPQGLP+VG G  GAG+LDFLR
Sbjct: 239 ARPPASAGQPANPPAQT---QQPAAAPASGPNANPLDLFPQGLPNVG-GNPGAGTLDFLR 294

Query: 270 NSPQFQVLRAMVQANPQLF-PCFKSWGNK 297
           NS QFQ LRAMVQANPQ+  P  +  G +
Sbjct: 295 NSQQFQALRAMVQANPQVLQPMLQELGKQ 323

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 =  312 bits (799), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 178/299 (59%), Positives = 217/299 (72%), Gaps = 16/299 (5%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MKIFVKTL G++F++EVKP D V DVK  IETV+G++ YPAA+QMLI+QGKVLKD+TTLE
Sbjct: 1   MKIFVKTLSGSNFEIEVKPADKVSDVKTAIETVKGAE-YPAAKQMLIHQGKVLKDETTLE 59

Query: 62  ENKVAENSFVVIMLTKNK-RPTGEGSTRSTAPTKAPQSSAPTPAATP-ATAPQTAVPIST 119
           EN V ENSF+VIML+K K  P+G     STA   AP ++ P   ATP  +AP  +VP+  
Sbjct: 60  ENNVVENSFIVIMLSKTKASPSG----ASTASAPAPSATQPQTVATPQVSAPTASVPV-- 113

Query: 120 EPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTV 179
                PT   A+A+  + +A+ ++ VYG AASNLVAG  LE  +QQILDMGGG+WDRDTV
Sbjct: 114 -----PTSGTATAAAPATAASVQTDVYGQAASNLVAGTTLESTVQQILDMGGGSWDRDTV 168

Query: 180 VRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSG 239
           VRALRAA+NNPERAVEYLYSGIP QAE+ PVA+AP  G+ A +P   PQ        + G
Sbjct: 169 VRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPATGEQAANPLAQPQQAAAPAAATGG 228

Query: 240 PNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF-PCFKSWGNK 297
           PNANPL+LFPQG+P      AGAG+LDFLRNS QFQ LRAMVQANPQ+  P  +  G +
Sbjct: 229 PNANPLNLFPQGMPAA-DAGAGAGNLDFLRNSQQFQALRAMVQANPQILQPMLQELGKQ 286

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 =  299 bits (765), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 173/308 (56%), Positives = 213/308 (69%), Gaps = 25/308 (8%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MKI VKTLKG++F +EV     V DVK  IET QG  +YPA QQMLI+QGKVLKDDTTL+
Sbjct: 1   MKISVKTLKGSTFQIEVDSAQKVADVKRIIETTQGQHIYPAEQQMLIHQGKVLKDDTTLD 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRST-APTKAPQSSAP-------TPAATPATAPQT 113
           ENKV ENSF+VIML +     G+GS+ S  A +KAP + AP        PA+    AP T
Sbjct: 61  ENKVLENSFLVIMLRQ-----GKGSSSSAPATSKAPSNQAPPTQTVPAAPASQAPVAPAT 115

Query: 114 AVPIS-TEPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGG 172
            VP++ + PTP  T +PA A    V+ +SE+  YG A SNLVAG+NLE  IQ IL+MGGG
Sbjct: 116 TVPVTVSAPTPTATASPAPA----VAVSSEADNYGQATSNLVAGSNLEATIQSILEMGGG 171

Query: 173 TWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQP 232
            WDRD V+ AL AA+NNPERAVEYLYSG+PEQ ++ PV   P + Q AN PTQ  Q TQP
Sbjct: 172 IWDRDIVLHALSAAFNNPERAVEYLYSGVPEQMDI-PV--PPPSIQPAN-PTQASQATQP 227

Query: 233 A--PVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF-P 289
           A   + SSGPNA+PLDLFPQ LP+  + AAG G+LD LRN+ QF+ L ++VQANPQ+  P
Sbjct: 228 AAPSILSSGPNASPLDLFPQALPNASTDAAGLGNLDALRNNAQFRTLLSLVQANPQILQP 287

Query: 290 CFKSWGNK 297
             +  G +
Sbjct: 288 LLQELGKQ 295

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 =  254 bits (650), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 145/301 (48%), Positives = 192/301 (63%), Gaps = 29/301 (9%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+ VKTLKG+ F++ V P DT+  VK  IE  QG D YP  QQ+LI+ GKVLKD+T+L 
Sbjct: 1   MKLTVKTLKGSHFEIRVLPSDTIMAVKKNIEDSQGKDNYPCGQQLLIHNGKVLKDETSLV 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEP 121
           ENKV E  F+V+ML+K+K     G +   A  +    S P  A T +T P  A P +T+ 
Sbjct: 61  ENKVTEEGFLVVMLSKSKS----GGSAGQASVQTSSVSQPVSATTSSTKP--AAPSTTQS 114

Query: 122 TPAP-TPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVV 180
           +P P +P PA    ++ + T     YG AAS LV+G++LE  +QQI++MGGG+WD++TV 
Sbjct: 115 SPVPASPIPAQEQPAAQTDT-----YGQAASTLVSGSSLEQMVQQIMEMGGGSWDKETVT 169

Query: 181 RALRAAYNNPERAVEYLYSGIPEQAEVQ---PVARAPGNGQAANSPTQMPQPTQPAPVTS 237
           RALRAAYNNPERAV+YLYSGIP+ AEV    P A+  G+G A         P  PA   S
Sbjct: 170 RALRAAYNNPERAVDYLYSGIPQTAEVAVPVPEAQIAGSGAA---------PVAPA---S 217

Query: 238 SGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF-PCFKSWGN 296
            GPN++PLDLFPQ      +G+   G+L+FLRN+ QFQ LR MV +NPQ+  P  +  G 
Sbjct: 218 GGPNSSPLDLFPQETV-AAAGSGDLGTLEFLRNNDQFQQLRTMVHSNPQILQPMLQELGK 276

Query: 297 K 297
           +
Sbjct: 277 Q 277

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 =  236 bits (603), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 137/299 (45%), Positives = 182/299 (60%), Gaps = 28/299 (9%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+ VKTLKG+ F++ V P DT+  VK  IE  Q  D YP  QQ+LI+ GKVLKD+TTL 
Sbjct: 1   MKLTVKTLKGSHFEIRVLPTDTIMAVKKNIEDSQSKDNYPCGQQLLIHNGKVLKDETTLV 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEP 121
           ENKV E  F+V+ML+K+K  +  G + +   +    + + T  A P+T    AVP S   
Sbjct: 61  ENKVTEEGFLVVMLSKSKTASSAGPSSTQPTSTTTSTISSTTLAAPSTTQSIAVPASNST 120

Query: 122 TPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVR 181
                P            T++S  YG AAS LV+G+++E  +QQI++MGGG+WD++TV R
Sbjct: 121 PVQEQP------------TAQSDTYGQAASTLVSGSSIEQMVQQIMEMGGGSWDKETVTR 168

Query: 182 ALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPN 241
           ALRAAYNNPERAV+YLYSGIPE   + P     G G          + T P P  S GPN
Sbjct: 169 ALRAAYNNPERAVDYLYSGIPETVTI-PATNLSGVGSGR-------ELTAPPP--SGGPN 218

Query: 242 ANPLDLFPQGLPDVGSGAAGA--GSLDFLRNSPQFQVLRAMVQANPQLF-PCFKSWGNK 297
           ++PLDLFPQ   +  S AAG   G+L+FLR + QFQ LR+MV +NPQ+  P  +  G +
Sbjct: 219 SSPLDLFPQ---EAVSDAAGGDLGTLEFLRGNDQFQQLRSMVNSNPQILQPMLQELGKQ 274

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 =  163 bits (412), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 115/322 (35%), Positives = 170/322 (52%), Gaps = 52/322 (16%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct: 1   MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 62  ENKVAENSFVVIMLTKNKRPT--GEGSTRSTAP-----------TKAPQSSAPTPAATPA 108
           E K+ E +FVV+M+TK K  +     +T+ +AP           T   Q+  P PA  P 
Sbjct: 61  EYKIDEKNFVVVMVTKPKAVSTPAPATTQQSAPASTTAVTSSTTTTVAQAPTPVPALAPT 120

Query: 109 TAPQTAVP----ISTEPTPA-------PTPAPA--------SASVSSVSATSESGVYGHA 149
           + P +  P     S+EP PA       P   PA        +A+ S+   +S S ++  A
Sbjct: 121 STPASITPASATASSEPAPASAAKQEKPAEKPAETPVATSPTATDSTSGDSSRSNLFEDA 180

Query: 150 ASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQP 209
            S LV G + E  + +I+ MG   ++R+ V+ ALRA++NNP+RAVEYL  GIP   E Q 
Sbjct: 181 TSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQA 237

Query: 210 VARAPGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLR 269
           V   P   QAA+  T  PQ +  A   ++                  + ++G   L+FLR
Sbjct: 238 VVDPP---QAAS--TGAPQSSAVAAAAATTTAT------------TTTTSSGGHPLEFLR 280

Query: 270 NSPQFQVLRAMVQANPQLFPCF 291
           N PQFQ +R ++Q NP L P  
Sbjct: 281 NQPQFQQMRQIIQQNPSLLPAL 302

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

Homo sapiens (taxid: 9606)

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

 Score =  159 bits (403), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 109/328 (33%), Positives = 159/328 (48%), Gaps = 64/328 (19%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct: 1   MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILSDDTALK 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTP------------------ 103
           E K+ E +FVV+M+TK K  T      +  P     SS P+P                  
Sbjct: 61  EYKIDEKNFVVVMVTKPKAVT------TAVPATTQPSSTPSPTAVSSSPAVAAAQAPAPT 114

Query: 104 -----AATPATAPQTAVPISTEPTPA-------PTPAPASASV--------SSVSATSES 143
                 +TPA+    +   S+EP PA       P   PA   V        S+   +S S
Sbjct: 115 PALPPTSTPASTAPASTTASSEPAPAGATQPEKPAEKPAQTPVLTSPAPADSTPGDSSRS 174

Query: 144 GVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPE 203
            ++  A S LV G + E  + +I+ MG   ++R+ V+ ALRA++NNP+RAVEYL  GIP 
Sbjct: 175 NLFEDATSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPG 231

Query: 204 QAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAG 263
             E Q V   P                 P  V++  P +  +           +  +G  
Sbjct: 232 DRESQAVVDPP-----------------PQAVSTGTPQSPAVAAAAATTTATTTTTSGGH 274

Query: 264 SLDFLRNSPQFQVLRAMVQANPQLFPCF 291
            L+FLRN PQFQ +R ++Q NP L P  
Sbjct: 275 PLEFLRNQPQFQQMRQIIQQNPSLLPAL 302

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

Mus musculus (taxid: 10090)

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

 Score =  154 bits (389), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 109/325 (33%), Positives = 158/325 (48%), Gaps = 58/325 (17%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct: 1   MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILSDDTALK 60

Query: 62  ENKVAENSFVVIMLTKNKRPTG----------------------------EGSTRSTAPT 93
           E K+ E +FVV+M+TK K  T                                T + APT
Sbjct: 61  EYKIDEKNFVVVMVTKPKAVTSAVPATTQQSSSPSTTTVSSSPAAAVAQAPAPTPALAPT 120

Query: 94  KAPQSSAPT-------PAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVY 146
             P S+ P        PA T AT P+       +     +PAPA    S+   +S S ++
Sbjct: 121 STPASTTPASTTASSEPAPTGATQPEKPAEKPAQTPVLTSPAPAD---STPGDSSRSNLF 177

Query: 147 GHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAE 206
             A S LV G + E  + +I+ MG   ++R+ V+ ALRA++NNP+RAVEYL  GIP   E
Sbjct: 178 EDATSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPGDRE 234

Query: 207 VQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLD 266
            Q V   P                 P  V++  P +  +           +  +G   L+
Sbjct: 235 SQAVVDPP-----------------PQAVSTGTPQSPAVAAAAATTTATTTTTSGGHPLE 277

Query: 267 FLRNSPQFQVLRAMVQANPQLFPCF 291
           FLRN PQFQ +R ++Q NP L P  
Sbjct: 278 FLRNQPQFQQMRQIIQQNPSLLPAL 302

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

Rattus norvegicus (taxid: 10116)

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

 Score =  150 bits (379), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 106/324 (32%), Positives = 160/324 (49%), Gaps = 57/324 (17%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M + +KTL+  +F +++ P++TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct: 1   MLVTLKTLQQQTFKIDIDPDETVRALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 62  ENKVAENSFVVIMLTKNK-----RPTGEGSTRSTAPTKAPQSS----------------- 99
           E K+ E +FVV+M+TK K      P     + S A T    S+                 
Sbjct: 61  EYKIDEKNFVVVMVTKPKAVTTPAPATTQQSNSAATTTVSSSTAPAVTQAPAPAPASAPT 120

Query: 100 --------APTPAAT---PATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGH 148
                   APT A++   PA+A +   P +  P   P     +++ S+   +S S ++  
Sbjct: 121 PTPVSVTPAPTTASSEPAPASAAKQEKP-AERPVETPVATTPTSTDSTSGDSSRSNLFED 179

Query: 149 AASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQ 208
           A S LV G + E  + +I+ MG   ++R+ V+ ALRA++NNP+RAVEYL  GIP   E Q
Sbjct: 180 ATSALVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQ 236

Query: 209 PVARAPGNGQAANSPTQMPQPTQPAPVTSSG-PNANPLDLFPQGLPDVGSGAAGAGSLDF 267
            V                     P P  S+G P ++             + ++G   L+F
Sbjct: 237 AV-------------------VDPPPAASTGAPQSSVAAAAATTTATTTTTSSGGHPLEF 277

Query: 268 LRNSPQFQVLRAMVQANPQLFPCF 291
           LRN PQFQ +R ++Q NP L P  
Sbjct: 278 LRNQPQFQQMRQIIQQNPSLLPAL 301

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 =  142 bits (358), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/289 (35%), Positives = 145/289 (50%), Gaps = 50/289 (17%)

Query: 4   IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEEN 63
           I +KTL+  +F + ++P++TV  +K KIE  +G D +P A Q LIY GK+L DD  + + 
Sbjct: 5   ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 64

Query: 64  KVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSS-----APTPAAT---PATAPQTAV 115
           ++ E +FVV+M+TK K   G  +    +PT AP+SS     APT   +   PA     + 
Sbjct: 65  RIDEKNFVVVMVTKTKAGQGTSAPPEASPTAAPESSTSFPPAPTSGMSHPPPAAREDKSP 124

Query: 116 PISTEPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWD 175
              + PT +P     S   S  S   E      AAS LV G+  E  + +I+ MG   ++
Sbjct: 125 SEESAPTTSPESVSGSVPSSGSSGREED-----AASTLVTGSEYETMLTEIMSMG---YE 176

Query: 176 RDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPV 235
           R+ VV ALRA+YNNP RAVEYL +GIP   E       P +G    S        QPA  
Sbjct: 177 RERVVAALRASYNNPHRAVEYLLTGIPGSPE-------PEHGSVQESQVS----EQPA-- 223

Query: 236 TSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQAN 284
                                + AAG   L+FLR+ PQFQ +R ++Q N
Sbjct: 224 ---------------------TEAAGENPLEFLRDQPQFQNMRQVIQQN 251

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	300
356536322	408	PREDICTED: putative DNA repair protein R	0.983	0.723	0.639	1e-103
225452017	381	PREDICTED: putative DNA repair protein R	0.96	0.755	0.688	1e-103
356575534	402	PREDICTED: putative DNA repair protein R	0.97	0.723	0.646	1e-102
356575536	399	PREDICTED: putative DNA repair protein R	0.96	0.721	0.630	6e-97
225423953	397	PREDICTED: putative DNA repair protein R	0.973	0.735	0.682	7e-97
363807216	400	uncharacterized protein LOC100813881 [Gl	0.973	0.73	0.660	7e-97
255636381	382	unknown [Glycine max]	0.96	0.753	0.661	3e-96
356575538	381	PREDICTED: putative DNA repair protein R	0.953	0.750	0.634	3e-95
225452019	361	PREDICTED: putative DNA repair protein R	0.95	0.789	0.653	1e-94
358248820	392	uncharacterized protein LOC100809066 [Gl	0.973	0.744	0.694	2e-93

>gi|356536322|ref|XP_003536688.1| PREDICTED: putative DNA repair protein RAD23-3-like [Glycine max]

 Score =  382 bits (980), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 202/316 (63%), Positives = 232/316 (73%), Gaps = 21/316 (6%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+FVKTLKGT F++EV P+DTV +VK  IETVQG+DVYPAAQQMLI+QGKVL+D +TLE
Sbjct: 1   MKVFVKTLKGTHFEIEVTPQDTVSEVKKNIETVQGADVYPAAQQMLIHQGKVLRDASTLE 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAP-TKAPQSSAPTPAATPATAPQTAVPISTE 120
           ENKV EN+F+VIML+K+K P+GEGST STAP TKAPQ+S   PA+TP  +          
Sbjct: 61  ENKVVENTFIVIMLSKSKSPSGEGSTTSTAPSTKAPQTST-VPASTPPASVVPQASAPAP 119

Query: 121 PTPAPTPAPASASVS------------------SVSATSESGVYGHAASNLVAGNNLEGA 162
                      ASV+                  S +A   S +YG AASNLVAG+NLEG 
Sbjct: 120 APAPAATGALPASVTAPISSPSPAPAPTPAPISSGTAVEGSDIYGQAASNLVAGSNLEGT 179

Query: 163 IQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANS 222
           IQQILDMGGG+WDRDTVVRALRAAYNNPERAVEYLY+GIPEQAE   VA+ P + Q  N 
Sbjct: 180 IQQILDMGGGSWDRDTVVRALRAAYNNPERAVEYLYTGIPEQAEAPLVAQVPASAQPTNP 239

Query: 223 PTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQ 282
           P   PQ  QPAPVTS+GPNANPLDLFPQGLP+VGSGAAGAGSLDFLRNS QFQ LRAMVQ
Sbjct: 240 PADAPQTAQPAPVTSAGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQ 299

Query: 283 ANPQLF-PCFKSWGNK 297
           ANPQ+  P  +  G +
Sbjct: 300 ANPQILQPMLQELGKQ 315

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  379 bits (974), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 206/299 (68%), Positives = 229/299 (76%), Gaps = 11/299 (3%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MKIFVKTLKGT F++EVKPEDTV DVK  IE V G+DVYPAAQQMLI+QGKVLKD TTL+
Sbjct: 1   MKIFVKTLKGTHFEIEVKPEDTVADVKKNIELVHGTDVYPAAQQMLIHQGKVLKDATTLD 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKA--PQSSAPTPAATPATAPQTAVPIST 119
           EN+VAE+SFVVIML+KNK   G  ST S APT    P SS+P  +  P+TAPQ   P+  
Sbjct: 61  ENQVAESSFVVIMLSKNKVSAGGASTTSAAPTSQAQPVSSSPPTSNQPSTAPQA--PVVA 118

Query: 120 EPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTV 179
            P   P PAPA A     S +S+S +YG AASNLVAGNNLE  IQQILDMGGG+WDRDTV
Sbjct: 119 LPEVIPEPAPAVAP----SISSDSDIYGQAASNLVAGNNLEVTIQQILDMGGGSWDRDTV 174

Query: 180 VRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSG 239
           VRALRAAYNNPERAVEYLYSGIPEQAE  P AR P +G A N PTQ PQ  Q   V SSG
Sbjct: 175 VRALRAAYNNPERAVEYLYSGIPEQAEGPPAARPPASGLAVNLPTQAPQGPQ-TTVASSG 233

Query: 240 PNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF-PCFKSWGNK 297
           PNANPLDLFPQGLP +GS A+ AG+LDFLRNSPQFQ LRAMVQANPQ+  P  +  G +
Sbjct: 234 PNANPLDLFPQGLPSMGSNAS-AGTLDFLRNSPQFQALRAMVQANPQILQPMLQELGKQ 291

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 203/314 (64%), Positives = 231/314 (73%), Gaps = 23/314 (7%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+FVKTLKGT F++EV P+DTV +VK  IETVQG+DVYPAAQQMLI+QGKVL+D TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVTPQDTVSEVKKNIETVQGADVYPAAQQMLIHQGKVLRDATTLE 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTA-PTKAPQSSAPTPAATPATAPQTAVPISTE 120
           ENKVAEN+F+VIML+K+K  +GEGST STA  TKAPQ+S       PA+ P  +V     
Sbjct: 61  ENKVAENTFIVIMLSKSKSTSGEGSTTSTALSTKAPQTST-----VPASTPPVSVAPQAP 115

Query: 121 PTPAPTPAPASASVSSV----------------SATSESGVYGHAASNLVAGNNLEGAIQ 164
              A    PAS +                    +A   S +YG AASNLVAG+NLEG IQ
Sbjct: 116 APAATGALPASVTAPVSSPSPAPAPAPAPISSGTAVEGSDIYGQAASNLVAGSNLEGTIQ 175

Query: 165 QILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPT 224
           QILDMGGG+WDRDTVVRALRAAYNNPERAVEYLY+GIPEQAE   VARAP + Q  N P 
Sbjct: 176 QILDMGGGSWDRDTVVRALRAAYNNPERAVEYLYTGIPEQAEAPLVARAPVSAQPTNPPA 235

Query: 225 QMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQAN 284
             PQ  QPA VTS+GPNANPLDLFPQGLP+VGSGAAGAGSLDFLRNS QFQ LRAMVQAN
Sbjct: 236 DAPQTAQPAAVTSAGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQAN 295

Query: 285 PQLF-PCFKSWGNK 297
           PQ+  P  +  G +
Sbjct: 296 PQILQPMLQELGKQ 309

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575536|ref|XP_003555896.1| PREDICTED: putative DNA repair protein RAD23-3-like isoform 2 [Glycine max]

 Score =  360 bits (923), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 198/314 (63%), Positives = 225/314 (71%), Gaps = 26/314 (8%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+FVKTLKGT F++EV P+DTV +VK  IETVQG+DVYPAAQQMLI+QGKVL+D TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVTPQDTVSEVKKNIETVQGADVYPAAQQMLIHQGKVLRDATTLE 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTA-PTKAPQSSAPTPAATPATAPQTAVPISTE 120
           ENKVAEN+F+VIML+K+K  +GEGST STA  TKAPQ+S       PA+ P  +V     
Sbjct: 61  ENKVAENTFIVIMLSKSKSTSGEGSTTSTALSTKAPQTST-----VPASTPPVSVAPQAP 115

Query: 121 PTPAPTPAPASASVSSV----------------SATSESGVYGHAASNLVAGNNLEGAIQ 164
              A    PAS +                    +A   S +YG AASNLVAG+NLEG IQ
Sbjct: 116 APAATGALPASVTAPVSSPSPAPAPAPAPISSGTAVEGSDIYGQAASNLVAGSNLEGTIQ 175

Query: 165 QILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPT 224
           QILDMGGG+WDRDTVVRALRAAYNNPERAVEYLY+GIPEQAE   VARAP + Q  N P 
Sbjct: 176 QILDMGGGSWDRDTVVRALRAAYNNPERAVEYLYTGIPEQAEAPLVARAPVSAQPTNPPA 235

Query: 225 QMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQAN 284
             PQ  QPA VTS+GPNANPLDLFPQ      SGAAGAGSLDFLRNS QFQ LRAMVQAN
Sbjct: 236 DAPQTAQPAAVTSAGPNANPLDLFPQ---VAISGAAGAGSLDFLRNSQQFQALRAMVQAN 292

Query: 285 PQLF-PCFKSWGNK 297
           PQ+  P  +  G +
Sbjct: 293 PQILQPMLQELGKQ 306

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225423953|ref|XP_002282352.1| PREDICTED: putative DNA repair protein RAD23-3 [Vitis vinifera] gi|297737829|emb|CBI27030.3| unnamed protein product [Vitis vinifera]

 Score =  359 bits (922), Expect = 7e-97,   Method: Compositional matrix adjust.
 Identities = 211/309 (68%), Positives = 233/309 (75%), Gaps = 17/309 (5%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MKIFVKTLKGT F+++VKPEDTV DVK  IE VQGSDVYPA+QQMLI+QGKVLKD TTL+
Sbjct: 1   MKIFVKTLKGTHFEIQVKPEDTVADVKANIEAVQGSDVYPASQQMLIHQGKVLKDGTTLD 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPT------------PAATPAT 109
           ENKVAENSFVV+ML+KNK  + EGST STAP  AP  +                  +  T
Sbjct: 61  ENKVAENSFVVVMLSKNKN-SSEGSTASTAPAPAPAPAPTPIVKAPSASAPPPTTTSTLT 119

Query: 110 APQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDM 169
           APQ  V     P   P PAPA+   S+V+  SE+  YG AASNLVAGNN E AIQQILDM
Sbjct: 120 APQAPVVALPPPATVPAPAPAATPASTVTVVSETDAYGQAASNLVAGNNFEEAIQQILDM 179

Query: 170 GGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQP 229
           GGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEV PVARAP +GQAAN P Q  QP
Sbjct: 180 GGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVPPVARAPASGQAANPPAQSQQP 239

Query: 230 TQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF- 288
             PAP  SSGPNANPLDLFPQG+P+VGS  AGAG+LDFLRNS QFQ LRAMVQANPQ+  
Sbjct: 240 V-PAP--SSGPNANPLDLFPQGIPNVGSNPAGAGTLDFLRNSQQFQALRAMVQANPQILQ 296

Query: 289 PCFKSWGNK 297
           P  +  G +
Sbjct: 297 PMLQELGKQ 305

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  359 bits (922), Expect = 7e-97,   Method: Compositional matrix adjust.
 Identities = 206/312 (66%), Positives = 232/312 (74%), Gaps = 20/312 (6%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+FVKTLKGT F++EV P DT+ +VK  IETVQG+DVYPAAQQMLI+QGKVLKD TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVNPSDTLSEVKKNIETVQGADVYPAAQQMLIHQGKVLKDGTTLE 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPIST-- 119
           ENKVAE+SF+VIML+K K  +GEGST STAP+  P S+ PT  +  +TAPQ   P ST  
Sbjct: 61  ENKVAESSFIVIMLSKTKSSSGEGSTTSTAPSAKP-SATPTSTSV-STAPQA--PASTGA 116

Query: 120 -------------EPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQI 166
                               PAPA A + S S+  ES +YG AASNLVAG+NLEG IQQI
Sbjct: 117 SATPVTAPTAAPAPAPAPAAPAPAPAPIFSGSSVPESDIYGQAASNLVAGSNLEGTIQQI 176

Query: 167 LDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQM 226
           LDMGGG+WDRDTVVR LRAAYNNPERAVEYLYSGIPEQAE  PV   P + Q +N P   
Sbjct: 177 LDMGGGSWDRDTVVRTLRAAYNNPERAVEYLYSGIPEQAEAPPVTGVPASAQPSNPPADT 236

Query: 227 PQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQ 286
           PQ  QPA V SSGPNANPLDLFPQGLP+VGSGAAGAGSLDFLRNS QFQ LRAMVQANPQ
Sbjct: 237 PQAAQPASVPSSGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANPQ 296

Query: 287 LF-PCFKSWGNK 297
           +  P  +  G +
Sbjct: 297 ILQPMLQELGKQ 308

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255636381|gb|ACU18529.1| unknown [Glycine max]

 Score =  357 bits (917), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 197/298 (66%), Positives = 223/298 (74%), Gaps = 10/298 (3%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+FVKTLKGT F++EV P DT+ +VK  IETVQG+DVYPAAQQMLI+QGKVLKD TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVNPSDTLSEVKKNIETVQGADVYPAAQQMLIHQGKVLKDGTTLE 60

Query: 62  ENKVAENSFVVIMLTK-NKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTE 120
           ENKVAE+SF+VIML+K +  PT      ST+ + APQ+ A T A+       TA      
Sbjct: 61  ENKVAESSFIVIMLSKPSATPT------STSVSTAPQAPASTGASATPVTAPTAA--PAP 112

Query: 121 PTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVV 180
                 PAPA A + S S+  ES +YG AASNLVAG+NLEG IQQILDMGGG+WDRDTVV
Sbjct: 113 APAPAAPAPAPAPIFSGSSVPESDIYGQAASNLVAGSNLEGTIQQILDMGGGSWDRDTVV 172

Query: 181 RALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGP 240
           R LRAAYNNPERAVEYLYSGIPEQAE  PV   P + Q +N P   PQ  QPA V SSGP
Sbjct: 173 RTLRAAYNNPERAVEYLYSGIPEQAEALPVTGVPASAQPSNPPADTPQAAQPASVPSSGP 232

Query: 241 NANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF-PCFKSWGNK 297
           NANPLDLFPQGLP+VGSGAAGAGSLDFLRNS QFQ LRAMVQANPQ+  P  +  G +
Sbjct: 233 NANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANPQILQPMLQELGKQ 290

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575538|ref|XP_003555897.1| PREDICTED: putative DNA repair protein RAD23-3-like isoform 3 [Glycine max]

 Score =  354 bits (909), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 189/298 (63%), Positives = 216/298 (72%), Gaps = 12/298 (4%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+FVKTLKGT F++EV P+DTV +VK  IETVQG+DVYPAAQQMLI+QGKVL+D TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVTPQDTVSEVKKNIETVQGADVYPAAQQMLIHQGKVLRDATTLE 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEP 121
           ENKVAEN+F+VIML+K           ST P   P  S    A  PA        ++   
Sbjct: 61  ENKVAENTFIVIMLSKT----------STVPASTPPVSVAPQAPAPAATGALPASVTAPV 110

Query: 122 TPAPTPAPASASVSSV-SATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVV 180
           +        + +  S  +A   S +YG AASNLVAG+NLEG IQQILDMGGG+WDRDTVV
Sbjct: 111 SSPSPAPAPAPAPISSGTAVEGSDIYGQAASNLVAGSNLEGTIQQILDMGGGSWDRDTVV 170

Query: 181 RALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGP 240
           RALRAAYNNPERAVEYLY+GIPEQAE   VARAP + Q  N P   PQ  QPA VTS+GP
Sbjct: 171 RALRAAYNNPERAVEYLYTGIPEQAEAPLVARAPVSAQPTNPPADAPQTAQPAAVTSAGP 230

Query: 241 NANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF-PCFKSWGNK 297
           NANPLDLFPQGLP+VGSGAAGAGSLDFLRNS QFQ LRAMVQANPQ+  P  +  G +
Sbjct: 231 NANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANPQILQPMLQELGKQ 288

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  352 bits (903), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 196/300 (65%), Positives = 219/300 (73%), Gaps = 15/300 (5%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MKIFVKTLKGT F++EVKPEDTV DVK  IE V G+DVYPAAQQMLI+QGKVLKD TTL+
Sbjct: 1   MKIFVKTLKGTHFEIEVKPEDTVADVKKNIELVHGTDVYPAAQQMLIHQGKVLKDATTLD 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKA--PQSSAPTPAATPATAPQTAVPIST 119
           EN+VAE+SFVVIML+KNK   G  ST S APT    P SS+P  +  P+TAPQ   P+  
Sbjct: 61  ENQVAESSFVVIMLSKNKVSAGGASTTSAAPTSQAQPVSSSPPTSNQPSTAPQA--PVVA 118

Query: 120 EPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTV 179
            P   P PAPA A     S +S+S +YG AASNLVAGNNLE  IQQILDMGGG+WDRDTV
Sbjct: 119 LPEVIPEPAPAVAP----SISSDSDIYGQAASNLVAGNNLEVTIQQILDMGGGSWDRDTV 174

Query: 180 VRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSG 239
           VRALRAAYNNPERAVEYLYSGIPEQAE  P AR P +G A N PTQ PQ  Q   V SSG
Sbjct: 175 VRALRAAYNNPERAVEYLYSGIPEQAEGPPAARPPASGLAVNLPTQAPQGPQ-TTVASSG 233

Query: 240 PNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWGNKIL 299
           PNANPLDLFPQGLP +GS A+ AG+LDFLRNSPQ      + + NP L    +      L
Sbjct: 234 PNANPLDLFPQGLPSMGSNAS-AGTLDFLRNSPQ-----ELGKQNPHLMRLIQEHQADFL 287

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  348 bits (893), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 211/304 (69%), Positives = 233/304 (76%), Gaps = 12/304 (3%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           MK+FVKTLKGT F++EV P DT+ +VK  IETVQG+DVYPAAQQMLI+QGKVLKD TTLE
Sbjct: 1   MKVFVKTLKGTHFEIEVNPSDTLSEVKKNIETVQGADVYPAAQQMLIHQGKVLKDGTTLE 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPIST-- 119
           ENKVAENSF+VIML+K K  +GEGST STAP+    S+ PT  +  A APQ   P ST  
Sbjct: 61  ENKVAENSFIVIMLSKTKSSSGEGSTTSTAPS-VKASATPTSTSVSA-APQA--PASTGA 116

Query: 120 -----EPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTW 174
                    AP  A A A +SS SA  ES +YG AASNLVAG+NLEG IQQILDMGGG+W
Sbjct: 117 TPTPVTAPAAPASAAAPAPISSGSAVPESDIYGQAASNLVAGSNLEGTIQQILDMGGGSW 176

Query: 175 DRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAP 234
           DRDTVVRALRAAYNNPERAVEYLYSGIPEQAE  PV R P + Q AN P   PQ  QPA 
Sbjct: 177 DRDTVVRALRAAYNNPERAVEYLYSGIPEQAEAPPVTREPASAQPANPPAAAPQAAQPAS 236

Query: 235 VTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF-PCFKS 293
           V SSGPNANPLDLFPQGLP+VGSGAAGAGSLDFLRNS QFQ LRAMVQANPQ+  P  + 
Sbjct: 237 VPSSGPNANPLDLFPQGLPNVGSGAAGAGSLDFLRNSQQFQALRAMVQANPQILQPMLQE 296

Query: 294 WGNK 297
            G +
Sbjct: 297 LGKQ 300

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	300
TAIR|locus:2076944	419	RAD23C "RADIATION SENSITIVE23C	0.496	0.355	0.690	4e-81
TAIR|locus:2177376	378	RAD23D "RADIATION SENSITIVE23D	0.95	0.753	0.538	1.5e-74
TAIR|locus:2200522	368	RAD23A "RADIATION SENSITIVE23A	0.676	0.551	0.430	2.8e-41
UNIPROTKB|F1SP32	408	RAD23B "Uncharacterized protei	0.27	0.198	0.493	5.8e-38
UNIPROTKB|P54727	409	RAD23B "UV excision repair pro	0.26	0.190	0.487	8.2e-38
UNIPROTKB|E2R4A5	406	RAD23B "Uncharacterized protei	0.27	0.199	0.469	1.4e-37
UNIPROTKB|Q29RK4	408	RAD23B "UV excision repair pro	0.27	0.198	0.469	3.8e-37
RGD|1562958	415	Rad23b "RAD23 homolog B (S. ce	0.27	0.195	0.481	4.7e-37
MGI|MGI:105128	416	Rad23b "RAD23b homolog (S. cer	0.27	0.194	0.481	4.8e-37
UNIPROTKB|K7ESE3	308	RAD23A "UV excision repair pro	0.273	0.266	0.416	2.2e-35

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

 Score = 510 (184.6 bits), Expect = 4.0e-81, Sum P(2) = 4.0e-81
 Identities = 107/155 (69%), Positives = 118/155 (76%)

Query:   145 VYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQ 204
             VYG AASNL AG+NLE  IQQILDMGGGTWDR+TVV ALRAA+NNPERAVEYLY+GIPEQ
Sbjct:   173 VYGQAASNLAAGSNLESTIQQILDMGGGTWDRETVVLALRAAFNNPERAVEYLYTGIPEQ 232

Query:   205 AEVQPVARAPGN-GQAANSXXXXXXXXXXXXXXSSGPNANPLDLFPQGLPDVGSGAAGAG 263
             AEV PVAR P + GQ AN               +SGPNANPLDLFPQGLP+VG G  GAG
Sbjct:   233 AEVPPVARPPASAGQPANPPAQTQQPAAAP---ASGPNANPLDLFPQGLPNVG-GNPGAG 288

Query:   264 SLDFLRNSPQFQVLRAMVQANPQLF-PCFKSWGNK 297
             +LDFLRNS QFQ LRAMVQANPQ+  P  +  G +
Sbjct:   289 TLDFLRNSQQFQALRAMVQANPQVLQPMLQELGKQ 323

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 = 752 (269.8 bits), Expect = 1.5e-74, P = 1.5e-74
 Identities = 160/297 (53%), Positives = 187/297 (62%)

Query:     2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
             MKIFVKTL G++F++EVKP D V DVK  IETV+G++ YPAA+QMLI+QGKVLKD+TTLE
Sbjct:     1 MKIFVKTLSGSNFEIEVKPADKVSDVKTAIETVKGAE-YPAAKQMLIHQGKVLKDETTLE 59

Query:    62 ENKVAENSFVVIMLTKNKRPTGEGSTRXXXXXXXXXXXXXXXXXXXXXXXXXXVPIXXXX 121
             EN V ENSF+VIML+K K      ST                           VP     
Sbjct:    60 ENNVVENSFIVIMLSKTKASPSGASTASAPAPSATQPQTVATPQVSAPTASVPVP----- 114

Query:   122 XXXXXXXXXXXXXXXXXXXXXXGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVR 181
                                    VYG AASNLVAG  LE  +QQILDMGGG+WDRDTVVR
Sbjct:   115 ----TSGTATAAAPATAASVQTDVYGQAASNLVAGTTLESTVQQILDMGGGSWDRDTVVR 170

Query:   182 ALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSXXXXXXXXXXXXXXSSGPN 241
             ALRAA+NNPERAVEYLYSGIP QAE+ PVA+AP  G+ A +              + GPN
Sbjct:   171 ALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPATGEQAANPLAQPQQAAAPAAATGGPN 230

Query:   242 ANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLF-PCFKSWGNK 297
             ANPL+LFPQG+P   +GA GAG+LDFLRNS QFQ LRAMVQANPQ+  P  +  G +
Sbjct:   231 ANPLNLFPQGMPAADAGA-GAGNLDFLRNSQQFQALRAMVQANPQILQPMLQELGKQ 286

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 = 438 (159.2 bits), Expect = 2.8e-41, P = 2.8e-41
 Identities = 93/216 (43%), Positives = 119/216 (55%)

Query:     2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
             MK+ VKTLKG+ F++ V P DT+  VK  IE  Q  D YP  QQ+LI+ GKVLKD+TTL 
Sbjct:     1 MKLTVKTLKGSHFEIRVLPTDTIMAVKKNIEDSQSKDNYPCGQQLLIHNGKVLKDETTLV 60

Query:    62 ENKVAENSFVVIMLTKNKRPTGEGSTRXXXXXXXXXXXXXXXXXXXXXXXXXXVPIXXXX 121
             ENKV E  F+V+ML+K+K  +  G +                           VP     
Sbjct:    61 ENKVTEEGFLVVMLSKSKTASSAGPSSTQPTSTTTSTISSTTLAAPSTTQSIAVP----- 115

Query:   122 XXXXXXXXXXXXXXXXXXXXXXGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVR 181
                                     YG AAS LV+G+++E  +QQI++MGGG+WD++TV R
Sbjct:   116 -------ASNSTPVQEQPTAQSDTYGQAASTLVSGSSIEQMVQQIMEMGGGSWDKETVTR 168

Query:   182 ALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNG 217
             ALRAAYNNPERAV+YLYSGIPE   + P     G G
Sbjct:   169 ALRAAYNNPERAVDYLYSGIPETVTI-PATNLSGVG 203

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

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

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

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

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

GO:0043130 "ubiquitin binding" evidence=IDA

GO:0070628 "proteasome binding" evidence=IDA

UNIPROTKB|F1SP32 RAD23B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 205 (77.2 bits), Expect = 5.8e-38, Sum P(3) = 5.8e-38
 Identities = 40/81 (49%), Positives = 58/81 (71%)

Query:     2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
             M+I +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct:     1 MQITLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query:    62 ENKVAENSFVVIMLTKNKRPT 82
             E K+ E +FVV+M+TK K  T
Sbjct:    61 EYKIDEKNFVVVMVTKPKAVT 81

GO:0071942 "XPC complex" evidence=IEA

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

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000715 "nucleotide-excision repair, DNA damage recognition" evidence=IEA

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

GO:0003684 "damaged DNA binding" evidence=IEA

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

 Score = 202 (76.2 bits), Expect = 8.2e-38, Sum P(3) = 8.2e-38
 Identities = 38/78 (48%), Positives = 57/78 (73%)

Query:     2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
             M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct:     1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query:    62 ENKVAENSFVVIMLTKNK 79
             E K+ E +FVV+M+TK K
Sbjct:    61 EYKIDEKNFVVVMVTKPK 78

GO:0003684 "damaged DNA binding" evidence=IEA

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

GO:0000502 "proteasome complex" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0071942 "XPC complex" evidence=IDA

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

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

GO:0031593 "polyubiquitin binding" evidence=IDA

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

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E2R4A5 RAD23B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 198 (74.8 bits), Expect = 1.4e-37, Sum P(3) = 1.4e-37
 Identities = 38/81 (46%), Positives = 57/81 (70%)

Query:     2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
             M + +KTL+  +F +++ P++TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct:     1 MLVTLKTLQQQTFKIDIDPDETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query:    62 ENKVAENSFVVIMLTKNKRPT 82
             E K+ E +FVV+M+TK K  T
Sbjct:    61 EYKIDEKNFVVVMVTKPKAVT 81

GO:0071942 "XPC complex" evidence=IEA

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

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000715 "nucleotide-excision repair, DNA damage recognition" evidence=IEA

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

GO:0003684 "damaged DNA binding" evidence=IEA

UNIPROTKB|Q29RK4 RAD23B "UV excision repair protein RAD23 homolog B" [Bos taurus (taxid:9913)]

 Score = 198 (74.8 bits), Expect = 3.8e-37, Sum P(3) = 3.8e-37
 Identities = 38/81 (46%), Positives = 57/81 (70%)

Query:     2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
             M + +KTL+  +F +++ P++TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct:     1 MLVTLKTLQQQTFKIDIDPDETVRALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query:    62 ENKVAENSFVVIMLTKNKRPT 82
             E K+ E +FVV+M+TK K  T
Sbjct:    61 EYKIDEKNFVVVMVTKPKAVT 81

GO:0071942 "XPC complex" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0000715 "nucleotide-excision repair, DNA damage recognition" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

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

GO:0003684 "damaged DNA binding" evidence=IEA

RGD|1562958 Rad23b "RAD23 homolog B (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 204 (76.9 bits), Expect = 4.7e-37, Sum P(3) = 4.7e-37
 Identities = 39/81 (48%), Positives = 58/81 (71%)

Query:     2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
             M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct:     1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILSDDTALK 60

Query:    62 ENKVAENSFVVIMLTKNKRPT 82
             E K+ E +FVV+M+TK K  T
Sbjct:    61 EYKIDEKNFVVVMVTKPKAVT 81

GO:0000502 "proteasome complex" evidence=IEA

GO:0000715 "nucleotide-excision repair, DNA damage recognition" evidence=IEA;ISO

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

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

GO:0007283 "spermatogenesis" evidence=IEA;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:0071942 "XPC complex" evidence=ISO;ISS

GO:0005730 "nucleolus" evidence=ISO

MGI|MGI:105128 Rad23b "RAD23b homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 204 (76.9 bits), Expect = 4.8e-37, Sum P(3) = 4.8e-37
 Identities = 39/81 (48%), Positives = 58/81 (71%)

Query:     2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
             M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct:     1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILSDDTALK 60

Query:    62 ENKVAENSFVVIMLTKNKRPT 82
             E K+ E +FVV+M+TK K  T
Sbjct:    61 EYKIDEKNFVVVMVTKPKAVT 81

GO:0000502 "proteasome complex" evidence=IEA

GO:0000715 "nucleotide-excision repair, DNA damage recognition" evidence=ISO

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

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

GO:0007283 "spermatogenesis" evidence=IMP

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:0071942 "XPC complex" evidence=ISO

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

 Score = 181 (68.8 bits), Expect = 2.2e-35, Sum P(3) = 2.2e-35
 Identities = 35/84 (41%), Positives = 57/84 (67%)

Query:     4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEEN 63
             I +KTL+  +F + ++P++TV  +K KIE  +G D +P A Q LIY GK+L DD  + + 
Sbjct:     5 ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 64

Query:    64 KVAENSFVVIMLTKNKRPTGEGST 87
             ++ E +FVV+M+TK K   G+G++
Sbjct:    65 RIDEKNFVVVMVTKTK--AGQGTS 86

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

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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	0.5616	0.9433	0.7219	yes	no
Q84L31	RD23C_ARATH	No assigned EC number	0.5896	0.9666	0.6921	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	300
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	5e-67
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	2e-34
smart00213	72	smart00213, UBQ, Ubiquitin homologues	4e-24
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	1e-21
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	3e-21
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	8e-14
cd01803	76	cd01803, Ubiquitin, Ubiquitin	7e-12
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	3e-11
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	3e-11
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	2e-10
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	3e-10
pfam00627	37	pfam00627, UBA, UBA/TS-N domain	2e-09
cd00194	38	cd00194, UBA, Ubiquitin Associated domain	1e-07
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	2e-07
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	8e-07
smart00165	37	smart00165, UBA, Ubiquitin associated domain	1e-06
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	3e-06
pfam09280	59	pfam09280, XPC-binding, XPC-binding domain	3e-06
cd01812	71	cd01812, BAG1_N, Ubiquitin-like domain of BAG1	3e-05
cd01793	74	cd01793, Fubi, Fubi ubiquitin-like protein	4e-05
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-04
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-04
cd01796	71	cd01796, DDI1_N, DNA damage inducible protein 1 ub	2e-04
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	3e-04
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	3e-04
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	0.001
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.002
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.002
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.002
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	0.002
cd01794	70	cd01794, DC_UbP_C, dendritic cell derived ubiquiti	0.002
PHA00350	399	PHA00350, PHA00350, putative assembly protein	0.002
PRK05641	153	PRK05641, PRK05641, putative acetyl-CoA carboxylas	0.002
pfam07462	574	pfam07462, MSP1_C, Merozoite surface protein 1 (MS	0.002
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.003
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.003
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	0.003
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	0.003
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.003
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.003
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	0.004

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

 Score =  213 bits (544), Expect = 5e-67
 Identities = 115/288 (39%), Positives = 160/288 (55%), Gaps = 16/288 (5%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M +  KTL+   F ++++P++TV ++K KIE  QG D YP AQQ LIY GK+L DD T++
Sbjct: 1   MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVK 60

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEP 121
           E K+ E  FVV+M++K K  TG+ +  +  PT AP +  P+P A+PA+    A   + E 
Sbjct: 61  EYKIKEKDFVVVMVSKPKTGTGKVAPPAATPTSAP-TPTPSPPASPASGMSAAPASAVEE 119

Query: 122 TPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVR 181
                 +  + +  S S +  S     AAS LV G+  E  I++I++MG   ++R+ V R
Sbjct: 120 KSPSEESATATAPESPSTSVPSSG-SDAASTLVVGSERETTIEEIMEMG---YEREEVER 175

Query: 182 ALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPN 241
           ALRAA+NNP+RAVEYL +GIPE  E QP          A + T+ PQ        + G  
Sbjct: 176 ALRAAFNNPDRAVEYLLTGIPEDPE-QPEPVQQTAASTAAATTETPQHGSVFEQAAQGGT 234

Query: 242 ANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFP 289
             P              A G   L+FLRN PQFQ LR +VQ NPQL P
Sbjct: 235 EQPAT----------EAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLP 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 =  119 bits (300), Expect = 2e-34
 Identities = 46/78 (58%), Positives = 57/78 (73%), Gaps = 1/78 (1%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          MKI  KTLK  +F +EV P+DTV ++K KIE  +G D YP  QQ LIY GK+LKDDTTLE
Sbjct: 1  MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCD-YPPEQQKLIYSGKILKDDTTLE 59

Query: 62 ENKVAENSFVVIMLTKNK 79
          E K+ E  FVV+M++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 = 92.7 bits (231), Expect = 4e-24
 Identities = 32/75 (42%), Positives = 48/75 (64%), Gaps = 3/75 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++ VKTL G +  +EVKP DTV ++K KI  + G    P  QQ LIY+GKVL+DD TL 
Sbjct: 1  IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGI---PPEQQRLIYKGKVLEDDRTLA 57

Query: 62 ENKVAENSFVVIMLT 76
          +  + + 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|215813 pfam00240, ubiquitin, Ubiquitin family

 Score = 85.7 bits (213), Expect = 1e-21
 Identities = 31/73 (42%), Positives = 45/73 (61%), Gaps = 4/73 (5%)

Query: 7  KTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVA 66
          KTL G +  +EV P DTV ++K KIE  +G    P  QQ LI+ GKVL+DDTTL E  + 
Sbjct: 1  KTLDGKTITLEVDPSDTVSELKEKIEDKEG---IPVDQQRLIFSGKVLEDDTTLSEYGIQ 57

Query: 67 ENSFVVIMLTKNK 79
          + S  + ++ + +
Sbjct: 58 DGS-TLHLVLRLR 69

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|176364 cd01769, UBL, Ubiquitin-like domain of UBL

 Score = 85.0 bits (211), Expect = 3e-21
 Identities = 32/72 (44%), Positives = 46/72 (63%), Gaps = 3/72 (4%)

Query: 5  FVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENK 64
           VKTL G +F++EV P+DTV ++K KI   +G    P  QQ LIY GK+LKDD TL +  
Sbjct: 1  TVKTLTGKTFELEVSPDDTVAELKAKIAAKEG---VPPEQQRLIYAGKILKDDKTLSDYG 57

Query: 65 VAENSFVVIMLT 76
          + + 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|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein

 Score = 64.9 bits (159), Expect = 8e-14
 Identities = 34/77 (44%), Positives = 42/77 (54%), Gaps = 7/77 (9%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVY-PAAQQMLIYQGKVLKDDTTL 60
          ++I VKTL   +    V+ E TV D+K KI      +V  P  QQ LIY G+VLKDD TL
Sbjct: 1  IEIKVKTLDSQTHTFTVEEEITVLDLKEKIA----EEVGIPVEQQRLIYSGRVLKDDETL 56

Query: 61 EENKVAENSFVVIMLTK 77
           E KV +     I L K
Sbjct: 57 SEYKVEDGH--TIHLVK 71

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|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 59.9 bits (145), Expect = 7e-12
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 62 ENKVAENSFVVIML 75
          +  + + 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|176352 cd00196, UBQ, Ubiquitin-like proteins

 Score = 57.9 bits (140), Expect = 3e-11
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 5  FVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENK 64
           VK   G + ++ V    TV D+K K+    G    P  QQ L+  GK+L D  TLE+  
Sbjct: 1  KVKLNDGKTVELLVPSGTTVADLKEKLAKKLG---LPPEQQRLLVNGKILPDSLTLEDYG 57

Query: 65 VAENSFVVIMLT 76
          + +   +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|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein

 Score = 57.9 bits (140), Expect = 3e-11
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + DD T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDDKTAA 57

Query: 62 ENKVAENSFVVIMLT 76
          + 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|185411 PTZ00044, PTZ00044, ubiquitin; Provisional

 Score = 56.0 bits (135), Expect = 2e-10
 Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+I +KTL G       +P++TV  VKM ++  +G DV    Q  LIY GK + DD  L 
Sbjct: 1  MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDV---KQIRLIYSGKQMSDDLKLS 57

Query: 62 ENKVAENSFVVIML 75
          + KV   S + ++L
Sbjct: 58 DYKVVPGSTIHMVL 71

Length = 76

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

 Score = 56.0 bits (135), Expect = 3e-10
 Identities = 26/66 (39%), Positives = 42/66 (63%), Gaps = 3/66 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++F++TL GT F++ V P +TV  VK KI+ ++G    P AQQ LI+    L+D+  L 
Sbjct: 28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEG---IPVAQQHLIWNNMELEDEYCLN 84

Query: 62 ENKVAE 67
          +  ++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|201355 pfam00627, UBA, UBA/TS-N domain

 Score = 51.7 bits (125), Expect = 2e-09
 Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 3/36 (8%)

Query: 162 AIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYL 197
            I+Q+ +MG   + R+   +ALRA   N ERAVEYL
Sbjct: 5   LIKQLREMG---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|238116 cd00194, UBA, Ubiquitin Associated domain

 Score = 47.1 bits (113), Expect = 1e-07
 Identities = 18/41 (43%), Positives = 26/41 (63%), Gaps = 3/41 (7%)

Query: 159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS 199
            E  ++Q+L+MG   + R+   +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|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like

 Score = 47.5 bits (114), Expect = 2e-07
 Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          ++I +K   G    ++VKP  T+  +       +G       Q  LI+ G+ L  + T+ 
Sbjct: 1  IRIKLKGKDGKEVFIKVKPTTTLSKLINAYRKKRGIP--ADQQVRLIFDGERLDPNDTVA 58

Query: 62 ENKVAENSFVVIML 75
          +  + +   + +++
Sbjct: 59 DYDIEDGDTIDVVI 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|176393 cd01798, parkin_N, amino-terminal ubiquitin-like of parkin protein

 Score = 45.5 bits (108), Expect = 8e-07
 Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 3/59 (5%)

Query: 4  IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEE 62
          ++V+T  G +F VEV 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|197551 smart00165, UBA, Ubiquitin associated domain

 Score = 43.6 bits (104), Expect = 1e-06
 Identities = 18/36 (50%), Positives = 24/36 (66%), Gaps = 3/36 (8%)

Query: 162 AIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYL 197
            I Q+L+MG   + R+  ++ALRAA  N ERA EYL
Sbjct: 4   KIDQLLEMG---FSREEALKALRAANGNVERAAEYL 36

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

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

 Score = 48.3 bits (116), Expect = 3e-06
 Identities = 18/62 (29%), Positives = 27/62 (43%)

Query: 81  PTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSAT 140
            T   +  + A   A  + A  PAA    AP  A P +  P   P PA A+A+ ++ +A 
Sbjct: 40  STAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAP 99

Query: 141 SE 142
             
Sbjct: 100 PA 101

Length = 1228

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

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 18/25 (72%), Positives = 20/25 (80%)

Query: 265 LDFLRNSPQFQVLRAMVQANPQLFP 289
           L FLRN+PQFQ LR MVQ NP+L P
Sbjct: 1   LAFLRNNPQFQQLRQMVQQNPELLP 25

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|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1

 Score = 40.8 bits (96), Expect = 3e-05
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++ VK   G S D+ +  + T  D+K  +  V G        Q LI++GK   D  TL+
Sbjct: 1  IRVRVKH-GGESHDLSISSQATFGDLKKMLAPVTG---VEPRDQKLIFKGKERDDAETLD 56

Query: 62 ENKVAENSFVVIM 74
           + 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|176388 cd01793, Fubi, Fubi ubiquitin-like protein

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++FV+     +   EV  ++TV D+K  +  ++G        Q+L+  G  L+DD TL 
Sbjct: 1  MQLFVRAQNTHTL--EVTGQETVSDIKAHVAGLEG---IDVEDQVLLLAGVPLEDDATLG 55

Query: 62 ENKVAENS 69
          +  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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 43.4 bits (102), Expect = 1e-04
 Identities = 37/187 (19%), Positives = 54/187 (28%), Gaps = 10/187 (5%)

Query: 76   TKNKRPTGEGSTRST---APTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASA 132
               + PT  G        AP   P      PA    +  + ++P   +P   P    A A
Sbjct: 2756 RPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPA 2815

Query: 133  SVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMG-----GGTWDRDTVVRALRAAY 187
            +    +A+    +    ++   A     G     L +G     GG   R    R+  A  
Sbjct: 2816 AALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKP 2875

Query: 188  NNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDL 247
              P R      +        +  A  P +        Q P P QP P     P   P   
Sbjct: 2876 AAPARPPVRRLARPAVSRSTESFALPP-DQPERPPQPQAPPPPQPQPQPPPPPQPQP-PP 2933

Query: 248  FPQGLPD 254
             P   P 
Sbjct: 2934 PPPPRPQ 2940

Length = 3151

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

 Score = 42.6 bits (101), Expect = 2e-04
 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 81  PTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSAT 140
                +  + A   A   +A  PAA     P  A P +  P PA   A A+A  +  +A 
Sbjct: 45  TAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAP-AAPPKPAAAAAAAAAPAAPPAAA 103

Query: 141 SE 142
           + 
Sbjct: 104 AA 105

Length = 1228

>gnl|CDD|176391 cd01796, DDI1_N, DNA damage inducible protein 1 ubiquitin-like domain

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 11 GTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSF 70
           T+F ++V P+  + + K   E   G    PA+QQ LIY G+ L D+  L      ++  
Sbjct: 9  ETTFSLDVDPDLELENFKALCEAESG---IPASQQQLIYNGRELVDNKRLLALYGVKDGD 65

Query: 71 VVIML 75
          +V++ 
Sbjct: 66 LVVLR 70

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. Length = 71

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

 Score = 41.8 bits (99), Expect = 3e-04
 Identities = 15/60 (25%), Positives = 24/60 (40%)

Query: 84  EGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSES 143
             +   TA   A  ++A  PAA PA     A   +     AP   P  A+ ++ +A   +
Sbjct: 39  GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAA 98

Length = 1228

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 8/69 (11%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQM--LIYQGKVLKDDTT 59
          +K+ VKT K    ++E+  + +V D K  +     S  + A Q+   LI+ GK+LKD  T
Sbjct: 1  IKVTVKTPK-DKEEIEIAEDASVKDFKEAV-----SKKFKANQEQLVLIFAGKILKDTDT 54

Query: 60 LEENKVAEN 68
          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|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 21/76 (27%), Positives = 29/76 (38%)

Query: 80  RPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSA 139
                 S    APT A  ++ P  AA P      A P +  P PAP P  A+A  +  + 
Sbjct: 380 GAPAPPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPARSAD 439

Query: 140 TSESGVYGHAASNLVA 155
            + +   G      VA
Sbjct: 440 PAAAASAGDRWRAFVA 455

Length = 576

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

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 13/65 (20%), Positives = 23/65 (35%)

Query: 81  PTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSAT 140
                +  + A   A ++ A    A PA A   A P       A     A  + ++ +A 
Sbjct: 49  AAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAP 108

Query: 141 SESGV 145
           + + V
Sbjct: 109 AAAAV 113

Length = 1228

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

 Score = 39.1 bits (92), Expect = 0.002
 Identities = 14/50 (28%), Positives = 19/50 (38%)

Query: 86  STRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVS 135
           +     P  A  ++ P PAA  A A   A P +     AP  A     V+
Sbjct: 69  APAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEVT 118

Length = 1228

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

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 16/62 (25%), Positives = 25/62 (40%)

Query: 90  TAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGHA 149
             P  A  ++AP   A  A AP  A   +     AP  A   A V++ +A + +     A
Sbjct: 382 ARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAA 441

Query: 150 AS 151
            +
Sbjct: 442 PA 443

Length = 618

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

 Score = 39.4 bits (92), Expect = 0.002
 Identities = 32/183 (17%), Positives = 45/183 (24%), Gaps = 17/183 (9%)

Query: 89  STAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGH 148
           S  P     + A   A  P  A   A   +  P  AP P   +      +          
Sbjct: 394 SAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKA 453

Query: 149 AASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQ 208
            A         E   Q   D G  +                   A     +      + +
Sbjct: 454 NARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPR--AAAPSAATPAAVPDAR 511

Query: 209 PVARAPGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFL 268
             A A      A +    P+   P P  ++                   GAA A  LD L
Sbjct: 512 APAAASREDAPAAAAPPAPEARPPTPAAAAPAAR-------------AGGAAAA--LDVL 556

Query: 269 RNS 271
           RN+
Sbjct: 557 RNA 559

Length = 830

>gnl|CDD|176389 cd01794, DC_UbP_C, dendritic cell derived ubiquitin-like protein

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 11 GTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSF 70
          G    + V  +DTV  +K +++  +G D      Q   + GK+L D T L+E K+ ++ +
Sbjct: 8  GKDVKLSVSSKDTVGQLKKQLQAAEGVD---PCCQRWFFSGKLLTDKTRLQETKIQKD-Y 63

Query: 71 VV 72
          VV
Sbjct: 64 VV 65

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. Length = 70

>gnl|CDD|222783 PHA00350, PHA00350, putative assembly protein

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 14/50 (28%), Positives = 16/50 (32%)

Query: 99  SAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGH 148
           S  TPA   A  P     +S    PA T  PA          + SG    
Sbjct: 254 SVKTPAEHQAQTPSGVPTVSGPARPAQTGKPAPVLGPLGDGCTGSGCGNE 303

Length = 399

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

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 16/40 (40%), Positives = 18/40 (45%)

Query: 96  PQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVS 135
             S+      TPA AP  AVP +  P     PAPA AS  
Sbjct: 44  DLSAVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPAPASAG 83

Length = 153

>gnl|CDD|219419 pfam07462, MSP1_C, Merozoite surface protein 1 (MSP1) C-terminus

 Score = 39.2 bits (91), Expect = 0.002
 Identities = 22/82 (26%), Positives = 28/82 (34%), Gaps = 17/82 (20%)

Query: 75  LTKNKRPTGEGSTRSTA-------------PTKAPQSSAPTPAATPATAPQTAVPISTEP 121
           L KNK  TG  +  +               P    Q +  T   TP  A     P+S   
Sbjct: 229 LIKNKNYTGNTNPENNPEVNEALEQYKELLPKGTTQEAKVTTVVTPPQADAAPSPLS--- 285

Query: 122 TPAPTPAPASASVSSVSATSES 143
              P  +  SAS S+   TS S
Sbjct: 286 -VRPAGSSGSASGSTQIPTSGS 306

This family represents the C-terminal region of merozoite surface protein 1 (MSP1) which are found in a number of Plasmodium species. MSP-1 is a 200-kDa protein expressed on the surface of the P. vivax merozoite. MSP-1 of Plasmodium species is synthesised as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19-kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunisation with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate. Length = 574

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

 Score = 39.1 bits (92), Expect = 0.003
 Identities = 12/65 (18%), Positives = 19/65 (29%)

Query: 81  PTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSAT 140
                   + A       +   PAA    AP      +        P  A+A+ +  +A 
Sbjct: 53  AAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAA 112

Query: 141 SESGV 145
            E  V
Sbjct: 113 VEDEV 117

Length = 1228

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

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 31/107 (28%), Positives = 46/107 (42%), Gaps = 11/107 (10%)

Query: 91  APTKAPQSSAPTPAATPATAPQT-AVPISTEPTPAPT---PAPASASVSSVSATSESGVY 146
           AP  AP + A  PA     AP+T A+P+   P PA     PAPA+A  ++    +E G  
Sbjct: 437 APAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTEEGDV 496

Query: 147 GHA------ASNLVAGNNLEGAIQ-QILDMGGGTWDRDTVVRALRAA 186
            HA      A+  +     E A+Q +++   G  W       +L   
Sbjct: 497 WHATVQQLAAAEAITALARELALQSELVARDGDQWLLRVERESLNQP 543

Length = 618

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

 Score = 38.8 bits (91), Expect = 0.003
 Identities = 21/84 (25%), Positives = 27/84 (32%), Gaps = 5/84 (5%)

Query: 86  STRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGV 145
           +  +  P   P         +     Q A   S  P  A  P P  A  +  S T  +  
Sbjct: 373 APANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTEPSPTPPA-- 430

Query: 146 YGHAASNLVAGNNLEGAIQQILDM 169
               A+N     NLE   QQIL  
Sbjct: 431 ---NAANAPPSLNLEELWQQILAK 451

Length = 620

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

 Score = 38.7 bits (91), Expect = 0.003
 Identities = 15/51 (29%), Positives = 18/51 (35%)

Query: 89  STAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSA 139
                    S+  T A T A AP  A  +   P  AP  APA     + S 
Sbjct: 371 PPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQ 421

Length = 647

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

 Score = 38.4 bits (90), Expect = 0.003
 Identities = 38/231 (16%), Positives = 57/231 (24%), Gaps = 48/231 (20%)

Query: 80  RPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAP-ASASVSSVS 138
            P+  G+  +      P ++AP+    PA A       +  P P   PAP A+ +  +  
Sbjct: 441 PPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAP 500

Query: 139 ATSESG----------------------------------------------VYGHAASN 152
           A                                                     G  A  
Sbjct: 501 AAPAGADDAATLRERWPEILAAVPKRSRKTWAILLPEATVLGVRGDTLVLGFSTGGLARR 560

Query: 153 LVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVAR 212
             +  N E  +  + +  GG W  + VV     A                E A     A 
Sbjct: 561 FASPGNAEVLVTALAEELGGDWQVEAVVGPAPGAAGGEGPPAPASSGPPEEAARPAAPA- 619

Query: 213 APGNGQAANSPTQMPQPTQPAPVTSSGPNANPLDLFPQGLPDVGSGAAGAG 263
           AP    A         P + +   + G  A         +PD   G  G  
Sbjct: 620 APAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWP 670

Length = 824

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

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 16/68 (23%), Positives = 23/68 (33%), Gaps = 3/68 (4%)

Query: 78  NKRPTGEGSTRSTAPTKA---PQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASV 134
                   +  S +P+++    Q SAP  A  PA  P T         P   P+ A  +V
Sbjct: 388 AAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAV 447

Query: 135 SSVSATSE 142
                  E
Sbjct: 448 RPAQFKEE 455

Length = 614

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

 Score = 38.3 bits (89), Expect = 0.004
 Identities = 14/68 (20%), Positives = 23/68 (33%)

Query: 69  SFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPA 128
           + +   L + ++      +  TA   A  +  P     P   P      S E  P   PA
Sbjct: 361 ADLTQRLNRLEKEVRSLRSAPTAAATAAGAPLPDFDPRPRGPPAPEPARSAEAPPLVAPA 420

Query: 129 PASASVSS 136
            A A ++ 
Sbjct: 421 AAPAGLAL 428

Length = 504

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	300
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	99.79
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.79
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.77
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.77
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.75
PTZ00044	76	ubiquitin; Provisional	99.74
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.73
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.73
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.72
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	99.71
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.71
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.71
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.7
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.69
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.69
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.68
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	99.61
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.6
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.6
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.56
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.53
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.5
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.49
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.46
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.45
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.4
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.37
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	99.3
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	99.13
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.09
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	99.01
PF09280	59	XPC-binding: XPC-binding domain; InterPro: IPR0153	99.0
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	99.0
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	98.99
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.95
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	98.93
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	98.9
PLN02560	308	enoyl-CoA reductase	98.86
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.86
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	98.76
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.71
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.56
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.51
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.44
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	98.38
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.26
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.19
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	98.07
KOG4495	110	consensus RNA polymerase II transcription elongati	97.71
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.56
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	97.5
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	97.47
COG5417	81	Uncharacterized small protein [Function unknown]	97.46
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	97.45
KOG0944	763	consensus Ubiquitin-specific protease UBP14 [Postt	97.39
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.34
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.17
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	97.06
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	97.05
KOG4583	391	consensus Membrane-associated ER protein involved	97.03
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	96.86
KOG0013	231	consensus Uncharacterized conserved protein [Funct	96.81
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	96.79
KOG1639	297	consensus Steroid reductase required for elongatio	96.79
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	96.75
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	96.67
KOG0418	200	consensus Ubiquitin-protein ligase [Posttranslatio	96.66
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	96.61
smart00546	43	CUE Domain that may be involved in binding ubiquit	96.59
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	96.43
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	96.42
PF13019	162	Telomere_Sde2: Telomere stability and silencing	96.18
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	95.9
PRK08364	70	sulfur carrier protein ThiS; Provisional	95.29
PF09288	55	UBA_3: Fungal ubiquitin-associated domain ; InterP	95.08
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	94.95
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	94.8
PF11626	87	Rap1_C: TRF2-interacting telomeric protein/Rap1 -	94.6
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	94.57
PF14453	57	ThiS-like: ThiS-like ubiquitin	94.48
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	94.25
PRK06437	67	hypothetical protein; Provisional	94.11
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	93.62
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	93.24
KOG0012	380	consensus DNA damage inducible protein [Replicatio	93.12
PF06972	60	DUF1296: Protein of unknown function (DUF1296); In	93.07
PF07499	47	RuvA_C: RuvA, C-terminal domain; InterPro: IPR0111	92.74
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	92.68
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	92.44
smart00727	41	STI1 Heat shock chaperonin-binding motif.	92.37
PRK06488	65	sulfur carrier protein ThiS; Validated	91.79
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	91.47
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	91.01
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	90.53
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	89.46
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	89.37
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	89.29
PF12754	309	Blt1: Cell-cycle control medial ring component; In	89.15
KOG0944	763	consensus Ubiquitin-specific protease UBP14 [Postt	88.86
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	88.79
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	88.77
PRK06083	84	sulfur carrier protein ThiS; Provisional	88.57
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	88.44
PRK05863	65	sulfur carrier protein ThiS; Provisional	87.86
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	87.63
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	87.53
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	87.43
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	87.13
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	86.87
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	86.54
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	86.31
PF08938	79	HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This	85.47
PRK05659	66	sulfur carrier protein ThiS; Validated	85.24
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	84.43
PRK07440	70	hypothetical protein; Provisional	84.04
KOG2982	418	consensus Uncharacterized conserved protein [Funct	84.03
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	83.82
PRK06944	65	sulfur carrier protein ThiS; Provisional	83.56
smart00455	70	RBD Raf-like Ras-binding domain.	83.41
PRK08053	66	sulfur carrier protein ThiS; Provisional	83.19
PRK12332	198	tsf elongation factor Ts; Reviewed	82.35
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	81.64
TIGR00116	290	tsf translation elongation factor Ts. This protein	80.95
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	80.88
PF11069	98	DUF2870: Protein of unknown function (DUF2870); In	80.27

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=100.00  E-value=5.1e-62  Score=468.40  Aligned_cols=271  Identities=41%  Similarity=0.658  Sum_probs=179.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|++.+++++|||||+||+|+|+++|++|+|+++++|+||++|+|..
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            89999999999999999999999999999999987555899999999999999999999999999999999999998775


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCcccccccccccCCChH
Q 022228           82 TGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPT-PAPASASVSSVSATSESGVYGHAASNLVAGNNLE  160 (300)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~s~l~~g~~~e  160 (300)
                      .+..+.+...+.+++.+++.++.. +...+..+ +........+. .++. ++...+++.+.......+.|+|++|++||
T Consensus        81 ~~~~~~~~~~~~~~p~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~s~l~~g~~~e  157 (378)
T TIGR00601        81 TGKSAPPAATPTSAPTPTPSPPAS-PASGMSAA-PASAVEEKSPSEESAT-ATAPESPSTSVPSSGSDAASTLVVGSERE  157 (378)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCC-CCCCCccccccCCCCC-CCCCCCCCccccccCCCcccccccchHHH
Confidence            332221110110000000000000 00000000 00000000000 0000 00000000000000124678999999999


Q ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCCccccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 022228          161 GAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGP  240 (300)
Q Consensus       161 ~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (300)
                      ++|++||+||   |+|+||++|||||||||||||||||+|||++++...    +.+.    +... .   .   ....++
T Consensus       158 ~~I~~i~eMG---f~R~qV~~ALRAafNNPdRAVEYL~tGIP~~~~~~~----~~~~----~~~~-~---~---~~~~~~  219 (378)
T TIGR00601       158 TTIEEIMEMG---YEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPE----PVQQ----TAAS-T---A---AATTET  219 (378)
T ss_pred             HHHHHHHHhC---CCHHHHHHHHHHHhCCHHHHHHHHHhCCCccccccc----cCCC----cccc-c---c---cccCCC
Confidence            9999999999   999999999999999999999999999999866211    1110    0000 0   0   011112


Q ss_pred             CCCCCCCCCCCCCCCC------CCCCCCCchhhhhCcHHHHHHHHHHHhCCCchHHHHhcc
Q 022228          241 NANPLDLFPQGLPDVG------SGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWG  295 (300)
Q Consensus       241 ~~~~~~lf~~~~~~~~------~~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~lq~~  295 (300)
                      +..+ |||++++.+..      .+ .|+++|+|||++|||++||++||+||+||++|||+-
T Consensus       220 ~~~~-~lf~~a~~~~~~~~~~~~~-~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLqql  278 (378)
T TIGR00601       220 PQHG-SVFEQAAQGGTEQPATEAA-QGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQI  278 (378)
T ss_pred             CCCc-chhhhhhcccccccccccc-cCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHHHH
Confidence            2233 99999864321      11 145699999999999999999999999999999863

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=1.5e-59  Score=433.73  Aligned_cols=246  Identities=50%  Similarity=0.774  Sum_probs=183.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      |+|+||+++|++|+|+|.+++||.++|++|+...|.| +|+++|||||+||+|+|+.++.+|+|+++++|+||++|+|..
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            7999999999999999999999999999999999988 999999999999999999999999999999999999999831


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccCCChHH
Q 022228           82 TGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEPTPAPTPAPASASVSSVSATSESGVYGHAASNLVAGNNLEG  161 (300)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~~g~~~e~  161 (300)
                      .+..    ++.+.++..   .+  ....+|..+ .       ..  ...++.   ...++....++.+.++|++|+++|+
T Consensus        80 ~t~~----ap~s~~~~~---~p--~~~~ap~~s-~-------a~--~~s~~~---~~~~~~~~~~~~aas~Lv~G~~~e~  137 (340)
T KOG0011|consen   80 STQV----APQSSAATH---LP--KAAEAPPSS-A-------AE--DASPAT---PAQTSQEDTYEIAASTLVVGSEYEQ  137 (340)
T ss_pred             ccCC----CCCCccccC---CC--ccCCCCCcc-c-------cc--cCCCCc---cccccccchhhhhhhhhhccchhHH
Confidence            1111    000000000   00  000000000 0       00  000000   0012233457788999999999999


Q ss_pred             HHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCCccccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 022228          162 AIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSSGPN  241 (300)
Q Consensus       162 ~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (300)
                      +|.+||+||   |+||+|+|||||||||||||||||++|||+..+...+...+++          .+  . .  +   .+
T Consensus       138 ~V~~Im~MG---y~re~V~~AlRAafNNPeRAVEYLl~GIP~~~~~~~~~~~~~~----------~~--~-~--p---~~  196 (340)
T KOG0011|consen  138 TVQQIMEMG---YDREEVERALRAAFNNPERAVEYLLNGIPEDAEVPEPEKSTAA----------AA--E-L--P---AN  196 (340)
T ss_pred             HHHHHHHhC---ccHHHHHHHHHHhhCChhhhHHHHhcCCcccccCCcccCCccc----------CC--C-C--C---CC
Confidence            999999999   9999999999999999999999999999998665543211110          00  0 0  0   03


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCchhhhhCcHHHHHHHHHHHhCCCchHHHHhcc
Q 022228          242 ANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWG  295 (300)
Q Consensus       242 ~~~~~lf~~~~~~~~~~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~lq~~  295 (300)
                      .+|+++|++++....    ++++|+|||++|||++||+|||+||+||++|||+-
T Consensus       197 ~~p~~~~~~~~~~~~----~~~~l~fLr~~~qf~~lR~~iqqNP~ll~~~Lqql  246 (340)
T KOG0011|consen  197 AQPLDLFPQGAVEAS----GGDPLEFLRNQPQFQQLRQMIQQNPELLHPLLQQL  246 (340)
T ss_pred             CChhhcCCccchhhh----cCCchhhhhccHHHHHHHHHHhhCHHHHHHHHHHH
Confidence            356899998765543    35899999999999999999999999999999974

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.79  E-value=3.7e-19  Score=133.91  Aligned_cols=73  Identities=26%  Similarity=0.432  Sum_probs=71.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+||+++|+++.++|++++||++||++|+++.|   +++++|+|+|+||.|+|+.+|++|||+++++|+++++.
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            79999999999999999999999999999999999   99999999999999999999999999999999999874

GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.79  E-value=6.1e-19  Score=132.91  Aligned_cols=72  Identities=19%  Similarity=0.308  Sum_probs=69.8

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      ||+|+||++.|+.+.++|++++||.+||++|++..|   +++++|||+|+|++|+|+++|++|||++|++||+..
T Consensus         1 ~~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~---~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791           1 MIEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTG---TRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             CEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhC---CChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence            899999999999999999999999999999999999   999999999999999999999999999999999863

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.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.77  E-value=1.6e-18  Score=130.89  Aligned_cols=75  Identities=59%  Similarity=0.860  Sum_probs=72.4

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCC--CCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVY--PAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~i--p~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|++|.++|++++||.+||++|++..|   +  ++++|||+|+|++|+|+.+|++|||++|++|++++++++
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            79999999999999999999999999999999999   7  999999999999999999999999999999999998864

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

>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF

Probab=99.77  E-value=1.8e-18  Score=131.90  Aligned_cols=74  Identities=26%  Similarity=0.395  Sum_probs=70.4

Q ss_pred             EEEEEEcCCCcE-EEEE-eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTS-FDVE-VKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~-~~ie-V~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+||+++|++ +.|+ +++++||.+||++|++..|   +++++|||+|+||+|+|+.+|++|||+++++|+++++.-
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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.75  E-value=6.1e-18  Score=127.36  Aligned_cols=73  Identities=27%  Similarity=0.402  Sum_probs=69.1

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+  ++++.++|++++||.+||.+|+++.|   +|+++|+|+|+||+|+|+++|++|+|+++++||++++.+.
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 MQLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEG---IDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLG   73 (74)
T ss_pred             CEEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhC---CCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            7999997  47899999999999999999999999   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=99.74  E-value=9.1e-18  Score=126.53  Aligned_cols=74  Identities=35%  Similarity=0.551  Sum_probs=71.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+||+++|+++.++|++++||.+||++|+...|   +|+++|||+|+|+.|+|+.+|++|+|+++++||++++.+
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            79999999999999999999999999999999999   999999999999999999999999999999999999864

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.73  E-value=1.5e-17  Score=133.33  Aligned_cols=75  Identities=36%  Similarity=0.635  Sum_probs=72.4

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|+++.|+|++++||.+||++|+++.|   +++++|||+|+||+|+|+++|++|+|+++++|+++++.+.
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=99.73  E-value=1.6e-17  Score=126.55  Aligned_cols=74  Identities=23%  Similarity=0.363  Sum_probs=70.5

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      .|+|+||+++|+.+.|+|+++.||.+||++|+++.+   +++++|||+|+||+|+|+ +|++|||++|++|+||.+..
T Consensus         1 ~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~---~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~   74 (78)
T cd01804           1 PMNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLK---VPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVE   74 (78)
T ss_pred             CeEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhC---CChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecc
Confidence            489999999999999999999999999999999999   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=99.72  E-value=3.5e-17  Score=122.79  Aligned_cols=74  Identities=36%  Similarity=0.600  Sum_probs=71.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+||+++|+++.++|++++||.+||++|+...|   ++++.|||+|+|+.|+|+++|++|+|++|++|+++++.+
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            79999999999999999999999999999999999   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=2e-17  Score=126.44  Aligned_cols=74  Identities=30%  Similarity=0.380  Sum_probs=71.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQML--IYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkL--i~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+||+++|+++.++|+++.||.+||++|++..+   +++++|||  +|+|++|+|+++|++|||++|++|+|+++|-
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            89999999999999999999999999999999999   99999999  9999999999999999999999999999864

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=2.7e-17  Score=123.86  Aligned_cols=72  Identities=26%  Similarity=0.315  Sum_probs=69.5

Q ss_pred             EEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         4 I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+||++.|+++.|+|++++||.+||++|+...|   +|+++|+|+|+||+|+|+++|++|||+++++|+++++..
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=99.71  E-value=4.6e-17  Score=122.11  Aligned_cols=74  Identities=42%  Similarity=0.670  Sum_probs=71.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+||+.+|+++.++|++++||.+||++|+...+   +++++|+|+|+|+.|+|+.+|++|+|+++++|+++++.+
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            79999999999999999999999999999999999   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=3.1e-17  Score=122.59  Aligned_cols=70  Identities=26%  Similarity=0.457  Sum_probs=67.0

Q ss_pred             EEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         4 I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      ++||.++|+++.++|++++||.+||.+|++..|   +++++|||+|+|++|+|+.+|++|+|+++++|||++.
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.

>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein

Probab=99.71  E-value=3.9e-17  Score=121.54  Aligned_cols=70  Identities=30%  Similarity=0.539  Sum_probs=67.6

Q ss_pred             EEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         4 I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+||++.|+++.++|++++||.+||++|+++.|   +++++|+|+|+|+.|+|+.+|++|+|+++++||++.|
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.

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.70  E-value=6.2e-17  Score=120.17  Aligned_cols=72  Identities=43%  Similarity=0.579  Sum_probs=69.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+|+||+++|+++.+++++++||.+||++|+...|   ++++.|+|+|+|++|+|+.+|++|||++|++|+++.+
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            78999999999999999999999999999999999   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.

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

Probab=99.69  E-value=7.7e-17  Score=122.96  Aligned_cols=73  Identities=25%  Similarity=0.254  Sum_probs=64.8

Q ss_pred             EEEEEEcCCCcE--EEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcc--cCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTS--FDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENK--VAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~--~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~g--I~~g~~I~v~v   75 (300)
                      |.|+||+.+|++  |.+++++++||.+||++|+...+.. .++++|||||+||+|+|+.+|++|.  ++++.+||++.
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            789999999998  5555689999999999999987421 5689999999999999999999996  99999999985

Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.

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

Probab=99.69  E-value=1.1e-16  Score=119.49  Aligned_cols=71  Identities=28%  Similarity=0.421  Sum_probs=67.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+|+||+.+|+ +.|+|++++||.+||++|++..|   ++.++|+|+|+||+|+|+++|++|||+++++||++++
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            58999999997 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=99.68  E-value=1.3e-16  Score=117.78  Aligned_cols=69  Identities=43%  Similarity=0.693  Sum_probs=66.1

Q ss_pred             EcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            7 KTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         7 Ktl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+++|+.|.|+|++++||.+||++|+...+   ++++.|+|+|+|++|+|+.+|++|||++|++|+++++++
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   999999999999999999999999999999999988753

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

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.66  E-value=2.3e-16  Score=119.11  Aligned_cols=70  Identities=31%  Similarity=0.460  Sum_probs=66.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe---CCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY---QGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~---~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|| |+|++|.|+|++++||.+||++|++.++   +|+++|||+|   +|++|+|+.+|++|+|++|++|+||.
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            578999 7999999999999999999999999999   9999999996   99999999999999999999999985

The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.

>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain

Probab=99.64  E-value=6.5e-16  Score=115.60  Aligned_cols=68  Identities=35%  Similarity=0.491  Sum_probs=64.3

Q ss_pred             EEEEcC-CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CchhhcccCCCcEEEEE
Q 022228            4 IFVKTL-KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDD-TTLEENKVAENSFVVIM   74 (300)
Q Consensus         4 I~VKtl-~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~-~tL~d~gI~~g~~I~v~   74 (300)
                      |+||+. +|+++.++|++++||.+||.+|+.+.|   +|+++|+|+|+||.|+|+ .+|++|||++|++||+-
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=99.61  E-value=2e-15  Score=111.89  Aligned_cols=70  Identities=30%  Similarity=0.428  Sum_probs=66.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+||+. |+.+.++|++++||.+||++|+..+|   +++++|||+|+|+.|+|+++|++|||++|++|+||.
T Consensus         1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~   70 (71)
T cd01812           1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTG---VEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhC---CChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence            68999986 99999999999999999999999999   999999999999999999999999999999999874

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

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

Probab=99.60  E-value=7.3e-16  Score=109.65  Aligned_cols=70  Identities=36%  Similarity=0.591  Sum_probs=68.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      |.|.||+++|+.+.|++++.++|..+|++|+++.|   +|+.+|||||.||.+.|+++-.+|++.-|++||++
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            68999999999999999999999999999999999   99999999999999999999999999999999974

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

Probab=99.60  E-value=4.3e-15  Score=112.49  Aligned_cols=68  Identities=28%  Similarity=0.468  Sum_probs=65.1

Q ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            9 LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         9 l~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      ++|+++.|+|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+.
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            5899999999999999999999999999   9999999999999999999999999999999999998754

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

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

Probab=99.56  E-value=1.3e-14  Score=141.50  Aligned_cols=77  Identities=34%  Similarity=0.592  Sum_probs=71.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      ++|+||+.++ ++.|.|..+.||++||++|....+   +++++++|||.||+|+|++||..|||++|.+||||++....+
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            7899999988 899999999999999999999998   899999999999999999999999999999999998765544


Q ss_pred             C
Q 022228           82 T   82 (300)
Q Consensus        82 ~   82 (300)
                      .
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=8.9e-14  Score=108.07  Aligned_cols=75  Identities=15%  Similarity=0.267  Sum_probs=72.1

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |.|+|++.+|+.+.+.|.+++||..||++++++.|   +++++|||+|+|+.|+|+.|+.+|+|.++++|+|+++...
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            88999999999999999999999999999999999   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=99.50  E-value=6.3e-14  Score=100.99  Aligned_cols=64  Identities=47%  Similarity=0.732  Sum_probs=61.1

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCc
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENS   69 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~   69 (300)
                      |+|+||+.+ +.+.++|+++.||.+||.+|+..++   ++++.|+|+|+|+.|+|+++|++|||++|+
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            789999998 7999999999999999999999999   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=118.66  Aligned_cols=76  Identities=41%  Similarity=0.639  Sum_probs=72.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |+++++++.|++..++|++++||..||.+|..+.|   +|+++|+|+|+||+|+|..||.+|||...++||++.+.+..
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            56788899999999999999999999999999999   99999999999999999999999999999999999988764

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

Probab=99.46  E-value=4e-14  Score=119.32  Aligned_cols=78  Identities=38%  Similarity=0.598  Sum_probs=74.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      |+|+|+++.++++.++|..++||..+|.+|++..+   ||+++|||||.|+.|+|..+|+||+|+..++|+++++.+...
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            78999999999999999999999999999999999   999999999999999999999999999999999999976654


Q ss_pred             C
Q 022228           82 T   82 (300)
Q Consensus        82 ~   82 (300)
                      .
T Consensus        78 k   78 (156)
T KOG0004|consen   78 K   78 (156)
T ss_pred             c
Confidence            3

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.45  E-value=1e-13  Score=104.65  Aligned_cols=55  Identities=25%  Similarity=0.189  Sum_probs=49.2

Q ss_pred             CCCCHHHHHHHHHHHhCCCCC-CCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228           20 PEDTVFDVKMKIETVQGSDVY-PAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus        20 ~~~TV~~LK~kI~~~~g~~~i-p~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      .++||.+||++|+++.+.. + ++++|||||+||+|+|+++|++|||++|++||++.
T Consensus        19 ~~~TV~~LK~kI~~~~~eg-i~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          19 GGYQVSTLKQLIAAQLPDS-LPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             ccCcHHHHHHHHHHhhccC-CCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            4689999999999996322 5 58999999999999999999999999999999985

BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.40  E-value=6.4e-13  Score=107.00  Aligned_cols=78  Identities=18%  Similarity=0.221  Sum_probs=64.7

Q ss_pred             EEEEEEcCCCcEE-EEEeCCCCCHHHHHHHHHHHhCC--CCCC--CCCeEEEeCCeecCCCCchhhcc------cCCCcE
Q 022228            2 MKIFVKTLKGTSF-DVEVKPEDTVFDVKMKIETVQGS--DVYP--AAQQMLIYQGKVLKDDTTLEENK------VAENSF   70 (300)
Q Consensus         2 M~I~VKtl~g~~~-~ieV~~~~TV~~LK~kI~~~~g~--~~ip--~~~qkLi~~GkiL~D~~tL~d~g------I~~g~~   70 (300)
                      +.|+||..+|..+ .+.+.+++||.+||++|++..+.  ..+|  +++|||||+||+|+|++||++|+      +....+
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            6788888888654 36788999999999999966632  1255  99999999999999999999999      777789


Q ss_pred             EEEEEecCC
Q 022228           71 VVIMLTKNK   79 (300)
Q Consensus        71 I~v~v~k~~   79 (300)
                      +||+++.+.
T Consensus        85 mHvvlr~~~   93 (113)
T cd01814          85 MHVVVQPPL   93 (113)
T ss_pred             EEEEecCCC
Confidence            999998654

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=99.37  E-value=2.5e-12  Score=93.81  Aligned_cols=68  Identities=47%  Similarity=0.758  Sum_probs=64.4

Q ss_pred             EEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            5 FVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         5 ~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      +||..+|+.+.++++++.||.+||++|+...+   ++++.|+|+|+|+.|+|+.+|.+|+|++++.|+|+.
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=3e-12  Score=96.93  Aligned_cols=66  Identities=23%  Similarity=0.273  Sum_probs=59.6

Q ss_pred             EEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCchhhcccC-CCcEEEEEE
Q 022228            6 VKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLK-DDTTLEENKVA-ENSFVVIML   75 (300)
Q Consensus         6 VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~-D~~tL~d~gI~-~g~~I~v~v   75 (300)
                      =|...|.++.|+|++++||.+||.+|+.+.|   +|++.||| |.|+.|. |+++|++|||+ +|++|++.+
T Consensus         7 ~~~~~~~t~~l~v~~~~TV~~lK~kI~~~~g---ip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799           7 DAQSHTVTIWLTVRPDMTVAQLKDKVFLDYG---FPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             ccccCCCeEEEEECCCCcHHHHHHHHHHHHC---cCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            3555788999999999999999999999999   99999999 9999985 66899999999 789999864

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=99.30  E-value=1.2e-11  Score=92.00  Aligned_cols=71  Identities=25%  Similarity=0.413  Sum_probs=65.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-CCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPA-AQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~-~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|++.+|+.+.+.|.++.+|..|+++++++.+   ++. +.++|+|+|+.|++++|+++|+|++|++|+|++
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~---i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKG---IPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHT---TTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhC---CCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            78999999999999999999999999999999999   889 999999999999999999999999999999874

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

>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=99.13  E-value=1e-10  Score=76.58  Aligned_cols=36  Identities=44%  Similarity=0.704  Sum_probs=33.7

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHH
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYL  197 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyL  197 (300)
                      .++.|++|++||   |++++|++||+.+.||.|+|++||
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 ....

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.09  E-value=3.1e-10  Score=89.38  Aligned_cols=62  Identities=23%  Similarity=0.253  Sum_probs=56.9

Q ss_pred             EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCC-CCchhhcccCCCcEEEEEEec
Q 022228           13 SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKD-DTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus        13 ~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D-~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      ...++|++++||++||.+|..+.+   +++.+|||+|+|+.|.| .+||++|||..++.|++.+..
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~---V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llide   78 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFS---VAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADE   78 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhc---CCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecC
Confidence            466889999999999999999999   99999999999999965 569999999999999998754

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,

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

Probab=99.01  E-value=4.2e-09  Score=85.60  Aligned_cols=76  Identities=21%  Similarity=0.347  Sum_probs=56.7

Q ss_pred             EEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCC----CCCCCCeEEEeCCeecCCCCchhhcccCCCc------E
Q 022228            2 MKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSD----VYPAAQQMLIYQGKVLKDDTTLEENKVAENS------F   70 (300)
Q Consensus         2 M~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~----~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~------~   70 (300)
                      +.|+++..+|+ ...+.+++++||.+||+.|......+    ...+..+||||.||+|+|+++|++|++..++      +
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            57888888999 78899999999999999999765322    1235689999999999999999999998777      4


Q ss_pred             EEEEEec
Q 022228           71 VVIMLTK   77 (300)
Q Consensus        71 I~v~v~k   77 (300)
                      +||+++.
T Consensus        83 mHlvvrp   89 (111)
T PF13881_consen   83 MHLVVRP   89 (111)
T ss_dssp             EEEEE-S
T ss_pred             EEEEecC
Confidence            5566554

>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=99.00  E-value=1.9e-10  Score=83.12  Aligned_cols=30  Identities=60%  Similarity=0.941  Sum_probs=27.8

Q ss_pred             hhhhhCcHHHHHHHHHHHhCCCchHHHHhc
Q 022228          265 LDFLRNSPQFQVLRAMVQANPQLFPCFKSW  294 (300)
Q Consensus       265 l~~Lr~~pqf~~lR~~vq~nP~~L~~~lq~  294 (300)
                      |+|||++|+|++||++||+||++|++|||+
T Consensus         1 L~~Lr~~Pqf~~lR~~vq~NP~lL~~lLqq   30 (59)
T PF09280_consen    1 LEFLRNNPQFQQLRQLVQQNPQLLPPLLQQ   30 (59)
T ss_dssp             CGGGTTSHHHHHHHHHHHC-GGGHHHHHHH
T ss_pred             ChHHHcChHHHHHHHHHHHCHHHHHHHHHH
Confidence            689999999999999999999999999986

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 ....

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

Probab=99.00  E-value=5.1e-10  Score=117.04  Aligned_cols=72  Identities=28%  Similarity=0.439  Sum_probs=68.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      ..|+||+++.++.+|.|+..+||++||+.|.++.+   |+.+.|||||.|++|.|++++.+|+| +|.+|||+-|.
T Consensus         3 ~~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~n---i~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlverp   74 (1143)
T KOG4248|consen    3 PNVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVN---IPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVERP   74 (1143)
T ss_pred             cceeeeecccceeEEEechHHHHHHHHHHHHHhcc---cccccceeeecceeeccchhhhhccC-CCeEEEeeccC
Confidence            35899999999999999999999999999999999   99999999999999999999999999 99999999883

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

Probab=98.99  E-value=2.9e-09  Score=82.21  Aligned_cols=72  Identities=24%  Similarity=0.369  Sum_probs=60.3

Q ss_pred             EEEEEEcC-CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE-EeCCe-----ec-CCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTL-KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQML-IYQGK-----VL-KDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl-~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkL-i~~Gk-----iL-~D~~tL~d~gI~~g~~I~v   73 (300)
                      ++|.|+.. +....+..+.+++||.+||++|+..+|   +++..|+| +|.|+     .| +|+++|.+|++++|..|||
T Consensus         2 v~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G---~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhV   78 (84)
T cd01789           2 VTVNITSSADSFSFEKKYSRGLTIAELKKKLELVVG---TPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHV   78 (84)
T ss_pred             EEEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHC---CCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEE
Confidence            46777653 344566679999999999999999999   99999999 58887     45 6778999999999999999


Q ss_pred             EEe
Q 022228           74 MLT   76 (300)
Q Consensus        74 ~v~   76 (300)
                      +-.
T Consensus        79 vD~   81 (84)
T cd01789          79 IDV   81 (84)
T ss_pred             EeC
Confidence            854

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.

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

Probab=98.95  E-value=7.5e-09  Score=74.91  Aligned_cols=72  Identities=43%  Similarity=0.638  Sum_probs=68.1

Q ss_pred             EEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         4 I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      ++++++.|+.+.+++....+|..+|.+|....+   ++...|+|+|.|+.|.|+.+|.+|+|..++++++..+.+
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=98.93  E-value=1.8e-09  Score=70.74  Aligned_cols=37  Identities=49%  Similarity=0.781  Sum_probs=35.2

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      ++.|++|++||   |+|++|++||+++.||.++|++||+.
T Consensus         2 ~~~v~~L~~mG---f~~~~~~~AL~~~~~d~~~A~~~L~~   38 (38)
T cd00194           2 EEKLEQLLEMG---FSREEARKALRATNNNVERAVEWLLE   38 (38)
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            57899999999   99999999999999999999999974

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.

>smart00165 UBA Ubiquitin associated domain

Probab=98.90  E-value=2.3e-09  Score=69.88  Aligned_cols=36  Identities=53%  Similarity=0.828  Sum_probs=34.6

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      ++.|++|++||   |++++|++||+...||.++|++||+
T Consensus         2 ~~~v~~L~~mG---f~~~~a~~aL~~~~~d~~~A~~~L~   37 (37)
T smart00165        2 EEKIDQLLEMG---FSREEALKALRAANGNVERAAEYLL   37 (37)
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence            67899999999   9999999999999999999999995

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

>PLN02560 enoyl-CoA reductase

Probab=98.86  E-value=6.2e-09  Score=98.62  Aligned_cols=70  Identities=30%  Similarity=0.425  Sum_probs=61.6

Q ss_pred             EEEEEEcCCCcEE---EEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---C----eecCCCCchhhcccCCCcEE
Q 022228            2 MKIFVKTLKGTSF---DVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ---G----KVLKDDTTLEENKVAENSFV   71 (300)
Q Consensus         2 M~I~VKtl~g~~~---~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~---G----kiL~D~~tL~d~gI~~g~~I   71 (300)
                      |+|+|+..+|+.+   +|+|+++.||++||++|+++.+.  +++++|||++.   |    +.|+|+++|++||++++++|
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            7899998889887   79999999999999999999771  37899999982   3    48899999999999999987


Q ss_pred             EE
Q 022228           72 VI   73 (300)
Q Consensus        72 ~v   73 (300)
                      ++
T Consensus        79 y~   80 (308)
T PLN02560         79 VF   80 (308)
T ss_pred             EE
Confidence            65

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

Probab=98.86  E-value=1e-08  Score=79.46  Aligned_cols=74  Identities=23%  Similarity=0.363  Sum_probs=59.7

Q ss_pred             CEEEEEEcCCC--cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC----C---eec-CCCCchhhcccCCCcE
Q 022228            1 MMKIFVKTLKG--TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ----G---KVL-KDDTTLEENKVAENSF   70 (300)
Q Consensus         1 mM~I~VKtl~g--~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~----G---kiL-~D~~tL~d~gI~~g~~   70 (300)
                      |++|+|.....  +.++..++.++||.+||.+|+..+|   ++++.|+|.|.    +   ..| +|+++|.+||+++|..
T Consensus         1 ~v~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~G---i~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~   77 (87)
T PF14560_consen    1 VVKLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTG---IPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMR   77 (87)
T ss_dssp             EEEEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHT---S-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEE
T ss_pred             CEEEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhC---CCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCE
Confidence            46788876554  4889999999999999999999999   99999999875    2   224 5678999999999999


Q ss_pred             EEEEEec
Q 022228           71 VVIMLTK   77 (300)
Q Consensus        71 I~v~v~k   77 (300)
                      |||.=..
T Consensus        78 i~V~D~~   84 (87)
T PF14560_consen   78 IHVVDTN   84 (87)
T ss_dssp             EEEEE-T
T ss_pred             EEEEeCC
Confidence            9998654

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=98.76  E-value=3.4e-08  Score=79.61  Aligned_cols=71  Identities=20%  Similarity=0.291  Sum_probs=59.8

Q ss_pred             EEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhccc-------CCCcEEEEEE
Q 022228            3 KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKV-------AENSFVVIML   75 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI-------~~g~~I~v~v   75 (300)
                      -|.|| .+..++.+++.++.||.+||++|+....   .|+++|+|+..+.+|+|++||+|||+       ....+|-+.+
T Consensus         4 FlmIr-R~KTTiF~dakes~tVlelK~~iegI~k---~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~   79 (119)
T cd01788           4 FLMIR-RHKTTIFTDAKESTTVYELKRIVEGILK---RPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAF   79 (119)
T ss_pred             EEEEE-ecceEEEeecCCcccHHHHHHHHHHHhc---CChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEE
Confidence            34444 2344677899999999999999999998   99999999988899999999999999       5577777777


Q ss_pred             ec
Q 022228           76 TK   77 (300)
Q Consensus        76 ~k   77 (300)
                      |+
T Consensus        80 r~   81 (119)
T cd01788          80 RS   81 (119)
T ss_pred             ec
Confidence            75

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.

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=98.71  E-value=4.1e-08  Score=74.38  Aligned_cols=69  Identities=25%  Similarity=0.249  Sum_probs=54.2

Q ss_pred             EEEEEcCC-CcEEEEEeC-CCCCHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecCCCCchhhcccCCCcEEEE
Q 022228            3 KIFVKTLK-GTSFDVEVK-PEDTVFDVKMKIETVQGSDVYPAAQQML--IYQGKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         3 ~I~VKtl~-g~~~~ieV~-~~~TV~~LK~kI~~~~g~~~ip~~~qkL--i~~GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      .|.++... .....++++ ++.||.+||+.|+...+.  +++++|||  ++.|++|.|+.+|.+|||++|++|+|
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            46666555 333334444 889999999999988651  57899888  58999999999999999999998876

Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.56  E-value=4.4e-07  Score=62.14  Aligned_cols=67  Identities=33%  Similarity=0.464  Sum_probs=60.7

Q ss_pred             EEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            6 VKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         6 VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+..++..+.+.+..+.||.+||++|..+.+   ++++.++|+++|..+.+...+.+|++.+++.|+++.
T Consensus         2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196           2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLG---LPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             eEecCCCEEEEEcCCCCcHHHHHHHHHHHHC---cChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            3444788899999999999999999999999   889999999999999999988999999999998864

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=98.51  E-value=1.9e-07  Score=71.60  Aligned_cols=68  Identities=26%  Similarity=0.345  Sum_probs=44.4

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---Ceec--CCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ---GKVL--KDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~---GkiL--~D~~tL~d~gI~~g~~I~v   73 (300)
                      |-|.|++.+| .+.|++++++||.+||++|.+..+   ++...+.|..+   ...|  .++++|+++||+.||.|++
T Consensus         5 milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~---~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL   77 (80)
T PF11543_consen    5 MILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLS---IPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYL   77 (80)
T ss_dssp             -EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS------TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE-
T ss_pred             EEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcC---CCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEE
Confidence            7899998777 788999999999999999999999   88888888543   2344  5678999999999999976

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=98.44  E-value=1.2e-06  Score=65.49  Aligned_cols=72  Identities=18%  Similarity=0.305  Sum_probs=63.1

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--eecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ---G--KVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~---G--kiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      ++|+||-+.+..+.+.|+|..+|.+||++|....+   + ...|||.|.   |  ..|.+.++|.+|||-.+-.|.|+-.
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~---~-~g~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lleT   76 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRN---C-SGLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLET   76 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhC---c-ccceEEEeecCCcccccccccccHhhhcceeccEEEEEec
Confidence            58999999999999999999999999999999999   5 469999993   3  4679999999999998888887764


Q ss_pred             c
Q 022228           77 K   77 (300)
Q Consensus        77 k   77 (300)
                      -
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.

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

Probab=98.38  E-value=1.5e-07  Score=68.45  Aligned_cols=71  Identities=20%  Similarity=0.295  Sum_probs=64.0

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      |+.|.+...-|++..|.+.+++||+++|+.|+..+|   ..++.+.|---+.+++|.-+|++|.|++|-.+.+.
T Consensus         1 miev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtG---T~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely   71 (73)
T KOG3493|consen    1 MIEVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY   71 (73)
T ss_pred             CceehhhhhcCceEEEEeCCcccccCHHHHHHHhhC---CChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence            678889989999999999999999999999999999   77888888766778899999999999999887664

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

Probab=98.26  E-value=2.1e-06  Score=84.12  Aligned_cols=72  Identities=24%  Similarity=0.400  Sum_probs=66.9

Q ss_pred             EEEEEcCCCcEEEEE-eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            3 KIFVKTLKGTSFDVE-VKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         3 ~I~VKtl~g~~~~ie-V~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      .|.|| |.|+.|.++ ++.++|+..||.+|...+|   +++++||++++|+.|.|+-.+..++||+|.+|++|.+.-
T Consensus         5 ~v~VK-W~gk~y~v~~l~~d~t~~vlKaqlf~LTg---V~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e   77 (473)
T KOG1872|consen    5 TVIVK-WGGKKYPVETLSTDETPSVLKAQLFALTG---VPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAE   77 (473)
T ss_pred             eEeee-ecCccccceeccCCCchHHHHHHHHHhcC---CCccceeEEEecccccccccccccccCCCCEEEeecccc
Confidence            36777 899999998 9999999999999999999   999999999999999999999999999999999998653

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

Probab=98.19  E-value=2.2e-06  Score=80.28  Aligned_cols=73  Identities=32%  Similarity=0.502  Sum_probs=62.5

Q ss_pred             EEEEEEcC---CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTL---KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl---~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |.|.|+.-   .-..+.|+|+.+..|.+||+.++...|   +|+++.|+||.||.|.|+.++..+.+...+.+|+|.-+
T Consensus         1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~g---vp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~lR   76 (446)
T KOG0006|consen    1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQG---VPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIMLLR   76 (446)
T ss_pred             CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhC---CChhheEEEEeccccccCceeecccccccchhhhhccC
Confidence            45566643   223588899999999999999999999   99999999999999999999999999888999988443

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

Probab=98.07  E-value=3.3e-05  Score=61.07  Aligned_cols=73  Identities=11%  Similarity=0.226  Sum_probs=66.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +.|+|+.-++....+.|..+.+.+.|++..++..|   +....+|++|+|+.+.+.+|-.+++++++|.|.++...
T Consensus        21 i~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~G---l~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q   93 (99)
T KOG1769|consen   21 INLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQG---LSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQ   93 (99)
T ss_pred             EEEEEecCCCCEEEEEeecCChHHHHHHHHHHHcC---CccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeec
Confidence            56777776677788999999999999999999999   88999999999999999999999999999999998754

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

Probab=97.71  E-value=5.6e-05  Score=59.30  Aligned_cols=61  Identities=26%  Similarity=0.362  Sum_probs=50.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe-CC-eecCCCCchhhcccC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY-QG-KVLKDDTTLEENKVA   66 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~-~G-kiL~D~~tL~d~gI~   66 (300)
                      |-|.||. ...++.++.+++.||.+||.+++....   -|++.|+|+. .- .+|+|.++|+|||..
T Consensus         3 ~f~~VrR-~kttif~da~es~tV~elK~~l~gi~~---~Pvn~qrL~kmd~eqlL~D~ktL~d~gft   65 (110)
T KOG4495|consen    3 VFLRVRR-HKTTIFTDAKESSTVFELKRKLEGILK---RPVNEQRLYKMDTEQLLDDGKTLGDCGFT   65 (110)
T ss_pred             eeeeeee-cceeEEeecCccccHHHHHHHHHHHHh---CCCcchheeecCHHHHhhccchhhhcccc
Confidence            4456663 345678899999999999999999998   8999999976 33 688999999999864

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

Probab=97.56  E-value=0.0002  Score=56.85  Aligned_cols=59  Identities=20%  Similarity=0.268  Sum_probs=46.0

Q ss_pred             EEEEcCC-CcEEEEEeC--CCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhc
Q 022228            4 IFVKTLK-GTSFDVEVK--PEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEEN   63 (300)
Q Consensus         4 I~VKtl~-g~~~~ieV~--~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~   63 (300)
                      |+||..+ -..+.++|.  .+.||..||+.|.+..+.+ ..-..+||||+||+|.|+..|...
T Consensus         3 l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~-~s~~rLRlI~~Gr~L~d~t~l~~~   64 (97)
T PF10302_consen    3 LTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPE-PSRRRLRLIYAGRLLNDHTDLSSE   64 (97)
T ss_pred             EEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCC-CccccEEeeecCcccCccchhhhh
Confidence            5566554 234677777  7899999999999998433 556789999999999998877664

They contain a characteristic GFDRL sequence motif.

>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=0.00028  Score=53.58  Aligned_cols=72  Identities=19%  Similarity=0.275  Sum_probs=51.1

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC---CeEEE-eCCeecCCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAA---QQMLI-YQGKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~---~qkLi-~~GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      ++|+|..-+|+.+.+.+..+.+|.+|...|.+..+.......   ..+|. -+|..|+++++|.++||.+|+.|++
T Consensus         3 ~rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L   78 (79)
T PF08817_consen    3 CRVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGDVLVL   78 (79)
T ss_dssp             EEEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred             EEEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence            567887655689999999999999999999988773212222   36676 6899999999999999999999986

Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.

>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=97.47  E-value=0.001  Score=50.50  Aligned_cols=69  Identities=23%  Similarity=0.326  Sum_probs=58.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCC-eEEE--eCCeecCCC--CchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQ-QMLI--YQGKVLKDD--TTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~-qkLi--~~GkiL~D~--~tL~d~gI~~g~~I~v   73 (300)
                      .+|.||..+|+.+...+..++||.+|...|.....   .+... .+|+  |-.+.|.++  ++|+++|+..+.+|+|
T Consensus         7 ~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~---~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    7 VRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLF---SPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             EEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHH---CTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcC---CCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence            57899999999999999999999999999988876   33443 7786  677888554  6999999999998876

The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.46  E-value=0.00071  Score=50.79  Aligned_cols=72  Identities=14%  Similarity=0.262  Sum_probs=58.8

Q ss_pred             EEEEE--EcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC--CCCeEEEeCCeecCCCCchhhcccCCCcEEEE
Q 022228            2 MKIFV--KTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP--AAQQMLIYQGKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~V--Ktl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip--~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      |+|+|  +.++|.+|.+.+....+|+.|-..+.+....+..+  -..+|..-++++|.++..|.+|+|.+||.+.+
T Consensus         5 ikVTvD~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei   80 (81)
T COG5417           5 IKVTVDFTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI   80 (81)
T ss_pred             EEEEEEeEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence            45554  67789999999999999999999887776532122  24678999999999999999999999999875

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

Probab=97.45  E-value=0.00022  Score=47.75  Aligned_cols=39  Identities=28%  Similarity=0.390  Sum_probs=35.2

Q ss_pred             hHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      +++.|+.|.+|  .   |+++.+.++|++.-+|.|+||++|+.|
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            36789999999  6   999999999999999999999999865

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.

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

Probab=97.39  E-value=0.00011  Score=75.01  Aligned_cols=43  Identities=35%  Similarity=0.649  Sum_probs=40.0

Q ss_pred             CChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 022228          157 NNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIP  202 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP  202 (300)
                      +.-|+.|..|++||   |.|.|++.||++..||.+|||||+++-+-
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   99999999999999999999999999865

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.34  E-value=0.0016  Score=49.38  Aligned_cols=69  Identities=14%  Similarity=0.141  Sum_probs=56.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLKD---DTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~D---~~tL~d~gI~~g~~I~v   73 (300)
                      .+|.||..+|+.+...+..++||.+|.+.|....+   ......+|+  |-.|.|.+   +++|.++|+..+.+|+|
T Consensus         5 ~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~---~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v   78 (80)
T smart00166        5 CRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALT---DGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL   78 (80)
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHccc---CCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence            47899999999999999999999999999966555   445567775  66788854   47999999988888765

Present in FAF1 and Shp1p.

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=97.17  E-value=0.0037  Score=47.02  Aligned_cols=67  Identities=24%  Similarity=0.330  Sum_probs=53.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLKD---DTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~D---~~tL~d~gI~~g~~I~v   73 (300)
                      .+|.||..+|+.+...+..++||.+|.+.|.....   . ....+|+  |-.|.|.|   +++|+++|+. .+.+++
T Consensus         3 t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~---~-~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~-~s~~~~   74 (77)
T cd01767           3 TKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGP---P-AEPFTLMTSFPRRVLTDLDYELTLQEAGLV-NEVVFQ   74 (77)
T ss_pred             EEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCC---C-CCCEEEEeCCCCccCCCCCccCcHHHcCCc-cceEEE
Confidence            47899999999999999999999999999987654   2 4567776  56788854   7899999999 455544

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.

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=97.06  E-value=0.0053  Score=46.65  Aligned_cols=68  Identities=19%  Similarity=0.408  Sum_probs=56.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLKD---DTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~D---~~tL~d~gI~~g~~I~v   73 (300)
                      .+|.||..+|+.+...+..++||.+|.+.|....+   . ....+|+  |-.|.+.+   +++|.++|+....+|+|
T Consensus         5 ~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~---~-~~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           5 TRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTG---N-GGPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             EEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCC---C-CCCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence            47899999999999999999999999999986654   2 2557776  67888854   47999999998888876

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.

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=97.05  E-value=0.0051  Score=46.90  Aligned_cols=65  Identities=22%  Similarity=0.278  Sum_probs=52.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC-CCchhhcccCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLKD-DTTLEENKVAEN   68 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~D-~~tL~d~gI~~g   68 (300)
                      -+|.||..+|+.+...+..++||.+|++.|....+.  .......|+  |-.|.|.| +.||+|.|+.+.
T Consensus         5 t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~--~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s   72 (79)
T cd01770           5 TSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPE--FAARPFTLMTAFPVKELSDESLTLKEANLLNA   72 (79)
T ss_pred             eEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCC--CCCCCEEEecCCCCcccCCCCCcHHHCCCcCc
Confidence            478999999999999999999999999999987641  223567776  67888854 679999999853

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.

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

Probab=97.03  E-value=0.00017  Score=68.32  Aligned_cols=75  Identities=21%  Similarity=0.267  Sum_probs=56.2

Q ss_pred             EEEEEEcCCC--cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCC--cEEEEEEec
Q 022228            2 MKIFVKTLKG--TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAEN--SFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g--~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g--~~I~v~v~k   77 (300)
                      +.+.||..+.  +...|..+..+||++||..++..+..+ --..+|||||.||.|.|...|+|.-+|..  -.+||+...
T Consensus        10 v~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPsk-pl~~dqrliYsgkllld~qcl~d~lrkq~k~Hv~hlvcns   88 (391)
T KOG4583|consen   10 VTLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSK-PLELDQRLIYSGKLLLDHQCLTDWLRKQVKEHVKHLVCNS   88 (391)
T ss_pred             eEEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCC-CchhhHHHHhhccccccchhHHHHHHHHHHHHHHHHhcCC
Confidence            3566776554  457788889999999999999987643 23578999999999999999999866543  344555443

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

Probab=96.86  E-value=0.0042  Score=48.36  Aligned_cols=70  Identities=17%  Similarity=0.200  Sum_probs=60.7

Q ss_pred             EEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            3 KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      .+.|-..+|.++.+.|..+.+...|.+..+...|   -.-+..|++|+|+.++-++|-.|+++.+++.|-++.
T Consensus        26 nLkvv~qd~telfFkiKktT~f~klm~af~~rqG---K~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~   95 (103)
T COG5227          26 NLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQG---KNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVT   95 (103)
T ss_pred             ceEEecCCCCEEEEEEeccchHHHHHHHHHHHhC---cCcceeEEEEcceecCCCCChhhcCCccchHHHHHH
Confidence            3555556788888999999999999999999999   447899999999999999999999999999876543

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.81  E-value=0.0025  Score=56.93  Aligned_cols=65  Identities=25%  Similarity=0.376  Sum_probs=55.9

Q ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCC--cEEEEEEec
Q 022228           10 KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAEN--SFVVIMLTK   77 (300)
Q Consensus        10 ~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g--~~I~v~v~k   77 (300)
                      .++.|.+.+...+||+++|.++....+   +.+-.|+++|+|++|-|...|.+|+|..|  -+|.++|..
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg---~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqviVlq  221 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEG---VDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQVIVLQ  221 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhc---cchhhheeeccCCceeccccceeeeecCCCEEEEEEEecc
Confidence            466788888899999999999999999   66889999999999999999999999999  444444443

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=96.79  E-value=0.013  Score=45.13  Aligned_cols=70  Identities=16%  Similarity=0.362  Sum_probs=59.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC---CCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLK---DDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~---D~~tL~d~gI~~g~~I~v~v   75 (300)
                      -+|.||..+|+..+-.+..++++.+|...|.. .|   .+.+..+|+  |--|.+.   .+.||++.|+....+|+|--
T Consensus         6 t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g---~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq~   80 (82)
T cd01773           6 ARLMLRYPDGKREQIALPEQAKLLALVRHVQS-KG---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE   80 (82)
T ss_pred             eEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cC---CCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEec
Confidence            47999999999999999999999999999988 56   678889997  5677773   34799999999999998753

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.

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

Probab=96.79  E-value=0.0027  Score=58.18  Aligned_cols=70  Identities=17%  Similarity=0.185  Sum_probs=52.7

Q ss_pred             EEEEEEcCCCc-EEE-EEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE----EeCCeecCCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGT-SFD-VEVKPEDTVFDVKMKIETVQGSDVYPAAQQML----IYQGKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~-~~~-ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkL----i~~GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      |.|++...++. ..+ .+.....||.|++++|..+..+  +.+..+|+    --+||.|.|+.+|++|+...+++|.|
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            68888877652 333 6777889999999888776653  44544443    34799999999999999999977755

>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly

Probab=96.75  E-value=0.0073  Score=44.49  Aligned_cols=63  Identities=17%  Similarity=0.144  Sum_probs=46.6

Q ss_pred             cCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEE
Q 022228            8 TLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         8 tl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      ..+++.+.|.|.++.++.++-+..+.+.+   +..++-.|.|++|.|+-+..+.-.|+-+|..+.+
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            46789999999999999999999999999   8889999999999999999999999999988754

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.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=96.67  E-value=0.0021  Score=62.78  Aligned_cols=38  Identities=37%  Similarity=0.524  Sum_probs=36.0

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      -.++|++|++||   |+|..|+.|-.|+-.|-+-|+.||+.
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            367999999999   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).

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

Probab=96.66  E-value=0.0024  Score=55.98  Aligned_cols=47  Identities=21%  Similarity=0.258  Sum_probs=43.8

Q ss_pred             cccccCCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          151 SNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       151 s~l~~g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ..+.++..+...|.+|.+||   |+|+.++.+|+-..-|..+|.|+|++|
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            34777889999999999999   999999999999999999999999987

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=96.61  E-value=0.021  Score=44.14  Aligned_cols=68  Identities=15%  Similarity=0.150  Sum_probs=56.1

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC--CeecC--------CCCchhhcccCCCcEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ--GKVLK--------DDTTLEENKVAENSFV   71 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~--GkiL~--------D~~tL~d~gI~~g~~I   71 (300)
                      .+|.||..+|+.+.-.+..++||++|...|.. .+   ..++...|+++  -|+|.        .+.||++.||....+|
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            57999999999999999999999999999964 34   44678888854  47885        3679999999988777


Q ss_pred             EE
Q 022228           72 VI   73 (300)
Q Consensus        72 ~v   73 (300)
                      +|
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.

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

Probab=96.59  E-value=0.0062  Score=40.79  Aligned_cols=39  Identities=26%  Similarity=0.418  Sum_probs=35.9

Q ss_pred             hHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .++.|..|.+|  .   ++++.|++.|++.-||.|+|++.|+.|
T Consensus         2 ~~~~v~~L~~mFP~---l~~~~I~~~L~~~~g~ve~~i~~LL~~   42 (43)
T smart00546        2 NDEALHDLKDMFPN---LDEEVIKAVLEANNGNVEATINNLLEG   42 (43)
T ss_pred             hHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            36789999999  6   899999999999999999999999876

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)

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

Probab=96.43  E-value=0.0099  Score=53.07  Aligned_cols=73  Identities=21%  Similarity=0.310  Sum_probs=57.5

Q ss_pred             CEEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE-EeCC-----eec-CCCCchhhcccCCCcEEE
Q 022228            1 MMKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQML-IYQG-----KVL-KDDTTLEENKVAENSFVV   72 (300)
Q Consensus         1 mM~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkL-i~~G-----kiL-~D~~tL~d~gI~~g~~I~   72 (300)
                      |++|.|.+...+ .++..+..+.||.+||.|++..+|   .+++.++| +|.|     -.| +++..|..|+..+|-.||
T Consensus         1 ~v~v~Iss~~~~~~~Ekr~~~~ltl~q~K~KLe~~~G---~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rih   77 (234)
T KOG3206|consen    1 MVRVVISSSLNDFRTEKRLSNSLTLAQFKDKLELLTG---TEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIH   77 (234)
T ss_pred             CeEEEEecccccchhhhhcCCcCcHHHHHhhhhhhhC---CCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEE
Confidence            567878654332 245567899999999999999999   88999999 5665     345 456799999999999999


Q ss_pred             EEEe
Q 022228           73 IMLT   76 (300)
Q Consensus        73 v~v~   76 (300)
                      |+=.
T Consensus        78 viD~   81 (234)
T KOG3206|consen   78 VIDS   81 (234)
T ss_pred             EEec
Confidence            8754

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=96.42  E-value=0.032  Score=42.66  Aligned_cols=69  Identities=19%  Similarity=0.247  Sum_probs=58.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC---CCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLK---DDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~---D~~tL~d~gI~~g~~I~v~   74 (300)
                      .+|.||..+|+.+.-.+..++++.+|...|..+ |   ++....+|+  |=-|.+.   .+.+|.+.|+....+|+|-
T Consensus         5 ~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~---~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~Ve   78 (80)
T cd01771           5 SKLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-G---YPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLILE   78 (80)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-C---CCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEEE
Confidence            579999999999999999999999999999764 6   667788886  6678774   2569999999998888763

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.

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=96.18  E-value=0.039  Score=47.73  Aligned_cols=75  Identities=17%  Similarity=0.273  Sum_probs=54.2

Q ss_pred             EEEEEEcCCC----cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCe-EEEe-CCeec--CCCCchhhcccCCCc----
Q 022228            2 MKIFVKTLKG----TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQ-MLIY-QGKVL--KDDTTLEENKVAENS----   69 (300)
Q Consensus         2 M~I~VKtl~g----~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~q-kLi~-~GkiL--~D~~tL~d~gI~~g~----   69 (300)
                      |.|+|++++|    .++.+.+..+.||.+|+.+|....+   ++...+ .|.+ .++.|  .++..++++.-...+    
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            6899999999    5899999999999999999999998   766663 3444 34444  556677777554443    


Q ss_pred             EEEEEEecCC
Q 022228           70 FVVIMLTKNK   79 (300)
Q Consensus        70 ~I~v~v~k~~   79 (300)
                      +|.|+++...
T Consensus        78 ~l~l~~rl~G   87 (162)
T PF13019_consen   78 TLRLSLRLRG   87 (162)
T ss_pred             EEEEEEeccC
Confidence            4555555544

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=95.90  E-value=0.034  Score=42.15  Aligned_cols=67  Identities=13%  Similarity=0.160  Sum_probs=47.4

Q ss_pred             CEEEEEEcCC------C-cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC--CCeEEEeCCeecCCCCchhhcccCCCcEE
Q 022228            1 MMKIFVKTLK------G-TSFDVEVKPEDTVFDVKMKIETVQGSDVYPA--AQQMLIYQGKVLKDDTTLEENKVAENSFV   71 (300)
Q Consensus         1 mM~I~VKtl~------g-~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~--~~qkLi~~GkiL~D~~tL~d~gI~~g~~I   71 (300)
                      ||+|+|+.+.      | ....+++....||.+|++.|......  +..  ....+..+|+...+     ++-|++||.|
T Consensus         1 ~m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~--l~~~~~~~~vavN~~~v~~-----~~~l~dgDeV   73 (82)
T PLN02799          1 SVEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPS--LEEVRSCCVLALNEEYTTE-----SAALKDGDEL   73 (82)
T ss_pred             CeEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChh--HHHHhhCcEEEECCEEcCC-----CcCcCCCCEE
Confidence            7999999764      4 45677888889999999999766420  111  22346678888753     3457889999


Q ss_pred             EEE
Q 022228           72 VIM   74 (300)
Q Consensus        72 ~v~   74 (300)
                      .++
T Consensus        74 ai~   76 (82)
T PLN02799         74 AII   76 (82)
T ss_pred             EEe
Confidence            886

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=95.29  E-value=0.14  Score=37.94  Aligned_cols=59  Identities=20%  Similarity=0.412  Sum_probs=44.1

Q ss_pred             CEEEEEEcCCCc--EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            1 MMKIFVKTLKGT--SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         1 mM~I~VKtl~g~--~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      ||+|+|.   |+  ...++++...||.+|.+.+    +   ++.....+..+|+++..     ++-+++||.|.++
T Consensus         4 mm~v~vn---g~~~~~~~~~~~~~tv~~ll~~l----~---~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii   64 (70)
T PRK08364          4 MIRVKVI---GRGIEKEIEWRKGMKVADILRAV----G---FNTESAIAKVNGKVALE-----DDPVKDGDYVEVI   64 (70)
T ss_pred             EEEEEEe---ccccceEEEcCCCCcHHHHHHHc----C---CCCccEEEEECCEECCC-----CcCcCCCCEEEEE
Confidence            4566664   44  5678888889999998765    5   66677788899999854     5568889998876

>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=95.08  E-value=0.024  Score=40.26  Aligned_cols=23  Identities=39%  Similarity=0.715  Sum_probs=19.5

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHH
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRA  185 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrA  185 (300)
                      ...|.++++||   |+|+.|+.|||-
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   999999999985

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

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

Probab=94.95  E-value=0.034  Score=52.93  Aligned_cols=38  Identities=34%  Similarity=0.474  Sum_probs=36.1

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .++|.+|++||   |+|.-|+.|-=|+..|=+-|++||+.-
T Consensus       299 ~eAIeRL~alG---F~ralViqayfACdKNEelAAN~Ll~~  336 (340)
T KOG0011|consen  299 KEAIERLEALG---FPRALVIQAYFACDKNEELAANYLLSH  336 (340)
T ss_pred             HHHHHHHHHhC---CcHHHHHHHHHhcCccHHHHHHHHHhh
Confidence            67999999999   999999999999999999999999964

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

Probab=94.80  E-value=0.04  Score=55.01  Aligned_cols=41  Identities=34%  Similarity=0.524  Sum_probs=37.1

Q ss_pred             CChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          157 NNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ..|..-.++|-+||   | +|+.-++||+|.+.+.++|||-|+.+
T Consensus       452 ~r~q~QLeQL~~MG---F~nre~nlqAL~atgGdi~aAverll~s  493 (493)
T KOG0010|consen  452 ERYQTQLEQLNDMG---FLDREANLQALRATGGDINAAVERLLGS  493 (493)
T ss_pred             HHHHHHHHHHHhcC---CccHHHHHHHHHHhcCcHHHHHHHHhcC
Confidence            45677799999999   9 99999999999999999999999853

>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=94.60  E-value=0.061  Score=41.63  Aligned_cols=36  Identities=28%  Similarity=0.488  Sum_probs=31.6

Q ss_pred             HHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCC
Q 022228          163 IQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGI  201 (300)
Q Consensus       163 I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GI  201 (300)
                      |+.+.+.|   |.++.|.+||++.-+++..|..|++++.
T Consensus         1 i~~~~~~g---~~~~~v~~aL~~tSgd~~~a~~~vl~~l   36 (87)
T PF11626_consen    1 IKHYEELG---YSREFVTHALYATSGDPELARRFVLNFL   36 (87)
T ss_dssp             -HHHHHHT---B-HHHHHHHHHHTTTBHHHHHHHHHHCH
T ss_pred             CchHHHhC---CCHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            56678899   9999999999999999999999999883

The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.

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

Probab=94.57  E-value=0.069  Score=40.43  Aligned_cols=56  Identities=23%  Similarity=0.262  Sum_probs=46.1

Q ss_pred             eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhc-ccCCCcEEEEEE
Q 022228           18 VKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEEN-KVAENSFVVIML   75 (300)
Q Consensus        18 V~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~-gI~~g~~I~v~v   75 (300)
                      |.++++|.+|++.|......  ..-....|.|+|+.|+|...|+++ |++++..|.|+.
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            56789999999999877541  346778999999999999899888 588899888774

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=94.48  E-value=0.1  Score=37.39  Aligned_cols=56  Identities=23%  Similarity=0.388  Sum_probs=40.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+|+|.   |+.  ++++.+.|+.+||.++...         .=.+||+|-..+++.     -+++||.|+++.|
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--IETEENTTLFELRKESKPD---------ADIVILNGFPTKEDI-----ELKEGDEVFLIKK   56 (57)
T ss_pred             CEEEEC---CEE--EEcCCCcCHHHHHHhhCCC---------CCEEEEcCcccCCcc-----ccCCCCEEEEEeC
Confidence            566663   554  6677888999999875432         226799999887754     5677999988753

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

Probab=94.25  E-value=0.29  Score=36.39  Aligned_cols=68  Identities=25%  Similarity=0.265  Sum_probs=51.3

Q ss_pred             EEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe----CC--eecCCCCchhhcccCCCcEEEEEE
Q 022228            6 VKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY----QG--KVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         6 VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~----~G--kiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+.++|...+++|+.+.|+.+|=++|+.+.+.  ...+-.-|.|    +|  .-|+.+++|.+...+.+....+..
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            56789999999999999999999999999983  3455667877    23  457889999999777334333333

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 ....

>PRK06437 hypothetical protein; Provisional

Probab=94.11  E-value=0.32  Score=35.73  Aligned_cols=54  Identities=22%  Similarity=0.282  Sum_probs=43.5

Q ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228           10 KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus        10 ~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      .++...++++...||.+|-+.    .+   ++.....+..+|+++.     .++-|++||.|.++-
T Consensus         9 g~~~~~~~i~~~~tv~dLL~~----Lg---i~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv~   62 (67)
T PRK06437          9 GHINKTIEIDHELTVNDIIKD----LG---LDEEEYVVIVNGSPVL-----EDHNVKKEDDVLILE   62 (67)
T ss_pred             CCcceEEEcCCCCcHHHHHHH----cC---CCCccEEEEECCEECC-----CceEcCCCCEEEEEe
Confidence            456677888888999988765    46   7788889999999997     566788999998764

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

Probab=93.62  E-value=0.075  Score=52.61  Aligned_cols=59  Identities=19%  Similarity=0.142  Sum_probs=51.8

Q ss_pred             EEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228           15 DVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus        15 ~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      .++...+.|-.+|..+|.++.|   ++-...|.|.+||+|.-.+||.+-|++.+..+.|++.
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            4566677788899999999999   8888999999999999999999999998887777665

>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=93.24  E-value=0.26  Score=32.94  Aligned_cols=37  Identities=27%  Similarity=0.403  Sum_probs=30.8

Q ss_pred             HHHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          160 EGAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       160 e~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      ++.|.+.|+. |   -+++.++.-|+.+.+|.++||+.-+.
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            4678999987 7   79999999999999999999987654

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

Probab=93.12  E-value=0.12  Score=49.93  Aligned_cols=69  Identities=14%  Similarity=0.180  Sum_probs=58.5

Q ss_pred             EEEEEEcC--CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC--CchhhcccCCCcEEEE
Q 022228            2 MKIFVKTL--KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDD--TTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl--~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~--~tL~d~gI~~g~~I~v   73 (300)
                      |.++|-+.  ..++|.|+|..+.....|+..+....|   +..+..-|||+++.|.++  ..|..||++.+++|.+
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            45555444  667889999999999999999999999   889999999999999765  5899999999998854

>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=93.07  E-value=0.28  Score=35.36  Aligned_cols=41  Identities=22%  Similarity=0.336  Sum_probs=37.1

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ...+|++|-|.-|+ +..+++...|+-++++||.||+-||+=
T Consensus         5 ~rk~VQ~iKEiv~~-hse~eIya~L~ecnMDpnea~qrLL~q   45 (60)
T PF06972_consen    5 SRKTVQSIKEIVGC-HSEEEIYAMLKECNMDPNEAVQRLLSQ   45 (60)
T ss_pred             HHHHHHHHHHHhcC-CCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence            46789999999766 899999999999999999999999974

>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=92.74  E-value=0.14  Score=35.02  Aligned_cols=37  Identities=24%  Similarity=0.493  Sum_probs=28.9

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      .++.+.-|+.+|   |.+.++.+|++....+++.-+|.++
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            478899999999   9999999999998755555566654

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.

>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=92.68  E-value=0.59  Score=35.83  Aligned_cols=43  Identities=21%  Similarity=0.255  Sum_probs=37.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG   51 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G   51 (300)
                      +||+++   + ++.|.|.++.+..+|+++|.++.+   ++.+..+|.|+.
T Consensus         5 vKV~f~---~-tIaIrvp~~~~y~~L~~ki~~kLk---l~~e~i~LsYkd   47 (80)
T cd06406           5 VKVHFK---Y-TVAIQVARGLSYATLLQKISSKLE---LPAEHITLSYKS   47 (80)
T ss_pred             EEEEEE---E-EEEEEcCCCCCHHHHHHHHHHHhC---CCchhcEEEecc
Confidence            455555   3 899999999999999999999999   989999999964

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

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=92.44  E-value=0.65  Score=34.42  Aligned_cols=57  Identities=14%  Similarity=0.108  Sum_probs=41.8

Q ss_pred             EEEEEeCCCCCHHHHHHHHHHHhCC-CCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228           13 SFDVEVKPEDTVFDVKMKIETVQGS-DVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus        13 ~~~ieV~~~~TV~~LK~kI~~~~g~-~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      ...++++...||.+|.+.+....+. .........+..+|+...     .++-|++||.|.++
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            4667887889999999999887541 001234566778999987     34568899999887

MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.

>smart00727 STI1 Heat shock chaperonin-binding motif

Probab=92.37  E-value=0.11  Score=34.27  Aligned_cols=28  Identities=29%  Similarity=0.292  Sum_probs=24.2

Q ss_pred             hhhhCcHHHHHHHHHHHhCCCchHHHHhc
Q 022228          266 DFLRNSPQFQVLRAMVQANPQLFPCFKSW  294 (300)
Q Consensus       266 ~~Lr~~pqf~~lR~~vq~nP~~L~~~lq~  294 (300)
                      ..|+ +|+|+++++-+++||+++..+++.
T Consensus         6 ~~l~-~P~~~~~l~~~~~nP~~~~~~~~~   33 (41)
T smart00727        6 LRLQ-NPQVQSLLQDMQQNPDMLAQMLQE   33 (41)
T ss_pred             HHHc-CHHHHHHHHHHHHCHHHHHHHHHh
Confidence            3444 999999999999999999999873

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=91.79  E-value=0.66  Score=33.55  Aligned_cols=60  Identities=17%  Similarity=0.283  Sum_probs=42.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|   +|+.+.+  + ..||.+|.+.+    +   +......+-++|+++.. ....+.-+++||.|-++-
T Consensus         1 m~i~~---Ng~~~~~--~-~~tl~~Ll~~l----~---~~~~~vavavN~~iv~~-~~~~~~~L~dgD~Ieiv~   60 (65)
T PRK06488          1 MKLFV---NGETLQT--E-ATTLALLLAEL----D---YEGNWLATAVNGELVHK-EARAQFVLHEGDRIEILS   60 (65)
T ss_pred             CEEEE---CCeEEEc--C-cCcHHHHHHHc----C---CCCCeEEEEECCEEcCH-HHcCccccCCCCEEEEEE
Confidence            45655   5777776  3 35899888764    5   55666777899999863 334566789999998864

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

Probab=91.47  E-value=0.24  Score=49.15  Aligned_cols=42  Identities=21%  Similarity=0.375  Sum_probs=38.7

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCCc
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQ  204 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~~  204 (300)
                      ...|.+|+.||   |++-..+.||++.-||.|.|.++|+--++..
T Consensus       430 ~~~la~Lv~mG---F~e~~A~~ALe~~gnn~~~a~~~L~~s~~n~  471 (568)
T KOG2561|consen  430 GISLAELVSMG---FEEGKARSALEAGGNNEDTAQRLLSASVANE  471 (568)
T ss_pred             hhhHHHHHHhc---cccchHHHHHHhcCCcHHHHHHHHHHhCCCC
Confidence            45799999999   9999999999999999999999999888753

>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=91.01  E-value=0.71  Score=35.86  Aligned_cols=47  Identities=19%  Similarity=0.326  Sum_probs=38.6

Q ss_pred             EEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe
Q 022228            3 KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY   49 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~   49 (300)
                      .+++|+.+|+.+.+.+.+++.+.+|+..|.++.|.+........|.|
T Consensus         2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Y   48 (86)
T cd06409           2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSY   48 (86)
T ss_pred             cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEE
Confidence            46788999999999999999999999999999993312225777777

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

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

Probab=90.53  E-value=0.33  Score=49.04  Aligned_cols=40  Identities=30%  Similarity=0.582  Sum_probs=35.2

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIP  202 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP  202 (300)
                      ..+|.+|++||   |+.+.+.|||-+..| +-+.|+.||+-.+-
T Consensus       559 qs~I~qL~~mG---fp~~~~~rAL~~tgNqDaEsAMNWLFqHMd  599 (749)
T COG5207         559 QSLIRQLVDMG---FPEEDAARALGITGNQDAESAMNWLFQHMD  599 (749)
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHhhccCcchHHHHHHHHhhcc
Confidence            45899999999   999999999998766 68899999998853

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

Probab=89.46  E-value=2.8  Score=32.70  Aligned_cols=62  Identities=16%  Similarity=0.232  Sum_probs=42.7

Q ss_pred             cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--e--CCe-ecC-CCCchhhcccCCCcEEEEEEec
Q 022228           12 TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--Y--QGK-VLK-DDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus        12 ~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~--~Gk-iL~-D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      ..+...+...+||..+++.+.+...   + ..+.||-  |  ++. .|. .+.||.|.+|.+|-.|++-.+.
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            3577789999999999999999988   8 6778884  2  232 454 4579999999999988776654

>smart00295 B41 Band 4

Probab=89.37  E-value=4  Score=35.21  Aligned_cols=71  Identities=20%  Similarity=0.178  Sum_probs=51.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-CCeEEEeC---C---eecCCCCchhhcccC-CCcEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPA-AQQMLIYQ---G---KVLKDDTTLEENKVA-ENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~-~~qkLi~~---G---kiL~D~~tL~d~gI~-~g~~I~v   73 (300)
                      +.|.|..++|....+.++.+.||.+|.+.|+.+.|   +.. ...-|.+.   +   ..|+...+|.+...+ ....+++
T Consensus         4 ~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~---l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~l~f   80 (207)
T smart00295        4 RVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLG---IRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVKSEPLTLYF   80 (207)
T ss_pred             EEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhC---CCccceeEEEEEcCCCCcCeeCCCccCHHHhcCCCCCcEEEE
Confidence            56888889999999999999999999999999999   532 33344431   2   356777788887665 2334444


Q ss_pred             EE
Q 022228           74 ML   75 (300)
Q Consensus        74 ~v   75 (300)
                      .+
T Consensus        81 r~   82 (207)
T smart00295       81 RV   82 (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.

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

Probab=89.29  E-value=2.3  Score=31.86  Aligned_cols=57  Identities=21%  Similarity=0.248  Sum_probs=41.7

Q ss_pred             Cc-EEEEEeCCC-CCHHHHHHHHHHHhCCCCCC--CCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228           11 GT-SFDVEVKPE-DTVFDVKMKIETVQGSDVYP--AAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus        11 g~-~~~ieV~~~-~TV~~LK~kI~~~~g~~~ip--~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      |+ ...+++..+ .||.+|++.+.+..+.  +-  .....+..+|+.+.+     +.-|++||.|.++
T Consensus        14 g~~~~~~~~~~~~~tv~~L~~~L~~~~p~--l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~   74 (80)
T TIGR01682        14 GTDEETLELPDESTTVGELKEHLAKEGPE--LAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFI   74 (80)
T ss_pred             CCCeEEEECCCCCcCHHHHHHHHHHhCch--hhhhccceEEEECCEEcCC-----CcCcCCCCEEEEe
Confidence            44 357888876 8999999999888641  11  134566789998875     4578889999887

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

>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=89.15  E-value=0.12  Score=49.08  Aligned_cols=62  Identities=24%  Similarity=0.432  Sum_probs=0.0

Q ss_pred             EEEEEEcCCCcEEEEEeC---C--CCCHHHHHHHHHH----------HhCCCCCCCCCeE-----EEeCCeecCCCCchh
Q 022228            2 MKIFVKTLKGTSFDVEVK---P--EDTVFDVKMKIET----------VQGSDVYPAAQQM-----LIYQGKVLKDDTTLE   61 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~---~--~~TV~~LK~kI~~----------~~g~~~ip~~~qk-----Li~~GkiL~D~~tL~   61 (300)
                      +.|++|.+.+-.+.|.+.   +  +.+|.+||..++.          +.+   +|.+.+|     |+|+.|.+.|.++|.
T Consensus        79 ItV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~---vp~dKik~~~~~lL~~kkPv~~~ktl~  155 (309)
T PF12754_consen   79 ITVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETR---VPLDKIKNFRCRLLYKKKPVGDSKTLA  155 (309)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhccccccccccc---CCHHHhhhhhhhheecCccCCCcCcHH
Confidence            457777776665555433   2  5789999999999          777   9999999     999999999999988


Q ss_pred             hcccC
Q 022228           62 ENKVA   66 (300)
Q Consensus        62 d~gI~   66 (300)
                      ++.-.
T Consensus       156 e~l~~  160 (309)
T PF12754_consen  156 EVLAD  160 (309)
T ss_dssp             -----
T ss_pred             HHHhc
Confidence            87433

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.

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

Probab=88.86  E-value=0.58  Score=48.58  Aligned_cols=41  Identities=27%  Similarity=0.451  Sum_probs=36.1

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCCC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIPE  203 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP~  203 (300)
                      +..|.+|++||   |+.+.|.|||-..-| +.+.|..||+.-+-+
T Consensus       572 ~s~i~qL~~MG---Fp~eac~rAly~tgN~~aEaA~NWl~~HMdD  613 (763)
T KOG0944|consen  572 RSVISQLVEMG---FPEEACRRALYYTGNSGAEAASNWLMEHMDD  613 (763)
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHhhhcCccHHHHHHHHHHhccC
Confidence            56799999999   999999999999844 889999999988643

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

Probab=88.79  E-value=0.15  Score=51.35  Aligned_cols=38  Identities=18%  Similarity=0.279  Sum_probs=36.5

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .|..++.|++||   |.-.+|++||--..||.+|+|+|.++
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   99999999999999999999999999

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=88.77  E-value=2.9  Score=31.99  Aligned_cols=53  Identities=23%  Similarity=0.296  Sum_probs=41.6

Q ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe-CCeecCCCCchhhcccCCCcEEEEEE
Q 022228           11 GTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY-QGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus        11 g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~-~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      +..+.++++...||+++-+.    .|   +|..+..+|+ +|+...-     +|-+++|+.|.|.-
T Consensus        22 ~~~~~~~~~~~~tvkd~IEs----LG---VP~tEV~~i~vNG~~v~~-----~~~~~~Gd~v~V~P   75 (81)
T PF14451_consen   22 GGPFTHPFDGGATVKDVIES----LG---VPHTEVGLILVNGRPVDF-----DYRLKDGDRVAVYP   75 (81)
T ss_pred             CCceEEecCCCCcHHHHHHH----cC---CChHHeEEEEECCEECCC-----cccCCCCCEEEEEe
Confidence            45678899999999987654    68   9999998875 8887654     36788999998863

>PRK06083 sulfur carrier protein ThiS; Provisional

Probab=88.57  E-value=1.8  Score=33.33  Aligned_cols=61  Identities=8%  Similarity=0.201  Sum_probs=43.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|   +|+.+.+  +...||.+|-+.    .+   ++....-+-++|.++.- ....++-+++||.|.++.
T Consensus        19 m~I~V---NG~~~~~--~~~~tl~~LL~~----l~---~~~~~vAVevNg~iVpr-~~w~~t~L~egD~IEIv~   79 (84)
T PRK06083         19 ITISI---NDQSIQV--DISSSLAQIIAQ----LS---LPELGCVFAINNQVVPR-SEWQSTVLSSGDAISLFQ   79 (84)
T ss_pred             EEEEE---CCeEEEc--CCCCcHHHHHHH----cC---CCCceEEEEECCEEeCH-HHcCcccCCCCCEEEEEE
Confidence            55544   5776544  567788877664    35   66777778899999943 345666799999998874

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

Probab=88.44  E-value=1.1  Score=32.91  Aligned_cols=60  Identities=15%  Similarity=0.123  Sum_probs=47.0

Q ss_pred             EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228           13 SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus        13 ~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      ...+.+....||.+|.+.+....... .......+..+|+.+.+  .-.+.-+++||.|.++-
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            66788899999999999998886411 12367888899999988  36666788999998873

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 ....

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=87.86  E-value=1.6  Score=31.65  Aligned_cols=60  Identities=15%  Similarity=0.209  Sum_probs=43.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|   +|+.+.+  ....||.+|-+.    .+   ++.....+.++|.++..+.- ..+ +++||.|-++.
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            45655   5776555  467788877654    46   77889999999998865443 245 89999998864

>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=87.63  E-value=3.2  Score=31.77  Aligned_cols=71  Identities=15%  Similarity=0.197  Sum_probs=47.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-CCeEEEeCCe----e-cCCCCchhh----cccCCCcEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPA-AQQMLIYQGK----V-LKDDTTLEE----NKVAENSFV   71 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~-~~qkLi~~Gk----i-L~D~~tL~d----~gI~~g~~I   71 (300)
                      |+|++. .+|..+.+.+.++.+..+|+++|.++.+   +.. ....|-|..-    + |..+.-|.+    |.....++|
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            345554 4678899999999999999999999988   543 5677777431    1 233333444    344455666


Q ss_pred             EEEEe
Q 022228           72 VIMLT   76 (300)
Q Consensus        72 ~v~v~   76 (300)
                      .+.+.
T Consensus        77 ~l~v~   81 (82)
T cd06407          77 RLLVH   81 (82)
T ss_pred             EEEee
Confidence            66553

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

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

Probab=87.53  E-value=2.6  Score=34.80  Aligned_cols=71  Identities=18%  Similarity=0.207  Sum_probs=49.4

Q ss_pred             EEcCCCcEEE---E-EeCC-CCCHHHHHHHHHHHhCC-------CCCCCCCeEEEeC-----------------Ceec--
Q 022228            6 VKTLKGTSFD---V-EVKP-EDTVFDVKMKIETVQGS-------DVYPAAQQMLIYQ-----------------GKVL--   54 (300)
Q Consensus         6 VKtl~g~~~~---i-eV~~-~~TV~~LK~kI~~~~g~-------~~ip~~~qkLi~~-----------------GkiL--   54 (300)
                      ||+..-+.+.   + .|+. +.||++|++.+.+....       ..+.-+.+||++.                 ..+|  
T Consensus         6 IkSFeyRn~K~~Vl~~vdL~~~Tv~~l~~~v~~~I~t~~~~~Pfrn~~yDtlKIy~~AHg~Kt~nLvInle~De~~iL~~   85 (122)
T PF10209_consen    6 IKSFEYRNVKNLVLHNVDLKDTTVKDLKEQVKQDIKTRPGLPPFRNVKYDTLKIYTKAHGSKTNNLVINLEDDEDWILDV   85 (122)
T ss_pred             EecccCCceeeeeeecCCcccCcHHHHHHHHHHHHhcCCCCCCceeeecceEEEEecCCCCCcCCceeeccCCcceeeec
Confidence            4555544433   4 4787 89999999998876431       1134456777753                 2567  


Q ss_pred             -CCCCchhhcccCCCcEEEEEEe
Q 022228           55 -KDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus        55 -~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                       +++++|.+|||.+...|-++.+
T Consensus        86 ~~~~~tL~~~gv~nETEiSfF~~  108 (122)
T PF10209_consen   86 SDDDKTLKELGVENETEISFFNM  108 (122)
T ss_pred             CCCCCcHHHcCCCccceeeeeCH
Confidence             7788999999999998887754

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=87.43  E-value=3  Score=31.65  Aligned_cols=59  Identities=14%  Similarity=0.263  Sum_probs=40.9

Q ss_pred             cEEEEEeCCCCCHHHHHHHHHHHhCC---CCCC-----CCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228           12 TSFDVEVKPEDTVFDVKMKIETVQGS---DVYP-----AAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus        12 ~~~~ieV~~~~TV~~LK~kI~~~~g~---~~ip-----~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      ....+++. ..||.+|.+.|.+++..   ..+.     .....+..+|+..+++..   .-|++||.|.++
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            35677776 88999999999887541   0010     123667779988765532   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.

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

Probab=87.13  E-value=3.2  Score=30.60  Aligned_cols=67  Identities=19%  Similarity=0.239  Sum_probs=52.1

Q ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE-eCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228           10 KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI-YQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus        10 ~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi-~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      +|+-..++.+....+--+..+--+..+...-|++...|- -+|.+|+-+++++|||+..+-++++.++
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            577788888888887777777666665332567766664 4799999999999999999999887664

>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=86.87  E-value=1.8  Score=33.51  Aligned_cols=61  Identities=13%  Similarity=0.126  Sum_probs=43.2

Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228           14 FDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus        14 ~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +...++-..++..||..++.+.+   +.-+.-.+......|+++++|-|-+|+-...|.+.+--
T Consensus         5 I~q~mDI~epl~~Lk~lLe~Rl~---~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQi   65 (88)
T PF11620_consen    5 IMQHMDIREPLSTLKKLLERRLG---ISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQI   65 (88)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHH----S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEEE
T ss_pred             EEEEEecCCcHHHHHHHHHHhhC---CCcCCCeEEeccceecCCccHHHhhccccCEEEEEEEE
Confidence            44567778899999999999999   66788888888888999999999999988888887654

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.

>smart00666 PB1 PB1 domain

Probab=86.54  E-value=3.2  Score=30.85  Aligned_cols=46  Identities=17%  Similarity=0.240  Sum_probs=37.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG   51 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G   51 (300)
                      ++|+++. ++..+.+.+..+.|..+|+.+|..+.+   +.....+|-|..
T Consensus         2 ~~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~---~~~~~~~l~Y~D   47 (81)
T smart00666        2 VDVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFG---LDNQSFTLKYQD   47 (81)
T ss_pred             ccEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhC---CCCCCeEEEEEC
Confidence            4566664 678888999999999999999999998   656788888863

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.

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

Probab=86.31  E-value=2.4  Score=31.71  Aligned_cols=64  Identities=22%  Similarity=0.100  Sum_probs=46.5

Q ss_pred             EEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC--C--eecCCCCchhhcccCCCcEEEE
Q 022228            4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ--G--KVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         4 I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~--G--kiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      +.|-..+|+.-.+.|.+..||.++-.++.++.|   +.++...|.+.  +  +.++.+....   +-.+..|.|
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---LNPECCDVFLLGLDEKKPLDLDTDSS---SLAGEELEV   69 (72)
T ss_pred             EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcC---CCHHHEEEEEecCCCcCCcCchhhhh---hhcCCEEEE
Confidence            456677899999999999999999999999999   77877766654  3  4454443333   334455544

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.

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

Probab=85.47  E-value=0.44  Score=36.19  Aligned_cols=27  Identities=30%  Similarity=0.428  Sum_probs=23.8

Q ss_pred             C-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          174 W-DRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       174 f-~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      . ++.+++.||.-.|+|+++||.||++-
T Consensus        43 ~~~e~~i~eal~~~~fDvekAl~~Ll~~   70 (79)
T PF08938_consen   43 VPPEEQIKEALWHYYFDVEKALDYLLSK   70 (79)
T ss_dssp             C--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence            5 89999999999999999999999987

; PDB: 1UFZ_A 3IZQ_1.

>PRK05659 sulfur carrier protein ThiS; Validated

Probab=85.24  E-value=3.7  Score=29.46  Aligned_cols=61  Identities=16%  Similarity=0.280  Sum_probs=42.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|   +|+.+  ++....||.+|-+.    .+   ++.....+.++|+++.... -.+.-+++||.|-++.
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            45555   57755  55667888887654    46   7778888889999886432 3344588999998764

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

Probab=84.43  E-value=1.6  Score=42.58  Aligned_cols=66  Identities=24%  Similarity=0.348  Sum_probs=51.4

Q ss_pred             EEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC-CCchhhcccCCCcE
Q 022228            3 KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLKD-DTTLEENKVAENSF   70 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~D-~~tL~d~gI~~g~~   70 (300)
                      .|.||.-+|+.....++.+.||.+|+..|.....-  .....+-|+  |--|.|.| +.||++-|+.+...
T Consensus       307 sIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~--~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsvl  375 (380)
T KOG2086|consen  307 SIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPG--DSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSVL  375 (380)
T ss_pred             eEEEEecCCceeeeeccCcccHHHHHHHHHhcCCC--CcCCceeeeecCCCcccCCcchhHHhccchhhhh
Confidence            47788889999999999999999999999988762  333456665  55788865 56999999986443

>PRK07440 hypothetical protein; Provisional

Probab=84.04  E-value=5.8  Score=29.29  Aligned_cols=62  Identities=16%  Similarity=0.262  Sum_probs=43.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      +|+|+|   +|+.  +++....||.+|-+    ..+   +.....-+-++|+++.. ....++-+++||.|.++.
T Consensus         4 ~m~i~v---NG~~--~~~~~~~tl~~lL~----~l~---~~~~~vav~~N~~iv~r-~~w~~~~L~~gD~IEIv~   65 (70)
T PRK07440          4 PITLQV---NGET--RTCSSGTSLPDLLQ----QLG---FNPRLVAVEYNGEILHR-QFWEQTQVQPGDRLEIVT   65 (70)
T ss_pred             ceEEEE---CCEE--EEcCCCCCHHHHHH----HcC---CCCCeEEEEECCEEeCH-HHcCceecCCCCEEEEEE
Confidence            366665   4765  45567788888765    345   66778888899999863 234455688999998764

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.03  E-value=1.3  Score=42.51  Aligned_cols=56  Identities=14%  Similarity=0.146  Sum_probs=45.4

Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe---CCeec-----CCCCchhhcccCCCcEEEEE
Q 022228           16 VEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY---QGKVL-----KDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus        16 ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~---~GkiL-----~D~~tL~d~gI~~g~~I~v~   74 (300)
                      .-|...-||.+||+++..+.|   +...++||+|   .||.-     ..++.|-.|+|.+||.+.|-
T Consensus       352 ~~I~~~~TV~D~~~~Ld~~VG---vk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~lvq  415 (418)
T KOG2982|consen  352 GLICMTRTVLDFMKILDPKVG---VKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFLVQ  415 (418)
T ss_pred             eEEEeehHHHHHHHHhccccc---cccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEeeee
Confidence            445566799999999999999   8899999987   45543     33578999999999998764

>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=83.82  E-value=4.7  Score=31.36  Aligned_cols=46  Identities=13%  Similarity=0.240  Sum_probs=36.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGK   52 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~Gk   52 (300)
                      |+|.|. ..|..+.|.|.++.+..+|..+|.++.+   +. ..++|-|...
T Consensus         3 ikVKv~-~~~Dv~~i~v~~~i~f~dL~~kIrdkf~---~~-~~~~iKykDE   48 (86)
T cd06408           3 IRVKVH-AQDDTRYIMIGPDTGFADFEDKIRDKFG---FK-RRLKIKMKDD   48 (86)
T ss_pred             EEEEEE-ecCcEEEEEcCCCCCHHHHHHHHHHHhC---CC-CceEEEEEcC
Confidence            455554 3678999999999999999999999999   63 5667767554

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

>PRK06944 sulfur carrier protein ThiS; Provisional

Probab=83.56  E-value=6.5  Score=28.00  Aligned_cols=60  Identities=13%  Similarity=0.148  Sum_probs=39.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|   +|+.+  ++....||.+|.+.+    +   +. ....+.++|+++..+. -.+.-+++||.|.++-
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            45555   47654  456678999888764    3   32 3456778999885432 2233488899998874

>smart00455 RBD Raf-like Ras-binding domain

Probab=83.41  E-value=4.9  Score=29.75  Aligned_cols=51  Identities=24%  Similarity=0.186  Sum_probs=42.0

Q ss_pred             EEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC--eecCCC
Q 022228            4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG--KVLKDD   57 (300)
Q Consensus         4 I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G--kiL~D~   57 (300)
                      +.|-..+|+...+.+.+..||.++-.+|.++.|   +.++...|.+.|  |.|+=+
T Consensus         2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~---l~~~~~~v~~~g~~k~ldl~   54 (70)
T smart00455        2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRG---LNPECCVVRLRGEKKPLDLN   54 (70)
T ss_pred             eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcC---CCHHHEEEEEcCCCcceecC
Confidence            345567899999999999999999999999999   888888888754  455433

>PRK08053 sulfur carrier protein ThiS; Provisional

Probab=83.19  E-value=6.2  Score=28.54  Aligned_cols=61  Identities=10%  Similarity=0.219  Sum_probs=41.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|   +|+.+.+  ....||.+|.+.    .+   +......+-++++++..+ .-.++-+++||.|.++-
T Consensus         1 m~i~v---Ng~~~~~--~~~~tl~~ll~~----l~---~~~~~vaVavN~~iv~r~-~w~~~~L~~gD~Ieii~   61 (66)
T PRK08053          1 MQILF---NDQPMQC--AAGQTVHELLEQ----LN---QLQPGAALAINQQIIPRE-QWAQHIVQDGDQILLFQ   61 (66)
T ss_pred             CEEEE---CCeEEEc--CCCCCHHHHHHH----cC---CCCCcEEEEECCEEeChH-HcCccccCCCCEEEEEE
Confidence            56665   4776555  566789988865    34   445667888999998532 23344588999998764

>PRK12332 tsf elongation factor Ts; Reviewed

Probab=82.35  E-value=2.2  Score=38.13  Aligned_cols=36  Identities=22%  Similarity=0.327  Sum_probs=32.4

Q ss_pred             HHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          161 GAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       161 ~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      ..|.+|-++ |   +.=-+|..||..+-+|.|.|++||--
T Consensus         6 ~~ik~LR~~tg---a~~~~ck~AL~~~~gd~~~A~~~lr~   42 (198)
T PRK12332          6 KLVKELREKTG---AGMMDCKKALEEANGDMEKAIEWLRE   42 (198)
T ss_pred             HHHHHHHHHHC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            568888887 7   88899999999999999999999973

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=81.64  E-value=5.3  Score=39.45  Aligned_cols=73  Identities=19%  Similarity=0.246  Sum_probs=57.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe----CCee--cCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY----QGKV--LKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~----~Gki--L~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |.+.+|.-.| ...++|+++++.+.|-.+|-.....+ +.++++.++-    .|.+  +..++++.|+|++.|+.|+|-.
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            5678887666 57799999999999999987766544 7778887764    3443  3467899999999999999887


Q ss_pred             e
Q 022228           76 T   76 (300)
Q Consensus        76 ~   76 (300)
                      +
T Consensus        79 s   79 (571)
T COG5100          79 S   79 (571)
T ss_pred             c
Confidence            4

>TIGR00116 tsf translation elongation factor Ts

Probab=80.95  E-value=2.5  Score=40.05  Aligned_cols=36  Identities=19%  Similarity=0.234  Sum_probs=32.4

Q ss_pred             HHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          161 GAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       161 ~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      ..|.+|-++ |   +.=-+|..||..+-||.|.|++||--
T Consensus         6 ~~IK~LRe~Tg---agm~dCKkAL~e~~gDiekAi~~LRk   42 (290)
T TIGR00116         6 QLVKELRERTG---AGMMDCKKALTEANGDFEKAIKNLRE   42 (290)
T ss_pred             HHHHHHHHHHC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            468888887 7   88899999999999999999999963

This protein is found in Bacteria, mitochondria, and chloroplasts.

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=80.88  E-value=6.6  Score=28.21  Aligned_cols=56  Identities=13%  Similarity=0.244  Sum_probs=40.0

Q ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228           10 KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus        10 ~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      +|+.+  +++...||.+|.+++    +   ++.+...+.++|+++..+ .-.++-|++||.|.++-
T Consensus         5 Ng~~~--~~~~~~tv~~ll~~l----~---~~~~~i~V~vNg~~v~~~-~~~~~~L~~gD~V~ii~   60 (65)
T cd00565           5 NGEPR--EVEEGATLAELLEEL----G---LDPRGVAVALNGEIVPRS-EWASTPLQDGDRIEIVT   60 (65)
T ss_pred             CCeEE--EcCCCCCHHHHHHHc----C---CCCCcEEEEECCEEcCHH-HcCceecCCCCEEEEEE
Confidence            56654  445678999988764    4   556788888999998653 23334688999998763

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=80.27  E-value=2.9  Score=33.21  Aligned_cols=32  Identities=22%  Similarity=0.364  Sum_probs=23.2

Q ss_pred             EEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228           46 MLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus        46 kLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      .|-|.||.|.++++|++| |..++...|+++..
T Consensus         3 ~LW~aGK~l~~~k~l~dy-~GkNEKtKiivKl~   34 (98)
T PF11069_consen    3 QLWWAGKELQRGKKLSDY-IGKNEKTKIIVKLQ   34 (98)
T ss_pred             eEEeccccccCCCcHHHh-cCCCcceeEEEEec
Confidence            577999999999999999 54444444454443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	300
1uel_A	95	Solution Structure Of Ubiquitin-Like Domain Of Hhr2		2e-15
1p1a_A	85	Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Le		2e-15
1oqy_A	368	Structure Of The Dna Repair Protein Hhr23a Length =		4e-14
2wyq_A	85	The Crystal Structure Of The Ubiquitin-Like (Ubl) D		3e-12
1p98_A	78	High-Resolution Nmr Structure Of The Ubl-Domain Of		2e-11
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		3e-09
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		1e-08
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		1e-08
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		1e-08
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		1e-08
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		2e-08
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		2e-08
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		2e-08
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		2e-08
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		2e-08
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-08
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		2e-08
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-08
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		2e-08
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		2e-08
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-08
1ify_A	49	Solution Structure Of The Internal Uba Domain Of Hh		2e-08
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		2e-08
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		2e-08
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-08
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		3e-08
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		3e-08
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		3e-08
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		3e-08
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		3e-08
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		3e-08
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		3e-08
3jvz_X	81	E2~ubiquitin-Hect Length = 81		3e-08
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		3e-08
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		3e-08
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		4e-08
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		4e-08
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		4e-08
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		4e-08
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		5e-08
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		5e-08
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		5e-08
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		5e-08
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		6e-08
3h7s_A	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		6e-08
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		7e-08
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		7e-08
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		8e-08
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		9e-08
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		9e-08
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		1e-07
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		1e-07
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		1e-07
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-07
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		2e-07
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		2e-07
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		2e-07
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-07
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		2e-07
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-07
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		3e-07
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		3e-07
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		3e-07
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		4e-07
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		4e-07
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		5e-07
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		6e-07
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		9e-07
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		9e-07
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		1e-06
4hk2_A	78	U7ub25.2540 Length = 78		2e-06
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		2e-06
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		3e-06
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		3e-06
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		9e-06
2kk8_A	84	Nmr Solution Structure Of A Putative Uncharacterize		1e-05
1ndd_B	76	Structure Of Nedd8 Length = 76		1e-05
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		1e-05
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		1e-05
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		1e-05
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		1e-05
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		2e-05
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		2e-05
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		2e-05
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		2e-05
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		2e-05
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		1e-04
2bwe_S	77	The Crystal Structure Of The Complex Between The Ub		1e-04
3m63_B	101	Crystal Structure Of Ufd2 In Complex With The Ubiqu		2e-04
1wh3_A	87	Solution Structure Of C-Terminal Ubiquitin Like Dom		7e-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 = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 57/78 (73%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60
Query: 62 ENKVAENSFVVIMLTKNK 79
          E K+ E +FVV+M+TK K
Sbjct: 61 EYKIDEKNFVVVMVTKPK 78

>pdb|1P1A|A Chain A, Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Length = 85

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 57/78 (73%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct: 4  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 63
Query: 62 ENKVAENSFVVIMLTKNK 79
          E K+ E +FVV+M+TK K
Sbjct: 64 EYKIDEKNFVVVMVTKPK 81

>pdb|1OQY|A Chain A, Structure Of The Dna Repair Protein Hhr23a Length = 368

Iteration: 1
 Score = 75.5 bits (184), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 50/136 (36%), Positives = 66/136 (48%), Gaps = 37/136 (27%)
Query: 149 AASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQ 208
           AAS LV G+  E  + +I+ MG   ++R+ VV ALRA+YNNP RAVEYL +GIP   E  
Sbjct: 158 AASTLVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIPGSPE-- 212
Query: 209 PVARAPGNGQAANSXXXXXXXXXXXXXXSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFL 268
                P +G    S              S  P                + AAG   L+FL
Sbjct: 213 -----PEHGSVQES------------QVSEQP---------------ATEAAGENPLEFL 240
Query: 269 RNSPQFQVLRAMVQAN 284
           R+ PQFQ +R ++Q N
Sbjct: 241 RDQPQFQNMRQVIQQN 256

>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 = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/76 (43%), Positives = 52/76 (68%)
Query: 4  IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEEN 63
          I +KTL+  +F + ++P++TV  +K KIE  +G D +P A Q LIY GK+L DD  + + 
Sbjct: 8  ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 67
Query: 64 KVAENSFVVIMLTKNK 79
          ++ E +FVV+M+TK K
Sbjct: 68 RIDEKNFVVVMVTKTK 83

>pdb|1P98|A Chain A, High-Resolution Nmr Structure Of The Ubl-Domain Of Hhr23a Length = 78

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/74 (43%), Positives = 51/74 (68%)
Query: 4  IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEEN 63
          I +KTL+  +F + ++P++TV  +K KIE  +G D +P A Q LIY GK+L DD  + + 
Sbjct: 5  ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 64
Query: 64 KVAENSFVVIMLTK 77
          ++ E +FVV+M+TK
Sbjct: 65 RIDEKNFVVVMVTK 78

>pdb|2K25|A Chain A, Automated Nmr Structure Of The Ubb By Fapsy Length = 103

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/74 (43%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 9  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 65
Query: 62 ENKVAENSFVVIML 75
          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 = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + 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 = 57.0 bits (136), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ L++  K L+D  TL 
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQKLLFARKQLEDGRTLS 59
Query: 62 ENKVAENSFVVIML 75
          +  + + SF+ ++L
Sbjct: 60 DYNIHKESFLYLVL 73

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 59
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 60 DYNIQKESTLHLVL 73

>pdb|3LDZ|F Chain F, Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin Length = 73

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + 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 = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|2XK5|B Chain B, Crystal Structure Of K6-Linked Diubiquitin Length = 76

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPQQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 62 ENKVAENSFVVIML 75
          +  +   S + ++L
Sbjct: 61 DYNIQRESTLHLVL 74

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 27/50 (54%), Positives = 36/50 (72%), Gaps = 3/50 (6%)
Query: 153 LVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIP 202
           LV G+  E  + +I+ MG   ++R+ VV ALRA+YNNP RAVEYL +GIP
Sbjct: 2   LVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 48

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 59 DYNIQKESTLHLVL 72

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/76 (40%), Positives = 48/76 (63%), Gaps = 2/76 (2%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQG--SDVYPAAQQMLIYQGKVLKDDTT 59
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G  +   P  QQ LI+ GK L+D  T
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGRWALAIPPDQQRLIFAGKQLEDGRT 60
Query: 60 LEENKVAENSFVVIML 75
          L +  + + S + ++L
Sbjct: 61 LSDYNIQKESTLHLVL 76

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92
Query: 62  ENKVAENSFVVIML 75
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 5  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 61
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 62 DYNIQKESTLHLVL 75

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 59 DYNIQKESTLHLVL 72

>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 = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92
Query: 62  ENKVAENSFVVIML 75
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

>pdb|3U30|A Chain A, Crystal Structure Of A Linear-Specific Ubiquitin Fab Bound To Linear Ubiquitin Length = 172

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 77
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 78 DYNIQKESTLHLVL 91

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G     A QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IAADQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3V6C|B Chain B, Crystal Structure Of Usp2 In Complex With Mutated Ubiquitin Length = 91

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFV TL GT   +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 18 MQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 74
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 75 DYNIQKESTLHLVL 88

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 6  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 62
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 63 DYNIQKESTLHLVL 76

>pdb|3AI5|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein Length = 307

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 290
Query: 62  ENKVAENSFVVIML 75
           +  + + S + ++L
Sbjct: 291 DYNIQKESTLHLVL 304

>pdb|1ZGU|B Chain B, Solution Structure Of The Human Mms2-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ G+ L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGRQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + 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 = 55.5 bits (132), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ G+ L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGRQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 59
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 60 DYNIQKESTLHLVL 73

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 77  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 133
Query: 62  ENKVAENSFVVIML 75
           +  + + S + ++L
Sbjct: 134 DYNIQKESTLHLVL 147

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          ++IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++FVKTL G +  VE++P DTV ++K KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQLFVKTLTGKTLTVELEPSDTVENLKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNLQKESTIHLVL 71

>pdb|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant Of Ubiquitin Length = 88

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 48/74 (64%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++F+KTL G +F VE++P DT+ ++K KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 66
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 67 DYNIQKESTLHLVL 80

>pdb|2Y5B|B Chain B, Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde Length = 152

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          ++IFVKTL G +  +EV+P DT+ +VK KI   Q  +  P  QQ LI+ GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKI---QDKEXIPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>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 = 54.7 bits (130), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/64 (45%), Positives = 41/64 (64%), Gaps = 3/64 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKV 65
          +  +
Sbjct: 58 DYNI 61

>pdb|4HJK|A Chain A, U7ub7 Disulfide Variant Length = 77

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 30/68 (44%), Positives = 42/68 (61%), Gaps = 3/68 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVK L G +  +EV+P DT+ +VK KI+   G   YP  QQ LI+ GK L+D  TL 
Sbjct: 2  MQIFVKCLTGKTNTLEVEPSDTIENVKAKIQDKIG---YPPDQQRLIFAGKQLEDGRTLS 58
Query: 62 ENKVAENS 69
          +  + + S
Sbjct: 59 DYNIQKES 66

>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 = 54.3 bits (129), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 46/73 (63%), Gaps = 3/73 (4%)
Query: 3   KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEE 62
           +IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL +
Sbjct: 107 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSD 163
Query: 63  NKVAENSFVVIML 75
             + + S + ++L
Sbjct: 164 YNIQKESTLHLVL 176

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++F+KTL G +  +EV+P DTV + K KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQVFLKTLTGKTVTIEVEPSDTVENFKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTIHLVL 71

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/73 (41%), Positives = 46/73 (63%), Gaps = 3/73 (4%)
Query: 3  KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEE 62
          +IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL +
Sbjct: 2  QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSD 58
Query: 63 NKVAENSFVVIML 75
            + + S + ++L
Sbjct: 59 YNIQKESTLHLVL 71

>pdb|2O6V|B Chain B, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ G  L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGXQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 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 = 53.9 bits (128), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          ++IFVKTL G +  +EV+P DT+ +VK KI   Q  +  P  QQ LI+ GK L+D  TL 
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKI---QDKEQIPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3MTN|B Chain B, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 85

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/68 (44%), Positives = 43/68 (63%), Gaps = 3/68 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 62 ENKVAENS 69
          +  + + S
Sbjct: 61 DYNIQKWS 68

>pdb|3V6E|B Chain B, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin Length = 91

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFV TL G    +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 18 MQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 74
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 75 DYNIQKESTLHLVL 88

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + 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 = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/68 (42%), Positives = 42/68 (61%), Gaps = 3/68 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK  +D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQXEDGRTLS 57
Query: 62 ENKVAENS 69
          +  + + S
Sbjct: 58 DYNIQKES 65

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 21 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 77
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 78 DYNIQKESTLHLVL 91

>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 = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + 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 = 52.8 bits (125), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|4HCN|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Ubiquitin Length = 98

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 79
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 80 DYNIQKESTLHLVL 93

>pdb|1ZW7|A Chain A, Elimination Of The C-Cap In Ubiquitin Structure, Dynamics And Thermodynamic Consequences Length = 82

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+   G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGATITLEVESSDTIDNVKSKIQAAPG---IPPDQQELIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/68 (42%), Positives = 42/68 (61%), Gaps = 3/68 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENS 69
          +  + + S
Sbjct: 58 DYNIQKES 65

>pdb|4A18|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1 Length = 129

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  ++V+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLDVEASDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>pdb|3N3K|B Chain B, The Catalytic Domain Of Usp8 In Complex With A Usp8 Specific Inhibitor Length = 85

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/68 (42%), Positives = 42/68 (61%), Gaps = 3/68 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+I VKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60
Query: 62 ENKVAENS 69
          +  +  +S
Sbjct: 61 DYNIHNHS 68

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/79 (39%), Positives = 47/79 (59%), Gaps = 5/79 (6%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQ-----GSDVYPAAQQMLIYQGKVLKD 56
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +     G    P  QQ LI+ GK L+D
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGGGGGGGGGIPPDQQRLIFAGKQLED 60
Query: 57 DTTLEENKVAENSFVVIML 75
            TL +  + + S + ++L
Sbjct: 61 GRTLSDYNIQKESTLHLVL 79

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P D++  +K KI+  +G    P  QQ LI+ GK L++  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEG---IPPDQQRLIFAGKQLEEGKTLS 60
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 61 DYNIQKESTLHLVL 74

>pdb|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>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 = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 42/68 (61%), Gaps = 3/68 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57
Query: 62 ENKVAENS 69
          +  + + S
Sbjct: 58 DYNIQKES 65

>pdb|3ZF7|SS Chain s, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 128

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L++  TL 
Sbjct: 1  MQIFVKTLTGKTIALEVEASDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEEGRTLA 57
Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P DT+  +K ++E  +G    P  QQ LIY GK L DD T +
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEG---IPPVQQRLIYAGKQLADDKTAK 57
Query: 62 ENKVAENSFVVIML 75
          +  +   S + ++L
Sbjct: 58 DYNIEGGSVLHLVL 71

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 3/68 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVK   G ++ +EV+P DT+ +VK KI+   G    P  QQ LI+ GK L+D  TL 
Sbjct: 3  MQIFVKFRTGKTYTLEVEPSDTIENVKAKIQDKLG---IPPDQQWLIFAGKRLEDGRTLS 59
Query: 62 ENKVAENS 69
          +  + + S
Sbjct: 60 DYNIQKES 67

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/81 (38%), Positives = 47/81 (58%), Gaps = 10/81 (12%)
Query: 2  MKIFVKTLK-------GTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVL 54
          M+IFVKTL        G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L
Sbjct: 1  MQIFVKTLTQVRELVGGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQL 57
Query: 55 KDDTTLEENKVAENSFVVIML 75
          +D  TL +  + + S + ++L
Sbjct: 58 EDGRTLSDYNIQKESTLHLVL 78

>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 = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFV+TL G +  +EV+  DT+ +V+ +I+  +G    P  QQ LI+ G+ L+D  TL 
Sbjct: 8  MQIFVRTLTGRTITLEVESSDTIDNVRARIQDREG---IPPDQQRLIFAGRQLEDGRTLA 64
Query: 62 ENKVAENSFVVIML 75
          +  +   S + ++L
Sbjct: 65 DYNIQRESTLHLVL 78

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 3/73 (4%)
Query: 3  KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEE 62
          +IF KTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL +
Sbjct: 11 QIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIWAGKQLEDGRTLSD 67
Query: 63 NKVAENSFVVIML 75
            +   S + ++L
Sbjct: 68 YNIQRESTLHLVL 80

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 36/54 (66%), Gaps = 3/54 (5%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLK 55
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLE 53

>pdb|2KK8|A Chain A, Nmr Solution Structure Of A Putative Uncharacterized Protein Obtained From Arabidopsis Thaliana: Northeast Structural Genomics Consortium Target Ar3449a Length = 84

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKV-LKDDTTL 60
          MK  V+ L G+SF++EV   DT+  VK KIE  Q     P ++Q LI  G V L++D T+
Sbjct: 11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQH---IPVSKQTLIVDGIVILREDLTV 67
Query: 61 EENKVAENS 69
          E+ ++   S
Sbjct: 68 EQCQIVPTS 76

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57
Query: 62 ENKVAENSFVVIML 75
          + 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 = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 7  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 63
Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 64 DYKILGGSVLHLVL 77

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 2  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 58
Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 59 DYKILGGSVLHLVL 72

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 3  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 59
Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 60 DYKILGGSVLHLVL 73

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57
Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 58 DYKILGGSVLHLVL 71

>pdb|2JVC|A Chain A, Nmr Solution Structure Of Ubiquitin Like Protein Length = 82

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  ++V   DTV  VK KI   +G    P  QQ LI+ GK L+D   + 
Sbjct: 6  MQIFVKTLTGKTITIDVDHADTVGAVKAKIYDKEG---IPPDQQRLIFGGKQLEDSNAMS 62
Query: 62 ENKVAENSFVVIML 75
          +  V + S + ++L
Sbjct: 63 DYNVQKESTLHLVL 76

>pdb|2GBJ|A Chain A, Crystal Structure Of The 9-10 8 Glycine Insertion Mutant Of Ubiquitin. Length = 84

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/82 (37%), Positives = 47/82 (57%), Gaps = 11/82 (13%)
Query: 2  MKIFVKTLKGT--------SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKV 53
          M+IFVKTL G         +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK 
Sbjct: 1  MQIFVKTLTGGGGGGGGGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQ 57
Query: 54 LKDDTTLEENKVAENSFVVIML 75
          L+D  TL +  + + S + ++L
Sbjct: 58 LEDGRTLSDYNIQKESTLHLVL 79

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 69
Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 70 DYKILGGSVLHLVL 83

>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 = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 6  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 62
Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 63 DYKILGGSVLHLVL 76

>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 = 46.2 bits (108), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 69
Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 70 DYKILGGSVLHLVL 83

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 4  IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEEN 63
          I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK   D+ T  + 
Sbjct: 8  IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQXNDEKTAADY 64
Query: 64 KVAENSFVVIML 75
          K+   S + ++L
Sbjct: 65 KIXGGSVLHLVL 76

>pdb|2BWE|S Chain S, The Crystal Structure Of The Complex Between The Uba And Ubl Domains Of Dsk2 Length = 77

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/58 (41%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 14 FDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFV 71
          ++V V PE TV   K  I    G    P A Q LIY GK+LKDD T+E   + +   V
Sbjct: 16 WEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTVESYHIQDGHSV 70

>pdb|3M63|B Chain B, Crystal Structure Of Ufd2 In Complex With The Ubiquitin-Like (Ubl) Domain Of Dsk2 Length = 101

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 14 FDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVI 73
          ++V V PE TV   K  I    G    P A Q LIY GK+LKDD T+E   + +   V +
Sbjct: 40 WEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHL 96
Query: 74 M 74
          +
Sbjct: 97 V 97

>pdb|1WH3|A Chain A, Solution Structure Of C-Terminal Ubiquitin Like Domain Of Human 2'-5'-Oligoadenylate Synthetase-Like Protain (P59 Oasl) Length = 87

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++FVK   G S+   + P   +  +K +IE  QG    P  QQ L +QG+VL+D   L 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLG 64
Query: 62 ENKVAENSFVVIMLTKNKRPT 82
             + ++  +++   K   P+
Sbjct: 65 IYGIQDSDTLILSKKKGSGPS 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	300
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	1e-51
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	3e-40
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	3e-39
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	5e-37
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	3e-34
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	8e-29
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	1e-28
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	6e-28
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	5e-25
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	8e-25
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	3e-24
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	3e-24
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	3e-24
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	3e-24
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	9e-24
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	1e-23
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	1e-23
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	2e-23
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	2e-23
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	3e-23
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	8e-23
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	1e-22
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	1e-22
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	2e-22
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	5e-22
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	9e-22
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	1e-21
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	2e-21
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	6e-21
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	2e-20
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	9e-20
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	1e-19
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	2e-19
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	4e-19
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	2e-18
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	7e-18
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	1e-17
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	1e-17
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	2e-17
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	5e-17
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	5e-17
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	2e-10
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	1e-16
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	4e-16
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	1e-09
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	1e-15
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	5e-12
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	9e-14
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	2e-12
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	4e-12
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	6e-12
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	7e-12
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	2e-11
1we6_A	111	Splicing factor, putative; structural genomics, ub	8e-11
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	2e-10
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	9e-10
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	7e-09
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	1e-08
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	2e-07
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	2e-07
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	3e-07
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	4e-07
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	4e-07
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	4e-07
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	5e-07
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	1e-06
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	1e-06
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	1e-06
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	3e-06
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	5e-06
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	2e-05
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	2e-05
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	6e-05
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	2e-04
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	2e-04
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	2e-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 =  173 bits (438), Expect = 1e-51
 Identities = 99/291 (34%), Positives = 147/291 (50%), Gaps = 40/291 (13%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           + I +KTL+  +F + ++P++TV  +K KIE  +G D +P A Q LIY GK+L DD  + 
Sbjct: 8   VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 67

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPISTEP 121
           + ++ E +FVV+M+TK K   G  +    +PT AP+SS   P A  +           + 
Sbjct: 68  DYRIDEKNFVVVMVTKTKAGQGTSAPPEASPTAAPESSTSFPPAPTSGMSHPPPAAREDK 127

Query: 122 TPAPTPAP---ASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDT 178
           +P+   AP     +   SV ++  SG    AAS LV G+  E  + +I+ MG   ++R+ 
Sbjct: 128 SPSEESAPTTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETMLTEIMSMG---YERER 184

Query: 179 VVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPAPVTSS 238
           VV ALRA+YNNP RAVEYL +GIP   E +                Q  Q ++       
Sbjct: 185 VVAALRASYNNPHRAVEYLLTGIPGSPEPEH------------GSVQESQVSEQP----- 227

Query: 239 GPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFP 289
                             + AAG   L+FLR+ PQFQ +R ++Q NP L P
Sbjct: 228 -----------------ATEAAGENPLEFLRDQPQFQNMRQVIQQNPALLP 261

>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 =  134 bits (340), Expect = 3e-40
 Identities = 33/79 (41%), Positives = 53/79 (67%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           + I +KTL+  +F + ++P++TV  +K KIE  +G D +P A Q LIY GK+L DD  +
Sbjct: 5  AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPI 64

Query: 61 EENKVAENSFVVIMLTKNK 79
           + ++ E +FVV+M+TK K
Sbjct: 65 RDYRIDEKNFVVVMVTKTK 83

>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 =  132 bits (333), Expect = 3e-39
 Identities = 40/98 (40%), Positives = 61/98 (62%), Gaps = 6/98 (6%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 62 ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSS 99
          E K+ E +FVV+M+TK K  +      + AP       
Sbjct: 61 EYKIDEKNFVVVMVTKPKAVS------TPAPATLEHHH 92

>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 =  126 bits (319), Expect = 5e-37
 Identities = 24/100 (24%), Positives = 47/100 (47%), Gaps = 3/100 (3%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           M+ +  K  K     ++++P +T+ + K K+           +Q  LIY GKVL+D  T+
Sbjct: 1   MVSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSIS---CEESQIKLIYSGKVLQDSKTV 57

Query: 61  EENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSA 100
            E  + +   VV M+++ K    + + R    +   + +A
Sbjct: 58  SECGLKDGDQVVFMVSQKKSTKTKVTERDPNSSSVDKLAA 97

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

 Score =  118 bits (299), Expect = 3e-34
 Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 4/76 (5%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKV-LKDDTTL 60
          MK  V+ L G+SF++EV   DT+  VK KIE  Q     P ++Q LI  G V L++D T+
Sbjct: 11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQH---IPVSKQTLIVDGIVILREDLTV 67

Query: 61 EENKVAENSFVVIMLT 76
          E+ ++   S + + ++
Sbjct: 68 EQCQIVPTSDIQLEVS 83

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

 Score =  105 bits (263), Expect = 8e-29
 Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDT-T 59
           + + VK      F VEV   +TV  +K KI  V+     P  +  L Y G  L DD   
Sbjct: 15 KIHVTVKFPSKQ-FTVEVDRTETVSSLKDKIHIVEN---TPIKRMQLYYSGIELADDYRN 70

Query: 60 LEENKVAENSFVVIMLTKNKRP 81
          L E  + E S +V+ L    R 
Sbjct: 71 LNEYGITEFSEIVVFLKSINRA 92

>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 =  104 bits (261), Expect = 1e-28
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57

Query: 62 ENKVAENSFVVIML 75
          + 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 =  102 bits (257), Expect = 6e-28
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 57

Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 58 DYKILGGSVLHLVL 71

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

 Score = 94.7 bits (236), Expect = 5e-25
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+I VKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60

Query: 62 ENKVAENSFVVIML 75
          +  +  +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 = 96.4 bits (240), Expect = 8e-25
 Identities = 6/74 (8%), Positives = 15/74 (20%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M      ++       V+    V       E VQ         ++         +     
Sbjct: 1  MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQ---AQTEIKLFNKWSFEEVEVKDAS 57

Query: 62 ENKVAENSFVVIML 75
               +    + + 
Sbjct: 58 LVDYVQVRQPIFVA 71

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

 Score = 94.4 bits (234), Expect = 3e-24
 Identities = 29/74 (39%), Positives = 45/74 (60%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G       QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPD---QQRLIFAGKQLEDGRTLS 57

Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 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 = 92.4 bits (230), Expect = 3e-24
 Identities = 31/74 (41%), Positives = 46/74 (62%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 62 ENKVAENSFVVIML 75
          +  +   S + ++L
Sbjct: 58 DYNIQRESTLHLVL 71

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

 Score = 92.8 bits (231), Expect = 3e-24
 Identities = 28/74 (37%), Positives = 48/74 (64%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++F+KTL G +F VE++P DT+ ++K KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 66

Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 67 DYNIQKESTLHLVL 80

>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 = 92.8 bits (231), Expect = 3e-24
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P D V  +K ++E  +G    P  QQ LIY GK + D+ T  
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAA 69

Query: 62 ENKVAENSFVVIML 75
          + K+   S + ++L
Sbjct: 70 DYKILGGSVLHLVL 83

>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 = 91.1 bits (227), Expect = 9e-24
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 2  MKIFVKTLKGTS-FDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          M + +    G   ++V V PE TV   K  I    G    P A Q LIY GK+LKDD T+
Sbjct: 3  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTV 59

Query: 61 EENKVAENSFVVIMLTK 77
          E   + +   V ++ ++
Sbjct: 60 ESYHIQDGHSVHLVKSQ 76

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A Length = 76

 Score = 90.8 bits (226), Expect = 1e-23
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M +FV+      F VEV  + ++  +K  +   QG    PA Q  +I+ GK L +  T++
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQG---VPADQLRVIFAGKELPNHLTVQ 57

Query: 62 ENKVAENSFVVIML 75
             + + S V I+ 
Sbjct: 58 NCDLEQQSIVHIVQ 71

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

 Score = 90.8 bits (226), Expect = 1e-23
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++ VK L+G    ++V  ++ V  +K  +         P  QQ L+++GK L D   L 
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLN---VPVRQQRLLFKGKALADGKRLS 64

Query: 62 ENKVAENSFVVIML 75
          +  +  NS + +++
Sbjct: 65 DYSIGPNSKLNLVV 78

>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 = 90.9 bits (226), Expect = 2e-23
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 60

Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 61 DYNIQKWSTLFLLL 74

>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 = 90.8 bits (226), Expect = 2e-23
 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 8/92 (8%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++ VKTL   +    V  +  V + K  I         P+ +Q LIYQG+VL+DD  L+
Sbjct: 6  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQ 62

Query: 62 ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPT 93
          E  V      ++      R   +    S A +
Sbjct: 63 EYNVGGKVIHLVE-----RAPPQTHLPSGASS 89

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

 Score = 90.6 bits (225), Expect = 3e-23
 Identities = 35/97 (36%), Positives = 54/97 (55%), Gaps = 7/97 (7%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 62 ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQS 98
          +  + + S + ++L    R  G     S++  K   +
Sbjct: 58 DYNIQKESTLHLVL----RLRGGRDPNSSSVDKLAAA 90

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score = 89.9 bits (223), Expect = 8e-23
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 92

Query: 62  ENKVAENSFVVIML 75
           +  + + S + ++L
Sbjct: 93  DYNIQKESTLHLVL 106

>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 = 89.3 bits (222), Expect = 1e-22
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           ++K+ VKT K    D  V    T+  +K +I            Q +LI+ GK+LKD  +L
Sbjct: 22  LIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSL 77

Query: 61  EENKVAENSFVVIMLTKNKRPTG 83
            +  V +   V +++ +  R  G
Sbjct: 78  AQCGVRDGLTVHLVIKRQHRAMG 100

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 88.5 bits (220), Expect = 1e-22
 Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++ VKTL   +    V  +  V + K  I         P+ +Q LIYQG+VL+DD  L+
Sbjct: 18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQ 74

Query: 62 ENKVAEN 68
          E  V   
Sbjct: 75 EYNVGGK 81

>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 = 88.6 bits (220), Expect = 2e-22
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           ++ ++   G    + V+  DTVF +K ++   +G        Q   + G+ L D    E
Sbjct: 24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG---VEPGSQRWFFSGRPLTDKMKFE 80

Query: 62 ENKVAENSFVVIMLTK 77
          E K+ ++  V +++++
Sbjct: 81 ELKIPKDYVVQVIVSQ 96

>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 = 87.5 bits (217), Expect = 5e-22
 Identities = 34/99 (34%), Positives = 52/99 (52%), Gaps = 7/99 (7%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 2   MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 58

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSA 100
           +  + + S + ++L    R  G    R     +     +
Sbjct: 59  DYNIQKESTLHLVL----RLRGYADLREDPDRQDHHPGS 93

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score = 86.6 bits (215), Expect = 9e-22
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 2   MKIFVKTLKGTS-FDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           M + +    G   ++V V PE TV   K  I    G    P A Q LIY GK+LKDD T+
Sbjct: 27  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTV 83

Query: 61  EENKVAENSFVVIMLTK 77
           E   + +   V ++ ++
Sbjct: 84  ESYHIQDGHSVHLVKSQ 100

>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 = 85.9 bits (213), Expect = 1e-21
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++FVK   G S+   + P   +  +K +IE  QG    P  QQ L +QG+VL+D   L 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLG 64

Query: 62 ENKVAENSFVVIML 75
             + ++  +++  
Sbjct: 65 IYGIQDSDTLILSK 78

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score = 86.4 bits (214), Expect = 2e-21
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           +IF KTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIWAGKQLEDGRTLS 66

Query: 62 ENKVAENSFVVIML 75
          +  +   S + ++L
Sbjct: 67 DYNIQRESTLHLVL 80

>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} SCOP: a.5.2.1 Length = 49

 Score = 82.9 bits (205), Expect = 6e-21
 Identities = 27/50 (54%), Positives = 36/50 (72%), Gaps = 3/50 (6%)

Query: 153 LVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIP 202
           LV G+  E  + +I+ MG   ++R+ VV ALRA+YNNP RAVEYL +GIP
Sbjct: 2   LVTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIP 48

>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 = 83.2 bits (206), Expect = 2e-20
 Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 4/93 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           ++K+ VKT K    D  V    T+  +K +I            Q +LI+ GK+LKD  +L
Sbjct: 17  LIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSL 72

Query: 61  EENKVAENSFVVIMLTKNKRPTGEGSTRSTAPT 93
            +  V +   V +++ +  R  G     S   +
Sbjct: 73  AQCGVRDGLTVHLVIKRQHRAMGNECPASGPSS 105

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

 Score = 80.9 bits (200), Expect = 9e-20
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          + I V+  KG S   EV+   TV  +K ++    G +        L ++GK L+D   L 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPLG 61

Query: 62 ENKVAENSFVVIML 75
          E  +   S V + L
Sbjct: 62 EYGLKPLSTVFMNL 75

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens} Length = 88

 Score = 80.9 bits (200), Expect = 1e-19
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          + I V+  KG S   EV+   TV  +K ++    G +        L ++GK L+D   L 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPLG 61

Query: 62 ENKVAENSFVVIML 75
          E  +   S V + L
Sbjct: 62 EYGLKPLSTVFMNL 75

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

 Score = 80.5 bits (199), Expect = 2e-19
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           +MK+ VKT K    +  V    +V   K +I     S      Q +LI+ GK+LKD  TL
Sbjct: 25  IMKVTVKTPKEK-EEFAVPENSSVQQFKEEISKRFKS---HTDQLVLIFAGKILKDQDTL 80

Query: 61  EENKVAENSFVVIMLTKNKRP 81
            ++ + +   V +++    RP
Sbjct: 81  SQHGIHDGLTVHLVIKTQNRP 101

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

 Score = 82.1 bits (202), Expect = 4e-19
 Identities = 12/62 (19%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++ VKTL+G +    ++   +V D+K +I        +      L+  G +  +   + 
Sbjct: 1  MQVQVKTLEGETKIYTLEQGTSVLDLKSQI---SQDMGFEIDMMTLVNNGFIAPNTELVT 57

Query: 62 EN 63
          ++
Sbjct: 58 DD 59

>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 = 77.4 bits (191), Expect = 2e-18
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 2  MKIFVKTLKG--TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
          M I V+T+ G  T     +     V +++ KI+ +          Q L Y+GK ++D  T
Sbjct: 3  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFH---VEPGLQRLFYRGKQMEDGHT 59

Query: 60 LEENKVAENSFVVIML 75
          L + +V  N  + +++
Sbjct: 60 LFDYEVRLNDTIQLLV 75

>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 = 76.3 bits (188), Expect = 7e-18
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          ++++ VKT +    +  +     V   K +I          A + +LI+ GK+L+D   L
Sbjct: 17 IIRVSVKTPQDC-HEFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDIL 72

Query: 61 EENKVAENSFVVIMLTKNKRPT 82
           +  + + S V +++  +  P+
Sbjct: 73 SQRGILDGSTVHVVVRSHSGPS 94

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score = 75.6 bits (186), Expect = 1e-17
 Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++FV+  +  +F+V    ++TV  +K  + +++G        Q+++  G  L+D+ TL 
Sbjct: 20 MQLFVRAQELHTFEVT--GQETVAQIKAHVASLEG---IAPEDQVVLLAGAPLEDEATLG 74

Query: 62 ENKVAENS 69
          +  V   +
Sbjct: 75 QCGVEALT 82

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

 Score = 76.4 bits (188), Expect = 1e-17
 Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 5/92 (5%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           +K+ VKT K    +  V    +V   K  I     S      Q +LI+ GK+LKD  TL 
Sbjct: 33  IKVTVKTPKE-KEEFAVPENSSVQQFKEAISKRFKS---QTDQLVLIFAGKILKDQDTLI 88

Query: 62  ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPT 93
           ++ +  +   V ++ K    +      + A  
Sbjct: 89  QHGI-HDGLTVHLVIKRDPNSSSVDKYAAALE 119

>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 = 74.6 bits (184), Expect = 2e-17
 Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 4/77 (5%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           +K+ VK   G S  + V P+ TV D+K +++ +          Q LI++GKVL + +TL
Sbjct: 12 TIKLTVK-FGGKSIPLSVSPDCTVKDLKSQLQPITN---VLPRGQKLIFKGKVLVETSTL 67

Query: 61 EENKVAENSFVVIMLTK 77
          +++ V   + +++M ++
Sbjct: 68 KQSDVGSGAKLMLMASQ 84

>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 = 73.6 bits (181), Expect = 5e-17
 Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 2  MKIFVKTLKG--TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
          M I V+T+ G  T    +V  + T+ +++ ++  +          Q L Y+GK L++  T
Sbjct: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD---VRPECQRLFYRGKQLENGYT 64

Query: 60 LEENKVAENSFVVIML 75
          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 = 75.4 bits (185), Expect = 5e-17
 Identities = 30/68 (44%), Positives = 43/68 (63%), Gaps = 3/68 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 62 ENKVAENS 69
          +  + + 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 = 57.3 bits (138), Expect = 2e-10
 Identities = 31/75 (41%), Positives = 47/75 (62%), Gaps = 3/75 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
            M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL
Sbjct: 76  GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTL 132

Query: 61  EENKVAENSFVVIML 75
            +  + + S + ++L
Sbjct: 133 SDYNIQKESTLHLVL 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 = 75.4 bits (185), Expect = 1e-16
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+  DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 62 ENKVAENSFVVIML 75
          +  + + S + ++L
Sbjct: 58 DYNIQKESTLHLVL 71

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 73.6 bits (180), Expect = 4e-16
 Identities = 30/68 (44%), Positives = 43/68 (63%), Gaps = 3/68 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 77

Query: 62 ENKVAENS 69
          +  + + S
Sbjct: 78 DYNIQKES 85

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 55.4 bits (133), Expect = 1e-09
 Identities = 31/75 (41%), Positives = 47/75 (62%), Gaps = 3/75 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
            M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL
Sbjct: 96  GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTL 152

Query: 61  EENKVAENSFVVIML 75
            +  + + S + ++L
Sbjct: 153 SDYNIQKESTLHLVL 167

>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 = 71.9 bits (176), Expect = 1e-15
 Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ--GKVLKDDTT 59
            + VK L G  F V +    +V ++K +I    G     A QQ L     G  L+D   
Sbjct: 3  WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG---VHAFQQRLAVHPSGVALQDRVP 59

Query: 60 LEENKVAENSFVVIM 74
          L    +   S V+++
Sbjct: 60 LASQGLGPGSTVLLV 74

>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 = 61.9 bits (150), Expect = 5e-12
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
            + I V+  KG S   EV+   TV  +K ++    G +        L ++GK L+D   L
Sbjct: 81  PLSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPL 137

Query: 61  EENKVAENSFVVIML 75
            E  +   S V + L
Sbjct: 138 GEYGLKPLSTVFMNL 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 = 65.6 bits (160), Expect = 9e-14
 Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           M       L G      +   D V  +K+KI    G    PA +Q L Y+G  +KD  +L
Sbjct: 35  MQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATG---MPAGKQKLQYEGIFIKDSNSL 91

Query: 61  EENKVAENSFVVIML 75
               +A  + + + L
Sbjct: 92  AYYNMASGAVIHLAL 106

>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 = 61.5 bits (149), Expect = 2e-12
 Identities = 21/97 (21%), Positives = 42/97 (43%), Gaps = 8/97 (8%)

Query: 2   MKIFVKTLK----GTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDD 57
           M I V  ++      +F ++V P+  + + ++  E   G    PA +  ++Y  ++L DD
Sbjct: 8   MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG---VPAEEAQIVYMEQLLTDD 64

Query: 58  T-TLEENKVAENSFVVIMLTKNKRPTGEGSTRSTAPT 93
             +L    + +   VV++   N      G T S   +
Sbjct: 65  HCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTPSGPSS 101

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 62.7 bits (152), Expect = 4e-12
 Identities = 30/75 (40%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
             +IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL
Sbjct: 105 GGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTL 161

Query: 61  EENKVAENSFVVIML 75
            +  + + S + ++L
Sbjct: 162 SDYNIQKESTLHLVL 176

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 60.0 bits (145), Expect = 6e-12
 Identities = 26/93 (27%), Positives = 40/93 (43%), Gaps = 8/93 (8%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDT-TL 60
          + + +K L  T      +PEDTV  +K K    Q S      Q  LIYQG++L+D   TL
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQES------QMKLIYQGRLLQDPARTL 61

Query: 61 EENKVAENSFVVIMLTKNKRPTGEGSTRSTAPT 93
              +  N  +    +        G + S+ P+
Sbjct: 62 SSLNITNNCVIHCHRSP-PGAAVSGPSASSGPS 93

>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 = 59.6 bits (144), Expect = 7e-12
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 3/83 (3%)

Query: 2  MKIFVKT--LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
          + + VK+   +    ++      +V  +K  +  V          Q LIY GK+L D   
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPER-PRPEDQRLIYSGKLLLDHQC 66

Query: 60 LEENKVAENSFVVIMLTKNKRPT 82
          L +    +    V+ L  N +  
Sbjct: 67 LRDLLPKQEKRHVLHLVCNVKSG 89

>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 = 58.6 bits (142), Expect = 2e-11
 Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 5/82 (6%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          ++ + +     T  DV+V  + T  ++K KI ++ G    P A Q ++Y+G  + +D TL
Sbjct: 17 LVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMYKGL-VPEDKTL 71

Query: 61 EENKVAENSFVVIMLTKNKRPT 82
           E KV   + ++++ +    P+
Sbjct: 72 REIKVTSGAKIMVVGSTISGPS 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 = 57.5 bits (139), Expect = 8e-11
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 2   MKIFVKT-LKGTSFDVEVKPE-DTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
           +++       G   ++ V+   + V  +K KI         PA +Q L  +   LKD+ +
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMS 86

Query: 60  LEENKVAENSFVVIML 75
           L    V     + + L
Sbjct: 87  LAHYNVGAGEILTLSL 102

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

 Score = 55.7 bits (134), Expect = 2e-10
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 2  MKIFVKT--LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
          + + +K    K +   +      TV  +K  +  V  S       Q L+Y G++L D   
Sbjct: 24 VTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKP-LTKDQRLVYSGRLLPDHLQ 82

Query: 60 LEENKVAENSFVVIML 75
          L++    ++ + ++ L
Sbjct: 83 LKDILRKQDEYHMVHL 98

>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 = 53.7 bits (129), Expect = 9e-10
 Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
            + VK  K     VE+  ++     K ++  + G      A+Q ++ +G  LKDD    
Sbjct: 8  YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTG---VQPARQKVMVKGGTLKDD-DWG 63

Query: 62 ENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKA 95
            K+     V++M + +  P  E S +++ P+  
Sbjct: 64 NIKMKNGMTVLMMGSADALPE-EPSAKTSGPSSG 96

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

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 19/104 (18%), Positives = 37/104 (35%), Gaps = 6/104 (5%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP-----AAQQMLIYQGKVLK 55
           M+ + +  + G + +    P D+  D+   +      D             LIYQG+ L 
Sbjct: 17  MINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLH 76

Query: 56  DDTTLEENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSS 99
            + TL   K+      V+ L   +    E +++     +    S
Sbjct: 77  GNVTLGALKLPFGKTTVMHLVA-RETLPEPNSQGQRNREKTGES 119

>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 = 51.0 bits (121), Expect = 2e-07
 Identities = 30/69 (43%), Positives = 43/69 (62%), Gaps = 3/69 (4%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
            M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL
Sbjct: 233 SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTL 289

Query: 61  EENKVAENS 69
            +  + + S
Sbjct: 290 SDYNIQKES 298

>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 = 47.3 bits (112), Expect = 2e-07
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          M+++ V    G    V+   ED+V D K  +    G+      + +L   G VLKD  +L
Sbjct: 21 MIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGT---QPNKIVLQKGGSVLKDHISL 77

Query: 61 EENKV 65
          E+ +V
Sbjct: 78 EDYEV 82

>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 = 47.1 bits (111), Expect = 3e-07
 Identities = 18/75 (24%), Positives = 27/75 (36%)

Query: 8   TLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAE 67
            L  T          ++  +K  I       V       LIY G+ LKDD TL+   +  
Sbjct: 31  QLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQP 90

Query: 68  NSFVVIMLTKNKRPT 82
            S V ++      P+
Sbjct: 91  GSTVHVLRKSWSGPS 105

>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 = 45.6 bits (108), Expect = 4e-07
 Identities = 15/28 (53%), Positives = 19/28 (67%)

Query: 262 AGSLDFLRNSPQFQVLRAMVQANPQLFP 289
              L+FLRN PQFQ +R ++Q NP L P
Sbjct: 1   GHPLEFLRNQPQFQQMRQIIQQNPSLLP 28

>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 = 45.6 bits (108), Expect = 4e-07
 Identities = 15/29 (51%), Positives = 19/29 (65%)

Query: 261 GAGSLDFLRNSPQFQVLRAMVQANPQLFP 289
               L+FLRN PQFQ +R ++Q NP L P
Sbjct: 2   SHMPLEFLRNQPQFQQMRQIIQQNPSLLP 30

>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 = 45.5 bits (108), Expect = 4e-07
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 4/58 (6%)

Query: 160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNG 217
           E  +  I+ MG   + RD  ++ALRA  N+ ERAV++++S   +  + +     P +G
Sbjct: 10  EDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSH-IDDLDAEAAMSGPSSG 63

>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 = 46.2 bits (109), Expect = 5e-07
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          M+++      G    V+   +DT+ D+K  I    G+      + +L     + KD  +L
Sbjct: 28 MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGT---RWNKIVLKKWYTIFKDHVSL 84

Query: 61 EENKV 65
           + ++
Sbjct: 85 GDYEI 89

>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 Length = 105

 Score = 45.7 bits (108), Expect = 1e-06
 Identities = 20/98 (20%), Positives = 32/98 (32%), Gaps = 16/98 (16%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQG------------SDVYPAAQQMLIY 49
           M + V  + G    V V    TV D+K  I+                S  Y      L  
Sbjct: 8   MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 50  QGKVLKDDT-TLEENKVAENS---FVVIMLTKNKRPTG 83
            G+ L +D   L +  +       F+  +  K+   +G
Sbjct: 68  AGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQKSGPSSG 105

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          + +    +   +  + V+P+ TV  +K  +    G   +P   Q  +   ++ +D  TL 
Sbjct: 27 VSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYG---FPPVLQQWVIGQRLARDQETLH 83

Query: 62 ENKVAENSFVV 72
           + V +N    
Sbjct: 84 SHGVRQNGDSA 94

>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 = 44.1 bits (104), Expect = 1e-06
 Identities = 8/40 (20%), Positives = 23/40 (57%), Gaps = 3/40 (7%)

Query: 160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS 199
           + ++  +L  G   +  D   +AL+A+  + E+A +++++
Sbjct: 30  QSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFN 66

>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 = 43.7 bits (103), Expect = 3e-06
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQML--IYQGKVLKDDTT 59
          + I VK          +  +DTV D+K  ++T+ G  V P  Q++L    +GK  ++D  
Sbjct: 8  LPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTG--VLPERQKLLGLKVKGKPAENDVK 65

Query: 60 LEENKVAENSFVVIMLTKNKRPT 82
          L   K+  N+ +++M T+   P+
Sbjct: 66 LGALKLKPNTKIMMMGTRESGPS 88

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster} Length = 320

 Score = 46.4 bits (109), Expect = 5e-06
 Identities = 18/130 (13%), Positives = 40/130 (30%), Gaps = 5/130 (3%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQML--IYQGKVLKDDTT 59
           + + VK   G  + V++  +DTV  ++ +I       V P  Q++L   Y+GK   D+  
Sbjct: 6   VVVIVK-WSGKEYPVDLTDQDTVEVLRHEIFRKTQ--VRPERQKLLNLKYKGKTAADNVK 62

Query: 60  LEENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATAPQTAVPIST 119
           +   ++  N  ++++ +         S                            +    
Sbjct: 63  ISALELKPNFKLMMVGSTEADIEDACSLPDNIGEVVDDFDDADEREESVAHSAVYLAKVQ 122

Query: 120 EPTPAPTPAP 129
                     
Sbjct: 123 RRVRDYKIKE 132

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1 Length = 116

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 17/81 (20%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP-----AAQQMLIYQGKVLK 55
          M+ + +  + G + +    P D+  D+   +      D             LIYQG+ L 
Sbjct: 16 MINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLH 75

Query: 56 DDTTLEENKVAENSFVVIMLT 76
           + TL   K+      V+ L 
Sbjct: 76 GNVTLGALKLPFGKTTVMHLV 96

>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 = 41.9 bits (98), Expect = 2e-05
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 2  MKIFVKTLKG-TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          M +F+   +  T+   + K   TVF++K  +E +      P  +Q L    ++L D  TL
Sbjct: 1  MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKR---PPEEQRLYKDDQLLDDGKTL 57

Query: 61 EENKVAENS 69
           E      +
Sbjct: 58 GECGFTSQT 66

>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 Length = 122

 Score = 40.7 bits (95), Expect = 6e-05
 Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 13/93 (13%)

Query: 1  MMKIFVKTLKGTSFDVEVK--PEDTVFDVKMKIETVQGSDVYPAAQQMLIY-------QG 51
          +  + + T   T F +E K     ++ D+K K+E V G+         +         +G
Sbjct: 6  VYDLEI-TTNATDFPMEKKYPAGMSLNDLKKKLELVVGT---TVDSMRIQLFDGDDQLKG 61

Query: 52 KVLKDDTTLEENKVAENSFVVIMLTKNKRPTGE 84
          ++     +L++  V +   +  +         +
Sbjct: 62 ELTDGAKSLKDLGVRDGYRIHAVDVTGGNEDFK 94

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 88

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 2/62 (3%)

Query: 6  VKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQM-LIYQGKVLKDDTTLEENK 64
           KT +   F  +V+P  T+ ++K    T      YPA Q + L  +GK LKD+  L++  
Sbjct: 18 AKTREKLCFLDKVEPHATIAEIKNLF-TKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLP 76

Query: 65 VA 66
          V 
Sbjct: 77 VG 78

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 100

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M  F    +  + DV ++   TV ++K  +E      +  +   +  ++   ++D T L+
Sbjct: 9  MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQ--IPVSKMLLKGWKTGDVEDSTVLK 66

Query: 62 ENKVAENSFVVIMLTKNKRPT 82
             + +N+ + ++      P+
Sbjct: 67 SLHLPKNNSLYVLTPDLPPPS 87

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

 Score = 39.5 bits (91), Expect = 2e-04
 Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 3/47 (6%)

Query: 164 QQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPV 210
             I  MG   + R+  ++ALRA  NN ERA+++++S    + +   V
Sbjct: 83  AIITSMG---FQRNQAIQALRATNNNLERALDWIFSHPEFEEDSDFV 126

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	300
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	100.0
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.84
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.8
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.8
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.8
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.8
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.79
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.79
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.79
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.79
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.78
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.78
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.78
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.78
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.77
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.76
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.76
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.76
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.76
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.76
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.76
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.76
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.76
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.76
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.75
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.75
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.75
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.75
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.75
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.75
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.74
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.74
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.74
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.74
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.73
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.73
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.73
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.73
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.73
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.73
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.73
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	99.73
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.72
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.72
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.71
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.71
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.71
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.71
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.54
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.69
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.69
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.69
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.69
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.68
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.67
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.67
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.67
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.67
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.67
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.66
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.66
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.66
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.66
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.66
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.66
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.66
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.65
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.65
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
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.62
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.61
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
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.55
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.55
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.53
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.49
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.49
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
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.45
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	99.45
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	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	99.4
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.4
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.39
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.37
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.37
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	99.37
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.36
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	99.36
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.35
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	99.34
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.33
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	99.31
2dna_A	67	Unnamed protein product; ubiquitin associated doma	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	99.29
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.28
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.26
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.25
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	99.23
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	99.23
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.23
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	99.22
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	99.19
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	99.19
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	99.19
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	99.16
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	99.15
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	99.12
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	99.12
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	99.11
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	99.11
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	99.06
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	99.02
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	99.02
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	99.0
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	98.95
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	98.87
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	98.86
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	98.79
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.77
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	98.75
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	98.74
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	98.72
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	98.68
2pjh_A	80	Protein NPL4, nuclear protein localization protein	98.64
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	98.61
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	98.59
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	98.51
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	98.45
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	98.43
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	98.38
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.36
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	98.3
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	98.25
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	98.19
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	98.19
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	98.08
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.07
2cos_A	54	Serine/threonine protein kinase LATS2; UBA domain,	97.99
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	97.97
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	97.95
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	97.89
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	97.81
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	97.79
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	97.77
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	97.6
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	97.54
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.53
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	97.11
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	96.85
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	96.67
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	96.66
2pwq_A	216	Ubiquitin conjugating enzyme; structural genomics	96.36
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	96.36
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	96.27
2dhy_A	67	CUE domain-containing protein 1; structural genomi	96.13
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	96.02
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	95.99
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	95.62
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	95.59
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	95.58
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	95.48
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	95.23
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	94.83
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	94.69
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	94.65
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	94.35
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	94.33
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	93.7
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	93.69
2qjl_A	99	URM1, ubiquitin-related modifier 1; ubiquitin-like	92.47
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	92.28
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	92.24
1q02_A	52	Sequestosome 1; helical bundle, protein binding; N	92.22
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	92.08
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	91.95
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	91.82
2l52_A	99	Methanosarcina acetivorans SAMP1 homolog; beta-grA	91.62
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	91.17
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	91.11
4dbg_B	162	Ring finger protein 31; ubiquitin fold, ubiquitina	91.09
1ip9_A	85	BEM1 protein; ubiquitin alpha/beta roll, signaling	90.02
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	89.82
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	89.42
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	89.4
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	88.73
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	88.3
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	88.25
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	87.55
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	86.63
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	86.25
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	85.68
3qij_A	296	Protein 4.1; cytoskeleton, structural genomics, st	85.52
2k5p_A	78	THis protein, thiamine-biosynthesis protein; NESG,	85.14
1tte_A	215	Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiq	84.81
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	84.62
2c7h_A	86	RBBP6, retinoblastoma-binding protein 6, isoform 3	84.42
2ns5_A	85	Partitioning-defective 3 homolog; cell polarity, N	83.72
1ixs_A	62	Holliday junction DNA helicase RUVA; heterodimeric	83.37
1ufz_A	83	Hypothetical protein BAB28515; HBS1-like domain, s	82.94
1p3q_Q	54	VPS9P, vacuolar protein sorting-associated protein	82.84
2hj1_A	97	Hypothetical protein; structural genomics, PSI, pr	81.48
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	81.43
1wgr_A	100	Growth factor receptor-bound protein 7; RA domain,	81.1
2k9x_A	110	Tburm1, uncharacterized protein; unknown function;	81.08
1aip_C	196	EF-TS, elongation factor TS; nucleotide exchange,	80.03

>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=7.2e-53  Score=403.66  Aligned_cols=255  Identities=36%  Similarity=0.618  Sum_probs=168.6

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||+++|++|.|+|++++||.+||++|+.+.++..+++++|||||+||+|+|+++|++|+|+++++|++|++|.+.
T Consensus         7 ~M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~~   86 (368)
T 1oqy_A            7 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKA   86 (368)
T ss_dssp             CCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCCS
T ss_pred             eEEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCCC
Confidence            58999999999999999999999999999999943211199999999999999999999999999999999777777664


Q ss_pred             CCCCCCCCC-CCCCCC--CCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCC--CCCCCCCCCCCCCCCCCCccccccccc
Q 022228           81 PTGEGSTRS-TAPTKA--PQSSAPTPAATPATAPQTAVPI--STEPTPAPT--PAPASASVSSVSATSESGVYGHAASNL  153 (300)
Q Consensus        81 ~~~~~~~~~-~~~~~~--~~~~~~~~~~~~~~~p~~~~p~--~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~s~l  153 (300)
                      .......++ .+.+.+  ..+.++.+...+  ++... +.  ...+...+.  .+|..++.. .........++.+.|+|
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~p~~~~~~-~~~~~~~~~~~~~~s~l  162 (368)
T 1oqy_A           87 GQGTSAPPEASPTAAPESSTSFPPAPTSGM--SHPPP-AAREDKSPSEESAPTTSPESVSGS-VPSSGSSGREEDAASTL  162 (368)
T ss_dssp             SSCCCCCSSCCCCCSSSCCCSCCCSSSCCC--CCCCS-SSSCCCCCSCSCCCCSSTTCSCCC-SCSCCCSCCCCCCCTTT
T ss_pred             CCCCCCCcccCCCCCccccCCCCCCCCCCC--CCCCc-cccccCCccccCCCCCCCCccccc-ccccccccccccccccc
Confidence            433111111 111100  000000000000  00000 00  000000000  011100000 01111123356678999


Q ss_pred             ccCCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCCccccCcccCCCCCCCCCCCCCCCCCCCCCC
Q 022228          154 VAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNGQAANSPTQMPQPTQPA  233 (300)
Q Consensus       154 ~~g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (300)
                      |+|+++|++|++||+||   |+|++|++|||++|||+|||||||++|||++.+....        ...   ...   . .
T Consensus       163 ~~g~~~~~~i~~l~~MG---f~~~~~~~AL~a~~nn~~~A~e~L~~gip~~~~~~~~--------~~~---~~~---~-~  224 (368)
T 1oqy_A          163 VTGSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLTGIPGSPEPEHG--------SVQ---ESQ---V-S  224 (368)
T ss_dssp             CCTTTHHHHHHHHHTTT---CCSHHHHHHHHHSCSSTTHHHHTTTTSSTTCSSCCCC--------CCC---CCC---S-S
T ss_pred             cCCcchHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCcccccccC--------Ccc---ccc---c-c
Confidence            99999999999999999   9999999999999999999999999999987442210        000   000   0 0


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCchhhhhCcHHHHHHHHHHHhCCCchHHHHhccC
Q 022228          234 PVTSSGPNANPLDLFPQGLPDVGSGAAGAGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSWGN  296 (300)
Q Consensus       234 ~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~lq~~~  296 (300)
                        .  .             . ..++ .+.++|+|||++|||++||++||+||+||++|||+-.
T Consensus       225 --~--~-------------~-~~~~-~~~~~l~~Lr~~pqf~~lR~~vq~nP~~l~~~lq~l~  268 (368)
T 1oqy_A          225 --E--Q-------------P-ATEA-AGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLG  268 (368)
T ss_dssp             --C--C-------------C-CSSC-CSCCTTHHHHHSHHHHHHHHSTTTCTTHHHHHHTTTT
T ss_pred             --c--c-------------c-Cccc-cccchHHHHhcChHHHHHHHHHHhChHHHHHHHHHHH
Confidence              0  0             0 0011 2567899999999999999999999999999999743

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

Probab=99.84  E-value=3.8e-21  Score=153.47  Aligned_cols=78  Identities=28%  Similarity=0.495  Sum_probs=70.9

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      ||+|+||+++|++|.|+|++++||.+||++|+.+.|   +++++|||+|+||+|+|+++|++|||++|++|+|++++++.
T Consensus         1 mm~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~~~   77 (106)
T 3m62_B            1 MVSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSIS---CEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQKKS   77 (106)
T ss_dssp             --CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTT---SCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC---
T ss_pred             CEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCCCC
Confidence            899999999999999999999999999999999999   99999999999999999999999999999999999997664


Q ss_pred             C
Q 022228           81 P   81 (300)
Q Consensus        81 ~   81 (300)
                      .
T Consensus        78 ~   78 (106)
T 3m62_B           78 T   78 (106)
T ss_dssp             -
T ss_pred             C
Confidence            4

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A

Probab=99.80  E-value=1.3e-19  Score=139.49  Aligned_cols=76  Identities=29%  Similarity=0.427  Sum_probs=71.8

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||+++|++|.|+|++++||.+||++|+.+.+   +++++|||+|+||.|+|+++|++|+| +|++|||+++.+..
T Consensus         5 ~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---ip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~~~   80 (90)
T 4dwf_A            5 SLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAPPQ   80 (90)
T ss_dssp             EEEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCCC-
T ss_pred             EEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCCCC
Confidence            499999999999999999999999999999999999   99999999999999999999999999 89999999986543

>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=99.80  E-value=1.4e-19  Score=140.85  Aligned_cols=72  Identities=26%  Similarity=0.348  Sum_probs=70.1

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      ||+|+||++.|+++.|+|++++||.+||++|+++.|   +|+++|||+|+||+|+|+.+|++|+|++|++|++..
T Consensus        21 mIqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~G---ip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~~   92 (93)
T 3plu_A           21 MIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIG---TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   92 (93)
T ss_dssp             EEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEE
T ss_pred             eEEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhC---CCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEEe
Confidence            799999999999999999999999999999999999   999999999999999999999999999999999863

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

Probab=99.80  E-value=3.6e-19  Score=133.62  Aligned_cols=75  Identities=28%  Similarity=0.342  Sum_probs=72.5

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      .|+|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|||+|+|+.|+|+++|++|+|++|++|+++++.+
T Consensus         4 ~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl~   78 (79)
T 3phx_B            4 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLR   78 (79)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCB
T ss_pred             CEEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcC---CCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            399999999999999999999999999999999999   999999999999999999999999999999999999865

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=6.1e-20  Score=141.75  Aligned_cols=75  Identities=28%  Similarity=0.517  Sum_probs=70.5

Q ss_pred             CEEEEEEcCCCcEEEEEeC--CCCCHHHHHHHH-HHHhCCCCCCCCCeEEEeCCeecCCCCchhhccc-CCCcEEEEEEe
Q 022228            1 MMKIFVKTLKGTSFDVEVK--PEDTVFDVKMKI-ETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKV-AENSFVVIMLT   76 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~--~~~TV~~LK~kI-~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI-~~g~~I~v~v~   76 (300)
                      ||+|+||+++|++|.|+|+  +++||.+||++| +...|   +|+++|||||+||+|+|+.+|++|+| .+|++|+|+++
T Consensus         1 mmqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~   77 (87)
T 2lxa_A            1 MVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKA---SHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIK   77 (87)
T ss_dssp             CCEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSC---SSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEEC
T ss_pred             CEEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcC---CChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcC
Confidence            8999999999999988755  999999999999 99989   99999999999999999999999999 69999999987


Q ss_pred             cC
Q 022228           77 KN   78 (300)
Q Consensus        77 k~   78 (300)
                      +.
T Consensus        78 ~~   79 (87)
T 2lxa_A           78 PN   79 (87)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=4.3e-19  Score=134.74  Aligned_cols=76  Identities=41%  Similarity=0.711  Sum_probs=70.7

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHH---hCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETV---QGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~---~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +|+|+||+++|+.|.++|++++||.+||++|+.+   .|   +++++|||+|+|+.|+|+++|++|+|++|++|+|++++
T Consensus         5 ~m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~   81 (85)
T 2wyq_A            5 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDA---FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTK   81 (85)
T ss_dssp             CEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTT---CCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC-
T ss_pred             eEEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccC---CCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcC
Confidence            5999999999999999999999999999999998   67   99999999999999999999999999999999999987


Q ss_pred             CC
Q 022228           78 NK   79 (300)
Q Consensus        78 ~~   79 (300)
                      ++
T Consensus        82 ~~   83 (85)
T 2wyq_A           82 TK   83 (85)
T ss_dssp             --
T ss_pred             CC
Confidence            65

>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=99.79  E-value=6.3e-19  Score=137.56  Aligned_cols=77  Identities=47%  Similarity=0.765  Sum_probs=72.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHH---hCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETV---QGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~---~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+||+++|+.|.++|++++||.+||++|+..   .|   +++++|||+|+||.|+|+++|++|||++|++|+|+++++
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            799999999999999999999999999999999   67   999999999999999999999999999999999999876


Q ss_pred             CCC
Q 022228           79 KRP   81 (300)
Q Consensus        79 ~~~   81 (300)
                      +..
T Consensus        78 ~~~   80 (95)
T 1uel_A           78 KAV   80 (95)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            544

>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=3.4e-19  Score=137.23  Aligned_cols=78  Identities=33%  Similarity=0.541  Sum_probs=72.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.+   +|+++|||+|+|+.|+|+++|++|+|++|++|+|+++.+...
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            79999999999999999999999999999999999   999999999999999999999999999999999999987655


Q ss_pred             C
Q 022228           82 T   82 (300)
Q Consensus        82 ~   82 (300)
                      .
T Consensus        78 ~   78 (88)
T 4fbj_B           78 G   78 (88)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.79  E-value=8.1e-19  Score=139.61  Aligned_cols=77  Identities=29%  Similarity=0.377  Sum_probs=72.0

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||+++|+ |.|+|++++||.+||++|+.+.+   +++++|||+|+||+|+|+++|++|+|+++++|||+++++..
T Consensus        17 ~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~~   92 (106)
T 1wx7_A           17 LIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   92 (106)
T ss_dssp             EEEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHT---CCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCCCC
T ss_pred             eEEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHC---cChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCCC
Confidence            599999999886 79999999999999999999999   99999999999999999999999999999999999987654


Q ss_pred             C
Q 022228           81 P   81 (300)
Q Consensus        81 ~   81 (300)
                      .
T Consensus        93 ~   93 (106)
T 1wx7_A           93 A   93 (106)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=6.7e-19  Score=136.07  Aligned_cols=75  Identities=41%  Similarity=0.647  Sum_probs=72.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      .|+|+||+++|++|.|+|++++||.+||++|+++.|   +++++|||+|+|+.|+|+++|++|||++|++|+|+++.+
T Consensus        17 ~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           17 SMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   91 (91)
T ss_dssp             SEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCCC
T ss_pred             eEEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhC---CChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEecC
Confidence            499999999999999999999999999999999999   999999999999999999999999999999999998864

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

Probab=99.78  E-value=6.1e-19  Score=134.98  Aligned_cols=72  Identities=39%  Similarity=0.592  Sum_probs=70.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCee-cCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKV-LKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~Gki-L~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+|+||++.|++|.++|++++||.+||++|+.+.|   +|+++|||+|+||. |+|+++|++|+|++|++|+|+++
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            99999999999999999999999999999999999   99999999999999 99999999999999999999875

>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=99.78  E-value=2.8e-19  Score=141.27  Aligned_cols=72  Identities=18%  Similarity=0.257  Sum_probs=69.8

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      ||+|+||++.|+++.|+|++++||.+||++|+++.|   +++++|||||.||+|+|+.+|++|+|+++++|+|+.
T Consensus        28 mm~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~G---ip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           28 MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHC---CCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             eEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhC---CCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEe
Confidence            699999999999999999999999999999999999   999999999999999999999999999999999864

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.78  E-value=5.6e-19  Score=139.29  Aligned_cols=74  Identities=26%  Similarity=0.508  Sum_probs=69.4

Q ss_pred             EEEEEEcCCCcEEEE--EeCCCCCHHHHHHHH-HHHhCCCCCCCCCeEEEeCCeecCCCCchhhccc-CCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDV--EVKPEDTVFDVKMKI-ETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKV-AENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~i--eV~~~~TV~~LK~kI-~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI-~~g~~I~v~v~k   77 (300)
                      |+|+||+++|++|.+  +|++++||.+||++| +...|   +++++|||||+||+|+|+.+|++|+| ++|++|+||+++
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            899999999998777  566999999999999 87878   99999999999999999999999999 999999999987


Q ss_pred             C
Q 022228           78 N   78 (300)
Q Consensus        78 ~   78 (300)
                      +
T Consensus        97 p   97 (98)
T 4a20_A           97 N   97 (98)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=2e-18  Score=134.18  Aligned_cols=77  Identities=40%  Similarity=0.632  Sum_probs=73.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      |+|+||+++|++|.|+|++++||.+||++|++..+   +++++|||+|+|+.|+|+++|++|+|+++++|+|+++.+...
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   999999999999999999999999999999999999977644

>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=1.8e-18  Score=131.96  Aligned_cols=76  Identities=34%  Similarity=0.562  Sum_probs=72.8

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      .|+|+||+++|++|.|+|++++||.+||++|+.+.+   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+.
T Consensus        12 ~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           12 SMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRG   87 (88)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCCCC
T ss_pred             cEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHC---cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            499999999999999999999999999999999999   9999999999999999999999999999999999988653

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.76  E-value=1.9e-18  Score=135.62  Aligned_cols=76  Identities=39%  Similarity=0.600  Sum_probs=73.0

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||+++|++|.|+|++++||.+||++|+++.+   +|+++|||+|+||.|+|+++|++|+|++|++|+|+++.+.
T Consensus        22 ~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           22 PMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   97 (98)
T ss_dssp             CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCSC
T ss_pred             eEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhC---CChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            489999999999999999999999999999999999   9999999999999999999999999999999999998753

>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=99.76  E-value=5e-18  Score=130.15  Aligned_cols=77  Identities=22%  Similarity=0.352  Sum_probs=72.9

Q ss_pred             CEEEEEEcCCC-cEEEE-EeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            1 MMKIFVKTLKG-TSFDV-EVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         1 mM~I~VKtl~g-~~~~i-eV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      +|+|+||+++| ++|.| +|++++||.+||++|+.+.+   +++++|||+|+|+.|+|+++|++|+|+++++|+|+++.+
T Consensus         7 ~m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~g---ip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~   83 (89)
T 1wy8_A            7 GMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD---VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPD   83 (89)
T ss_dssp             CEEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSC---CCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECCC
T ss_pred             cEEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHC---cChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeCC
Confidence            59999999999 79999 59999999999999999999   999999999999999999999999999999999999876


Q ss_pred             CC
Q 022228           79 KR   80 (300)
Q Consensus        79 ~~   80 (300)
                      ..
T Consensus        84 gG   85 (89)
T 1wy8_A           84 SG   85 (89)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

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

Probab=99.76  E-value=3e-18  Score=128.59  Aligned_cols=74  Identities=26%  Similarity=0.418  Sum_probs=71.4

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +|+|+||+++|+.+.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|||++|++|+|+++.
T Consensus         7 ~m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~---i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A            7 GMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLN---VPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             SEEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTC---CCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             cEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            499999999999999999999999999999999999   99999999999999999999999999999999999875

>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=99.76  E-value=4.1e-18  Score=128.86  Aligned_cols=77  Identities=40%  Similarity=0.624  Sum_probs=73.8

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||+++|+++.|+|++++||.+||++|+++.+   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+..
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~---i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~GG   79 (85)
T 3mtn_B            3 HMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRGG   79 (85)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCCCC
T ss_pred             eEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHC---cChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECcCC
Confidence            599999999999999999999999999999999999   99999999999999999999999999999999999987653

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.76  E-value=2.3e-18  Score=137.18  Aligned_cols=78  Identities=21%  Similarity=0.422  Sum_probs=74.0

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||+++|++|.|+|++++||.+||++|+.+.|   +++++|||+|+||.|+|+++|++|+|++|++|||+++++..
T Consensus        23 ~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           23 ECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG---VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQ   99 (106)
T ss_dssp             SEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTC---CCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSSC
T ss_pred             eEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHC---cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            499999999999999999999999999999999999   99999999999999999999999999999999999987654


Q ss_pred             C
Q 022228           81 P   81 (300)
Q Consensus        81 ~   81 (300)
                      .
T Consensus       100 ~  100 (106)
T 1ttn_A          100 N  100 (106)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=3.4e-18  Score=127.83  Aligned_cols=74  Identities=26%  Similarity=0.363  Sum_probs=70.8

Q ss_pred             CEEEEEEcCCCcEE-EEE-eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            1 MMKIFVKTLKGTSF-DVE-VKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         1 mM~I~VKtl~g~~~-~ie-V~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      .|+|+||+++|+++ .++ |++++||.+||++|+.+.|   +++++|||+|+|+.|+|+++|++|+|++|++|+++++.
T Consensus         2 ~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            2 SMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFH---VEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   77 (78)
T ss_dssp             CEEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             cEEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHC---cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeC
Confidence            49999999999985 999 9999999999999999999   99999999999999999999999999999999999875

>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=4.2e-18  Score=125.86  Aligned_cols=74  Identities=35%  Similarity=0.592  Sum_probs=71.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+||+++|+++.++|++++||.+||++|++..+   +++++|||+|+|+.|+|+.+|++|+|++|++|+++++.+
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            79999999999999999999999999999999999   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=99.76  E-value=2.2e-18  Score=130.47  Aligned_cols=77  Identities=39%  Similarity=0.588  Sum_probs=72.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||+++|+++.|+|++++||.+||++|+++.+   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+..
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~---ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~GG   79 (85)
T 3n3k_B            3 HMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGG   79 (85)
T ss_dssp             -CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC--
T ss_pred             eEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            589999999999999999999999999999999999   99999999999999999999999999999999999987653

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.75  E-value=3.1e-18  Score=131.19  Aligned_cols=72  Identities=31%  Similarity=0.453  Sum_probs=69.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      +|+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++|+| +|++||+++|
T Consensus        17 ~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           17 SLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVER   88 (88)
T ss_dssp             EEEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEEC
T ss_pred             eEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCEECCCCCcHHHcCC-CCcEEEEEEC
Confidence            389999999999999999999999999999999999   99999999999999999999999999 8999999875

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

Probab=99.75  E-value=5.3e-18  Score=129.37  Aligned_cols=76  Identities=29%  Similarity=0.480  Sum_probs=73.2

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||+++|+++.++|++++||.+||++|+++.+   +++++|||+|+|+.|+|+++|++|+|+++++|+|+++.+.
T Consensus         7 ~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            7 GIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGS   82 (87)
T ss_dssp             SEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTC---CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCC
T ss_pred             CEEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhC---CChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccC
Confidence            599999999999999999999999999999999999   9999999999999999999999999999999999998765

>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=3.9e-18  Score=127.94  Aligned_cols=75  Identities=17%  Similarity=0.262  Sum_probs=72.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|+++.++|++++||.+||++|+++.|   +++++|||+|+|+.|+|+++|++|+|+++++|+++++.+.
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~g---i~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~G   78 (79)
T 2uyz_B            4 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   78 (79)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHC---CCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998653

>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=2.6e-18  Score=132.10  Aligned_cols=75  Identities=28%  Similarity=0.348  Sum_probs=70.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|+++.++|++++||.+||++|+...|   +|+++|||+|+|+.|+|+++|++|+|++|++|+|+++.+.
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            99999999999999999999999999999999999   9999999999999999999999999999999999998754

>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=99.75  E-value=5.9e-18  Score=131.74  Aligned_cols=75  Identities=29%  Similarity=0.313  Sum_probs=69.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDD-TTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~-~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||+++|+.|.|+|++++||.+||++|+.+.      +++|||||+||.|+|+ ++|++|+|++|++|||++++++
T Consensus         7 ~m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~------~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~~   80 (95)
T 1wia_A            7 GINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ------ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPG   80 (95)
T ss_dssp             SEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST------TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCC
T ss_pred             eEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC------cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCC
Confidence            49999999999999999999999999999998773      7899999999999999 9999999999999999998765


Q ss_pred             CC
Q 022228           80 RP   81 (300)
Q Consensus        80 ~~   81 (300)
                      .+
T Consensus        81 ~~   82 (95)
T 1wia_A           81 AA   82 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=7.3e-18  Score=124.55  Aligned_cols=75  Identities=41%  Similarity=0.652  Sum_probs=71.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+.+|+++.++|++++||.+||++|++..+   +++++|+|+|+|+.|+|+.+|++|+|++|++|+++++.+.
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~---i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~G   75 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRG   75 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            79999999999999999999999999999999999   9999999999999999999999999999999999988653

>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=5.9e-18  Score=131.35  Aligned_cols=77  Identities=19%  Similarity=0.241  Sum_probs=71.3

Q ss_pred             CEEEEEEcCCCc--EEEEEeCCCCCHHHHHHHHHHHh--CCCCCCCCCeEEEeCCeecCCCCchhhc--ccCCCcEEEEE
Q 022228            1 MMKIFVKTLKGT--SFDVEVKPEDTVFDVKMKIETVQ--GSDVYPAAQQMLIYQGKVLKDDTTLEEN--KVAENSFVVIM   74 (300)
Q Consensus         1 mM~I~VKtl~g~--~~~ieV~~~~TV~~LK~kI~~~~--g~~~ip~~~qkLi~~GkiL~D~~tL~d~--gI~~g~~I~v~   74 (300)
                      +|+|+||+.+++  .+.|+|++++||.+||++|+.+.  +   +++++|||||+||+|+|+++|++|  +|+++++|||+
T Consensus         7 ~m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~---i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv   83 (93)
T 1wgd_A            7 GVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPER---PRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLV   83 (93)
T ss_dssp             CCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTC---CCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEE
T ss_pred             EEEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCC---CChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEE
Confidence            489999999998  67788889999999999999998  8   999999999999999999999999  99999999999


Q ss_pred             EecCCC
Q 022228           75 LTKNKR   80 (300)
Q Consensus        75 v~k~~~   80 (300)
                      ++.+..
T Consensus        84 ~~~~gg   89 (93)
T 1wgd_A           84 CNVKSG   89 (93)
T ss_dssp             CCCCCC
T ss_pred             eCCCCC
Confidence            887654

>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=3.3e-18  Score=136.43  Aligned_cols=78  Identities=21%  Similarity=0.241  Sum_probs=71.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---------------CCeEEEeCCeecC-CCCchhhcc
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPA---------------AQQMLIYQGKVLK-DDTTLEENK   64 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~---------------~~qkLi~~GkiL~-D~~tL~d~g   64 (300)
                      .|+|+||+++|++|.|+|++++||.+||++|+++.+   +++               ++|+|||+||+|. |+++|++||
T Consensus         7 ~M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~---i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dyg   83 (105)
T 1v2y_A            7 GMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ---LKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYG   83 (105)
T ss_dssp             SEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHH---HHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHT
T ss_pred             cEEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhC---CCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHcC
Confidence            499999999999999999999999999999999998   665               4679999999996 568999999


Q ss_pred             cCCCcEEEEEEecCCCC
Q 022228           65 VAENSFVVIMLTKNKRP   81 (300)
Q Consensus        65 I~~g~~I~v~v~k~~~~   81 (300)
                      |++|++|||+.+.+...
T Consensus        84 I~~g~~l~lv~~lr~~~  100 (105)
T 1v2y_A           84 IRNRDEVSFIKKLGQKS  100 (105)
T ss_dssp             CCSSEEEEEEECSCSCC
T ss_pred             CCCCCEEEEEehhccCC
Confidence            99999999999987653

>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=99.74  E-value=8.8e-18  Score=132.85  Aligned_cols=77  Identities=23%  Similarity=0.416  Sum_probs=70.8

Q ss_pred             CEEEEEEcCCC----cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTLKG----TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDD-TTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl~g----~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~-~tL~d~gI~~g~~I~v~v   75 (300)
                      +|+|+||+..+    ++|.|+|++++||.+||++|+.+++   +++++|||+|+||.|+|+ ++|++|+|+++++|+|+.
T Consensus         7 ~m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~   83 (102)
T 1v5o_A            7 GMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG---VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQ   83 (102)
T ss_dssp             CEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTC---CCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECB
T ss_pred             eEEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHC---cChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEE
Confidence            59999998754    7999999999999999999999999   999999999999999988 699999999999999998


Q ss_pred             ecCCC
Q 022228           76 TKNKR   80 (300)
Q Consensus        76 ~k~~~   80 (300)
                      +.+..
T Consensus        84 ~~~gg   88 (102)
T 1v5o_A           84 KDNVG   88 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=5.8e-18  Score=132.73  Aligned_cols=76  Identities=17%  Similarity=0.258  Sum_probs=72.9

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||+++|+++.|+|++++||.+||++|+.+.|   +++++|||+|+|+.|+|+++|++|+|+++++|+|+++.+.
T Consensus        21 ~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           21 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   96 (97)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSSC
T ss_pred             cEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecCC
Confidence            389999999999999999999999999999999999   9999999999999999999999999999999999998653

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

Probab=99.73  E-value=8.9e-18  Score=129.22  Aligned_cols=75  Identities=37%  Similarity=0.661  Sum_probs=69.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|+++.++|++++||.+||++|++..+   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+.
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   9999999999999999999999999999999999988754

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

Probab=99.73  E-value=1.7e-17  Score=129.50  Aligned_cols=76  Identities=34%  Similarity=0.437  Sum_probs=71.9

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDD-TTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~-~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      .|+|+||+++| ++.|+|++++||.+||++|+.+.|   +|+++|||+|+||+|+|+ ++|++|+|+++++|+|+++.+.
T Consensus        15 ~~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~g   90 (94)
T 2kan_A           15 KIHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVEN---TPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSIN   90 (94)
T ss_dssp             CEEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSS---SCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCCS
T ss_pred             CEEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHC---cCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCCC
Confidence            38999999888 899999999999999999999999   999999999999999999 9999999999999999998765


Q ss_pred             C
Q 022228           80 R   80 (300)
Q Consensus        80 ~   80 (300)
                      .
T Consensus        91 g   91 (94)
T 2kan_A           91 R   91 (94)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.73  E-value=9.8e-18  Score=132.42  Aligned_cols=72  Identities=22%  Similarity=0.135  Sum_probs=65.2

Q ss_pred             EEEEEEcCC----CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLK----GTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~----g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      ..|.|+..+    +++|.|+|++++||.+||++|+++.|   +|+++|||||+||+|+|+++|++|+|++|++|+||+.
T Consensus        16 ati~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~g---ip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti~vl~l   91 (100)
T 1wju_A           16 ATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG---LQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLEL   91 (100)
T ss_dssp             EEEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTT---CCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECC
T ss_pred             EEEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHC---cCHHHeEEEeCCeECCCCCcHHHcCCCCCCEEEEEEE
Confidence            456677666    77999999999999999999999999   9999999999999999999999999999999955543

>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=99.73  E-value=5.7e-18  Score=131.98  Aligned_cols=76  Identities=21%  Similarity=0.340  Sum_probs=72.1

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||+. |++|.|+|++++||.+||++|+.+.+   +++++|||+|+||.|+|+++|++|+|+++++|||+++.+..
T Consensus        17 ~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           17 IIRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSG   92 (96)
T ss_dssp             EEEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTC---SCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSSC
T ss_pred             cEEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCCC
Confidence            489999998 99999999999999999999999999   99999999999999999999999999999999999887653

>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=99.73  E-value=1.8e-17  Score=133.11  Aligned_cols=76  Identities=41%  Similarity=0.644  Sum_probs=73.1

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||+++|++|.|+|++++||.+||++|+.+.+   +|+++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
T Consensus        35 ~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           35 AMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  110 (111)
T ss_dssp             CEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECCCC
T ss_pred             cEEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhC---CChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            499999999999999999999999999999999999   9999999999999999999999999999999999998753

>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=2.4e-17  Score=122.52  Aligned_cols=71  Identities=37%  Similarity=0.624  Sum_probs=68.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+|+||+ +|+.+.++|++++||.+||++|+...|   +++++|||+|+|+.|+|+++|++|||++|++|+|+.+
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            8999998 999999999999999999999999999   9999999999999999999999999999999999865

>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=99.73  E-value=1.4e-17  Score=131.48  Aligned_cols=76  Identities=29%  Similarity=0.381  Sum_probs=71.4

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||+++|+ |.|+|++++||.+||++|+++.+   +++++|||+|+||.|+|+++|++|+|++|++|+|+++.+..
T Consensus        22 ~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~~   97 (100)
T 1yqb_A           22 LIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   97 (100)
T ss_dssp             EEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             eEEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHC---cChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCCC
Confidence            499999999886 79999999999999999999999   99999999999999999999999999999999999987653

>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=99.73  E-value=2.7e-18  Score=118.70  Aligned_cols=49  Identities=55%  Similarity=0.981  Sum_probs=47.1

Q ss_pred             ccccCCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 022228          152 NLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPE  203 (300)
Q Consensus       152 ~l~~g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~  203 (300)
                      +|++|+.+++.|++|++||   |+|++|++|||+++||+|||+|||++|||+
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            4788999999999999999   999999999999999999999999999995

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

Probab=99.72  E-value=2.1e-17  Score=135.62  Aligned_cols=77  Identities=25%  Similarity=0.348  Sum_probs=70.0

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      +|+|+||++ |++|.|+|++++||.+||++|+.+.+   +++++|||+|+||+|+|+++|++|+|++|++|+|+++++..
T Consensus        32 ~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~gg  107 (125)
T 1j8c_A           32 IIKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFK---SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPN  107 (125)
T ss_dssp             CEEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHC---SCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC----
T ss_pred             cEEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHC---cCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCCC
Confidence            499999998 99999999999999999999999999   99999999999999999999999999999999999987654


Q ss_pred             C
Q 022228           81 P   81 (300)
Q Consensus        81 ~   81 (300)
                      .
T Consensus       108 ~  108 (125)
T 1j8c_A          108 S  108 (125)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=2.8e-17  Score=129.88  Aligned_cols=75  Identities=27%  Similarity=0.366  Sum_probs=71.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||+. |+.+.|+|++++||.+||++|+...|   +++++|||+|+||+|+|+++|++|||++|++|+|+++++.
T Consensus        25 ~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           25 IMKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFK---SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQN   99 (101)
T ss_dssp             CEEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHT---CCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCSS
T ss_pred             eEEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHC---cChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCC
Confidence            489999998 89999999999999999999999999   9999999999999999999999999999999999988654

>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=7.3e-17  Score=130.82  Aligned_cols=77  Identities=18%  Similarity=0.272  Sum_probs=66.0

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHH------hCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcE--EE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETV------QGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSF--VV   72 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~------~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~--I~   72 (300)
                      .|+|+||+++|+++.|+|++++||.+||++|+..      .+.. +++++|||||.||+|+|+++|++|+|+.+++  ||
T Consensus        16 ~m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p-~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlh   94 (116)
T 1wgh_A           16 MINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQV-SSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMH   94 (116)
T ss_dssp             SEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCC-CCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEE
T ss_pred             eEEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCC-CChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEE
Confidence            3899999999999999999999999999999994      3411 3699999999999999999999999987754  55


Q ss_pred             EEEecC
Q 022228           73 IMLTKN   78 (300)
Q Consensus        73 v~v~k~   78 (300)
                      |+++..
T Consensus        95 Lvlr~~  100 (116)
T 1wgh_A           95 LVARET  100 (116)
T ss_dssp             EEECSS
T ss_pred             EEccCC
Confidence            555543

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

Probab=99.71  E-value=3.8e-17  Score=127.85  Aligned_cols=76  Identities=41%  Similarity=0.643  Sum_probs=72.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |+|+||+.+|+++.++|++++||.+||++|+...|   +++++|||+|+||.|+|+++|++|+|++|++|+|+++.+..
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            79999999999999999999999999999999999   99999999999999999999999999999999999987643

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.71  E-value=2.9e-17  Score=127.75  Aligned_cols=74  Identities=22%  Similarity=0.346  Sum_probs=69.8

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||+  |+++.|+|++++||.+||++|+++.+   +++++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
T Consensus        19 ~m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~G   92 (93)
T 2l7r_A           19 SMQLFVRA--QELHTFEVTGQETVAQIKAHVASLEG---IAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLG   92 (93)
T ss_dssp             -CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHT---CCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCCC
T ss_pred             cEEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhC---cChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            48999997  89999999999999999999999999   9999999999999999999999999999999999988653

>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=99.71  E-value=2.2e-17  Score=129.46  Aligned_cols=73  Identities=23%  Similarity=0.334  Sum_probs=68.4

Q ss_pred             CEEEEEEcCCCcEE-EEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            1 MMKIFVKTLKGTSF-DVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         1 mM~I~VKtl~g~~~-~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      ||+|+|| +.|++| .|+|++++||.+||++|++++|   +++++|||+|+||+|+|+ +|++|+|+++++|+||.+..
T Consensus         7 ~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            7 GYSVTVK-WGKEKFEGVELNTDEPPMVFKAQLFALTG---VQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             EEEEEEE-ETTEEEEEEEEESSSCHHHHHHHHHHHTC---CCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCC
T ss_pred             EEEEEEE-ECCEEEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecch
Confidence            5899999 578999 6999999999999999999999   999999999999999999 99999999999999987643

>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=99.54  E-value=8.5e-19  Score=130.38  Aligned_cols=75  Identities=28%  Similarity=0.464  Sum_probs=72.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+.+|++|.++|++++||.+||++|+...|   +++++|+|+|+|+.|+|+++|++|+|++|++|+++++.+.
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlrg   75 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQG---VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   75 (76)
Confidence            89999999999999999999999999999999999   9999999999999999999999999999999999998653

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

Probab=99.69  E-value=1.1e-16  Score=131.43  Aligned_cols=75  Identities=19%  Similarity=0.293  Sum_probs=66.5

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHH------HhCCCCC--CCCCeEEEeCCeecCCCCchhhcccCCCcE--
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIET------VQGSDVY--PAAQQMLIYQGKVLKDDTTLEENKVAENSF--   70 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~------~~g~~~i--p~~~qkLi~~GkiL~D~~tL~d~gI~~g~~--   70 (300)
                      +|+|+||+++|+++.|+|++++||.+||++|+.      +.+   +  ++++|||||+||+|+|+++|++|+|+++++  
T Consensus        17 ~m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~---ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~t   93 (125)
T 2gow_A           17 MINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEE---QVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTV   93 (125)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCC---TTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEE
T ss_pred             eEEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccC---CCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceE
Confidence            499999999999999999999999999999998      455   6  589999999999999999999999998885  


Q ss_pred             EEEEEecC
Q 022228           71 VVIMLTKN   78 (300)
Q Consensus        71 I~v~v~k~   78 (300)
                      |||+++.+
T Consensus        94 lhlv~r~~  101 (125)
T 2gow_A           94 MHLVARET  101 (125)
T ss_dssp             EEEEECSC
T ss_pred             EEEEecCC
Confidence            55555544

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.69  E-value=1.4e-16  Score=127.78  Aligned_cols=76  Identities=41%  Similarity=0.644  Sum_probs=72.8

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||+++|+.+.++|++++||.+||++|+.+.+   +++++|||+|+||.|+|+++|++|+|+++++|+|+++.+.
T Consensus        35 ~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           35 AMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  110 (111)
T ss_dssp             CEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHC---CCTTTEEEEETTEECCSSCBTTTTTCCTTCEEEEEECCCC
T ss_pred             eEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHC---cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            499999999999999999999999999999999999   9999999999999999999999999999999999998653

>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=99.69  E-value=1.5e-16  Score=123.07  Aligned_cols=74  Identities=28%  Similarity=0.430  Sum_probs=68.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCC-----CCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCC-CCchhhcccCCCcEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPE-----DTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKD-DTTLEENKVAENSFVVIM   74 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~-----~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D-~~tL~d~gI~~g~~I~v~   74 (300)
                      ||+|+||+ .|+.|.|+|+++     +||.+||++|+..+|   +++++|||+|+||.|+| +++|++|+|+++++|+|+
T Consensus         7 ~~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~g---ip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~   82 (92)
T 1wxv_A            7 GLTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIG---VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLI   82 (92)
T ss_dssp             SEEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTC---CCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEE
T ss_pred             eEEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHC---cCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEE
Confidence            69999997 588999999995     999999999999999   99999999999999998 568999999999999998


Q ss_pred             EecC
Q 022228           75 LTKN   78 (300)
Q Consensus        75 v~k~   78 (300)
                      .++.
T Consensus        83 ~~~~   86 (92)
T 1wxv_A           83 GKKN   86 (92)
T ss_dssp             SCCS
T ss_pred             ecCC
Confidence            7654

>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=1.2e-16  Score=137.43  Aligned_cols=77  Identities=39%  Similarity=0.591  Sum_probs=73.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      |+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+|+.|+|+++|++|+|++|++|||+++.+...
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            79999999999999999999999999999999999   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=99.68  E-value=1.1e-16  Score=127.73  Aligned_cols=74  Identities=23%  Similarity=0.198  Sum_probs=68.6

Q ss_pred             EEEEEEcCCC---cEEEEEeC--------C-CCCHHHHHHHHHHHh--CCCCCCCCC-eEEEeCCeecCCCCchhhcccC
Q 022228            2 MKIFVKTLKG---TSFDVEVK--------P-EDTVFDVKMKIETVQ--GSDVYPAAQ-QMLIYQGKVLKDDTTLEENKVA   66 (300)
Q Consensus         2 M~I~VKtl~g---~~~~ieV~--------~-~~TV~~LK~kI~~~~--g~~~ip~~~-qkLi~~GkiL~D~~tL~d~gI~   66 (300)
                      |+|+||+.++   ++|.|+|+        + ++||.+||++|+.+.  +   +++++ |||||+||.|+|+++|++|+|+
T Consensus        13 ~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~g---ip~~~~qrLi~~Gk~L~D~~tL~~y~i~   89 (107)
T 1x1m_A           13 WHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQES---VPDPELIDLIYCGRKLKDDQTLDFYGIQ   89 (107)
T ss_dssp             CCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTT---CCCSSSEEEEETTEECCTTCBHHHHTCC
T ss_pred             eEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccC---CChhhcEEEEECCeECCCCCcHHHcCCC
Confidence            7899999999   89999954        4 499999999999999  8   99999 9999999999999999999999


Q ss_pred             CCcEEEEEEecC
Q 022228           67 ENSFVVIMLTKN   78 (300)
Q Consensus        67 ~g~~I~v~v~k~   78 (300)
                      ++++|||+++.+
T Consensus        90 ~g~~i~lv~~~~  101 (107)
T 1x1m_A           90 PGSTVHVLRKSW  101 (107)
T ss_dssp             TTCEEEEEESSC
T ss_pred             CCCEEEEEeCCC
Confidence            999999998764

>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=1.9e-16  Score=129.95  Aligned_cols=79  Identities=16%  Similarity=0.230  Sum_probs=67.7

Q ss_pred             EEEEEEcCCCcEE-EEEeCCCCCHHHHHHHHHHHhC--CCCCCC--CCeEEEeCCeecCCCCchhhcccCCC------cE
Q 022228            2 MKIFVKTLKGTSF-DVEVKPEDTVFDVKMKIETVQG--SDVYPA--AQQMLIYQGKVLKDDTTLEENKVAEN------SF   70 (300)
Q Consensus         2 M~I~VKtl~g~~~-~ieV~~~~TV~~LK~kI~~~~g--~~~ip~--~~qkLi~~GkiL~D~~tL~d~gI~~g------~~   70 (300)
                      |+|+||+++|+.| .+++++++||.+||++|+...+  ++.+|+  ++|||||+||+|+|+++|++|+|.++      .+
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            8999999999998 6999999999999999965432  112775  89999999999999999999999998      56


Q ss_pred             EEEEEecCCC
Q 022228           71 VVIMLTKNKR   80 (300)
Q Consensus        71 I~v~v~k~~~   80 (300)
                      |||+++.+..
T Consensus        97 mhlVlrl~g~  106 (126)
T 1se9_A           97 MHVIIQAPVT  106 (126)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEeccCCc
Confidence            8888876643

>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=2.4e-16  Score=133.24  Aligned_cols=76  Identities=28%  Similarity=0.339  Sum_probs=72.4

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |+|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|||+|+|+.|+|+++|++|+|++|++||++++.+..
T Consensus        82 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---ip~~~q~L~~~G~~L~d~~tL~~y~i~~g~~l~l~~rl~GG  157 (159)
T 3rt3_B           82 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGG  157 (159)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC--
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHC---CCHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            89999999999999999999999999999999999   99999999999999999999999999999999999987653

>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=1.6e-16  Score=122.79  Aligned_cols=73  Identities=30%  Similarity=0.453  Sum_probs=69.0

Q ss_pred             CEEEEEEcCCCcEEEE-EeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE---eCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            1 MMKIFVKTLKGTSFDV-EVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI---YQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         1 mM~I~VKtl~g~~~~i-eV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi---~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      +|+|+||. .|++|.| +|++++||.+||++|++++|   +|+++|||+   |+||+|+|+.+|++|+|++|++|+||.+
T Consensus         7 ~m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~g---ip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~   82 (90)
T 1v5t_A            7 GLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTG---VLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGT   82 (90)
T ss_dssp             SCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTC---CCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECC
T ss_pred             eEEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHC---cCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEec
Confidence            48999994 8899999 99999999999999999999   999999999   9999999999999999999999999875


Q ss_pred             c
Q 022228           77 K   77 (300)
Q Consensus        77 k   77 (300)
                      .
T Consensus        83 ~   83 (90)
T 1v5t_A           83 R   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.67  E-value=1e-16  Score=126.55  Aligned_cols=71  Identities=21%  Similarity=0.280  Sum_probs=64.4

Q ss_pred             EEEEEEcCCCc--EEEEEeCCCCCHHHHHHHHHHHh-CCCCCCCCCeEEEeCCeecCCCCchhhc--ccCCCcEEEEE
Q 022228            2 MKIFVKTLKGT--SFDVEVKPEDTVFDVKMKIETVQ-GSDVYPAAQQMLIYQGKVLKDDTTLEEN--KVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~--~~~ieV~~~~TV~~LK~kI~~~~-g~~~ip~~~qkLi~~GkiL~D~~tL~d~--gI~~g~~I~v~   74 (300)
                      |+|+||+++|+  ++.|+|++++||.+||++|+.+. |.  .++++|||||+||+|+|+++|++|  +|+++++|+|+
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            89999999998  67899999999999999999874 51  446999999999999999999999  99999999874

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.67  E-value=3.2e-16  Score=134.42  Aligned_cols=75  Identities=41%  Similarity=0.655  Sum_probs=72.5

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      +|+|+||+++|++|.|+|++++||.+||++|+.+.|   +++++|||+|+|+.|+|+.+|++|+|+++++|+|+++.+
T Consensus        20 ~m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~   94 (172)
T 3u30_A           20 HMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   94 (172)
T ss_dssp             CEEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCC
T ss_pred             cEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cChHHEEEEECCccccccCCHhHcCCcccceeeeeeccc
Confidence            599999999999999999999999999999999999   999999999999999999999999999999999998754

>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=99.66  E-value=1.2e-16  Score=124.79  Aligned_cols=72  Identities=29%  Similarity=0.459  Sum_probs=66.9

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +|+|+|| +.|++|.|+|++++||.+||++|+.+++   +++++|||+|+||.| |+.+|++|+|+++++|+||.++
T Consensus        17 ~~~i~Vk-~~g~~~~i~v~~~~TV~~LK~~I~~~tg---ip~~~QrL~~~Gk~L-dd~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           17 LVDLKII-WNKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMYKGLVP-EDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             CEEEEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHC---SCSTTCCCBSSSBCC-SSSBHHHHCCCTTEEEEECCSS
T ss_pred             eEEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCeeC-CcCcHHHCCCCCCCEEEEEecc
Confidence            4899999 6799999999999999999999999999   999999999999999 5569999999999999998754

>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=99.66  E-value=1.2e-16  Score=129.59  Aligned_cols=72  Identities=24%  Similarity=0.343  Sum_probs=65.3

Q ss_pred             EEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccC-------CCcEEEE
Q 022228            2 MKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVA-------ENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~-------~g~~I~v   73 (300)
                      |.|+|+...++ ++.|+|++++||.+||++|+.+.|   +|+++|||||+||+|+|+++|++|||+       .+++|++
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            45555555565 599999999999999999999999   999999999999999999999999999       6999999


Q ss_pred             EEe
Q 022228           74 MLT   76 (300)
Q Consensus        74 ~v~   76 (300)
                      +++
T Consensus        78 ~lr   80 (118)
T 2fnj_B           78 AFR   80 (118)
T ss_dssp             EEB
T ss_pred             Eec
Confidence            998

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=3.6e-16  Score=126.19  Aligned_cols=76  Identities=37%  Similarity=0.572  Sum_probs=72.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      ++|+||+++|+++.++|++++||.+||++|+...|   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+..
T Consensus        10 ~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~GG   85 (114)
T 2kdi_A           10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG   85 (114)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCSS
T ss_pred             EEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHC---cChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCC
Confidence            58999999999999999999999999999999999   99999999999999999999999999999999999987654

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=99.66  E-value=2.3e-16  Score=133.28  Aligned_cols=73  Identities=29%  Similarity=0.384  Sum_probs=70.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE-e-CCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI-Y-QGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi-~-~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+||+++|++|.++|++++||.+||++|+...|   +|+++|||+ | +|+.|+|+++|++|+|++|++|+++++.
T Consensus         3 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~~   77 (159)
T 3rt3_B            3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG---VHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   77 (159)
T ss_dssp             CEEEEEETTSCEEEEECCTTCCHHHHHHHHHHHHC---CCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEECC
T ss_pred             eEEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHhC---CCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEccC
Confidence            89999999999999999999999999999999999   999999999 9 7999999999999999999999999873

>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=99.66  E-value=1.5e-16  Score=128.82  Aligned_cols=73  Identities=23%  Similarity=0.336  Sum_probs=67.8

Q ss_pred             EEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCC-------CcEEEE
Q 022228            2 MKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAE-------NSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~-------g~~I~v   73 (300)
                      |.|+|+...++ ++.++|++++||.+||++|+.+.|   +|+++|||||+||+|+|++||++|||++       +++|++
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            56777766666 788999999999999999999999   9999999999999999999999999999       999999


Q ss_pred             EEec
Q 022228           74 MLTK   77 (300)
Q Consensus        74 ~v~k   77 (300)
                      ++|.
T Consensus        78 vlr~   81 (118)
T 4ajy_B           78 AFRA   81 (118)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.66  E-value=5.5e-17  Score=128.29  Aligned_cols=72  Identities=36%  Similarity=0.622  Sum_probs=68.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+||+ .|++|.|+|++++||.+||++|+++.|   +++++|||+|+||.|+|+++|++|||++|++|+|+.+.
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            6788997 899999999999999999999999999   99999999999999999999999999999999998764

>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=2.5e-16  Score=126.22  Aligned_cols=77  Identities=23%  Similarity=0.284  Sum_probs=72.8

Q ss_pred             CEEEEEEcC---CCcEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            1 MMKIFVKTL---KGTSFDVEVKP-EDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         1 mM~I~VKtl---~g~~~~ieV~~-~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      .|+|+||+.   +|+.+.++|++ ++||.+||++|+...|   +|+++|||+|+|++|+|+++|++|+|++|++|+|+++
T Consensus        27 ~i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~g---ip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r  103 (111)
T 1we6_A           27 PATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLR  103 (111)
T ss_dssp             CEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTT---CCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECS
T ss_pred             cEEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHC---CCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEE
Confidence            389999998   89999999998 9999999999999999   9999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022228           77 KNKR   80 (300)
Q Consensus        77 k~~~   80 (300)
                      .+..
T Consensus       104 ~~GG  107 (111)
T 1we6_A          104 ERSG  107 (111)
T ss_dssp             SCCS
T ss_pred             cCCC
Confidence            7654

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.65  E-value=5.1e-16  Score=118.81  Aligned_cols=70  Identities=27%  Similarity=0.460  Sum_probs=65.9

Q ss_pred             EEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         4 I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      +++++++|++|.++|++++||.+||++|+...|   +|+++|||+|+||.|+|+++|++|+|++|++|+|+.+
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            456678999999999999999999999999999   9999999999999999999999999999999999864

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.65  E-value=4.1e-16  Score=136.49  Aligned_cols=78  Identities=38%  Similarity=0.572  Sum_probs=74.2

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      .|+|+||+++|++|.|+|++++||.+||++|+.+.+   +|+++|||+|+|+.|+|+++|++|+|+++++|+|+++.+..
T Consensus       105 eMqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~g---Ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~LvlrlrGG  181 (189)
T 3q3f_A          105 GGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  181 (189)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCCCC
T ss_pred             ceeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccC---CCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCC
Confidence            399999999999999999999999999999999999   99999999999999999999999999999999999987654


Q ss_pred             C
Q 022228           81 P   81 (300)
Q Consensus        81 ~   81 (300)
                      .
T Consensus       182 ~  182 (189)
T 3q3f_A          182 G  182 (189)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=9.5e-16  Score=122.02  Aligned_cols=73  Identities=19%  Similarity=0.258  Sum_probs=68.8

Q ss_pred             EEEEEEcCCC--cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhccc-CCCcEEEEEEec
Q 022228            2 MKIFVKTLKG--TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKV-AENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g--~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI-~~g~~I~v~v~k   77 (300)
                      |+|+|++..+  .++.|+|++++||.+||++|++++|   +|+++|||+|+|+.|+|+++|.+||| ++|++||+++-.
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            8999999875  6899999999999999999999999   99999999999999999999999999 599999999854

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.6e-15  Score=122.43  Aligned_cols=75  Identities=20%  Similarity=0.291  Sum_probs=69.2

Q ss_pred             EEEEEE-cCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVK-TLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VK-tl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |.|+|+ ...++.|.++++++.||++||++|+.+.+   +|++.|+|||+||+|+|+.||++|||++|.+|||+++...
T Consensus        16 itvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~---iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~~   91 (118)
T 2daf_A           16 ATVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLG---IPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFSTN   91 (118)
T ss_dssp             EEEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHT---CCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEESC
T ss_pred             EEEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhC---CChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecCC
Confidence            567776 56788999999999999999999999999   9999999999999999999999999999999999998643

>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=3.2e-17  Score=134.78  Aligned_cols=76  Identities=39%  Similarity=0.606  Sum_probs=0.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+++.+..
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

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=5.2e-16  Score=119.82  Aligned_cols=70  Identities=21%  Similarity=0.272  Sum_probs=64.4

Q ss_pred             CEEEEEEcCCCcEE--EE-EeCCCCCHHHHHHHHHHH-hCCCCCCCCCeEEEeC--CeecCCCCchhhcccCCCcEEEE
Q 022228            1 MMKIFVKTLKGTSF--DV-EVKPEDTVFDVKMKIETV-QGSDVYPAAQQMLIYQ--GKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         1 mM~I~VKtl~g~~~--~i-eV~~~~TV~~LK~kI~~~-~g~~~ip~~~qkLi~~--GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      ||+|+||+++|+++  .| +|++++||.+||++|++. .+   +++++|||+|.  ||+|+|+++|++|+|+++++|+|
T Consensus        10 ~M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~---i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           10 HYEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQ---WYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             CEEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSS---SCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             EEEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcC---CChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            69999999998775  58 999999999999999995 67   99999999976  99999999999999999999875

>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=2.8e-15  Score=124.76  Aligned_cols=73  Identities=42%  Similarity=0.677  Sum_probs=70.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+.+.
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g---ip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~   73 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   73 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHC---cChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeec
Confidence            79999999999999999999999999999999999   99999999999999999999999999999999999864

>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=3.5e-15  Score=124.15  Aligned_cols=75  Identities=41%  Similarity=0.656  Sum_probs=72.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|+++.++|++++||.+||++|+.+.|   +++++|+|+|+|+.|+|+++|++|+|++|++|+|+++.+.
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            78999999999999999999999999999999999   9999999999999999999999999999999999998753

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.60  E-value=1.9e-15  Score=129.60  Aligned_cols=75  Identities=41%  Similarity=0.656  Sum_probs=69.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |.|+||+++|+++.++|++++||.+||++|+.+.|   +|+++|+|+|+|+.|+|+++|.+|+|++|++|||+++.+.
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            78999999999999999999999999999999999   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=4.1e-15  Score=119.93  Aligned_cols=76  Identities=26%  Similarity=0.405  Sum_probs=70.1

Q ss_pred             EEEEEEcC----------CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEE
Q 022228            2 MKIFVKTL----------KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFV   71 (300)
Q Consensus         2 M~I~VKtl----------~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I   71 (300)
                      |+|+|+..          +|+++.|+|++++||.+||++|+...|   +++++|||+|+|+.|+|+++|++|+|+++++|
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            56777764          478999999999999999999999999   99999999999999999999999999999999


Q ss_pred             EEEEecCCC
Q 022228           72 VIMLTKNKR   80 (300)
Q Consensus        72 ~v~v~k~~~   80 (300)
                      ||+++.+..
T Consensus       103 ~lv~rl~GG  111 (115)
T 1we7_A          103 HLALKERSG  111 (115)
T ss_dssp             EEEECCCSC
T ss_pred             EEEEEcCCC
Confidence            999987654

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=99.58  E-value=1.9e-16  Score=134.15  Aligned_cols=77  Identities=39%  Similarity=0.591  Sum_probs=0.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      |+|+||+++|++|.|+|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+++.+...
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GGg   77 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG   77 (152)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhC---CCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCCC
Confidence            89999999999999999999999999999999999   999999999999999999999999999999999999876543

>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=5.7e-15  Score=116.68  Aligned_cols=72  Identities=21%  Similarity=0.282  Sum_probs=65.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY--QGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~--~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |.++++.+.|+++.|+|++++||.+||++|++++|   +|+++|||+|  .|+ |+|+.+|++|+|+.|++||+++..
T Consensus         9 m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tg---Ipp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~~   82 (100)
T 2dzm_A            9 MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQ---IPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTPD   82 (100)
T ss_dssp             EEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHC---CCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCSS
T ss_pred             eEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHC---CChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEecC
Confidence            66777779999999999999999999999999999   9999999997  566 999999999999999999987653

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.55  E-value=1.4e-14  Score=135.28  Aligned_cols=75  Identities=41%  Similarity=0.655  Sum_probs=70.4

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      +|+|+||+++|+++.|+|++++||.+||++|+.+.+   +++++|||+|+||+|+|+++|++|+|+++++|+|++|.+
T Consensus       233 ~MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~G---Ip~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRLr  307 (307)
T 3ai5_A          233 SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  307 (307)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC---CCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC---
T ss_pred             eEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            589999999999999999999999999999999999   999999999999999999999999999999999998753

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.53  E-value=1.1e-14  Score=111.96  Aligned_cols=74  Identities=12%  Similarity=0.077  Sum_probs=65.3

Q ss_pred             EEEEEE--cCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe-------CCeecCCCCchhhcccCCCcEEE
Q 022228            2 MKIFVK--TLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY-------QGKVLKDDTTLEENKVAENSFVV   72 (300)
Q Consensus         2 M~I~VK--tl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~-------~GkiL~D~~tL~d~gI~~g~~I~   72 (300)
                      ++|.|.  ..+.+.+++.+++++||.+||++|+.++|   +|+++|||||       .|+.|+|+++|++|+|++|++||
T Consensus         3 V~v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~~G---ip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ih   79 (86)
T 4b6w_A            3 VKVSLTHSASRMRVPEKRYGLAQTIESIKENVFTHFA---TPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIH   79 (86)
T ss_dssp             EEEEEEETTCSCCEEEEEEETTSBHHHHHHHHHTTSC---CCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEE
T ss_pred             EEEEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHHHC---CCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEE
Confidence            445554  45667889999999999999999999999   9999999997       48999999999999999999999


Q ss_pred             EEEecC
Q 022228           73 IMLTKN   78 (300)
Q Consensus        73 v~v~k~   78 (300)
                      |+-+.|
T Consensus        80 lvd~~P   85 (86)
T 4b6w_A           80 VVDLQP   85 (86)
T ss_dssp             EEECCC
T ss_pred             EEeCCC
Confidence            997654

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.49  E-value=1.1e-13  Score=108.21  Aligned_cols=70  Identities=19%  Similarity=0.243  Sum_probs=62.9

Q ss_pred             EEEEEEcCCC--cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC--Ce---ec-CCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKG--TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ--GK---VL-KDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g--~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~--Gk---iL-~D~~tL~d~gI~~g~~I~v   73 (300)
                      ++|+|+...+  +.++++|++++||.+||++|+.++|   +|+++|||+|.  |+   .| +|+++|++|+|++|++|+|
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            6788887655  4899999999999999999999999   99999999997  55   34 8999999999999999998


Q ss_pred             E
Q 022228           74 M   74 (300)
Q Consensus        74 ~   74 (300)
                      +
T Consensus        93 v   93 (95)
T 2kjr_A           93 V   93 (95)
T ss_dssp             E
T ss_pred             E
Confidence            6

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.49  E-value=4.9e-14  Score=112.32  Aligned_cols=71  Identities=21%  Similarity=0.240  Sum_probs=65.7

Q ss_pred             EEEEEEcCCCcEEEEEeC-CCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCe-----------e----cCCCCchhhccc
Q 022228            2 MKIFVKTLKGTSFDVEVK-PEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGK-----------V----LKDDTTLEENKV   65 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~-~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~Gk-----------i----L~D~~tL~d~gI   65 (300)
                      |+|+||+.+|+. .|+|+ +++||.+||++|+.+++   +++++|+|+|.|+           .    ++|+++|++|||
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            899999999965 79999 99999999999999999   9999999999988           3    588999999999


Q ss_pred             CCCcEEEEEEe
Q 022228           66 AENSFVVIMLT   76 (300)
Q Consensus        66 ~~g~~I~v~v~   76 (300)
                      ++|++|||+..
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=2.1e-13  Score=107.08  Aligned_cols=72  Identities=17%  Similarity=0.074  Sum_probs=63.2

Q ss_pred             EEEEEEcCC--CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC---ee----cCCCCchhhcccCCCcEEE
Q 022228            2 MKIFVKTLK--GTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG---KV----LKDDTTLEENKVAENSFVV   72 (300)
Q Consensus         2 M~I~VKtl~--g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G---ki----L~D~~tL~d~gI~~g~~I~   72 (300)
                      +.|+|+...  ++.++++|++++||.+||++|+.++|   +|+++|||+|.|   +.    ++|+++|++|+|++|++|+
T Consensus        15 v~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~G---ip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ih   91 (97)
T 2kj6_A           15 VHLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCG---TSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLH   91 (97)
T ss_dssp             EEEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHC---CCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEE
T ss_pred             EEEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHC---cCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEE
Confidence            567777543  45799999999999999999999999   999999999988   43    5899999999999999999


Q ss_pred             EEEe
Q 022228           73 IMLT   76 (300)
Q Consensus        73 v~v~   76 (300)
                      |+-.
T Consensus        92 lvd~   95 (97)
T 2kj6_A           92 IIDL   95 (97)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8864

>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=1.4e-13  Score=102.52  Aligned_cols=46  Identities=20%  Similarity=0.349  Sum_probs=43.1

Q ss_pred             CCChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhCCCCc
Q 022228          156 GNNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSGIPEQ  204 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~GIP~~  204 (300)
                      ...|++.|++|++||   | +|+.+++||++++||++||||||++|||+.
T Consensus        26 e~~ye~qi~qL~eMG---F~dr~~~~~AL~~t~Gnve~Ave~L~~~~~~~   72 (74)
T 1vej_A           26 EGRYQQELEELKALG---FANRDANLQALVATDGDIHAAIEMLLGASGPS   72 (74)
T ss_dssp             TTTSHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHTCCCCC
T ss_pred             hHHHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHhCCCCC
Confidence            467899999999999   9 899999999999999999999999999863

>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=99.45  E-value=1.9e-13  Score=106.44  Aligned_cols=74  Identities=20%  Similarity=0.234  Sum_probs=64.7

Q ss_pred             CEEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC---ee----cCCCCchhhcccCCCcEEE
Q 022228            1 MMKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG---KV----LKDDTTLEENKVAENSFVV   72 (300)
Q Consensus         1 mM~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G---ki----L~D~~tL~d~gI~~g~~I~   72 (300)
                      +|.|+|+..... .++++|++++||.+||++|+.+.|   +|+++|||+|.|   +.    |+|+++|.+|+|++|++||
T Consensus         7 ~v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~g---ip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~   83 (95)
T 1v6e_A            7 GVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVG---SPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIH   83 (95)
T ss_dssp             CEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTC---SCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEE
T ss_pred             EEEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHC---CCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEE
Confidence            378888876543 689999999999999999999999   999999999986   54    5899999999999999999


Q ss_pred             EEEec
Q 022228           73 IMLTK   77 (300)
Q Consensus        73 v~v~k   77 (300)
                      |+...
T Consensus        84 v~d~~   88 (95)
T 1v6e_A           84 VIDHS   88 (95)
T ss_dssp             EBCCS
T ss_pred             EEECC
Confidence            87643

>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.45  E-value=1.1e-13  Score=92.82  Aligned_cols=40  Identities=20%  Similarity=0.307  Sum_probs=38.2

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGI  201 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GI  201 (300)
                      .++.|++|++||   |+|++|++||++++||+++|+|||++||
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            378899999999   9999999999999999999999999987

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

Probab=99.44  E-value=8e-15  Score=127.97  Aligned_cols=71  Identities=20%  Similarity=0.274  Sum_probs=0.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |+|+||+++|++|.|+|++++||.+||.+|+...|   +|+++|+|||+|++|+|+.+|+     ++++|||+++.+..
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keG---IP~~qQRLIf~GK~LeD~~TLs-----~~STLhLvlRLrGG   71 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMG---FEIDMMTLVNNGFIAPNTELVT-----DDVTYYLSLKLLGG   71 (189)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhC---cChhHEEEEecCeECCCCCccc-----CCCEEEEEEecCCC
Confidence            89999999999999999999999999999999999   9999999999999999999998     88999999987643

>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=4.4e-13  Score=104.62  Aligned_cols=76  Identities=11%  Similarity=0.194  Sum_probs=72.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |+|+||+.+|+.+.+.|.+++++..||++++++.|   ++++++||+|+|+.|.++.|+++|+|.++|+|+|+++.+..
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            89999999999999999999999999999999999   99999999999999999999999999999999999987654

>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=1.7e-13  Score=101.95  Aligned_cols=44  Identities=39%  Similarity=0.385  Sum_probs=40.9

Q ss_pred             CCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 022228          156 GNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIP  202 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP  202 (300)
                      ...+++.|++||+||   |+|++|++|||+++||+|||||||++|+.
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            356799999999999   99999999999999999999999999954

>2bwb_A Ubiquitin-like protein DSK2; UBA, signaling protein; 2.3A {Saccharomyces cerevisiae} SCOP: a.5.2.1 PDB: 2bwe_A

Probab=99.40  E-value=2.8e-13  Score=92.13  Aligned_cols=41  Identities=34%  Similarity=0.489  Sum_probs=38.3

Q ss_pred             CChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          157 NNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ..|+..|++|++||   | +|+.+++||++++||++||||||++|
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            35789999999999   9 79999999999999999999999987

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.40  E-value=3.2e-13  Score=103.23  Aligned_cols=71  Identities=14%  Similarity=0.267  Sum_probs=63.3

Q ss_pred             EEEEEEcCCCcEEEEE-eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC--CeecC---CCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVE-VKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ--GKVLK---DDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ie-V~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~--GkiL~---D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+||+.+|+. .++ |++++||.+||++|+++.|   +++++|+|+|+  +|.|+   |+++|++|||++|++|+|..
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            789999999964 577 9999999999999999999   99999999987  48874   68899999999999998865


Q ss_pred             e
Q 022228           76 T   76 (300)
Q Consensus        76 ~   76 (300)
                      .
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=2e-12  Score=95.77  Aligned_cols=71  Identities=11%  Similarity=0.207  Sum_probs=68.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|++.+|+.+.+.|.+++++..|+++++++.|   +++..+||+|.|+.|.++.|.++|++.+|++|+|++
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            78999999999999999999999999999999999   999999999999999999999999999999999874

>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=99.37  E-value=1.5e-12  Score=106.15  Aligned_cols=73  Identities=12%  Similarity=0.117  Sum_probs=64.8

Q ss_pred             EEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC---ee----cCCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG---KV----LKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G---ki----L~D~~tL~d~gI~~g~~I~v   73 (300)
                      |.|+|+...+. .++++|++++||.+||.+|+.+.|   +|+++|||+|.|   +.    ++|+++|.+|||.+|++|||
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            78888876553 688999999999999999999999   999999999977   43    48999999999999999999


Q ss_pred             EEec
Q 022228           74 MLTK   77 (300)
Q Consensus        74 ~v~k   77 (300)
                      +...
T Consensus        84 vd~~   87 (122)
T 1t0y_A           84 VDVT   87 (122)
T ss_dssp             EECT
T ss_pred             EeCC
Confidence            8754

>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=2.9e-12  Score=99.44  Aligned_cols=75  Identities=11%  Similarity=0.201  Sum_probs=71.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+|++.+|+.+.+.|.+++++..||++++++.|   +++.++||+|+|+.|.++.|+++|++.+||+|+|++....
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            78999999999999999999999999999999999   9999999999999999999999999999999999988764

>2knz_A Ubiquilin-4; cytoplasm, endoplasmic reticulum, nucleus, phosphoprotein, protein binding; NMR {Mus musculus}

Probab=99.37  E-value=7.1e-13  Score=92.82  Aligned_cols=43  Identities=23%  Similarity=0.351  Sum_probs=40.8

Q ss_pred             CChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 022228          157 NNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSGIP  202 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~GIP  202 (300)
                      ..|++.|++|++||   | +|+.|++||++++||++||||||++|++
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            46899999999999   9 9999999999999999999999999975

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.36  E-value=5.3e-13  Score=125.60  Aligned_cols=72  Identities=21%  Similarity=0.337  Sum_probs=66.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE---eCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI---YQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi---~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+|| ++|++|.|+|++++||.+||++|++++|   +|+++||||   |+||+|+|+.+|++|+|++|++|+||.+.
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            789999 6899999999999999999999999999   999999999   89999999999999999999999999654

>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=7.5e-13  Score=100.60  Aligned_cols=44  Identities=30%  Similarity=0.378  Sum_probs=40.9

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh--C-CCCcc
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS--G-IPEQA  205 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~--G-IP~~~  205 (300)
                      .++.|++||+||   |+|++|++|||+++||++||+|||++  | ||+.+
T Consensus        29 ~ee~I~~Lv~MG---F~~~~A~~AL~~t~gdve~A~e~L~sh~~~ip~~~   75 (83)
T 1veg_A           29 SQESINQLVYMG---FDTVVAEAALRVFGGNVQLAAQTLAHHGGSLPPDL   75 (83)
T ss_dssp             CHHHHHHHHHHS---CCHHHHHHHHHHTTTCHHHHHHHHHHHTSSCCTTS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCCCchhh
Confidence            488999999999   99999999999999999999999999  7 77654

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.35  E-value=6.2e-12  Score=94.88  Aligned_cols=70  Identities=9%  Similarity=0.240  Sum_probs=67.6

Q ss_pred             EEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      |+|+|++.+|+ .+.+.|..++++..||++++++.|   ++++++||+|.|+.|.++.|+++|++.+||+|+|+
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            89999999996 899999999999999999999999   89999999999999999999999999999999986

>2jy5_A Ubiquilin-1; UBA, alternative splicing, cytoplasm, nucleus, phosphoprotein, proteasome, signaling protein; NMR {Homo sapiens} PDB: 2jy6_B

Probab=99.34  E-value=1.4e-12  Score=90.94  Aligned_cols=42  Identities=24%  Similarity=0.387  Sum_probs=39.7

Q ss_pred             CCChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          156 GNNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ...|+..|++|++||   | +|+.|++||++++||++||||||++|
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            457899999999999   9 99999999999999999999999986

>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=99.33  E-value=7e-12  Score=97.52  Aligned_cols=74  Identities=11%  Similarity=0.208  Sum_probs=70.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |.|+|++.+|+.+.|.|..++++..|+++++++.|   ++++.+||+|.|+.|.++.|+.+|++.+|++|+|+++..
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            78999999999999999999999999999999999   899999999999999999999999999999999998754

>1wji_A Tudor domain containing protein 3; UBA domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.31  E-value=2.1e-12  Score=93.57  Aligned_cols=42  Identities=29%  Similarity=0.381  Sum_probs=39.2

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPE  203 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~  203 (300)
                      .+++|++|++||   |+|++|++|||+++||++||+|||+++..+
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   999999999999999999999999999544

>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.31  E-value=2.2e-12  Score=94.11  Aligned_cols=46  Identities=17%  Similarity=0.184  Sum_probs=41.9

Q ss_pred             CCChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhCCCCc
Q 022228          156 GNNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSGIPEQ  204 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~GIP~~  204 (300)
                      ...|+..|++|++||   | +|+.+++|||+++||++||||||++++++.
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            346789999999999   9 788889999999999999999999998863

>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=7.9e-12  Score=99.26  Aligned_cols=75  Identities=11%  Similarity=0.206  Sum_probs=71.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+|++.+|+.+.|.|..++++..||++++++.|   +++..+||+|.|+.|.++.|+.+|+|.++|+|+|++....
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            78999999999999999999999999999999999   8999999999999999999999999999999999987654

>1wr1_B Ubiquitin-like protein DSK2; UBA domain, UBA-ubiquitin complex, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.29  E-value=2.9e-12  Score=91.26  Aligned_cols=43  Identities=33%  Similarity=0.431  Sum_probs=39.9

Q ss_pred             CCChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhCC
Q 022228          156 GNNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSGI  201 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~GI  201 (300)
                      ...|+..|++|++||   | +|+.+++||+++++|++||||||++|.
T Consensus        14 e~~~~~qi~~L~~MG---F~d~~~~~~AL~~~~gnve~Ave~L~~~~   57 (58)
T 1wr1_B           14 EERYEHQLRQLNDMG---FFDFDRNVAALRRSGGSVQGALDSLLNGD   57 (58)
T ss_dssp             HHHTHHHHHHHHHHT---CCCHHHHHHHHHHHTSCHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHcC---CCcHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence            457899999999999   9 799999999999999999999999983

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.28  E-value=2.1e-12  Score=93.58  Aligned_cols=44  Identities=39%  Similarity=0.671  Sum_probs=40.8

Q ss_pred             ChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCCc
Q 022228          158 NLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQ  204 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~~  204 (300)
                      ..++.|++||+||   |+|++|++|||+++||++||+|||+.++++.
T Consensus         8 ~~~~~v~~L~~MG---F~~~~a~~AL~~t~~nve~A~e~L~~~~~d~   51 (63)
T 2dak_A            8 PPEDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSHIDDL   51 (63)
T ss_dssp             CCHHHHHHHHHHT---CCHHHHHHHHHHTTSCSHHHHHHHHHHHHSC
T ss_pred             CCHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCCc
Confidence            3588999999999   9999999999999999999999999997753

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.26  E-value=1.3e-11  Score=99.03  Aligned_cols=75  Identities=13%  Similarity=0.221  Sum_probs=71.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |.|+|++.+|+.+.|.|..++++..||++++++.|   +++.++||+|.|+.|.++.|+.+|++.++|+|+|++....
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            89999999999999999999999999999999999   9999999999999999999999999999999999987653

>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=99.25  E-value=2.3e-11  Score=96.87  Aligned_cols=73  Identities=14%  Similarity=0.196  Sum_probs=69.4

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+|++ +|+.+.|.|..++++..||++++++.|   +++..+||+|.|+.|.++.|..+|++.++|+|+|+++..
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            7899999 999999999999999999999999999   889999999999999999999999999999999998754

>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=99.23  E-value=9.3e-12  Score=92.72  Aligned_cols=41  Identities=20%  Similarity=0.463  Sum_probs=38.6

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIP  202 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP  202 (300)
                      .++.|++|++||   |+|++|++|||+++||++||||||+++..
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   99999999999999999999999999854

>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=99.23  E-value=5e-12  Score=91.85  Aligned_cols=45  Identities=22%  Similarity=0.354  Sum_probs=40.6

Q ss_pred             CChHHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCCCc
Q 022228          157 NNLEGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIPEQ  204 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP~~  204 (300)
                      ...+..|++|++||   |+|++|++||++++| |+++|+|||+.++++.
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            34466899999999   999999999999999 9999999999998753

>2dag_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5 (USP 5), UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=1.1e-11  Score=92.63  Aligned_cols=43  Identities=26%  Similarity=0.391  Sum_probs=40.1

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCCCc
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIPEQ  204 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP~~  204 (300)
                      .++.|++||+||   |+|++|++|||+.+| |+++|+|||++++++.
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

>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} SCOP: a.5.2.1

Probab=99.22  E-value=1.2e-11  Score=81.23  Aligned_cols=39  Identities=31%  Similarity=0.464  Sum_probs=36.3

Q ss_pred             CChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          157 NNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      +++++.|++|++||   |+|++|++||+++.||+++|++||+
T Consensus         2 ~~~~~~i~~L~~mG---f~~~~a~~AL~~~~~n~e~A~~~L~   40 (40)
T 1z96_A            2 PGLNSKIAQLVSMG---FDPLEAAQALDAANGDLDVAASFLL   40 (40)
T ss_dssp             -CHHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             chHHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHC
Confidence            35788999999999   9999999999999999999999995

>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=99.19  E-value=1.1e-11  Score=90.06  Aligned_cols=41  Identities=24%  Similarity=0.412  Sum_probs=38.1

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCCC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIPE  203 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP~  203 (300)
                      ++.|++||+||   |+|++|++|||+++| |+++|+|||++++-+
T Consensus        20 e~~i~~L~~MG---F~~~~a~~AL~~t~~~nve~A~ewL~~~~~d   61 (64)
T 2cpw_A           20 GSALDVLLSMG---FPRARAQKALASTGGRSVQTACDWLFSHSGP   61 (64)
T ss_dssp             CCHHHHHHHHT---CCHHHHHHHHHHTTTSCHHHHHHHHHSCCSC
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHcCCCCHHHHHHHHHhCCCC
Confidence            56899999999   999999999999998 999999999998643

>2ekk_A UBA domain from E3 ubiquitin-protein ligase HUWE1; ubiquitin associated domain, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=1.6e-11  Score=83.65  Aligned_cols=38  Identities=34%  Similarity=0.581  Sum_probs=35.6

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .++.|++|++||   |+|++|++|||+. ||+++|+|||++.
T Consensus         9 ~~~~v~~L~~MG---F~~~~a~~AL~~~-~n~e~A~~~L~~h   46 (47)
T 2ekk_A            9 NQQQLQQLMDMG---FTREHAMEALLNT-STMEQATEYLLTH   46 (47)
T ss_dssp             CHHHHHHHHHHH---CCHHHHHHHHHHS-CSHHHHHHHHHTC
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHc-CCHHHHHHHHHcC
Confidence            478999999999   9999999999999 7999999999864

>1whc_A RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain, structural genomics, riken structural genomics/proteomics initiative, unknown function; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.19  E-value=1.1e-11  Score=89.96  Aligned_cols=42  Identities=21%  Similarity=0.366  Sum_probs=38.7

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhc-CChHHHHHHHHhCCCCc
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAY-NNPERAVEYLYSGIPEQ  204 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAaf-nNpdrAvEyLl~GIP~~  204 (300)
                      ++.|++||+||   |+|++|++|||+++ +|+++|+|||+.++++.
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            46799999999   99999999999995 89999999999998764

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.16  E-value=9.1e-11  Score=91.44  Aligned_cols=74  Identities=16%  Similarity=0.265  Sum_probs=63.8

Q ss_pred             CEEEEEEc---CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC------ee-c-CCCCchhhcccCCCc
Q 022228            1 MMKIFVKT---LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG------KV-L-KDDTTLEENKVAENS   69 (300)
Q Consensus         1 mM~I~VKt---l~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G------ki-L-~D~~tL~d~gI~~g~   69 (300)
                      |++|+|+.   .+|+.+++.+..++||.+||.+|+..+|   +|+..|||+|.+      .+ | +|+++|.+|+|.+|+
T Consensus         9 ~v~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~g---ip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~   85 (97)
T 1wjn_A            9 LLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLK---VPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGD   85 (97)
T ss_dssp             EEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTT---CCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTC
T ss_pred             cEEEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHC---CChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCC
Confidence            36787875   5788899999999999999999999999   999999999863      22 5 677899999999999


Q ss_pred             EEEEEEec
Q 022228           70 FVVIMLTK   77 (300)
Q Consensus        70 ~I~v~v~k   77 (300)
                      +|||....
T Consensus        86 ~I~V~d~~   93 (97)
T 1wjn_A           86 CLLVRWSG   93 (97)
T ss_dssp             EEEEECCS
T ss_pred             EEEEEecC
Confidence            99998754

>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=99.15  E-value=1.7e-11  Score=87.89  Aligned_cols=32  Identities=47%  Similarity=0.858  Sum_probs=30.5

Q ss_pred             CchhhhhCcHHHHHHHHHHHhCCCchHHHHhc
Q 022228          263 GSLDFLRNSPQFQVLRAMVQANPQLFPCFKSW  294 (300)
Q Consensus       263 ~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~lq~  294 (300)
                      ++|+|||++|||++||++||+||++|++|||+
T Consensus         2 ~~l~~Lr~~Pqf~~lR~~vq~NP~~L~~lLqq   33 (61)
T 2f4m_B            2 HPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQ   33 (61)
T ss_dssp             CGGGGGTTCHHHHHHHHHHHHCGGGHHHHHHH
T ss_pred             chHHHHHcChHHHHHHHHHHHCHHHHHHHHHH
Confidence            47999999999999999999999999999986

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

Probab=99.12  E-value=5.2e-11  Score=90.73  Aligned_cols=43  Identities=23%  Similarity=0.387  Sum_probs=40.1

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCCc
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQ  204 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~~  204 (300)
                      .++.|++||+||   |+|++|++|||+++||+++|+|||++++.+.
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            478999999999   9999999999999999999999999997653

>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.12  E-value=5.7e-11  Score=84.29  Aligned_cols=38  Identities=24%  Similarity=0.599  Sum_probs=36.5

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ++.|..|++||   |.++|+.+||++.-||.|||+|||++-
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            67899999999   999999999999999999999999975

>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=99.11  E-value=9.6e-12  Score=91.90  Aligned_cols=33  Identities=45%  Similarity=0.803  Sum_probs=31.2

Q ss_pred             CCchhhhhCcHHHHHHHHHHHhCCCchHHHHhc
Q 022228          262 AGSLDFLRNSPQFQVLRAMVQANPQLFPCFKSW  294 (300)
Q Consensus       262 ~~~l~~Lr~~pqf~~lR~~vq~nP~~L~~~lq~  294 (300)
                      .++|+|||++|||++||++||+||++|++|||+
T Consensus         3 ~~~l~~Lr~~Pqf~qlR~~vqqNP~lL~~lLqq   35 (72)
T 1pve_A            3 HMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQ   35 (72)
T ss_dssp             TCTTGGGTTCTTTTTHHHHHTTCGGGHHHHHHH
T ss_pred             CchHHHHHcChHHHHHHHHHHHCHHHHHHHHHH
Confidence            467999999999999999999999999999986

>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=99.11  E-value=7.3e-11  Score=90.16  Aligned_cols=43  Identities=23%  Similarity=0.349  Sum_probs=39.8

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCCCc
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIPEQ  204 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP~~  204 (300)
                      .+++|++||+||   |+|++|++|||+++| |+++|+|||++++++.
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

>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=99.06  E-value=1.4e-10  Score=81.40  Aligned_cols=41  Identities=27%  Similarity=0.405  Sum_probs=37.5

Q ss_pred             ChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhCC
Q 022228          158 NLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSGI  201 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~GI  201 (300)
                      .|++.|++|++||   | +++.+++||+++.+|.+||||||+++.
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            6789999999999   9 666689999999999999999999874

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

Probab=99.02  E-value=2.6e-10  Score=93.29  Aligned_cols=41  Identities=37%  Similarity=0.601  Sum_probs=39.6

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIP  202 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP  202 (300)
                      .++.|++|++||   |+|++|++|||+++||++||+|||++|++
T Consensus        78 ~e~~v~~L~~MG---F~~~~a~~AL~~~~~~~e~A~e~L~~~~~  118 (126)
T 2lbc_A           78 PEEIVAIITSMG---FQRNQAIQALRATNNNLERALDWIFSHPE  118 (126)
T ss_dssp             CHHHHHHHHHHT---SCHHHHHHHHHHHTSCHHHHHHHHHTCCS
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            588999999999   99999999999999999999999999987

>2cwb_A Chimera of immunoglobulin G binding protein G and ubiquitin-like protein SB132; helical bundle, protein binding; NMR {Streptococcus SP} PDB: 2den_A

Probab=99.02  E-value=3.3e-10  Score=90.14  Aligned_cols=43  Identities=30%  Similarity=0.481  Sum_probs=39.9

Q ss_pred             CChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 022228          157 NNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSGIP  202 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~GIP  202 (300)
                      ..|++.|++|++||   | +|+++++||+++++|++||||||++|.+
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            36789999999999   9 8899999999999999999999999954

>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=99.00  E-value=2.2e-09  Score=86.46  Aligned_cols=73  Identities=18%  Similarity=0.272  Sum_probs=69.4

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+|++.+|+.+.|.|..++++..|++.++++.|   ++...+||+|.|+.|.++.|..++++.+||+|.|++..
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            67899999999999999999999999999999999   99999999999999999999999999999999999754

>2dkl_A Trinucleotide repeat containing 6C protein; TNRC6C, KIAA1582 protein, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.95  E-value=7.5e-10  Score=84.67  Aligned_cols=39  Identities=28%  Similarity=0.406  Sum_probs=37.2

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGI  201 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GI  201 (300)
                      ++.|++|++||   |+|++|++||++.++|+++|+|||+...
T Consensus        22 ~~~I~qL~~MG---F~~~~a~~AL~~~n~n~e~A~ewL~~h~   60 (85)
T 2dkl_A           22 SRLIKQLTDMG---FPREPAEEALKSNNMNLDQAMSALLEKK   60 (85)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHTTS
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHHCc
Confidence            78999999999   9999999999999999999999999873

>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=98.87  E-value=4.5e-10  Score=76.58  Aligned_cols=42  Identities=24%  Similarity=0.299  Sum_probs=38.9

Q ss_pred             ChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 022228          158 NLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIP  202 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP  202 (300)
                      +-+++|++|++||   |+|.+|++||.+.-+|.++|++||++++-
T Consensus         3 ~e~eaI~rL~~mG---F~~~~a~~Al~a~~~n~e~A~~~Lf~~~~   44 (47)
T 1dv0_A            3 QEKEAIERLKALG---FPESLVIQAYFACEKNENLAANFLLSQNF   44 (47)
T ss_dssp             CCHHHHTTTTTTT---CCHHHHHHHHTTTTSCHHHHHHHTTSCCC
T ss_pred             chHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHHhCcC
Confidence            4478999999999   99999999999999999999999998853

>2ooa_A E3 ubiquitin-protein ligase CBL-B; alpha-helical domain; 1.56A {Homo sapiens} PDB: 2oob_A 2jnh_A 2do6_A

Probab=98.79  E-value=6.2e-09  Score=71.41  Aligned_cols=38  Identities=32%  Similarity=0.406  Sum_probs=35.6

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .+..|++||+||   |+|++|++||+.+.||.|-|..+|+.
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

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.77  E-value=3.2e-08  Score=86.94  Aligned_cols=76  Identities=13%  Similarity=0.155  Sum_probs=70.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKRP   81 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~~   81 (300)
                      |+|+|+ .+|+.+.+.|..++++..||+.++++.|   ++..++||+|.|+.|.++.|..++++.+||+|+|+.......
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            678887 4899999999999999999999999999   999999999999999999999999999999999999876544

>2d9s_A CBL E3 ubiquitin protein ligase; UBA domain, dimer, protein binding, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.75  E-value=1.1e-08  Score=70.45  Aligned_cols=38  Identities=29%  Similarity=0.400  Sum_probs=35.5

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .|..|..||+||   |+|++|++||+.+.||.|-|..+|+.
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            467799999999   99999999999999999999999974

>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=1.8e-08  Score=87.60  Aligned_cols=75  Identities=13%  Similarity=0.170  Sum_probs=69.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |.|+|+ .+|+.+.|.|..++++..|++.++++.|   ++...+||+|+|+.|.++.|..++++.+||+|.|++.....
T Consensus        58 InLKVk-~dG~eV~FKIKrtTpL~KLmeAYcERqG---L~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~GG  132 (207)
T 3tix_A           58 INLKVS-DGSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGG  132 (207)
T ss_dssp             EEEEEE-CSSCEEEEEEETTSCTHHHHHHHHHHTT---CCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCTT
T ss_pred             EEEEEe-cCCCEEEEEEccCChHHHHHHHHHHHhC---CCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            678887 4899999999999999999999999999   89999999999999999999999999999999999877553

>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=98.72  E-value=9.4e-09  Score=83.24  Aligned_cols=39  Identities=18%  Similarity=0.312  Sum_probs=37.0

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      +.+.|.+|++||   |++++|+.||+...||.|||||||+++
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

>2oo9_A E3 ubiquitin-protein ligase CBL; alpha-helical domain, homodimer; 2.10A {Homo sapiens}

Probab=98.68  E-value=2.6e-08  Score=66.30  Aligned_cols=41  Identities=29%  Similarity=0.435  Sum_probs=38.6

Q ss_pred             CCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          156 GNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      |+.+|..|..||+||   |+|+.|++||-.+-||.+-|.+.|+.
T Consensus         1 ~~~~e~~I~~L~s~G---f~~~~~~rAL~ia~Nnie~A~nIL~e   41 (46)
T 2oo9_A            1 GSQLSSEIENLMSQG---YSYQDIQKALVIAQNNIEMAKNILRE   41 (46)
T ss_dssp             CCHHHHHHHHHHHTT---BCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHcC---CCHHHHHHHHHHhhccHHHHHHHHHH
Confidence            567899999999999   99999999999999999999999973

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=98.64  E-value=1.6e-08  Score=76.31  Aligned_cols=70  Identities=11%  Similarity=0.171  Sum_probs=58.3

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCee---c--CCCCchhhcccCCCcEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKV---L--KDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~Gki---L--~D~~tL~d~gI~~g~~I~v~   74 (300)
                      +|.|+||+.+| .+.|+|++++||.+||++|.+..+   ++.+.+.|.++-..   |  .++.+|+++||+.||.|+|.
T Consensus         4 ~m~lRvrs~~G-~~Ri~v~~~~t~~~L~~~I~~~~~---i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A            4 SIIIRVQSPDG-VKRITATKRETAATFLKKVAKEFG---FQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCCEEECSSE-EEECCCCSSCCHHHHHHHHHHHTC---CCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             cEEEEEECCCC-CEEEEcCCcChHHHHHHHHHHHcC---CCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            37899998877 788999999999999999999999   88788777654433   3  47789999999999999874

>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=98.61  E-value=3.1e-07  Score=68.47  Aligned_cols=71  Identities=14%  Similarity=0.256  Sum_probs=66.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC-CeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAA-QQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~-~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      +.+.++..+...+.+.|.++.+|.+|-+..+.+.+   ++.+ .++|.|.|..|+.+.++.||++.++|.|.||+
T Consensus        10 ~~~~~~~~~~~dl~f~I~~~t~v~kLi~ayc~~~~---I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           10 ITLLLRSSKSEDLRLSIPVDFTVKDLIKRYCTEVK---ISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             EEEEEEESSSCCEEEEEETTSBHHHHHHHHHHHHT---CCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HHHhhhccCCCCeEEEecCCCCHHHHHHHHHHHcC---CCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            56778888888899999999999999999999999   9898 99999999999999999999999999999986

>2juj_A E3 ubiquitin-protein ligase CBL; alpha helix, UBA domain, calcium, cytoplasm, metal- binding, phosphorylation, proto-oncogene, SH2 domain; NMR {Homo sapiens}

Probab=98.59  E-value=5.6e-08  Score=67.14  Aligned_cols=39  Identities=28%  Similarity=0.343  Sum_probs=36.6

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .|..|..||+||   |+|+.|++||+.+-||.+-|..+|+.=
T Consensus         7 ~e~~Ia~L~smG---fsr~da~~AL~ia~Ndv~~AtNiLlEf   45 (56)
T 2juj_A            7 LSSEIENLMSQG---YSYQDIQKALVIAQNNIEMAKNILREF   45 (56)
T ss_dssp             HHHHHHHHHTTT---CCHHHHHHHHHHTTTCSHHHHHHHHHS
T ss_pred             ChHHHHHHHHcC---CCHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            478999999999   999999999999999999999999854

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=98.51  E-value=6.2e-07  Score=70.08  Aligned_cols=70  Identities=9%  Similarity=0.219  Sum_probs=65.0

Q ss_pred             EEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      +.|+|+..+|+ .+.|.|..+.++..|.+..+++.|   ++....||+|.|..|..+.|..++++.+||+|.|+
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            67888888884 788999999999999999999999   88999999999999999999999999999999886

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=98.45  E-value=2.2e-08  Score=88.16  Aligned_cols=75  Identities=13%  Similarity=0.170  Sum_probs=0.4

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |.|+| ..+|+.+.|.|..++++..||+.++++.|   +++..+||+|+|+.|.++.|..++++.+||+|.|+......
T Consensus        22 InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqG---Ls~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~GG   96 (227)
T 3v7o_A           22 INLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG   96 (227)
T ss_dssp             ------------------------------------------------------------------------------C
T ss_pred             EEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhC---CCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccCC
Confidence            67888 67899999999999999999999999999   89999999999999999999999999999999999876553

>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=98.43  E-value=1.6e-07  Score=82.54  Aligned_cols=42  Identities=31%  Similarity=0.445  Sum_probs=39.6

Q ss_pred             cCCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          155 AGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       155 ~g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .+..+++.|++|++||   |+|++|+.||+...+|.++|+|||++
T Consensus       159 ~~~~~eekV~~l~~MG---f~~~~a~~AL~~~~wd~~~A~e~L~~  200 (201)
T 3k9o_A          159 SSPEYTKKIENLCAMG---FDRNAVIVALSSKSWDVETATELLLS  200 (201)
T ss_dssp             CCHHHHHHHHHHHTTT---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            4567899999999999   99999999999999999999999986

>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=98.38  E-value=4.3e-07  Score=71.41  Aligned_cols=43  Identities=30%  Similarity=0.581  Sum_probs=40.9

Q ss_pred             ChHHHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 022228          158 NLEGAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPE  203 (300)
Q Consensus       158 ~~e~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~  203 (300)
                      ++++.|..||+| |   |++++|+.||.-+.++.++|++||+.|.++
T Consensus        38 d~eekVk~L~EmtG---~seeeAr~AL~~~ngDl~~AI~~Lleg~~~   81 (104)
T 1wj7_A           38 DFEEKVKQLIDITG---KNQDECVIALHDCNGDVNRAINVLLEGNPD   81 (104)
T ss_dssp             HHHHHHHHHHHHTC---CCHHHHHHHHHHHTSCHHHHHHHHHTCSSS
T ss_pred             cHHHHHHHHHHhhC---CCHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            468899999999 9   999999999999999999999999999985

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.36  E-value=3.1e-06  Score=65.57  Aligned_cols=72  Identities=10%  Similarity=0.178  Sum_probs=67.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +.|+|+ .+|..+.+.|..+...+.|.+..+.+.|   +.+..+|++|.|..+.++.|-.++++.++|+|.+++.+
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            678888 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=98.30  E-value=5.9e-07  Score=72.63  Aligned_cols=39  Identities=28%  Similarity=0.617  Sum_probs=36.4

Q ss_pred             ChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          158 NLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .-.+.|++|++||   |+++.|++||++..||+++|+|||+.
T Consensus         7 ~e~~~v~~l~~MG---Fp~~~~~kAl~~~g~~~e~amewL~~   45 (118)
T 4ae4_A            7 SERQCVETVVNMG---YSYECVLRAMKAAGANIEQILDYLFA   45 (118)
T ss_dssp             HHHHHHHHHHHTT---CCHHHHHHHHHHHCSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC---CCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            3467899999999   99999999999999999999999986

>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=98.25  E-value=9e-07  Score=61.58  Aligned_cols=42  Identities=21%  Similarity=0.321  Sum_probs=39.0

Q ss_pred             CCChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          156 GNNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .+.|...+.+|.|||   | +++..++|||...+|.++||++|+.+
T Consensus         6 ee~~a~~L~~L~eMG---F~D~~~N~~aL~~~~gnv~~aI~~Ll~~   48 (54)
T 2cp8_A            6 SGQTAALMAHLFEMG---FCDRQLNLRLLKKHNYNILQVVTELLQL   48 (54)
T ss_dssp             CTTHHHHHHHHHHHT---CCCHHHHHHHHTTTTTCHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHcC---CCcHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            456788999999999   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=98.19  E-value=4.8e-06  Score=73.46  Aligned_cols=74  Identities=14%  Similarity=0.189  Sum_probs=68.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +.|+|++ +|+.+.+.|..++++..||+..+++.|   ++..++||+|.|+.+.+++|..++.+.++|+|.++.....
T Consensus        22 i~ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g---~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~eq~G   95 (209)
T 3uf8_A           22 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (209)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECSCTT
T ss_pred             EEEEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhC---CChheEEEEECCEeccCCCChHHhhhcccccchhhccccc
Confidence            5678887 778888999999999999999999999   9999999999999999999999999999999999977655

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

Probab=98.19  E-value=8.2e-07  Score=72.37  Aligned_cols=41  Identities=22%  Similarity=0.370  Sum_probs=37.6

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCCC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIPE  203 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP~  203 (300)
                      ++.|++|++||   |++..|++|||+..| |.++|++||+...++
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 899999999998654

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.07  E-value=1.6e-05  Score=61.66  Aligned_cols=68  Identities=16%  Similarity=0.182  Sum_probs=52.0

Q ss_pred             EEEEcC-CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeec--CCCCchhhcccCC-CcEEEEE
Q 022228            4 IFVKTL-KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVL--KDDTTLEENKVAE-NSFVVIM   74 (300)
Q Consensus         4 I~VKtl-~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL--~D~~tL~d~gI~~-g~~I~v~   74 (300)
                      |.|=.+ ++..+.+.|++++||..||++|++++|   +++++|+|||.||.|  +.++.-..|--.. ..-|+++
T Consensus        15 vHVf~~~~a~~h~v~I~~~etv~~~ke~V~eqTg---Ip~~~Q~LL~eg~~l~l~p~~~a~~~p~Tt~~~Pl~L~   86 (94)
T 4efo_A           15 IHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTK---IISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVV   86 (94)
T ss_dssp             EEEEETTTTEEEEEEEETTCBHHHHHHHHHHHHC---CCGGGEEEEETTEEECCCTTCBGGGSCCCBTTBCEEEE
T ss_pred             EEEEEcccceEEEEEeccchHHHHHHHHHHHHhC---CCHHHHHHHhCCCccccCCCCccccCCCCCCCCCEEEE
Confidence            444444 567889999999999999999999999   999999999999865  5556666664433 3444444

>2cos_A Serine/threonine protein kinase LATS2; UBA domain, structure genomics, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=97.99  E-value=8.9e-06  Score=56.11  Aligned_cols=39  Identities=26%  Similarity=0.399  Sum_probs=35.0

Q ss_pred             ChHHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHh
Q 022228          158 NLEGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYS  199 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~  199 (300)
                      ...++++.|++||   |+++.|++||+..-| ..+.|+|||.-
T Consensus         8 vn~qmlq~L~eMG---Fd~erae~Alk~Tg~~Gle~AmewL~k   47 (54)
T 2cos_A            8 VNRQMLQELVNAG---CDQEMAGRALKQTGSRSIEAALEYISK   47 (54)
T ss_dssp             CCHHHHHHHHHHH---CCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcC---CCHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            3468899999999   999999999999877 79999999973

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=97.97  E-value=9.7e-07  Score=83.78  Aligned_cols=74  Identities=14%  Similarity=0.189  Sum_probs=0.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +.|+|++ +|+.+.+.|..++++..|++..+++.|   ++.+.+|++|+|+.|.++.|.+++++++||+|.|+.....
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            5677776 678888999999999999999999999   8899999999999999999999999999999999987543

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=97.95  E-value=1.8e-05  Score=59.67  Aligned_cols=71  Identities=17%  Similarity=0.229  Sum_probs=60.5

Q ss_pred             EEEEEEc--CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-C--CCeEEEeCCeecCCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKT--LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP-A--AQQMLIYQGKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKt--l~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip-~--~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      +.|+|..  ..++.|.+.+....||+.|++.+.+.++.+ .+ .  -++|+.-+|.+|.+++.|.||+|.+||.|.+
T Consensus         5 I~ITidl~~y~~~~~DLRIP~~~tvK~Li~~l~ea~~l~-~~~~~~~~irv~NK~~~L~~~~~L~d~~ItnGD~Lei   80 (81)
T 2bps_A            5 IDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVS-MPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEI   80 (81)
T ss_dssp             EEEEEECTTTTCCEEEEEEETTSBTTHHHHHHHHHSCCC-SCCCTTCEEEEGGGTEEEETTSBTGGGTCCTTCEEEE
T ss_pred             EEEEEEeeccCCceEEEECCCchhHHHHHHHHHHHhCCC-cCCCCCCEEEEecCCEEEcCCCEEeeCCcCCCCEEEE
Confidence            5677774  689999999999999999999999998843 22 1  2568888999999999999999999999976

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=97.89  E-value=2.2e-05  Score=64.12  Aligned_cols=68  Identities=26%  Similarity=0.291  Sum_probs=56.4

Q ss_pred             EEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC-------------------------------------Ce
Q 022228            3 KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAA-------------------------------------QQ   45 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~-------------------------------------~q   45 (300)
                      .|+|+.++|+..++.|+.+.||.+++..|+.+.|   +...                                     .+
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            4899999999999999999999999999999999   5422                                     34


Q ss_pred             EEEe--CCeecCCCCchhhcccCCCcEEEE
Q 022228           46 MLIY--QGKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus        46 kLi~--~GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      ||..  .+..|+++++|.++||.++++|.+
T Consensus        90 kL~~dd~~~WLD~srtL~EQGI~e~~tllL  119 (128)
T 2kc2_A           90 KLHTDDELNWLDHGRTLREQGVEEHETLLL  119 (128)
T ss_dssp             SCCCSSSEEEECSSSCHHHHTCCTTSEEEE
T ss_pred             HhcccCCCCcccCCCcHHHcCCCCCCEEEE
Confidence            4422  236788899999999999999654

>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=97.81  E-value=4.9e-06  Score=79.45  Aligned_cols=41  Identities=24%  Similarity=0.353  Sum_probs=38.5

Q ss_pred             CChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          157 NNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .+-+++|++|++||   |+|++|++||+++.+|.+||++||+++
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            45688999999999   999999999999999999999999986

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=97.79  E-value=8.7e-05  Score=56.89  Aligned_cols=75  Identities=16%  Similarity=0.180  Sum_probs=69.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |.|+|-..+++.+.|.|.++.++.++-+..++++|   +.+++-.|.|++|.|+-+..+.-.||-+|..|.++.+.+.
T Consensus        10 m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~g---l~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~s~s   84 (90)
T 2al3_A           10 SAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQD---FNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVSRS   84 (90)
T ss_dssp             CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTT---CCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSSSC
T ss_pred             cEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhC---CChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEccCC
Confidence            58999999999999999999999999999999999   8889999999999999999999999999999999876543

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=97.77  E-value=3.4e-06  Score=80.72  Aligned_cols=74  Identities=12%  Similarity=0.180  Sum_probs=0.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +.|+|+. +++...|.|..++++..||+..+++.|   ++..+++|+|+|+.|.+++|.+++++++||+|.+++....
T Consensus        31 i~lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g---~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~g  104 (389)
T 4da1_A           31 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIG  104 (389)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             EEEEEec-CCcEEEEEECCCChHHHHHHHHHHHhC---CCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeecccc
Confidence            4567776 677788999999999999999999999   9999999999999999999999999999999999987664

>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=97.60  E-value=0.00025  Score=53.34  Aligned_cols=69  Identities=14%  Similarity=0.226  Sum_probs=58.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeec---CCCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVL---KDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL---~D~~tL~d~gI~~g~~I~v~   74 (300)
                      .+|.||..+|+.+.-.+..++||.+|...|.. .+   +.....+|+  |-.|.|   +.+++|.++|+..+.+|+|-
T Consensus         8 ~~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            8 SKLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KG---FPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   81 (84)
T ss_dssp             EEEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TT---CCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEEE
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cC---CCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEEE
Confidence            57899999999988899999999999999987 56   567888998  557888   34689999999998888774

>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=7e-05  Score=67.97  Aligned_cols=42  Identities=29%  Similarity=0.405  Sum_probs=39.5

Q ss_pred             cCCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          155 AGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       155 ~g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .+.+|++.|++|++||   |+|++|+.||+-...|.++|+|||+.
T Consensus       211 ~~~~~~~~v~~l~~mg---f~~~~~~~al~~~nWd~~~A~e~L~~  252 (253)
T 3e46_A          211 SSPEYTKKIENLCAAG---FDRNAVIVALSSKSWDVETATELLLS  252 (253)
T ss_dssp             CCHHHHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            4567899999999999   99999999999999999999999985

>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=97.53  E-value=0.0011  Score=52.44  Aligned_cols=72  Identities=15%  Similarity=0.233  Sum_probs=60.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC--C-CCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLK--D-DTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~--D-~~tL~d~gI~~g~~I~v~v~   76 (300)
                      .+|.||..+|+.+.-.+..++||.+|...|....+   .+.....|+  |-.|.|.  | +++|+++|+....+|+|...
T Consensus        14 t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~---~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~~   90 (109)
T 2dzk_A           14 ARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVG---NTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLPA   90 (109)
T ss_dssp             EEEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHT---TSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEECC
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccC---CCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEEC
Confidence            57999999999999999999999999999999877   556777886  5678886  3 67999999998877766543

>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=97.11  E-value=0.0014  Score=52.99  Aligned_cols=70  Identities=17%  Similarity=0.367  Sum_probs=59.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeec--CC-CCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVL--KD-DTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL--~D-~~tL~d~gI~~g~~I~v~v   75 (300)
                      .+|.||..+|+.+.-.+..++||.+|...|... +   +.....+|+  |-.|.|  .| +++|.++|+.....|+|..
T Consensus        44 t~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~---~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~~  118 (124)
T 1wj4_A           44 AQLMLRYPDGKREQITLPEQAKLLALVKHVQSK-G---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE  118 (124)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-H---CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEEE
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C---CCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEEE
Confidence            579999999999999999999999999999876 6   666788887  568888  34 6899999999988887653

>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=96.85  E-value=0.0093  Score=46.92  Aligned_cols=70  Identities=11%  Similarity=0.141  Sum_probs=57.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC--CCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLK--DDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~--D~~tL~d~gI~~g~~I~v~v   75 (300)
                      .+|.||..+|+.+.-.+..++||.+|...|... +   +.....+|+  |-.|.|.  .+++|+++||....+|+|..
T Consensus        24 ~~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~---~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve~   97 (109)
T 2cr5_A           24 VTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-G---YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEE   97 (109)
T ss_dssp             EEEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-T---CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C---CCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEEe
Confidence            579999999999888999999999999999865 4   446778887  5578886  36899999999888776643

>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=96.67  E-value=0.0058  Score=49.53  Aligned_cols=67  Identities=18%  Similarity=0.304  Sum_probs=54.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC-CCchhhcccCCCcE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLKD-DTTLEENKVAENSF   70 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~D-~~tL~d~gI~~g~~   70 (300)
                      .+|.||..+|+.+.-.+..++||.+|+..|..... + +......|+  |-.|.|.| +++|.++|+.....
T Consensus        53 t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~-~-~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psav  122 (127)
T 1s3s_G           53 TNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARP-A-MAATSFVLMTTFPNKELADENQTLKEANLLNAVI  122 (127)
T ss_dssp             CCEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCS-G-GGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEE
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCc-C-CCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceE
Confidence            46889999999999999999999999999988632 1 445677887  56899975 58999999997443

>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=96.66  E-value=0.0019  Score=45.59  Aligned_cols=40  Identities=25%  Similarity=0.327  Sum_probs=37.3

Q ss_pred             ChHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          158 NLEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       158 ~~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ..|+.|..|.+|  .   ++++.++..|++.-||.|+|++.|+.-
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            458999999999  7   899999999999999999999999975

>2pwq_A Ubiquitin conjugating enzyme; structural genomics consortium, SGC, ligase; 1.90A {Plasmodium yoelii}

Probab=96.36  E-value=0.00056  Score=60.56  Aligned_cols=41  Identities=29%  Similarity=0.291  Sum_probs=0.0

Q ss_pred             ChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCC
Q 022228          158 NLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGI  201 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GI  201 (300)
                      .+++.|+++++||   |+|+++++||+-.--+.++|+|.|+.|+
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            4578999999999   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=96.36  E-value=0.024  Score=42.79  Aligned_cols=71  Identities=14%  Similarity=0.184  Sum_probs=60.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe---CCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY---QGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~---~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      +++.|.....+++.+.|.+..++.+|--.|+++..   +.++...|..   .+..|+-+++|.||||++   |+.+-.++
T Consensus        11 vRLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kce---fdp~~~~Ll~d~~~~e~LdLskSLndlgirE---Lya~d~~~   84 (91)
T 2daj_A           11 VRVVINFKKTQKTIVRVSPHASLQELAPIICSKCE---FDPLHTLLLKDYQSQEPLDLTKSLNDLGLRE---LYAMDVNR   84 (91)
T ss_dssp             EEEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTT---CCTTSEEEESCSSCCCBCCTTSCHHHHTCSE---EEEEECCC
T ss_pred             EEEEEeecCcceeEEEeCCCCcHHHHHHHHhhccc---CChhhEEEecCCCCCcccchhcchhhhhhhh---hheecccc
Confidence            56778877888899999999999999999999988   8899888875   467889999999999997   66666554

>1otr_A Protein CUE2; protein-protein complex, cell cycle; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.4

Probab=96.27  E-value=0.0065  Score=41.27  Aligned_cols=39  Identities=15%  Similarity=0.240  Sum_probs=36.0

Q ss_pred             hHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      -+..|+.|+||  .   -++++|.++|+++.+|.||||..||++
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   699999999999999999999999987

>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.13  E-value=0.018  Score=41.66  Aligned_cols=44  Identities=20%  Similarity=0.242  Sum_probs=39.9

Q ss_pred             ccCCChHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          154 VAGNNLEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       154 ~~g~~~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      +.+.++++.|++|.+|  -   ++++-++..|++.-+|.|+|++-||.-
T Consensus        13 ~~~~~~~~~v~~L~~MFP~---lD~~vI~~vL~a~~G~vd~aId~LL~m   58 (67)
T 2dhy_A           13 VRRLEFNQAMDDFKTMFPN---MDYDIIECVLRANSGAVDATIDQLLQM   58 (67)
T ss_dssp             CCCCCSHHHHHHHHHHCSS---SCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            3467889999999999  5   799999999999999999999999863

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=96.02  E-value=0.053  Score=42.93  Aligned_cols=73  Identities=22%  Similarity=0.219  Sum_probs=49.9

Q ss_pred             EEEEEEcC--CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCCeEEEe----CCeecCCC------------
Q 022228            2 MKIFVKTL--KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP------AAQQMLIY----QGKVLKDD------------   57 (300)
Q Consensus         2 M~I~VKtl--~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip------~~~qkLi~----~GkiL~D~------------   57 (300)
                      |.|+|-..  .+..+.+.|-..+||.++|+||-...-+. +|      ++.+.|-+    .|++|.|.            
T Consensus        12 ltl~v~~~~~~~~~i~vkVLdCDTItQvKeKiLd~vyk~-~pyS~rP~~~~~dLEwr~g~~~~iL~D~D~ts~~~~~wkr   90 (111)
T 4e71_A           12 LTVSVIVQDEGVDAIPVKVLNCDTISQVKEKIIDQVYRG-QPCSCWPRPDSVVLEWRPGSTAQILSDLDLTSQREGRWKR   90 (111)
T ss_dssp             EEEEEEETTSCCCCEEEEEETTCBHHHHHHHHHHHHTC----------CCSEEEEEC--CCCEECCSSCTTSCC---CCC
T ss_pred             EEEEEEecCCCCCceeeeeeccCcHHHHHHHHHHHHHcC-CccccCCCCCceeeEEecCCCCccccccCccceecCcceE
Confidence            34444432  24557788889999999999997765322 33      34666765    35777662            


Q ss_pred             -CchhhcccCCCcEEEEEE
Q 022228           58 -TTLEENKVAENSFVVIML   75 (300)
Q Consensus        58 -~tL~d~gI~~g~~I~v~v   75 (300)
                       .||..|+|.+|.+|.++-
T Consensus        91 LNTL~HY~V~dgatl~l~~  109 (111)
T 4e71_A           91 VNTLMHYNVRDGATLILSK  109 (111)
T ss_dssp             CCBHHHHTCCTTCEEEEEE
T ss_pred             ecchhhcCCCCCCEEEEEe
Confidence             379999999999998764

>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=95.99  E-value=0.0054  Score=64.38  Aligned_cols=42  Identities=40%  Similarity=0.692  Sum_probs=38.3

Q ss_pred             CChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCC
Q 022228          157 NNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGI  201 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GI  201 (300)
                      ...++.|..|++||   |+++++++||++..||.+||||||++..
T Consensus       718 ~~~~e~i~~l~~mG---f~~~~a~~aL~~t~~~~eraidwlfs~~  759 (854)
T 3ihp_A          718 PPPEDCVTTIVSMG---FSRDQALKALRATNNSLERAVDWIFSHI  759 (854)
T ss_dssp             -CCHHHHHHHHTTT---CCHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcC---CCHHHHHHHHHhhcCcHHHHHHhhhcCc
Confidence            34578999999999   9999999999999999999999999863

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=95.62  E-value=0.1  Score=37.47  Aligned_cols=62  Identities=16%  Similarity=0.201  Sum_probs=46.7

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      +|+|+|..-. ....+++....||.+|.+.+    +   ++.....+..+|+++..+.     -+++||.|.++-
T Consensus         4 ~m~i~vNg~~-~~~~~~~~~~~tv~~Ll~~l----~---~~~~~v~vavN~~~v~~~~-----~L~~gD~V~ii~   65 (70)
T 1ryj_A            4 GMKFTVITDD-GKKILESGAPRRIKDVLGEL----E---IPIETVVVKKNGQIVIDEE-----EIFDGDIIEVIR   65 (70)
T ss_dssp             CEEEEEEETT-EEEEEEESSCCBHHHHHHHT----T---CCTTTEEEEETTEECCTTS-----BCCTTCEEEEEE
T ss_pred             eEEEEEeCcc-CceeEECCCCCcHHHHHHHh----C---CCCCCEEEEECCEECCCcc-----cCCCCCEEEEEe
Confidence            3888887432 34566777888999998875    4   5567777889999997665     688999998863

>2di0_A Activating signal cointegrator 1 complex subunit 2; ASCC2, CUE domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=95.59  E-value=0.034  Score=40.55  Aligned_cols=50  Identities=16%  Similarity=0.329  Sum_probs=43.3

Q ss_pred             ccCCChHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHhC-CCCccc
Q 022228          154 VAGNNLEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYSG-IPEQAE  206 (300)
Q Consensus       154 ~~g~~~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~G-IP~~~~  206 (300)
                      +++.+.+..|.+|.++  -   |....|.++|..-.+|+|+.|.+|+.| +|.++.
T Consensus         8 ~~~~~l~s~I~qV~DLfPd---LG~gfi~~~L~~y~~nvE~vin~LLE~~LPp~L~   60 (71)
T 2di0_A            8 MCGVELDSLISQVKDLLPD---LGEGFILACLEYYHYDPEQVINNILEERLAPTLS   60 (71)
T ss_dssp             CSSHHHHHHHHHHHHHCCS---SCHHHHHHHHHHTTTCHHHHHHHHHTTCCCTTTT
T ss_pred             CcHHHHHHHHHHHHHHccc---CCHHHHHHHHHHhCCCHHHHHHHHHccCCCHHHH
Confidence            4677889999999998  5   779999999999778999999999999 776643

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=95.58  E-value=0.03  Score=41.02  Aligned_cols=60  Identities=17%  Similarity=0.263  Sum_probs=46.4

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      |+|+||....+...+++....||.+|-++    .+   ++++..-+..+|+++..+.      +.+||.|.++
T Consensus         1 M~v~Vkl~g~~~~~~ev~~g~Tv~dLL~~----Lg---l~~~~VvV~vNG~~v~~d~------~l~GD~VeIv   60 (74)
T 2l32_A            1 MNVTVEVVGEETSEVAVDDDGTYADLVRA----VD---LSPHEVTVLVDGRPVPEDQ------SVEVDRVKVL   60 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHHT----TC---CCSSCCCEECCCCCCCTTS------SSCCCCEEEC
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHHH----cC---CCcceEEEEECCEECCHHH------CCCCCEEEEE
Confidence            79999977555566899999999998654    56   8888887788999986665      2348888765

>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=95.48  E-value=0.076  Score=43.56  Aligned_cols=65  Identities=23%  Similarity=0.269  Sum_probs=47.8

Q ss_pred             cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC------CCeEEEe----CCe-ecCCC-------------CchhhcccCC
Q 022228           12 TSFDVEVKPEDTVFDVKMKIETVQGSDVYPA------AQQMLIY----QGK-VLKDD-------------TTLEENKVAE   67 (300)
Q Consensus        12 ~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~------~~qkLi~----~Gk-iL~D~-------------~tL~d~gI~~   67 (300)
                      ..+.+.|-..|||.++|+||-+..-++ +|.      +++-|-+    .|+ +|.|.             .||..|+|.+
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            457888889999999999998876543 543      3455554    344 46653             2899999999


Q ss_pred             CcEEEEEEec
Q 022228           68 NSFVVIMLTK   77 (300)
Q Consensus        68 g~~I~v~v~k   77 (300)
                      |.+|.++-+.
T Consensus       120 ga~l~l~~~~  129 (138)
T 2r2o_A          120 GATVALVPCL  129 (138)
T ss_dssp             TCEEEEEEC-
T ss_pred             CCEEEEEECC
Confidence            9999887654

>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.2

Probab=95.23  E-value=0.03  Score=40.10  Aligned_cols=36  Identities=14%  Similarity=0.174  Sum_probs=33.3

Q ss_pred             HHHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          160 EGAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       160 e~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      .+.|..|.++ |   +...+|..||..+.+|.+.|++||-
T Consensus        10 ~~~Vk~LRe~TG---ag~~dcKkAL~e~~GDi~~Ai~~Lr   46 (64)
T 2cp9_A           10 KELLMKLRRKTG---YSFVNCKKALETCGGDLKQAEIWLH   46 (64)
T ss_dssp             CHHHHHHHHHHC---CCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            3679999997 8   9999999999999999999999995

>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=94.83  E-value=0.19  Score=44.41  Aligned_cols=61  Identities=16%  Similarity=0.259  Sum_probs=50.5

Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhCCCCCCCC-CeEEEe-C----CeecCC-CCchhhcccCCCcEEEEEEec
Q 022228           14 FDVEVKPEDTVFDVKMKIETVQGSDVYPAA-QQMLIY-Q----GKVLKD-DTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus        14 ~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~-~qkLi~-~----GkiL~D-~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +++.+...+||.+|+++++...+   ++.+ +.||-. .    ...|.| +.+|.+++|.++..|+|=++.
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~---i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE~r~  221 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFN---IPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQN  221 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTT---CCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEEECC
T ss_pred             EEEEecccCcHHHHHHHHHHHhC---CCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEEEec
Confidence            55778999999999999999999   8887 688853 2    346665 589999999999999887775

>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=94.69  E-value=0.26  Score=37.53  Aligned_cols=68  Identities=16%  Similarity=0.246  Sum_probs=48.7

Q ss_pred             EEEEEEcCC------C-cEEEEEeCCCCCHHHHHHHHHHHhCC--CCC------CCCCeEEEeCCeecCCCCchhhcccC
Q 022228            2 MKIFVKTLK------G-TSFDVEVKPEDTVFDVKMKIETVQGS--DVY------PAAQQMLIYQGKVLKDDTTLEENKVA   66 (300)
Q Consensus         2 M~I~VKtl~------g-~~~~ieV~~~~TV~~LK~kI~~~~g~--~~i------p~~~qkLi~~GkiL~D~~tL~d~gI~   66 (300)
                      |+|+||.+.      | ....+++....||.+|.+.+......  ..+      ......+..+|+....     ++-|+
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            889998764      3 46778888889999999999876320  000      0244667789988763     56789


Q ss_pred             CCcEEEEE
Q 022228           67 ENSFVVIM   74 (300)
Q Consensus        67 ~g~~I~v~   74 (300)
                      +||.|.++
T Consensus        85 dGDeV~i~   92 (98)
T 1vjk_A           85 DGDVVGVF   92 (98)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEE
Confidence            99998876

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=94.65  E-value=0.27  Score=39.69  Aligned_cols=66  Identities=27%  Similarity=0.294  Sum_probs=48.0

Q ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCCeEEEe----CCe-ecCCC-------------Cchhhccc
Q 022228           10 KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP------AAQQMLIY----QGK-VLKDD-------------TTLEENKV   65 (300)
Q Consensus        10 ~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip------~~~qkLi~----~Gk-iL~D~-------------~tL~d~gI   65 (300)
                      .+..+.+.|-..|||.++|+||-...-+. +|      ++++.|-|    .|+ +|.|.             .||..|+|
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            44567888889999999999998765332 44      35667765    244 46652             37899999


Q ss_pred             CCCcEEEEEEe
Q 022228           66 AENSFVVIMLT   76 (300)
Q Consensus        66 ~~g~~I~v~v~   76 (300)
                      .+|.+|.++.+
T Consensus        94 ~dgatv~l~~~  104 (127)
T 3h6n_A           94 PEGASLAMSLI  104 (127)
T ss_dssp             CTTCEEEEEEC
T ss_pred             CCCCEEEEEEc
Confidence            99999988754

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=94.35  E-value=0.2  Score=40.01  Aligned_cols=65  Identities=29%  Similarity=0.382  Sum_probs=45.8

Q ss_pred             cEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCCeEEEe-C---Ce-ecCCC-------------CchhhcccCC
Q 022228           12 TSFDVEVKPEDTVFDVKMKIETVQGSDVYP------AAQQMLIY-Q---GK-VLKDD-------------TTLEENKVAE   67 (300)
Q Consensus        12 ~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip------~~~qkLi~-~---Gk-iL~D~-------------~tL~d~gI~~   67 (300)
                      ..+.+.|-..+||.++|+||-...-+. +|      ++.+.|-+ .   |+ +|.|.             .||.+|+|.+
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            347778889999999999997765322 44      34556655 2   33 45541             3799999999


Q ss_pred             CcEEEEEEec
Q 022228           68 NSFVVIMLTK   77 (300)
Q Consensus        68 g~~I~v~v~k   77 (300)
                      |.+|.++-+.
T Consensus       106 gatl~l~~~~  115 (117)
T 4e74_A          106 GSVVALVSKQ  115 (117)
T ss_dssp             TCEEEEEECC
T ss_pred             CCEEEEEeCC
Confidence            9999887553

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=94.33  E-value=0.22  Score=43.59  Aligned_cols=61  Identities=18%  Similarity=0.320  Sum_probs=50.5

Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhCCCCCCCC-CeEEE--e-CC--eecCC-CCchhhcccCCCcEEEEEEec
Q 022228           14 FDVEVKPEDTVFDVKMKIETVQGSDVYPAA-QQMLI--Y-QG--KVLKD-DTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus        14 ~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~-~qkLi--~-~G--kiL~D-~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +.+.+...+||.+|++++....+   ++.+ +.||-  | .+  ..|+| +++|.+++|.++..|+|-++.
T Consensus       142 ~~~~~Sk~~ti~~l~~~~~~~~~---i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~r~  209 (217)
T 4a3p_A          142 VTRRFSKADTIDTIEKEIRKIFS---IPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKN  209 (217)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTT---CCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEECC
T ss_pred             eEEEEcccchHHHHHHHHHHHhC---CCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEEec
Confidence            66788999999999999999999   8876 68884  3 22  45666 579999999999999887774

>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=93.70  E-value=0.28  Score=46.00  Aligned_cols=71  Identities=13%  Similarity=0.113  Sum_probs=54.7

Q ss_pred             EEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCC-CCCCCCeEEEe------CCeecCCCCchhhcccCCCcEEEEE
Q 022228            3 KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSD-VYPAAQQMLIY------QGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~-~ip~~~qkLi~------~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      .++|... +.+-++.++++.||.++..+|.++.... ..+.++--|..      +|+-|+++++|..|++.+++.|...
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            4445433 6677899999999999999998886410 13466667766      5678999999999999999988765

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=93.69  E-value=0.15  Score=36.86  Aligned_cols=65  Identities=5%  Similarity=0.180  Sum_probs=44.2

Q ss_pred             EEEEEEcCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCC--CCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGT-SFDVEVKPEDTVFDVKMKIETVQGSDVYPA--AQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~-~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~--~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      |+|+||.+..- .-.+++ ...||.+|++.+....+   +..  ....+..+|+.+.+    .+.-+++||.|.++
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            56888866431 134666 56899999999986543   221  45667778888543    24568899999886

>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A

Probab=92.47  E-value=0.82  Score=34.72  Aligned_cols=69  Identities=12%  Similarity=0.116  Sum_probs=42.9

Q ss_pred             CEEEEEEcCC-------C-cEEEEEeC--CCCCHHHHHHHHHHHhCCCCCCC--------C----CeEEEeCCeecCCCC
Q 022228            1 MMKIFVKTLK-------G-TSFDVEVK--PEDTVFDVKMKIETVQGSDVYPA--------A----QQMLIYQGKVLKDDT   58 (300)
Q Consensus         1 mM~I~VKtl~-------g-~~~~ieV~--~~~TV~~LK~kI~~~~g~~~ip~--------~----~qkLi~~GkiL~D~~   58 (300)
                      ||+|+|+...       | +.+++++.  ...||.+|.+.+.++...  ...        .    ...+..+|+..+   
T Consensus         1 mM~i~V~~fa~lre~~~g~~~~~~~l~~~~~~Tv~~L~~~L~~~~~~--~~~~l~~~~~~~~lr~~~~v~VN~~~~~---   75 (99)
T 2qjl_A            1 MVNVKVEFLGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMIN--NPNDVSIFIEDDSIRPGIITLINDTDWE---   75 (99)
T ss_dssp             CEEEEEEEETTGGGGTTTCCEEEEEECSCSCCBHHHHHHHHHHHTCS--SGGGHHHHEETTEECTTEEEEETTEEGG---
T ss_pred             CcEEEEEEchHHHHHhCCCcEEEEecCCCCCCcHHHHHHHHHHHCch--hhHHHhhhccCCccccCeEEEECCEEcc---
Confidence            7999998652       2 45667776  678999999999888631  100        1    112333444211   


Q ss_pred             ch--hhcccCCCcEEEEE
Q 022228           59 TL--EENKVAENSFVVIM   74 (300)
Q Consensus        59 tL--~d~gI~~g~~I~v~   74 (300)
                      .+  .++-+++||.|.++
T Consensus        76 ~~~~~d~~L~dgDeVa~~   93 (99)
T 2qjl_A           76 LEGEKDYILEDGDIISFT   93 (99)
T ss_dssp             GGTGGGCBCCTTCEEEEE
T ss_pred             ccCCCCcCcCCCCEEEEE
Confidence            11  35679999998876

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=92.28  E-value=0.19  Score=37.89  Aligned_cols=61  Identities=10%  Similarity=0.188  Sum_probs=43.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPE-DTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~-~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|   +|+.+  ++... .||.+|.+.+    +   ++.....+..+|+++..+ ...+.-|++||.|-|+-
T Consensus        21 M~I~v---NGe~~--el~~~~~Tv~dLL~~L----~---~~~~~vaVavNg~iV~~~-~~~~~~L~dGD~Vei~~   82 (87)
T 1tyg_B           21 HMLQL---NGKDV--KWKKDTGTIQDLLASY----Q---LENKIVIVERNKEIIGKE-RYHEVELCDRDVIEIVH   82 (87)
T ss_dssp             -CEEE---TTEEE--CCSSSCCBHHHHHHHT----T---CTTSCCEEEETTEEECGG-GTTTSBCCSSSEEEEEE
T ss_pred             eEEEE---CCEEE--ECCCCCCcHHHHHHHh----C---CCCCCEEEEECCEECChh-hcCCcCCCCCCEEEEEc
Confidence            55555   57654  45665 8999998865    5   556777888999998543 34455689999998874

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=92.24  E-value=0.93  Score=33.46  Aligned_cols=58  Identities=14%  Similarity=0.124  Sum_probs=41.5

Q ss_pred             cEEEEEeCCCCCHHHHHHHHHHHhCCC---CCC-----CCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228           12 TSFDVEVKPEDTVFDVKMKIETVQGSD---VYP-----AAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus        12 ~~~~ieV~~~~TV~~LK~kI~~~~g~~---~ip-----~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      +...+++....||.+|++.+......-   .+.     .....+..+|+....     ++-+++||.|.++
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~~~~~~l~~~g~l~~~~~v~VN~~~v~~-----~~~l~~gDeV~i~   83 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPALESRVFGDDGELYDHINVLRNGEAAAL-----GEATAAGDELALF   83 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGGGHHHHBCTTSCBCTTSEEEETTEECCT-----TSBCCTTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcHHHHHHhccCCcccccEEEEECCEECCC-----CcccCCCCEEEEE
Confidence            567888888889999999998775300   000     023577789988865     4568899999886

>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=92.22  E-value=0.09  Score=35.83  Aligned_cols=37  Identities=22%  Similarity=0.362  Sum_probs=32.3

Q ss_pred             ChHHHHHHHHhccCCCCCHHHH--HHHHHHhcCChHHHHHHH
Q 022228          158 NLEGAIQQILDMGGGTWDRDTV--VRALRAAYNNPERAVEYL  197 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f~r~qv--~~ALrAafnNpdrAvEyL  197 (300)
                      ..+++|.+|++||   |+-+--  .+.|.+..+|..+|++-|
T Consensus         9 rl~~al~qMl~MG---F~negGWLt~LL~~k~gDI~~aLD~l   47 (52)
T 1q02_A            9 RLIESLSQMLSMG---FSDEGGWLTRLLQTKNYDIGAALDTI   47 (52)
T ss_dssp             HHHHHHHHHHTTT---CCCTTSHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHcC---CCccccHHHHHHHHccCCHHHHHHHh
Confidence            4678999999999   976654  699999999999999987

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

Probab=92.08  E-value=0.1  Score=54.65  Aligned_cols=42  Identities=26%  Similarity=0.406  Sum_probs=37.3

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCC-hHHHHHHHHhCCCC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNN-PERAVEYLYSGIPE  203 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnN-pdrAvEyLl~GIP~  203 (300)
                      .++.|++|++||   |++..+++||.+.-|+ .++|++||+..+-+
T Consensus       652 d~~~l~~L~~mG---f~~~~~~kal~~t~n~~~e~a~~wl~~hmdd  694 (854)
T 3ihp_A          652 DESVIIQLVEMG---FPMDACRKAVYYTGNSGAEAAMNWVMSHMDD  694 (854)
T ss_dssp             -CHHHHHHHHHT---CCHHHHHHHHHHTTSCCHHHHHHHHHHHTTS
T ss_pred             CHHHHHHHHhcC---CCHHHHHHHHhhcCCCchHHHhHHHhhccCc
Confidence            357899999999   9999999999999885 99999999988654

>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=91.95  E-value=0.38  Score=36.02  Aligned_cols=45  Identities=11%  Similarity=0.069  Sum_probs=39.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG   51 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G   51 (300)
                      |+|+|..-  -++.|.|..+.+..+|.++|.++.+   ++.+..+|.|+.
T Consensus         6 ~~VKV~~~--~tvairvp~~~~y~~L~~~l~~kL~---l~~~~~~LsYk~   50 (83)
T 1oey_A            6 YTLKVHYK--YTVVMKTQPGLPYSQVRDMVSKKLE---LRLEHTKLSYRP   50 (83)
T ss_dssp             EEEEEESS--SEEEEEECTTCCHHHHHHHHHHHTT---CCGGGCCEEECC
T ss_pred             EEEEEEEE--EEEEEECCCCCCHHHHHHHHHHHhC---CCcceeEEEeeC
Confidence            67777754  6899999999999999999999999   888999999964

>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=91.82  E-value=0.24  Score=39.23  Aligned_cols=69  Identities=12%  Similarity=0.100  Sum_probs=42.3

Q ss_pred             EEEEEEcCC------C--cEEEEEeCC---CCCHHHHHHHHHHHhCCCCCCCCCeEEEe-CCe------ecCCCCc---h
Q 022228            2 MKIFVKTLK------G--TSFDVEVKP---EDTVFDVKMKIETVQGSDVYPAAQQMLIY-QGK------VLKDDTT---L   60 (300)
Q Consensus         2 M~I~VKtl~------g--~~~~ieV~~---~~TV~~LK~kI~~~~g~~~ip~~~qkLi~-~Gk------iL~D~~t---L   60 (300)
                      |+|+|+...      |  +.+++++..   ..||.+|...|.+.+.     ...-+|+. +|+      +|-++..   |
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            899998664      3  366788873   3699999999887752     12222221 121      2222221   1


Q ss_pred             --hhcccCCCcEEEEEE
Q 022228           61 --EENKVAENSFVVIML   75 (300)
Q Consensus        61 --~d~gI~~g~~I~v~v   75 (300)
                        .++-+++||.|.++-
T Consensus        87 ~gldt~L~dGDeV~iip  103 (114)
T 1wgk_A           87 GELDYQLQDQDSILFIS  103 (114)
T ss_dssp             CTTTCBCCSSEEEEEEE
T ss_pred             CCcCcCCCCCCEEEEeC
Confidence              357799999987764

>2l52_A Methanosarcina acetivorans SAMP1 homolog; beta-grAsp fold, protein binding, E1-like, SAMP activator, ELSA, adenylation, ubiquitin; NMR {Methanosarcina acetivorans}

Probab=91.62  E-value=0.54  Score=35.85  Aligned_cols=70  Identities=16%  Similarity=0.236  Sum_probs=43.8

Q ss_pred             CEEEEEEcCC------C-cEEEEEeCCCCCHHHHHHHHHHHhCC--CCC-CC----CCe-------EEEeCCeecCCCCc
Q 022228            1 MMKIFVKTLK------G-TSFDVEVKPEDTVFDVKMKIETVQGS--DVY-PA----AQQ-------MLIYQGKVLKDDTT   59 (300)
Q Consensus         1 mM~I~VKtl~------g-~~~~ieV~~~~TV~~LK~kI~~~~g~--~~i-p~----~~q-------kLi~~GkiL~D~~t   59 (300)
                      ||+|+|+...      | +.++++   ..||.+|.+.+......  ..+ ..    ...       .+..+|+...... 
T Consensus         3 mm~v~V~~fa~lr~~~g~~~~~l~---~~tv~~ll~~L~~~~p~l~~~l~~~g~l~~~v~~~~~~~~v~VNg~~v~~~~-   78 (99)
T 2l52_A            3 MAEVKVKLFANLREAAGTPELPLS---GEKVIDVLLSLTDKYPALKYVIFEKGDEKSEILILCGSINILINGNNIRHLE-   78 (99)
T ss_dssp             CCEEEEEECTHHHHHHSSSEEEEE---CSSHHHHHHHHHHHCGGGTTTSBCSCCTTSSCCCBCSSCEEEETTSCGGGTT-
T ss_pred             ceEEEEEEeHHHHHHhCCCeEEEe---CCcHHHHHHHHHHHChhHHHHHhcccccccceeccccccEEEECCEEccccC-
Confidence            7899999765      3 344444   58999999999877420  001 00    123       5677887763221 


Q ss_pred             hhhcccCCCcEEEEE
Q 022228           60 LEENKVAENSFVVIM   74 (300)
Q Consensus        60 L~d~gI~~g~~I~v~   74 (300)
                      -.++-+++||.|.++
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            124468999998876

>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=91.17  E-value=1.2  Score=39.98  Aligned_cols=74  Identities=16%  Similarity=0.211  Sum_probs=56.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-CCCeEEEe---CC--eecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP-AAQQMLIY---QG--KVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip-~~~qkLi~---~G--kiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |.|.|..++| ++++.|+.+.|+.+|-+.|+.+.|   +. .+..-|.|   +|  ..|+.++.|.+.+++.+..+.+..
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            6788998998 788999999999999999999999   43 34455655   34  347888899888776666666666


Q ss_pred             ecCC
Q 022228           76 TKNK   79 (300)
Q Consensus        76 ~k~~   79 (300)
                      +++-
T Consensus        78 r~kf   81 (294)
T 1ef1_A           78 RAKF   81 (294)
T ss_dssp             EESS
T ss_pred             EEEE
Confidence            6543

>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=91.11  E-value=1.3  Score=40.21  Aligned_cols=73  Identities=14%  Similarity=0.104  Sum_probs=56.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-CCCeEEEe--CCe--ecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP-AAQQMLIY--QGK--VLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip-~~~qkLi~--~Gk--iL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |.+.|..++| ++.+.|+.+.|+.+|-+.|+.+.|   +. .+..-|.|  +|.  .|+.+++|.+.+++.+..+.+..+
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            5788999998 888999999999999999999999   43 34455555  443  478889999987766666655555


Q ss_pred             cC
Q 022228           77 KN   78 (300)
Q Consensus        77 k~   78 (300)
                      ++
T Consensus        99 ~k  100 (314)
T 1h4r_A           99 AK  100 (314)
T ss_dssp             ES
T ss_pred             EE
Confidence            54

>4dbg_B Ring finger protein 31; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens}

Probab=91.09  E-value=0.14  Score=42.85  Aligned_cols=37  Identities=19%  Similarity=0.201  Sum_probs=31.6

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHH
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYL  197 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyL  197 (300)
                      +...|.+|++.|  -|+|++|+.||+.+-+|.++|+--|
T Consensus       102 R~~K~~eL~s~G--~~~~~~~~~aL~~~~Gdv~~Al~eL  138 (162)
T 4dbg_B          102 RRRKVQELQSLG--FGPEEGSLQALFQHGGDVSRALTEL  138 (162)
T ss_dssp             HHHHHHHHHHTT--CCGGGTHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHhcC--CchHHHHHHHHHHcCCcHHHHHHHH
Confidence            345788899999  3399999999999999999999655

>1ip9_A BEM1 protein; ubiquitin alpha/beta roll, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 1ipg_A 2kfk_A

Probab=90.02  E-value=0.67  Score=34.78  Aligned_cols=42  Identities=21%  Similarity=0.141  Sum_probs=33.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY   49 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~   49 (300)
                      |||+|- .++..|.|.|..+.+..+||.||..+..   +  +.+.|++
T Consensus        13 ~KVK~y-y~DDIiAIrvP~di~~~~L~dKi~~RLk---~--~~~~l~~   54 (85)
T 1ip9_A           13 TKIKFY-YKDDIFALMLKGDTTYKELRSKIAPRID---T--DNFKLQT   54 (85)
T ss_dssp             EEEEEC-BTTCCEEEEECSCCCHHHHHHHHHHHHT---S--SCEEEEE
T ss_pred             eEEEEE-ecCcEEEEECCCCCCHHHHHHHHHHHhc---c--cceEEEE
Confidence            666665 3567999999999999999999999988   4  4555543

>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=89.82  E-value=1  Score=33.54  Aligned_cols=71  Identities=18%  Similarity=0.138  Sum_probs=44.1

Q ss_pred             EEEEEEcCC------CcEEEEEeCCCCCHHHHHHHHHHHhCC------C----CCCCCCeEEEeCCeecCCCCchhhccc
Q 022228            2 MKIFVKTLK------GTSFDVEVKPEDTVFDVKMKIETVQGS------D----VYPAAQQMLIYQGKVLKDDTTLEENKV   65 (300)
Q Consensus         2 M~I~VKtl~------g~~~~ieV~~~~TV~~LK~kI~~~~g~------~----~ip~~~qkLi~~GkiL~D~~tL~d~gI   65 (300)
                      |+|+|+.+.      |...++++ ...||.+|.+.+..++..      +    .--.....+..+|+...+..-+ ++-|
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 MNVTVSIPTILRPHTGGQKSVSA-SGDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVNIYVNDEDVRFSGGL-ATAI   78 (93)
T ss_dssp             -CEEEECCGGGGGGTTTCSEEEE-CCSBHHHHHHHHHHHSTTHHHHHBCSSSTTSBCTTEEEEETTEEGGGTTGG-GCBC
T ss_pred             CEEEEEEeHHHHHHhCCCeEEec-CCCCHHHHHHHHHHHChhHHHHHhccccCCcccCCEEEEECCEEccCcCCC-CcCC
Confidence            677887553      33334665 457999999999877531      0    0001135677788877643222 4568


Q ss_pred             CCCcEEEEE
Q 022228           66 AENSFVVIM   74 (300)
Q Consensus        66 ~~g~~I~v~   74 (300)
                      ++||.|.++
T Consensus        79 ~~gDeV~i~   87 (93)
T 3dwg_C           79 ADGDSVTIL   87 (93)
T ss_dssp             CTTCEEEEE
T ss_pred             CCCCEEEEE
Confidence            999999886

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=89.42  E-value=1.1  Score=33.60  Aligned_cols=60  Identities=13%  Similarity=0.119  Sum_probs=51.9

Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228           16 VEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus        16 ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      -.+|-..++..||+.++.+.+   +.-+.-.+...+..|+++++|.|-+|+-...|.+.+--+
T Consensus         7 qhmDI~epL~~Lk~LLe~Rl~---i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqik   66 (89)
T 2juo_A            7 QAIDINEPIGNLKKLLEPRLQ---CSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQVI   66 (89)
T ss_dssp             EEEESSSBGGGHHHHSHHHHC---SCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEEE
T ss_pred             hhccccCcHHHHHHHHHHHhc---CCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEEE
Confidence            456667899999999999999   778888888899889999999999999888888877643

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=89.40  E-value=1.4  Score=35.48  Aligned_cols=60  Identities=25%  Similarity=0.261  Sum_probs=41.0

Q ss_pred             cEEEEEeCCCCCHHHHHHHHHHH----hCCCCCC----CCCeEEEe-C---CeecCC----------C----Cchhhccc
Q 022228           12 TSFDVEVKPEDTVFDVKMKIETV----QGSDVYP----AAQQMLIY-Q---GKVLKD----------D----TTLEENKV   65 (300)
Q Consensus        12 ~~~~ieV~~~~TV~~LK~kI~~~----~g~~~ip----~~~qkLi~-~---GkiL~D----------~----~tL~d~gI   65 (300)
                      ..+.+.|-..|||.++|+||-..    .+   +|    ++.+.|-| .   |++|.|          .    .||..|+|
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            46788888999999999998643    35   43    34455544 1   233332          1    36788999


Q ss_pred             CCCcEEEEE
Q 022228           66 AENSFVVIM   74 (300)
Q Consensus        66 ~~g~~I~v~   74 (300)
                      .+|.+|-++
T Consensus       116 ~Dgatlal~  124 (126)
T 3kuz_A          116 SNGSTIKVF  124 (126)
T ss_dssp             CTTCEEEEE
T ss_pred             CCCCEEEEe
Confidence            999999765

>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=88.73  E-value=1.7  Score=43.46  Aligned_cols=75  Identities=13%  Similarity=0.111  Sum_probs=57.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--eecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ---G--KVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~---G--kiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |.|.|..++| ++.|.|+.+.|+.+|-..|+...|.  ...+.+-|.|.   |  ..|+.+++|.+.+++.+..+.+..+
T Consensus         5 i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~LgL--~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L~FR   81 (575)
T 2i1j_A            5 MNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIGL--REVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQFKFR   81 (575)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTC--CCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcCC--CCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEEEEE
Confidence            6788999998 7889999999999999999999992  12345666652   2  4578888999887777776666666


Q ss_pred             cCC
Q 022228           77 KNK   79 (300)
Q Consensus        77 k~~   79 (300)
                      ++-
T Consensus        82 vkf   84 (575)
T 2i1j_A           82 AKF   84 (575)
T ss_dssp             ESS
T ss_pred             EEE
Confidence            544

>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=88.30  E-value=2  Score=43.31  Aligned_cols=64  Identities=23%  Similarity=0.281  Sum_probs=45.1

Q ss_pred             EEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCCeEEEe----CCe-ecCCC-------------CchhhcccCCC
Q 022228           13 SFDVEVKPEDTVFDVKMKIETVQGSDVYP------AAQQMLIY----QGK-VLKDD-------------TTLEENKVAEN   68 (300)
Q Consensus        13 ~~~ieV~~~~TV~~LK~kI~~~~g~~~ip------~~~qkLi~----~Gk-iL~D~-------------~tL~d~gI~~g   68 (300)
                      .+.+.|-..|||.++|+||-+..-+. +|      ++++.|-+    .|+ +|.|.             .||.+|+|.+|
T Consensus       275 ~i~VkVLdCDTItQVKeKiLDavYk~-~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  353 (644)
T 3hm6_X          275 GVPVKVLDCDTISQAKEKMLDQLYKG-VPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  353 (644)
T ss_dssp             CEEEEEETTSBHHHHHHHHHHHHTTT-SCGGGSCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBTTTTTCCTT
T ss_pred             ceeeEeeccCcHHHHHHHHHHHHHcC-CCcccCCCCCCcceEEeeCCCCceeecccCccceecCcceeecchhhcCCCCC
Confidence            47788889999999999998654322 43      34555654    244 46553             38999999999


Q ss_pred             cEEEEEEec
Q 022228           69 SFVVIMLTK   77 (300)
Q Consensus        69 ~~I~v~v~k   77 (300)
                      .+|.++-+.
T Consensus       354 a~v~L~p~~  362 (644)
T 3hm6_X          354 ATVALVPCL  362 (644)
T ss_dssp             CEEEEEEC-
T ss_pred             cEEEEEecc
Confidence            999876543

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=88.25  E-value=2.5  Score=42.47  Aligned_cols=75  Identities=19%  Similarity=0.294  Sum_probs=50.3

Q ss_pred             EEEEEEcCC---CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCCeEEEe----CCe-ecCCC----------
Q 022228            2 MKIFVKTLK---GTSFDVEVKPEDTVFDVKMKIETVQGSDVYP------AAQQMLIY----QGK-VLKDD----------   57 (300)
Q Consensus         2 M~I~VKtl~---g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip------~~~qkLi~----~Gk-iL~D~----------   57 (300)
                      |.|+|-...   ...+.+.|-..|||.++|+||-+..-+. +|      ++++.|-+    .|+ +|.|.          
T Consensus       234 ltL~v~~~~~~~~~~i~vkVLdCDTItQVKeKiLdavYk~-~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~w  312 (627)
T 3ig3_A          234 LTLHCVCPESEGSAQVPVKVLNCDSITQAKDKLLDTVYKG-IPYSQRPKAEDMDLEWRQGRMARIILQDEDITTKIECDW  312 (627)
T ss_dssp             EEEEEECTTTC--CEEEEEEETTCBHHHHHHHHHHHHTTT-SCGGGSCCGGGEEEEEESCSSCEEEECSSSTTCCEETTE
T ss_pred             EEEEEeccCCCCCCceeeEeeccCcHHHHHHHHHHHHHcC-CCcccCCCCCccceeEeeCCCCceeeccCCccccccCce
Confidence            455554433   2457788889999999999998765322 33      34566654    233 45542          


Q ss_pred             ---CchhhcccCCCcEEEEEEec
Q 022228           58 ---TTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus        58 ---~tL~d~gI~~g~~I~v~v~k   77 (300)
                         .||.+|+|.+|.+|.++-+.
T Consensus       313 krLNTL~HY~V~Dga~v~L~p~~  335 (627)
T 3ig3_A          313 KRVNSLAHYQVTDGSLVALVPKQ  335 (627)
T ss_dssp             EECCBTTTTTCCTTCEEEEEEC-
T ss_pred             eEecchhhcCCCCCceEEEEecc
Confidence               37899999999999886554

>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=87.55  E-value=2.8  Score=39.00  Aligned_cols=73  Identities=23%  Similarity=0.233  Sum_probs=55.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC---------eecCCCCchhhcccCCCcEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQG---------KVLKDDTTLEENKVAENSFVV   72 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~G---------kiL~D~~tL~d~gI~~g~~I~   72 (300)
                      +.+.|..++|....+.|+.+.|+.+|-+.|+.+.|.  ...+..-|.+..         +-|+.+++|.+.++.....++
T Consensus        86 ~~~~V~l~dg~~~~~~vd~~tt~~el~~~v~~~l~L--~e~~~FgL~~~~~~~~~~~~~~wL~~~k~l~~q~~~~~~~l~  163 (371)
T 3ivf_A           86 RPLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGI--TNHDEYSLVRELMEEKKDDELNWLDHGRTLREQGVEEHETLL  163 (371)
T ss_dssp             EEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHTTC--SCGGGEEEECCC----------CCCTTSBTGGGTCCTTCEEE
T ss_pred             eEEEEECcCCCEEEEEECCCCCHHHHHHHHHHHcCC--CCccccEEEEEecccccchHHHHHhcCchhHhhCCCCCceEE
Confidence            578899999999999999999999999999999983  234566776632         346667788877766666655


Q ss_pred             EEEe
Q 022228           73 IMLT   76 (300)
Q Consensus        73 v~v~   76 (300)
                      +.++
T Consensus       164 frvK  167 (371)
T 3ivf_A          164 LRRK  167 (371)
T ss_dssp             EEEC
T ss_pred             EEEE
Confidence            5443

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=86.63  E-value=0.89  Score=31.83  Aligned_cols=60  Identities=12%  Similarity=0.277  Sum_probs=42.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      |+|+|   +|+.+  ++....||.+|.+.+    +   ++.....+..+|+++..+ ...+.-+++||.|.++
T Consensus         1 m~i~v---Ng~~~--~~~~~~tv~~ll~~l----~---~~~~~v~vavN~~~v~~~-~~~~~~L~~gD~v~i~   60 (66)
T 1f0z_A            1 MQILF---NDQAM--QCAAGQTVHELLEQL----D---QRQAGAALAINQQIVPRE-QWAQHIVQDGDQILLF   60 (66)
T ss_dssp             CCEEE---SSCEE--CCCTTCCHHHHHHHH----T---CCCSSEEEEETTEEECHH-HHTTCCCCTTEEECEE
T ss_pred             CEEEE---CCEEE--EcCCCCcHHHHHHHc----C---CCCCCEEEEECCEECCch-hcCCcCCCCCCEEEEE
Confidence            45544   57654  556778999998876    4   556777888899988542 2234468899999876

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=86.25  E-value=1.5  Score=30.80  Aligned_cols=63  Identities=16%  Similarity=0.135  Sum_probs=40.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+|+|...+|+.  +++....|+.+|-+.|....+     ....-...+|++.+-+     +-|++|+.|.++..
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            556777667876  456678899999888744332     1222334688877554     45667888877654

>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=85.68  E-value=3.3  Score=31.20  Aligned_cols=47  Identities=4%  Similarity=0.112  Sum_probs=37.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC-CeEEEeCCe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAA-QQMLIYQGK   52 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~-~qkLi~~Gk   52 (300)
                      |+|++. .+|..+.+.|+++.+..+|.++|.+..+   +... .+.|-|...
T Consensus         7 vkvK~~-~~gdi~~~~v~~~i~~~~L~~kv~~~~~---~~~~~~f~lky~DE   54 (89)
T 1vd2_A            7 VRVKAY-YRGDIMITHFEPSISFEGLCNEVRDMCS---FDNEQLFTMKWIDE   54 (89)
T ss_dssp             EEEEEE-SSSCEEEEEECTTCCHHHHHHHHHHHTT---CCSSCCEEEEECCS
T ss_pred             EEEEEE-eCCeEEEEECCCCCCHHHHHHHHHHHhC---CCCCCeEEEEEECC
Confidence            666666 4678899999999999999999999988   6544 477778643

>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=85.52  E-value=3.1  Score=37.66  Aligned_cols=70  Identities=10%  Similarity=-0.033  Sum_probs=51.1

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--eecCCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ---G--KVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~---G--kiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      |.+.|..++|....+.|+...|+.+|-+.|+.+.|.  ...+..-|.|.   |  ..|+.++.|.+........+++
T Consensus        18 ~~~~V~lldgt~~~~~vd~~tt~~el~~~v~~~l~L--~e~~~FgL~~~~~~~~~~wLd~~k~i~~q~~~~~~~l~f   92 (296)
T 3qij_A           18 GHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNL--LEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTF   92 (296)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHTC--SSGGGEEEEEEEETTEEEECCTTSBHHHHC---CCEEEE
T ss_pred             EEEEEEccCCCEEEEEECCCCCHHHHHHHHHHHcCC--CCcceeEEEEEcCCCccchhccchhHHHhcCCCCcEEEE
Confidence            678999999999999999999999999999999993  23344566552   3  3578888888764333334444

>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=85.14  E-value=0.78  Score=33.64  Aligned_cols=63  Identities=17%  Similarity=0.242  Sum_probs=44.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-CCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYP-AAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip-~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|   +|+.+.+......||.+|.+.+    +   ++ ....-+.++|.++.. ....++-+++||.|-++-
T Consensus         1 M~I~v---NGe~~e~~~~~~~Tl~~LL~~l----~---~~~~~~vAVavNg~iVpr-~~~~~~~L~dGD~IEIv~   64 (78)
T 2k5p_A            1 MNLTV---NGKPSTVDGAESLNVTELLSAL----K---VAQAEYVTVELNGEVLER-EAFDATTVKDGDAVEFLY   64 (78)
T ss_dssp             CEEEE---TTEEEECSSCSCEEHHHHHHHH----T---CSCTTTCCEEETTEECCT-THHHHCEECSSBCEEECC
T ss_pred             CEEEE---CCEEEEcCCCCCCcHHHHHHHc----C---CCCCCcEEEEECCEECCh-HHcCcccCCCCCEEEEEe
Confidence            56655   5776544321568999987753    5   66 667778899999855 345667789999998764

>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=84.81  E-value=0.59  Score=40.99  Aligned_cols=24  Identities=25%  Similarity=0.527  Sum_probs=21.7

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHh
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAA  186 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAa  186 (300)
                      +..|+++++||   |+++.|+.||+-.
T Consensus       170 ~~~v~~~~~mg---~~~~~~~~al~~~  193 (215)
T 1tte_A          170 HDLIDEFESQG---FEKDKIVEVLRRL  193 (215)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHHS
T ss_pred             HHHHHHHHHcC---CCHHHHHHHHHHc
Confidence            67999999999   9999999999643

>2c7h_A RBBP6, retinoblastoma-binding protein 6, isoform 3; P53-associated, mRNA processing, splicing-associated, oesophageal cancer; NMR {Homo sapiens}

Probab=84.42  E-value=2.5  Score=31.78  Aligned_cols=44  Identities=20%  Similarity=0.068  Sum_probs=32.0

Q ss_pred             CEEEEEEcCCCcE-EEEEeC-CCCCHHHHHHHHHHHhCCCCCCCCCeEE
Q 022228            1 MMKIFVKTLKGTS-FDVEVK-PEDTVFDVKMKIETVQGSDVYPAAQQML   47 (300)
Q Consensus         1 mM~I~VKtl~g~~-~~ieV~-~~~TV~~LK~kI~~~~g~~~ip~~~qkL   47 (300)
                      |..|+.|....+. ..|.++ ...+|.+||+.|..+.+   +-..+.-|
T Consensus         6 mS~V~YKFkS~k~~~~v~fdG~~Isv~dLKr~I~~~~k---l~~~dfDL   51 (86)
T 2c7h_A            6 MSCVHYKFSSKLNYDTVTFDGLHISLCDLKKQIMGREK---LKAADCDL   51 (86)
T ss_dssp             BEEEEEEETTCSSEEEEEESSSEEEHHHHHHHHHHHHT---CCTTTEEE
T ss_pred             eeEEEEEEeecCCcceEEEcCCEEEHHHHHHHHHHHhC---CCCCcccE
Confidence            5678888776654 447777 67899999999998887   43344544

>2ns5_A Partitioning-defective 3 homolog; cell polarity, N-terminal domain, PB1 domain, asymmetric membrane localization, signaling protein; NMR {Rattus norvegicus}

Probab=83.72  E-value=11  Score=28.07  Aligned_cols=73  Identities=21%  Similarity=0.146  Sum_probs=47.9

Q ss_pred             CEEEEEEcCCCcEEEEEeC-CCCCHHHHHHHHHHHhCCC-CC-CCCCeE---EEe-CCeecCCCCchhhcccCCCcEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVK-PEDTVFDVKMKIETVQGSD-VY-PAAQQM---LIY-QGKVLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~-~~~TV~~LK~kI~~~~g~~-~i-p~~~qk---Li~-~GkiL~D~~tL~d~gI~~g~~I~v   73 (300)
                      .|+|+|+. .+..+.|-+. ...||..|-++--.++-+. .. +.....   |-+ .|-+|+.+..|.+. +.++++|+-
T Consensus         2 ~MKvtV~f-g~~~vvVPC~dg~~tV~~L~~~A~~RY~K~~~k~~~~~v~V~~l~~~~ggiLD~DD~l~dV-ldD~e~i~A   79 (85)
T 2ns5_A            2 EFKVTVCF-GRTRVDVPCGDGRMKVFSLIQQAVTRYRKAVAKDPNYWIQVHRLEHGDGGILDLDDILCDV-ADDKDRLVA   79 (85)
T ss_dssp             CEEEEEEE-TTEEEEEEESSSCCCHHHHHHHHHHHHHHHTTCCTTSCEEEEEEECSSSCEECTTSCHHHH-SCTTEEEEE
T ss_pred             ccEEEEEE-CCEEEEEECCCCcccHHHHHHHHHHHHHHhcCCCCCcEEEEEEEEeCCCcEeCcccchhhh-ccCcceEEE
Confidence            48999995 5677788875 4569999877654443210 02 122222   224 78899999999997 678888876


Q ss_pred             EE
Q 022228           74 ML   75 (300)
Q Consensus        74 ~v   75 (300)
                      +.
T Consensus        80 ~~   81 (85)
T 2ns5_A           80 VF   81 (85)
T ss_dssp             EE
T ss_pred             Ee
Confidence            54

>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=83.37  E-value=0.92  Score=31.89  Aligned_cols=28  Identities=11%  Similarity=0.210  Sum_probs=24.5

Q ss_pred             CCChHHHHHHHHhccCCCCCHHHHHHHHHHh
Q 022228          156 GNNLEGAIQQILDMGGGTWDRDTVVRALRAA  186 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAa  186 (300)
                      +...+++|.-|+.+|   |.+.++.+|++..
T Consensus        14 ~~~~~ea~~AL~aLG---Y~~~ea~kav~~v   41 (62)
T 1ixs_A           14 SEAAEEAVMALAALG---FKEAQARAVVLDL   41 (62)
T ss_dssp             CHHHHHHHHHHHHTT---CCHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHcC---CCHHHHHHHHHHH
Confidence            345578999999999   9999999999876

>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=82.94  E-value=2.8  Score=31.23  Aligned_cols=41  Identities=10%  Similarity=0.157  Sum_probs=34.3

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ..-+.+|-+.=|.+.++.+.+.|.-.+-+|++||+.|+|+.
T Consensus        35 ~SCLd~iR~VlGdsV~e~~Lv~ailk~dfD~ekALd~vL~~   75 (83)
T 1ufz_A           35 YSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQ   75 (83)
T ss_dssp             HHHHHHHHHHTTTTSCHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccCCHHHHHHHHHHhcCCHHHHHHHHHhc
Confidence            44567777765678999999999888999999999999964

>1p3q_Q VPS9P, vacuolar protein sorting-associated protein VPS9; trafficking, post translational modification, mono- ubiquitination; 1.70A {Saccharomyces cerevisiae} SCOP: a.5.2.4 PDB: 1mn3_A

Probab=82.84  E-value=0.46  Score=32.71  Aligned_cols=40  Identities=20%  Similarity=0.209  Sum_probs=31.2

Q ss_pred             CChHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          157 NNLEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       157 ~~~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .+.++.|++|.+|  .   ++++=++.-|++--+|.|-+|+.||.
T Consensus        10 ~e~~~~~~~L~~MFP~---lD~evI~~Vl~a~~G~~~~~IdaLLq   51 (54)
T 1p3q_Q           10 NERKDTLNTLQNMFPD---MDPSLIEDVCIAAASRIGPCVDALLS   51 (54)
T ss_dssp             HHHHHHHHHHHHHSTT---SCHHHHHHHHHHSCC--CGGGC----
T ss_pred             HHHHHHHHHHHHHccc---CCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            3568899999999  5   89999999999999999999999973

>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative, NEW research center for structural genomics, nysgxrc; 2.10A {Haemophilus influenzae} SCOP: d.15.3.4

Probab=81.48  E-value=2  Score=32.86  Aligned_cols=70  Identities=10%  Similarity=-0.050  Sum_probs=47.4

Q ss_pred             CEEEEEEcC-C--CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTL-K--GTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl-~--g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      ||+|.|..- .  +..+.+++....||.++-+...-......+.....++-.+|++..     .+.-+++||.|-++-
T Consensus        12 ~~~v~v~ya~p~rq~~~~~~v~~g~TV~daI~~~gi~~~~peIdl~~~~V~Vng~~v~-----~d~~L~dGDRVEIyr   84 (97)
T 2hj1_A           12 QINIEIAYAFPERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIGIFSRPIK-----LTDVLKEGDRIEIYR   84 (97)
T ss_dssp             EEEEEEEEEETTEEEEEEEEEETTCBHHHHHHHHTHHHHCTTCCTTTSEEEEEECSCC-----TTCBCCTTCEEEECC
T ss_pred             eEEEEEEEeCCCCCEEEEEEcCCCCcHHHHHHHcCCCccCCcccccccEEEEcCEECC-----CCccCCCCCEEEEEe
Confidence            467777543 2  335667888999999998876542221014455678888888887     444588899998763

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=81.43  E-value=3.1  Score=29.53  Aligned_cols=54  Identities=9%  Similarity=0.085  Sum_probs=39.6

Q ss_pred             cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCe--EEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228           12 TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQ--MLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus        12 ~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~q--kLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      +...+++....||.+|.+.+......    ....  .+..+|+....+     .-+++||.|.++
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            35667777778999999998876420    1233  778899988753     568899998876

>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=81.10  E-value=5.9  Score=30.49  Aligned_cols=73  Identities=19%  Similarity=0.066  Sum_probs=50.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE------eCCeecCCCCchhhc----ccCCCcEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI------YQGKVLKDDTTLEEN----KVAENSFV   71 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi------~~GkiL~D~~tL~d~----gI~~g~~I   71 (300)
                      +.|+|-..+|....|.|+..+|+.++-+++..+.++. . ...--|+      +--+.|+|...|-+.    .+.....+
T Consensus        10 ~vvkvf~~Dgssksi~V~~~~Ta~dv~~~L~~K~~~~-~-~~~WaLvE~~P~L~~ER~~EDHE~vvevl~~W~~~s~nr~   87 (100)
T 1wgr_A           10 HVVKVYSEDGACRSVEVAAGATARHVCEMLVQRAHAL-S-DETWGLVECHPHLALERGLEDHESVVEVQAAWPVGGDSRF   87 (100)
T ss_dssp             EEEEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCC-C-CCCCCEEEEETTTTEEEEECSSSCHHHHHTTSCSSSCCEE
T ss_pred             EEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCC-C-CCCeEEEEecCCCCcEEeccCchhHHHHHhhCccCCCcEE
Confidence            3466667899999999999999999999999998842 1 2222232      134788998776555    45556666


Q ss_pred             EEEEe
Q 022228           72 VIMLT   76 (300)
Q Consensus        72 ~v~v~   76 (300)
                      ++..+
T Consensus        88 ~F~kr   92 (100)
T 1wgr_A           88 VFRKN   92 (100)
T ss_dssp             EECSC
T ss_pred             EEecc
Confidence            55433

>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei}

Probab=81.08  E-value=0.33  Score=38.20  Aligned_cols=69  Identities=12%  Similarity=0.062  Sum_probs=41.1

Q ss_pred             EEEEEEcCC------CcEEEEEeCC----CCCHHHHHHHHHHHhCCCCCCCCCeEEE-eCC--e------ecCCCCch--
Q 022228            2 MKIFVKTLK------GTSFDVEVKP----EDTVFDVKMKIETVQGSDVYPAAQQMLI-YQG--K------VLKDDTTL--   60 (300)
Q Consensus         2 M~I~VKtl~------g~~~~ieV~~----~~TV~~LK~kI~~~~g~~~ip~~~qkLi-~~G--k------iL~D~~tL--   60 (300)
                      |+|+||...      |+..++++..    ..||.+|-..|.+...     ..+-+|+ -+|  +      +|-+++.+  
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            677887654      3555677763    2499999888877743     2222332 123  1      33333333  


Q ss_pred             ---hhcccCCCcEEEEEE
Q 022228           61 ---EENKVAENSFVVIML   75 (300)
Q Consensus        61 ---~d~gI~~g~~I~v~v   75 (300)
                         .+|-+++||.|.++-
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

>1aip_C EF-TS, elongation factor TS; nucleotide exchange, GTP-binding, complex of two elongation factors; 3.00A {Thermus thermophilus} SCOP: a.5.2.2 d.43.1.1

Probab=80.03  E-value=2.5  Score=36.56  Aligned_cols=37  Identities=30%  Similarity=0.268  Sum_probs=33.1

Q ss_pred             HHHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          160 EGAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       160 e~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      -.+|.+|-++ |   ..=-+|..||..+.+|.|.|+|||--
T Consensus         4 a~~VKeLRe~TG---agmmdCKkAL~e~~GD~ekAie~LR~   41 (196)
T 1aip_C            4 MELIKKLREATG---AGMMDVKRALEDAGWDEEKAVQLLRE   41 (196)
T ss_dssp             HHHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            3578999988 7   88899999999999999999999963

---

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	300
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	4e-29
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	7e-26
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	7e-22
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	3e-21
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	4e-21
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	1e-19
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	2e-19
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	6e-19
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	6e-19
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	9e-19
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	2e-18
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	3e-18
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	1e-17
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	5e-17
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	6e-17
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	9e-17
d1oqya1	41	a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Hum	3e-16
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	4e-16
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	3e-15
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	5e-15
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	1e-14
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	1e-14
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	2e-14
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	2e-14
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	4e-14
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	4e-14
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	5e-14
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	4e-12
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	5e-12
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	2e-11
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	2e-11
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	3e-10
d1wjia_	63	a.5.2.1 (A:) Tudor domain containing protein 3, TD	3e-10
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	3e-09
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	5e-09
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	5e-09
d1wiva_	73	a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress	5e-09
d1wgna_	63	a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1	2e-08
d2f4mb1	58	a.189.1.1 (B:275-332) XPC-binding domain of Rad23	9e-08
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	1e-07
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	3e-07
d1vg5a_	73	a.5.2.1 (A:) Rhomboid family protein At3g58460 {Th	1e-06
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	1e-06
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	1e-05
d1whca_	64	a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus	2e-04
d2bwba1	44	a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharom	0.001

>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 =  104 bits (260), Expect = 4e-29
 Identities = 31/75 (41%), Positives = 51/75 (68%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          + I +KTL+  +F + ++P++TV  +K KIE  +G D +P A Q LIY GK+L DD  + 
Sbjct: 3  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 62

Query: 62 ENKVAENSFVVIMLT 76
          + ++ E +FVV+M+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 = 96.3 bits (239), Expect = 7e-26
 Identities = 38/86 (44%), Positives = 58/86 (67%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M++ +KTL+  +F +++ PE+TV  +K KIE+ +G D +P A Q LIY GK+L DDT L+
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 62 ENKVAENSFVVIMLTKNKRPTGEGST 87
          E K+ E +FVV+M+TK K  +     
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 = 84.9 bits (210), Expect = 7e-22
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M I VKTL G   +++++P DT+  +K ++E  +G    P  QQ LIY GK L DD T +
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEG---IPPVQQRLIYAGKQLADDKTAK 57

Query: 62 ENKVAENSFVVIML 75
          +  +   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 = 83.4 bits (206), Expect = 3e-21
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 3/74 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M+IFVKTL G +  +EV+P DT+ +VK KI+  +G    P  QQ LI+ GK L+D  TL 
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLS 57

Query: 62 ENKVAENSFVVIML 75
          +  + + 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 = 83.0 bits (205), Expect = 4e-21
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           + I V+  KG S   EV+   TV  +K ++    G +        L ++GK L+D   L
Sbjct: 3  PLSILVRNNKGRSSTYEVRLTQTVAHLKQQV---SGLEGVQDDLFWLTFEGKPLEDQLPL 59

Query: 61 EENKVAENSFVVIML 75
           E  +   S V + L
Sbjct: 60 GEYGLKPLSTVFMNL 74

>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 = 79.6 bits (196), Expect = 1e-19
 Identities = 26/110 (23%), Positives = 42/110 (38%), Gaps = 23/110 (20%)

Query: 2   MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDT-TL 60
           + + +K L  T      +PEDTV  +K K    Q S      Q  LIYQG++L+D   TL
Sbjct: 8   INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQES------QMKLIYQGRLLQDPARTL 61

Query: 61  EENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTPAATPATA 110
               +  N  +    +                      S P+ ++ P++ 
Sbjct: 62  SSLNITNNCVIHCHRSPPG----------------AAVSGPSASSGPSSG 95

>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 = 78.6 bits (194), Expect = 2e-19
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          + I +K+ +   ++V V PE TV   K  I    G    P A Q LIY GK+LKDD T+E
Sbjct: 2  LNIHIKSGQDK-WEVNVAPESTVLQFKEAINKANG---IPVANQRLIYSGKILKDDQTVE 57

Query: 62 ENKVAENSFVVIMLTKNK 79
             + +     + L K++
Sbjct: 58 SYHIQDGH--SVHLVKSQ 73

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.2 bits (190), Expect = 6e-19
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++ VKTL   +    V  +  V + K  I         P+ +Q LIYQG+VL+DD  L+
Sbjct: 1  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS---IPSEKQRLIYQGRVLQDDKKLQ 57

Query: 62 ENKVAENSFVVIM 74
          E  V      ++ 
Sbjct: 58 EYNVGGKVIHLVE 70

>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 = 77.2 bits (190), Expect = 6e-19
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          M +FV+      F VEV  + ++  +K  +   QG    PA Q  +I+ GK L +  T++
Sbjct: 3  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQG---VPADQLRVIFAGKELPNHLTVQ 59

Query: 62 ENKVAENSFVVIMLTKNKRPTGE 84
             + + S V I+     RP   
Sbjct: 60 NCDLEQQSIVHIVQ----RPRRR 78

>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 = 77.3 bits (190), Expect = 9e-19
 Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +++FVK   G S+   + P   +  +K +IE  QG    P  QQ L +QG+VL+D   L 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLG 64

Query: 62 ENKVAENSFVVIMLTKNKRPT 82
             + ++  +++   K   P+
Sbjct: 65 IYGIQDSDTLILSKKKGSGPS 85

>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 = 76.1 bits (187), Expect = 2e-18
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 3/82 (3%)

Query: 2  MKIFVKTL--KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
          + + VK+   +    ++      +V  +K  +  V          Q LIY GK+L D   
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERP-RPEDQRLIYSGKLLLDHQC 66

Query: 60 LEENKVAENSFVVIMLTKNKRP 81
          L +    +    V+ L  N + 
Sbjct: 67 LRDLLPKQEKRHVLHLVCNVKS 88

>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 = 76.6 bits (188), Expect = 3e-18
 Identities = 22/108 (20%), Positives = 36/108 (33%), Gaps = 15/108 (13%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKI-----ETVQGSDVYPAAQQMLIYQGKVLK 55
           M+ + +  + G + +    P D+  D+   +        +   V       LIYQG+ L 
Sbjct: 16  MINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLH 75

Query: 56  DDTTLEENKVAENSFVVIMLTKNKRPTGEGSTRSTAPTKAPQSSAPTP 103
            + TL   K+      V+ L            R T P    Q     P
Sbjct: 76  GNVTLGALKLPFGKTTVMHLVA----------RETLPEPNSQGQRSGP 113

>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 = 73.4 bits (180), Expect = 1e-17
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 9/82 (10%)

Query: 2  MKIFVKTLKG--TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
          M I V+T+ G  T    +V  + T+ +++ ++  +          Q L Y+GK L++  T
Sbjct: 1  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD---VRPECQRLFYRGKQLENGYT 57

Query: 60 LEENKVAENSFVVIMLTKNKRP 81
          L +  V  N  + +++    RP
Sbjct: 58 LFDYDVGLNDIIQLLV----RP 75

>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 = 72.3 bits (177), Expect = 5e-17
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
           ++ ++   G    + V+  DTVF +K ++   +G        Q   + G+ L D    E
Sbjct: 4  CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG---VEPGSQRWFFSGRPLTDKMKFE 60

Query: 62 ENKVAENSFVVIMLTK 77
          E K+ ++  V +++++
Sbjct: 61 ELKIPKDYVVQVIVSQ 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 = 71.9 bits (176), Expect = 6e-17
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 4  IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ--GKVLKDDTTLE 61
          + VK L G  F V +    +V ++K +I    G     A QQ L     G  L+D   L 
Sbjct: 3  LTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG---VHAFQQRLAVHPSGVALQDRVPLA 59

Query: 62 ENKVAENSFVVIMLTK 77
             +   S V++++ K
Sbjct: 60 SQGLGPGSTVLLVVDK 75

>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 = 71.5 bits (175), Expect = 9e-17
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 2  MKIFVKTLKG--TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
          M I V+T+ G  T     +     V +++ KI+ +          Q L Y+GK ++D  T
Sbjct: 1  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFH---VEPGLQRLFYRGKQMEDGHT 57

Query: 60 LEENKVAENSFVVIMLTKN 78
          L + +V  N  + +++ ++
Sbjct: 58 LFDYEVRLNDTIQLLVRQS 76

>d1oqya1 a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]} Length = 41

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.8 bits (169), Expect = 3e-16
 Identities = 22/44 (50%), Positives = 31/44 (70%), Gaps = 3/44 (6%)

Query: 156 GNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS 199
           G+  E  + +I+ MG   ++R+ VV ALRA+YNNP RAVEYL +
Sbjct: 1   GSEYETMLTEIMSMG---YERERVVAALRASYNNPHRAVEYLLT 41

>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 = 70.0 bits (171), Expect = 4e-16
 Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 6/85 (7%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY---QGKVLKDD 57
           + I VK          +  +DTV D+K  ++T+ G       +Q L+    +GK  ++D
Sbjct: 7  GLPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTG---VLPERQKLLGLKVKGKPAEND 63

Query: 58 TTLEENKVAENSFVVIMLTKNKRPT 82
            L   K+  N+ +++M T+   P+
Sbjct: 64 VKLGALKLKPNTKIMMMGTRESGPS 88

>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 = 68.1 bits (166), Expect = 3e-15
 Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          M+++      G    V+   +DT+ D+K  I    G       + +L     + KD  +L
Sbjct: 28 MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRWNKIVLKKWYTIFKDHVSL 84

Query: 61 EENKVAENSFV 71
           + ++ +   +
Sbjct: 85 GDYEIHDGMNL 95

>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 = 66.6 bits (162), Expect = 5e-15
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          M+++ V    G    V+   ED+V D K  +            + +L   G VLKD  +L
Sbjct: 1  MIEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQI---GTQPNKIVLQKGGSVLKDHISL 57

Query: 61 EENKVAENSFV 71
          E+ +V + + +
Sbjct: 58 EDYEVHDQTNL 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 = 66.6 bits (162), Expect = 1e-14
 Identities = 17/103 (16%), Positives = 29/103 (28%), Gaps = 21/103 (20%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQM-------------- 46
            M + V  + G    V V    TV D+K  I+           ++               
Sbjct: 7   GMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ---LKQEREGGVQHISWSYVWRTY 63

Query: 47  -LIYQGKVLKDDT-TLEENKVAENSFVVIMLTKNKRPTGEGST 87
            L   G+ L +D   L +  +       +   K        S+
Sbjct: 64  HLTSAGEKLTEDRKKLRDYGIRNRD--EVSFIKKLGQKSGPSS 104

>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 = 66.2 bits (161), Expect = 1e-14
 Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 8/97 (8%)

Query: 2   MKIFV----KTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDD 57
           M I V    + L   +F ++V P+  + + ++  E   G    PA +  ++Y  ++L DD
Sbjct: 8   MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG---VPAEEAQIVYMEQLLTDD 64

Query: 58  T-TLEENKVAENSFVVIMLTKNKRPTGEGSTRSTAPT 93
             +L    + +   VV++   N      G T S   +
Sbjct: 65  HCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTPSGPSS 101

>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 = 65.8 bits (160), Expect = 2e-14
 Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
             + VK  K     VE+  ++     K ++  + G       +Q ++ +G  LKDD   
Sbjct: 7  GYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPA---RQKVMVKGGTLKDD-DW 62

Query: 61 EENKVAENSFVVIMLTKNKRPTGEGSTRSTAPT 93
             K+     V++M + +  P  E S +++ P+
Sbjct: 63 GNIKMKNGMTVLMMGSADALPE-EPSAKTSGPS 94

>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 = 65.0 bits (158), Expect = 2e-14
 Identities = 16/78 (20%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          ++++ VKT +    +  +     V   K +I          A + +LI+ GK+L+D   L
Sbjct: 10 IIRVSVKTPQDC-HEFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDIL 65

Query: 61 EENKVAENSFVVIMLTKN 78
           +  + + S V +++  +
Sbjct: 66 SQRGILDGSTVHVVVRSH 83

>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 = 64.5 bits (157), Expect = 4e-14
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 9  LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAEN 68
          L G      +   D V  +K+KI    G    PA +Q L Y+G  +KD  +L    +A  
Sbjct: 19 LNGQVLVFTLPLTDQVSVIKVKIHEATG---MPAGKQKLQYEGIFIKDSNSLAYYNMANG 75

Query: 69 SFVVIML 75
          + + + L
Sbjct: 76 AVIHLAL 82

>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 = 65.0 bits (158), Expect = 4e-14
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 2   MKIFV--KTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
           +++F+  +  K     +E +   T  +++ KI    G          ++   K L+   T
Sbjct: 18  IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG---LQENYIKIVINKKQLQLGKT 74

Query: 60  LEENKVAENSFVVIMLTKNKRPTGEG 85
           LEE  VA N   +++  K       G
Sbjct: 75  LEEQGVAHNVKAMVLELKQSSGPSSG 100

>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 = 64.9 bits (158), Expect = 5e-14
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 7/97 (7%)

Query: 4  IFVKTLKG-TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEE 62
          +F+   +  T+   + K   TVF++K  +E +      P  +Q L    ++L D  TL E
Sbjct: 2  VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK---RPPDEQRLYKDDQLLDDGKTLGE 58

Query: 63 NKVAENSFVV---IMLTKNKRPTGEGSTRSTAPTKAP 96
                +        +    R           P  +P
Sbjct: 59 CGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSP 95

>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 = 58.7 bits (142), Expect = 4e-12
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 10/83 (12%)

Query: 2  MKIFVKTLKGTSFDVEVKP-----EDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLK- 55
          + + V        D+ V       E  V D+   +E V G    P + Q LI++GK LK 
Sbjct: 2  LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIG---VPQSFQKLIFKGKSLKE 57

Query: 56 DDTTLEENKVAENSFVVIMLTKN 78
           +T L    + +   V+++  KN
Sbjct: 58 METPLSALGIQDGCRVMLIGKKN 80

>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 = 58.9 bits (142), Expect = 5e-12
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 4/80 (5%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          ++K+ VKT K    D  V    T+  +K +I            Q +LI+ GK+LKD  +L
Sbjct: 7  LIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSL 62

Query: 61 EENKVAENSFVVIMLTKNKR 80
           +  V +   V +++ +  R
Sbjct: 63 AQCGVRDGLTVHLVIKRQHR 82

>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 = 57.6 bits (139), Expect = 2e-11
 Identities = 13/80 (16%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 2  MKIFVKTLKGTSFD-VEVKPEDTVFDVKMKIETVQGSD----VYPAAQQMLIYQGKVLKD 56
          ++I  +   G+           TV  +K  + +    +         +  LI  GKVL++
Sbjct: 8  LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLEN 67

Query: 57 DTTLEENKVAENSFVVIMLT 76
            T+++ +   ++    + T
Sbjct: 68 SKTVKDYRSPVSNLAGAVTT 87

>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 = 57.3 bits (138), Expect = 2e-11
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 1   MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
           ++K+ VKT K    +  V    +V   K  I            Q +LI+ GK+LKD  TL
Sbjct: 32  IIKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFK---SQTDQLVLIFAGKILKDQDTL 87

Query: 61  EENKVAENSFVVIML 75
            ++ + +   V +++
Sbjct: 88  IQHGIHDGLTVHLVI 102

>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 = 54.2 bits (130), Expect = 3e-10
 Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 5/82 (6%)

Query: 1  MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTL 60
          ++ + +     T  DV+V  + T  ++K KI ++ G    P A Q ++Y   ++ +D TL
Sbjct: 17 LVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMY-KGLVPEDKTL 71

Query: 61 EENKVAENSFVVIMLTKNKRPT 82
           E KV   + ++++ +    P+
Sbjct: 72 REIKVTSGAKIMVVGSTISGPS 93

>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 = 52.9 bits (127), Expect = 3e-10
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQAEVQPVARAPGNG 217
           E A++ I +MG   + ++   +AL    NN E A+  L +   ++  + P +  P +G
Sbjct: 10  EKALKHITEMG---FSKEASRQALMDNGNNLEAALNVLLTSNKQKPVMGPPS-GPSSG 63

>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 = 51.4 bits (123), Expect = 3e-09
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 3  KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEE 62
          K  ++  +    +       ++  +K  I       V       LIY G+ LKDD TL+ 
Sbjct: 20 KSILQLPETELGEY-SLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDF 78

Query: 63 NKVAENSFVVIML 75
            +   S V ++ 
Sbjct: 79 YGIQPGSTVHVLR 91

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (120), Expect = 5e-09
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 7/82 (8%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          +K+ V     +    +VK    +  +K      QG    P      +++G+ + D+ T +
Sbjct: 3  IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPK 59

Query: 62 ENKVAENSFVVIMLTKNKRPTG 83
          E  + E   + +        TG
Sbjct: 60 ELGMEEEDVIEVYQ----EQTG 77

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {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 domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.7 bits (121), Expect = 5e-09
 Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 11/89 (12%)

Query: 2  MKIFVKT-LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGK-------V 53
          + +F+ + L     +       T+ + K K+E V G    PA+   L   G        +
Sbjct: 8  VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVG---SPASCMELELYGADDKFYSKL 64

Query: 54 LKDDTTLEENKVAENSFVVIMLTKNKRPT 82
           ++D  L    V +   + ++      P+
Sbjct: 65 DQEDALLGSYPVDDGCRIHVIDHSGSGPS 93

>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 = 5e-09
 Identities = 8/41 (19%), Positives = 23/41 (56%), Gaps = 3/41 (7%)

Query: 160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG 200
           + ++  +L  G   +  D   +AL+A+  + E+A +++++ 
Sbjct: 30  QSSVDTLLSFG---FAEDVARKALKASGGDIEKATDWVFNN 67

>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 = 47.8 bits (114), Expect = 2e-08
 Identities = 12/58 (20%), Positives = 30/58 (51%), Gaps = 3/58 (5%)

Query: 142 ESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS 199
            SG  G  +   +   +    ++ +++MG   +  + V+RA++    N E+ ++YL++
Sbjct: 2   SSGSSGAYSELQMLSPSERQCVETVVNMG---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 = 45.8 bits (109), Expect = 9e-08
 Identities = 15/25 (60%), Positives = 19/25 (76%)

Query: 265 LDFLRNSPQFQVLRAMVQANPQLFP 289
           L+FLRN PQFQ +R ++Q NP L P
Sbjct: 2   LEFLRNQPQFQQMRQIIQQNPSLLP 26

>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 = 46.0 bits (109), Expect = 1e-07
 Identities = 10/74 (13%), Positives = 24/74 (32%), Gaps = 4/74 (5%)

Query: 2  MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLE 61
          + + V     +    ++K    +  +       QG           +Y G  ++ D T E
Sbjct: 5  INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPE 60

Query: 62 ENKVAENSFVVIML 75
          +  + +N  +    
Sbjct: 61 DLDMEDNDIIEAHR 74

>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 = 45.2 bits (107), Expect = 3e-07
 Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 15/86 (17%)

Query: 1  MMKIFVKTLKGTSFDVEVK--PEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGK------ 52
          +  + + T   T F +E K     ++ D+K K+E V G          +           
Sbjct: 4  VYDLEITT-NATDFPMEKKYPAGMSLNDLKKKLELVVG---TTVDSMRIQLFDGDDQLKG 59

Query: 53 -VLKDDTTLEENKVAENSFVVIMLTK 77
           +     +L++  V +     I    
Sbjct: 60 ELTDGAKSLKDLGVRDGY--RIHAVD 83

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Rhomboid family protein At3g58460
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 130 ASASVSSVSATSESGVYGHAASNLVAGNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNN 189
           +S S  S  A   +      +   VA +  E  IQ+++ MG   +DR  V  AL AA ++
Sbjct: 2   SSGSSGSRQAPIANAAVLPQSQGRVAAS--EEQIQKLVAMG---FDRTQVEVALAAADDD 56

Query: 190 PERAVEYLYSGIPEQA 205
              AVE L S     +
Sbjct: 57  LTVAVEILMSQSGPSS 72

>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 = 43.8 bits (103), Expect = 1e-06
 Identities = 11/88 (12%), Positives = 31/88 (35%), Gaps = 14/88 (15%)

Query: 1  MMKIFVK---TLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLK-- 55
          ++ + +K     +    + ++    TV  VK  +  +      P ++ +L Y+   +   
Sbjct: 9  LLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLK---VPVSELLLSYESSKMPGR 65

Query: 56 ------DDTTLEENKVAENSFVVIMLTK 77
                D   L+   V     +++  + 
Sbjct: 66 EIELENDLQPLQFYSVENGDCLLVRWSG 93

>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 = 16/76 (21%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 2   MKIFVKTL-KGTSFDVEVKPE-DTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTT 59
           +++       G   ++ V+   + V  +K KI         PA +Q L  +   LKD+ +
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMS 86

Query: 60  LEENKVAENSFVVIML 75
           L    V     + + L
Sbjct: 87  LAHYNVGAGEILTLSL 102

>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 = 36.7 bits (85), Expect = 2e-04
 Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 5/59 (8%)

Query: 160 EGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIPEQAEVQPVARAPGNG 217
             A++ +++MG   + R    +AL    N   E A+++L     +    +P++  P +G
Sbjct: 10  LTALESLIEMG---FPRGRAEKALALTGNQGIEAAMDWLMEHEDDPDVDEPLS-GPSSG 64

>d2bwba1 a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 44

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 33.8 bits (78), Expect = 0.001
 Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 2/38 (5%)

Query: 163 IQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG 200
           ++Q+ DMG   +D D  V 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	300
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	99.83
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.83
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.83
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.82
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.82
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.81
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.81
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	99.79
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.79
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.79
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.78
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.78
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.77
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.76
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.76
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.76
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.75
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.73
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.72
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.72
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.71
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.71
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.68
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.67
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.67
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	99.67
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.66
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.65
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.56
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.51
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.43
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.4
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.37
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	99.37
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	99.36
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	99.34
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.32
d2f4mb1	58	XPC-binding domain of Rad23 homolog B (Hhr23b) {Hu	99.3
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	99.24
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.22
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	99.09
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	98.99
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	98.8
d2bwba1	44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.73
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	98.73
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	98.71
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	98.69
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	98.56
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	98.49
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	98.49
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.41
d3e46a1	42	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal	97.69
d1z96a1	38	UBA-domain protein mud1 {Schizosaccharomyces pombe	97.63
d1oqya2	44	DNA repair protein Hhr23a {Human (Homo sapiens) [T	97.59
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.53
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	97.42
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	97.01
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.97
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	96.87
d1wj7a1	91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	96.85
d2cosa1	41	Serine/threonine protein kinase LATS2 {Mouse (Mus	96.82
d1vega_	83	NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculu	96.54
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	95.92
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	95.38
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	95.1
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	94.96
d1ttea1	55	Ubiquitin-protein ligase ubc1 {Baker's yeast (Sacc	94.59
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	94.28
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	93.86
d2dkla1	72	Trinucleotide repeat containing 6c protein, TNRC6C	91.93
d1x3zb1	57	Rad23 STI1 domain {Baker's yeast (Saccharomyces ce	91.86
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	91.53
d2cp8a1	41	Migration-inducing protein 19 NBR1 {Human (Homo sa	91.19
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	89.85
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	89.01
d1h4ra3	84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	88.02
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	87.86
d1v92a_	46	NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {	87.67
d2di0a1	63	Activating signal cointegrator 1 complex subunit 2	87.19
d1ip9a_	85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	84.19
d1cuka1	48	DNA helicase RuvA subunit, C-terminal domain {Esch	82.94
d1t3qa2	81	Quinoline 2-oxidoreductase small subunit QorS, N-d	82.66
d2k0bx1	52	Sequestosome 1 (Sqstm1) {Human (Homo sapiens) [Tax	80.27

>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=1.8e-21  Score=150.57  Aligned_cols=79  Identities=48%  Similarity=0.802  Sum_probs=74.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |+|+||+++|++|.|+|++++||.+||++|+++.+.+.+++++|||||+||+|+|+++|++|||++|++|++++++++.
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~~   79 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKA   79 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCCC
Confidence            8999999999999999999999999999999998755589999999999999999999999999999999999986553

>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=4e-21  Score=141.61  Aligned_cols=73  Identities=37%  Similarity=0.614  Sum_probs=71.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+||+++|++|.++|++++||.+||++|+++.|   +++++|||+|+||.|+|+.+|++|+|++|++||+++|.
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            89999999999999999999999999999999999   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=99.83  E-value=9.4e-21  Score=144.27  Aligned_cols=76  Identities=29%  Similarity=0.480  Sum_probs=73.2

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      .|+|+||+++|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||+|+|+++|++|+|+++++||++.+++.
T Consensus         7 ~mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~   82 (87)
T d1wh3a_           7 GIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG---LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGS   82 (87)
T ss_dssp             SEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTC---CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCC
T ss_pred             cEEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHC---cChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCC
Confidence            499999999999999999999999999999999999   9999999999999999999999999999999999988764

>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=1.1e-20  Score=140.30  Aligned_cols=75  Identities=41%  Similarity=0.656  Sum_probs=72.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|++|.++|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+.+|++|+|++|++|+++++.+.
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=99.83  E-value=1.2e-20  Score=141.01  Aligned_cols=75  Identities=28%  Similarity=0.462  Sum_probs=73.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|++|.|+|++++||.+||++|+++.|   +|+++|||+|+||.|+|+++|++|+|+++++||++.|.+.
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            99999999999999999999999999999999999   9999999999999999999999999999999999998764

>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=2.4e-20  Score=138.35  Aligned_cols=74  Identities=28%  Similarity=0.346  Sum_probs=71.8

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +|+|+||+++|+++.++|++++||.+||++|+.+.|   +++++|||+|+||.|+|+++|++|||++|++||+++|.
T Consensus         3 ~~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~g---i~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lRL   76 (76)
T d1z2ma2           3 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG---VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhc---CChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            599999999999999999999999999999999999   99999999999999999999999999999999999873

>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=8.3e-21  Score=141.32  Aligned_cols=76  Identities=41%  Similarity=0.730  Sum_probs=72.1

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      .|+|+||+++|++|.|+|++++||.+||++|+.+.|.+.+|+++|||+|+||+|+|+++|++|||++|++|+||++
T Consensus         2 ~~~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           2 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT   77 (77)
T ss_dssp             CCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEEC
Confidence            4899999999999999999999999999999999885558999999999999999999999999999999999985

>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=99.81  E-value=2.6e-20  Score=139.63  Aligned_cols=75  Identities=21%  Similarity=0.445  Sum_probs=72.6

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+||+++|++|.|+|++++||.+||.+|+++.|   +|+++|||+|+||.|+|+++|++|+|+++++||++++++.
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            79999999999999999999999999999999999   9999999999999999999999999999999999998753

>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=99.81  E-value=3.4e-20  Score=136.75  Aligned_cols=72  Identities=26%  Similarity=0.356  Sum_probs=70.2

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      ||+|+||+..|+++.++|++++||.+||++|+.+.|   +++++|||+|+||.|+|+.+|++|||++|++|++..
T Consensus         1 mi~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~---i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~~   72 (73)
T d1m94a_           1 MIEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIG---TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             CEEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHC---CTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEEE
T ss_pred             CeEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhc---ccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEEE
Confidence            899999999999999999999999999999999999   999999999999999999999999999999999863

>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=5.2e-20  Score=136.87  Aligned_cols=73  Identities=26%  Similarity=0.390  Sum_probs=70.2

Q ss_pred             EEEEEEcCCCc-EEEEE-eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGT-SFDVE-VKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~-~~~ie-V~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+||+++|+ ++.++ +++++||.+||.+|+++.|   +|+++|||+|+||.|+|+.+|++|||+++++||+++|+
T Consensus         1 M~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1           1 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFH---VEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHC---CCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHC---cChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            89999999996 78885 9999999999999999999   99999999999999999999999999999999999986

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.7e-20  Score=138.26  Aligned_cols=73  Identities=30%  Similarity=0.447  Sum_probs=69.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+||+++|++|.++|++++||.+||++|+.+.|   +|+++|||+|+||.|+|+++|++|+| ++++||++.|.|
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 579998887653

>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=99.79  E-value=2.2e-19  Score=133.46  Aligned_cols=73  Identities=23%  Similarity=0.381  Sum_probs=69.4

Q ss_pred             EEEEEEcCCC-cEEEE-EeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKG-TSFDV-EVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g-~~~~i-eV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+||+++| +++.+ +|++++||.+||.+|+.+.|   +|+++|||+|+||.|+|+++|++|||++|++||+++|.
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            8999999999 57887 59999999999999999999   99999999999999999999999999999999999873

>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=99.79  E-value=1.5e-19  Score=136.69  Aligned_cols=76  Identities=29%  Similarity=0.381  Sum_probs=71.1

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      ||+|+||+.++ +|.|+|++++||.+||++|+++.|   +++++|||+|+||.|+|+.+|++|||++|++|||++|+++.
T Consensus         7 ~i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~g---i~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~~   82 (84)
T d1yqba1           7 LIKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFK---AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   82 (84)
T ss_dssp             EEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHT---CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             EEEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHC---cCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCCC
Confidence            59999999755 689999999999999999999999   99999999999999999999999999999999999887653

>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=99.79  E-value=2.2e-19  Score=140.67  Aligned_cols=75  Identities=24%  Similarity=0.451  Sum_probs=69.1

Q ss_pred             EEEEE----EcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFV----KTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLK-DDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~V----Ktl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~-D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+|+|    |++++++|.|+|++++||.+||++|+.+.+   +|+++|||||+||.|. |+++|++|||++|++|+|+.+
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            89999    788899999999999999999999999999   9999999999999996 567999999999999988866


Q ss_pred             cCC
Q 022228           77 KNK   79 (300)
Q Consensus        77 k~~   79 (300)
                      +..
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=3.1e-19  Score=132.48  Aligned_cols=72  Identities=29%  Similarity=0.399  Sum_probs=70.1

Q ss_pred             EEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            3 KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY--QGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~--~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +|+||+++|++|.|+|++++||.+||.+|+.+.|   +|+++|||+|  +||+|+|+.+|++|||++|++|+|++++
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  7999999999999999999999999986

>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=137.10  Aligned_cols=74  Identities=27%  Similarity=0.287  Sum_probs=67.3

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCchhhcccCCCcEEEEEEecCCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLK-DDTTLEENKVAENSFVVIMLTKNKR   80 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~-D~~tL~d~gI~~g~~I~v~v~k~~~   80 (300)
                      |+|+||+++|+.|.|+|++++||.+||++|+   .   ++.++|||||+||+|. |.++|++|+|.+|++|||+++++..
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            8999999999999999999999999999985   3   5679999999999996 5579999999999999999987665


Q ss_pred             C
Q 022228           81 P   81 (300)
Q Consensus        81 ~   81 (300)
                      .
T Consensus        82 ~   82 (95)
T d1wiaa_          82 A   82 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=7.1e-19  Score=129.45  Aligned_cols=72  Identities=36%  Similarity=0.607  Sum_probs=68.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|+||+. +++|.|+|++++||.+||++|+...|   +|+++|||+|+||.|+|+.+|++|||++|++||++.++
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            89999974 56799999999999999999999999   99999999999999999999999999999999999864

>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=99.76  E-value=1.8e-18  Score=138.43  Aligned_cols=76  Identities=22%  Similarity=0.305  Sum_probs=68.1

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHH--------HHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIE--------TVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVV   72 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~--------~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~   72 (300)
                      +|+|+||+++|+++.|+|++++||.+||++|.        ++.+   +++++|||||.||+|+|+.+|++|+|.+|++++
T Consensus        16 ~i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~---~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~   92 (116)
T d1wgha_          16 MINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQV---SSPNILRLIYQGRFLHGNVTLGALKLPFGKTTV   92 (116)
T ss_dssp             SEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCC---CCTTTEEEEETTEEECSSCBTTTTTCCSSCEEE
T ss_pred             eEEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccC---CChHHeEEEECCEEecCCCCHHHcCCCCCCEEE
Confidence            58999999999999999999999999999995        4455   899999999999999999999999999999866


Q ss_pred             EEEecCC
Q 022228           73 IMLTKNK   79 (300)
Q Consensus        73 v~v~k~~   79 (300)
                      |++..++
T Consensus        93 lhlv~r~   99 (116)
T d1wgha_          93 MHLVARE   99 (116)
T ss_dssp             EEEEECS
T ss_pred             EEEEeCC
Confidence            6555444

>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=99.76  E-value=6.6e-19  Score=136.40  Aligned_cols=75  Identities=23%  Similarity=0.251  Sum_probs=69.2

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +|+|+||..+++.+.|+|++++||.+||++|+..++   +|+++|||||+||.|+|+ +|++|||++|++|+||.++..
T Consensus         7 ~~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~g---vp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~t~~~   81 (96)
T d1wgga_           7 GYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTG---VQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSADA   81 (96)
T ss_dssp             EEEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTC---CCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCCC
T ss_pred             ceEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcC---ccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEeeCCc
Confidence            389999998888889999999999999999999999   999999999999999986 799999999999999875443

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.8e-18  Score=135.52  Aligned_cols=72  Identities=28%  Similarity=0.365  Sum_probs=68.4

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      +|+|+||+.++ ++.|+|++++||.+||++|+.++|   +++++|||+|+||+|+|+++|++|||++|++|||++|
T Consensus        32 ~i~V~Vk~~~~-~~~i~V~~~~tV~~LK~~I~~~~g---i~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~lvlr  103 (103)
T d1j8ca_          32 IIKVTVKTPKE-KEEFAVPENSSVQQFKEAISKRFK---SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             CEEEEEECSSC-EEEEEECTTCCHHHHHHHHHHHHC---SCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             eEEEEEECCCc-cEEEEECCCChHHHHHHHHHHHHC---cCHHHeeeeeeeecccCCCcHHHcCCCCCCEEEEEEC
Confidence            59999998765 689999999999999999999999   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=99.75  E-value=7.2e-19  Score=137.22  Aligned_cols=72  Identities=18%  Similarity=0.257  Sum_probs=69.9

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v   75 (300)
                      ||+|+||+..|++|.|+|++++||.+||++|+.+.|   +|+++|||+|+||+|+|+.+|++|||++|++|+|+.
T Consensus        28 ~i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~g---ip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI~L~~   99 (100)
T d1uh6a_          28 MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHC---CCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             eEEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHC---CCcceEEEEEEeecccCcCCHHHcCCCCCCEEEEEE
Confidence            479999999999999999999999999999999999   999999999999999999999999999999999975

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.4e-18  Score=130.91  Aligned_cols=73  Identities=22%  Similarity=0.364  Sum_probs=68.4

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      +|+|+||+.++ .+.|+|++++||.+||++|++..+   +++++|||+|+||+|+|+++|++|||++|++|+|++|.
T Consensus        10 ~i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~---v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1          10 IIRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLH---CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             EEEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTC---SCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             eEEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhC---CChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEeC
Confidence            48999998755 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=99.72  E-value=1.3e-17  Score=126.58  Aligned_cols=68  Identities=28%  Similarity=0.443  Sum_probs=65.5

Q ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            9 LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         9 l~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      ++|+++.|+|++++||.+||++|+.+.|   +|+++|+|+|+|+.|+|+++|++|||++|++||+++|++.
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~---ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~RG   86 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATG---MPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG   86 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTC---CCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhc---CChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            6899999999999999999999999999   9999999999999999999999999999999999998763

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=1.9e-18  Score=135.90  Aligned_cols=78  Identities=21%  Similarity=0.267  Sum_probs=72.0

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeE---------------EEeCCeecCCC-Cchhhcc
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQM---------------LIYQGKVLKDD-TTLEENK   64 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qk---------------Li~~GkiL~D~-~tL~d~g   64 (300)
                      .|+|+||+++|++|.|+|++++||.+||++|++..+   +++++||               |+|+|+.|.|+ .+|.+|+
T Consensus         7 ~M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~---ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~g   83 (105)
T d1v2ya_           7 GMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ---LKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYG   83 (105)
T ss_dssp             SEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHH---HHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHT
T ss_pred             cEEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHC---cCHHHhcccccccccccccceEEEECCEECcccCCCHHHcC
Confidence            499999999999999999999999999999999999   9999987               99999999776 5899999


Q ss_pred             cCCCcEEEEEEecCCCC
Q 022228           65 VAENSFVVIMLTKNKRP   81 (300)
Q Consensus        65 I~~g~~I~v~v~k~~~~   81 (300)
                      |++|++|||+.++++..
T Consensus        84 I~~g~~l~lv~r~~~~~  100 (105)
T d1v2ya_          84 IRNRDEVSFIKKLGQKS  100 (105)
T ss_dssp             CCSSEEEEEEECSCSCC
T ss_pred             CCCCCEEEEEEecCCCC
Confidence            99999999998866543

>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=6.4e-18  Score=131.79  Aligned_cols=77  Identities=22%  Similarity=0.234  Sum_probs=69.9

Q ss_pred             EEEEE--EcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFV--KTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~V--Ktl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      |+|+|  |...|++|.|+|++++||.+||++|+.+.+   +++++|||||+||+|+|+++|.+|+|+++++|+||..+..
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            56666  567899999999999999999999999999   9999999999999999999999999999999999877654


Q ss_pred             CC
Q 022228           80 RP   81 (300)
Q Consensus        80 ~~   81 (300)
                      ..
T Consensus        95 ~~   96 (100)
T d1wjua_          95 SG   96 (100)
T ss_dssp             CC
T ss_pred             CC
Confidence            33

>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=2.7e-17  Score=128.11  Aligned_cols=78  Identities=17%  Similarity=0.233  Sum_probs=68.6

Q ss_pred             EEEEEEcCCCcEE-EEEeCCCCCHHHHHHHHHHHhCC--CCCC--CCCeEEEeCCeecCCCCchhhcccCCCc------E
Q 022228            2 MKIFVKTLKGTSF-DVEVKPEDTVFDVKMKIETVQGS--DVYP--AAQQMLIYQGKVLKDDTTLEENKVAENS------F   70 (300)
Q Consensus         2 M~I~VKtl~g~~~-~ieV~~~~TV~~LK~kI~~~~g~--~~ip--~~~qkLi~~GkiL~D~~tL~d~gI~~g~------~   70 (300)
                      |.|+||+++|+.+ .+.|++++||.+||++|+....+  ..+|  +++|||||+||+|+|+++|++|+|..|+      +
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            8999999999987 59999999999999999987321  1276  7799999999999999999999999998      9


Q ss_pred             EEEEEecCC
Q 022228           71 VVIMLTKNK   79 (300)
Q Consensus        71 I~v~v~k~~   79 (300)
                      +||++|.+.
T Consensus        88 mHlVvrpp~   96 (101)
T d1se9a_          88 MHVIIQAPV   96 (101)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999998644

>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=99.68  E-value=2.7e-17  Score=126.96  Aligned_cols=72  Identities=28%  Similarity=0.460  Sum_probs=68.0

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      ||+|+|+ +++++|.|+|++++||.+||++|+..++   +|+++|||+|+|+ |+|+++|++|+|++|++|+||.+.
T Consensus        17 ~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_          17 LVDLKII-WNKTKHDVKVPLDSTGSELKQKIHSITG---LPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             CEEEEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHC---SCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSS
T ss_pred             EEEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHhC---CChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecC
Confidence            5899998 7899999999999999999999999999   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=99.67  E-value=5.2e-17  Score=123.96  Aligned_cols=74  Identities=30%  Similarity=0.463  Sum_probs=67.7

Q ss_pred             CEEEEEEcCCCcEEEE-EeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE---eCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228            1 MMKIFVKTLKGTSFDV-EVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI---YQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         1 mM~I~VKtl~g~~~~i-eV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi---~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      +|+|+|| +.|+.|.+ +|++++||.+||++|+.+++   +|+++||||   |+||+|+|+.+|.+|+|++|++|+|+.+
T Consensus         7 ~~~i~Vk-~~~~~~~i~~v~~~~tV~~LK~~i~~~t~---vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s   82 (90)
T d1v5ta_           7 GLPIIVK-WGGQEYSVTTLSEDDTVLDLKQFLKTLTG---VLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGT   82 (90)
T ss_dssp             SCCEEEE-ETTEEEEECSCCSSSBHHHHHHHHHHHTC---CCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECC
T ss_pred             cEEEEEE-ECCeEEEEEEeCCCCcHHHHHHHHHHHHc---CCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEee
Confidence            4899999 56777877 79999999999999999999   999999999   5899999999999999999999999876


Q ss_pred             cC
Q 022228           77 KN   78 (300)
Q Consensus        77 k~   78 (300)
                      +.
T Consensus        83 ~~   84 (90)
T d1v5ta_          83 RE   84 (90)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>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=99.67  E-value=9.8e-17  Score=123.34  Aligned_cols=75  Identities=19%  Similarity=0.240  Sum_probs=64.7

Q ss_pred             EEEEEEcCCCc--EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCc--EEEEEEec
Q 022228            2 MKIFVKTLKGT--SFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENS--FVVIMLTK   77 (300)
Q Consensus         2 M~I~VKtl~g~--~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~--~I~v~v~k   77 (300)
                      |+|+||+.+++  .+.|+|++++||.+||++|+++.+.+ +++++|||||+||+|+|+.+|++|.++.++  +||++++.
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            79999998775  48899999999999999999996533 889999999999999999999999765444  77777544

>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=8.9e-18  Score=109.91  Aligned_cols=41  Identities=54%  Similarity=0.963  Sum_probs=39.8

Q ss_pred             CCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          156 GNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      |+++|++|++||+||   |+|++|++|||+++||+|||+|||++
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

>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=99.66  E-value=2.2e-16  Score=118.26  Aligned_cols=73  Identities=30%  Similarity=0.428  Sum_probs=66.4

Q ss_pred             EEEEEEcCCCcEEEEEe-----CCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCchhhcccCCCcEEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEV-----KPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLK-DDTTLEENKVAENSFVVIML   75 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV-----~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~-D~~tL~d~gI~~g~~I~v~v   75 (300)
                      |+|+|+ +.++.|.|+|     ++++||.+||++|+..+|   +|+++|||+|+|+.|. |+++|++|||++|++|+|+.
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            789997 5778899988     578899999999999999   9999999999999996 56799999999999999998


Q ss_pred             ecC
Q 022228           76 TKN   78 (300)
Q Consensus        76 ~k~   78 (300)
                      ++.
T Consensus        78 ~~~   80 (81)
T d1wxva1          78 KKN   80 (81)
T ss_dssp             CCS
T ss_pred             ecC
Confidence            764

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.65  E-value=8.3e-17  Score=127.64  Aligned_cols=76  Identities=21%  Similarity=0.296  Sum_probs=69.3

Q ss_pred             EEEEEEcC-CCcEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTL-KGTSFDVEVKP-EDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl-~g~~~~ieV~~-~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      ++|+|++. +|+++.|+|++ ++||.+||.+|+++.|   +|+++|||+|+||.|+|+.+|++|+|++|++|||++|.+.
T Consensus        30 i~V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~g---ip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rG  106 (111)
T d1we6a_          30 IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ---IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERS  106 (111)
T ss_dssp             EEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTT---CCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCC
T ss_pred             EEEEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHC---CCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCC
Confidence            45566554 68999999986 9999999999999999   9999999999999999999999999999999999999876


Q ss_pred             C
Q 022228           80 R   80 (300)
Q Consensus        80 ~   80 (300)
                      .
T Consensus       107 G  107 (111)
T d1we6a_         107 G  107 (111)
T ss_dssp             S
T ss_pred             C
Confidence            3

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=6.1e-15  Score=115.14  Aligned_cols=72  Identities=24%  Similarity=0.349  Sum_probs=61.0

Q ss_pred             EEEEcCCC-cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCc-------EEEEEE
Q 022228            4 IFVKTLKG-TSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENS-------FVVIML   75 (300)
Q Consensus         4 I~VKtl~g-~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~-------~I~v~v   75 (300)
                      |+|+...+ +++.|+|++++||.+||++|+++.|   +++++|||||+||.|+|+++|++|||.+++       ++++.+
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            45554444 4788999999999999999999999   999999999999999999999999996654       666666


Q ss_pred             ecC
Q 022228           76 TKN   78 (300)
Q Consensus        76 ~k~   78 (300)
                      +..
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=1.6e-14  Score=111.12  Aligned_cols=75  Identities=20%  Similarity=0.248  Sum_probs=67.8

Q ss_pred             CEEEEEEc-CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCe-------ecCCCCchhhcccCCCcEEE
Q 022228            1 MMKIFVKT-LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGK-------VLKDDTTLEENKVAENSFVV   72 (300)
Q Consensus         1 mM~I~VKt-l~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~Gk-------iL~D~~tL~d~gI~~g~~I~   72 (300)
                      .|.|+|++ +++..++..+++++||.+||++|+..+|   +|++.|||+|.|+       +++|+++|.+|+|.+|++||
T Consensus         7 ~v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tG---ip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ih   83 (95)
T d1v6ea_           7 GVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVG---SPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIH   83 (95)
T ss_dssp             CEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTC---SCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEE
T ss_pred             cEEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhC---cCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEE
Confidence            37899987 4666789999999999999999999999   9999999999887       57899999999999999999


Q ss_pred             EEEecC
Q 022228           73 IMLTKN   78 (300)
Q Consensus        73 v~v~k~   78 (300)
                      |+.+.+
T Consensus        84 lvd~~p   89 (95)
T d1v6ea_          84 VIDHSG   89 (95)
T ss_dssp             EBCCSC
T ss_pred             EEeCCC
Confidence            997764

>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=99.43  E-value=2.2e-13  Score=100.95  Aligned_cols=74  Identities=14%  Similarity=0.189  Sum_probs=68.2

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecCC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKNK   79 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~~   79 (300)
                      +.|+|+. +|+.+.+.|..++++..||+.++++.+   +++++++|+|+|+.|+++.|+.+|+|++|++|+++++...
T Consensus         5 I~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~---i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~G   78 (79)
T d1euvb_           5 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG---KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   78 (79)
T ss_dssp             EEEEEES-SSCEEEEEEETTSCTHHHHHHHHHHTT---CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCBC
T ss_pred             EEEEECC-CCeEEEEEECCCCcHHHHHHHHHHHhC---CChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEeccC
Confidence            5677775 788888999999999999999999999   9999999999999999999999999999999999998653

>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=99.40  E-value=2.5e-13  Score=104.63  Aligned_cols=75  Identities=16%  Similarity=0.219  Sum_probs=64.6

Q ss_pred             EEEEEEc---CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCee-------c-CCCCchhhcccCCCcE
Q 022228            2 MKIFVKT---LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKV-------L-KDDTTLEENKVAENSF   70 (300)
Q Consensus         2 M~I~VKt---l~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~Gki-------L-~D~~tL~d~gI~~g~~   70 (300)
                      +.|+|+.   .+++.++++|+.++||.+||.+|+..+|   +|++.|+|+|.|+.       | +|+++|.+|+|++|++
T Consensus        10 iti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~g---ip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~   86 (97)
T d1wjna_          10 LTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLK---VPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDC   86 (97)
T ss_dssp             EEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTT---CCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCE
T ss_pred             EEEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHC---cChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCE
Confidence            5677774   4578899999999999999999999999   99999999998862       4 4778999999999999


Q ss_pred             EEEEEecCC
Q 022228           71 VVIMLTKNK   79 (300)
Q Consensus        71 I~v~v~k~~   79 (300)
                      |+|....++
T Consensus        87 I~V~~~~P~   95 (97)
T d1wjna_          87 LLVRWSGPS   95 (97)
T ss_dssp             EEEECCSSC
T ss_pred             EEEEeCCCC
Confidence            998765543

>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=99.37  E-value=1.1e-12  Score=96.62  Aligned_cols=74  Identities=18%  Similarity=0.271  Sum_probs=70.8

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEecC
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTKN   78 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k~   78 (300)
                      |+|+|++.+|+.+.+.|..+.++..||..++++.+   +++.+++|+|+|+.|.++.|+.+|+|++|++|+|+++..
T Consensus         3 I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~---~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q~   76 (77)
T d2uyzb1           3 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG---VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQT   76 (77)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT---CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC---CChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            78999999999999999999999999999999999   899999999999999999999999999999999998653

>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=99.37  E-value=7e-13  Score=96.98  Aligned_cols=40  Identities=43%  Similarity=0.481  Sum_probs=38.2

Q ss_pred             ChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          158 NLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      ..|+.|++||+||   |+|++|++||++++||+|||||||++.
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            4589999999999   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=99.36  E-value=2.5e-13  Score=96.57  Aligned_cols=43  Identities=23%  Similarity=0.532  Sum_probs=39.5

Q ss_pred             CChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC-CC
Q 022228          157 NNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG-IP  202 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G-IP  202 (300)
                      ...|++|++||+||   |+|++|++|||++.||++||||||++. +|
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            34589999999999   999999999999999999999999985 44

>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=99.34  E-value=6.3e-13  Score=94.57  Aligned_cols=43  Identities=28%  Similarity=0.384  Sum_probs=40.3

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCCc
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPEQ  204 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~~  204 (300)
                      .+++|++||+||   |+|++|++||++..||+++||+||+++..+.
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

>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=99.32  E-value=1.5e-12  Score=99.63  Aligned_cols=57  Identities=26%  Similarity=0.207  Sum_probs=50.1

Q ss_pred             CCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEe
Q 022228           20 PEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus        20 ~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      .+.||.+||++|+.+.......+++|||||+||.|+|+++|++|+|++|++||++.|
T Consensus        36 ~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r   92 (94)
T d1x1ma1          36 GGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK   92 (94)
T ss_dssp             CCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEES
T ss_pred             CccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEe
Confidence            367999999999998763312469999999999999999999999999999999976

>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=99.30  E-value=4.9e-13  Score=92.83  Aligned_cols=31  Identities=48%  Similarity=0.900  Sum_probs=29.9

Q ss_pred             chhhhhCcHHHHHHHHHHHhCCCchHHHHhc
Q 022228          264 SLDFLRNSPQFQVLRAMVQANPQLFPCFKSW  294 (300)
Q Consensus       264 ~l~~Lr~~pqf~~lR~~vq~nP~~L~~~lq~  294 (300)
                      ||+|||++|||++||++||+||++|++|||+
T Consensus         1 pL~~Lr~~PqFq~lR~~vq~nP~~L~~lLqq   31 (58)
T d2f4mb1           1 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQ   31 (58)
T ss_dssp             GGGGGTTCHHHHHHHHHHHHCGGGHHHHHHH
T ss_pred             CcHHHhcChHHHHHHHHHHHCHHHHHHHHHH
Confidence            6899999999999999999999999999986

>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=99.24  E-value=3.2e-12  Score=93.44  Aligned_cols=39  Identities=21%  Similarity=0.515  Sum_probs=37.5

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .++.|++||+||   |+|++|++|||++.||.+||||||++.
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=2.1e-11  Score=92.43  Aligned_cols=74  Identities=12%  Similarity=0.111  Sum_probs=62.5

Q ss_pred             EEEEEEc-CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCe-------ecCCCCchhhcccCCCcEEEE
Q 022228            2 MKIFVKT-LKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGK-------VLKDDTTLEENKVAENSFVVI   73 (300)
Q Consensus         2 M~I~VKt-l~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~Gk-------iL~D~~tL~d~gI~~g~~I~v   73 (300)
                      +.|.|.+ ..+..++..++.+.||.+||.+|+..+|   +|+..|+|+|.|+       .++|+++|.+|||++|.+|||
T Consensus         5 ~~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~G---ip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihv   81 (90)
T d1t0ya_           5 YDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVG---TTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHA   81 (90)
T ss_dssp             EEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHC---CCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEE
T ss_pred             EEEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHC---CChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEE
Confidence            4566664 2344578889999999999999999999   9999999999886       457889999999999999999


Q ss_pred             EEecC
Q 022228           74 MLTKN   78 (300)
Q Consensus        74 ~v~k~   78 (300)
                      +-...
T Consensus        82 vd~~~   86 (90)
T d1t0ya_          82 VDVTG   86 (90)
T ss_dssp             EECTT
T ss_pred             EeCCC
Confidence            76543

>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=99.09  E-value=6.2e-11  Score=84.25  Aligned_cols=41  Identities=24%  Similarity=0.402  Sum_probs=37.8

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCCC
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIPE  203 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP~  203 (300)
                      +++|++|++||   |+|++|++||++..| ++++|||||++..-+
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   999999999999998 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=98.99  E-value=1.1e-10  Score=79.22  Aligned_cols=37  Identities=27%  Similarity=0.504  Sum_probs=34.5

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHh
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYS  199 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~  199 (300)
                      +..|++|++||   |++++|++||++.-| |.++|||||++
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            45799999999   999999999999988 99999999985

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.80  E-value=1.8e-08  Score=72.67  Aligned_cols=70  Identities=11%  Similarity=0.218  Sum_probs=66.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~   74 (300)
                      ++|+|+..+|+.+.+.|..+.++..|+...+...+   +++..++|+|+|+.|..+.|.+++++++||.|.|.
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            67899998999999999999999999999999999   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=98.73  E-value=7.9e-09  Score=67.43  Aligned_cols=40  Identities=35%  Similarity=0.494  Sum_probs=37.7

Q ss_pred             ChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          158 NLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .|..-+++|-+||   | +++..++||+++.+|.++|||+|++|
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            4677899999999   9 99999999999999999999999998

>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=98.73  E-value=5.8e-09  Score=70.55  Aligned_cols=38  Identities=26%  Similarity=0.416  Sum_probs=34.6

Q ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCC
Q 022228          161 GAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGI  201 (300)
Q Consensus       161 ~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GI  201 (300)
                      +.|++|++||   |+|.+|++||++.-| |.++||+||+...
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   999999999999876 9999999999763

>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=98.71  E-value=6.1e-09  Score=77.61  Aligned_cols=41  Identities=24%  Similarity=0.345  Sum_probs=37.7

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHHhCCC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLYSGIP  202 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl~GIP  202 (300)
                      .+++|++|++||   |+|..|++||++..| |.++|++||+...-
T Consensus        29 d~~~v~~L~~MG---F~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~   70 (84)
T d1veka_          29 NEEIVAQLVSMG---FSQLHCQKAAINTSNAGVEEAMNWLLSHMD   70 (84)
T ss_dssp             CHHHHHHHHHHT---CCHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHcC---CCHHHHHHHHHHHcCCCHHHHHHHHHHcCC
Confidence            378999999999   999999999999987 99999999998743

>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=98.69  E-value=1.4e-08  Score=64.92  Aligned_cols=39  Identities=21%  Similarity=0.321  Sum_probs=36.9

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .+.+|++|++||   |+++++++||+-+..|.+.|+.||+-|
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

>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=98.56  E-value=7e-08  Score=67.09  Aligned_cols=41  Identities=22%  Similarity=0.417  Sum_probs=37.8

Q ss_pred             CCChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          156 GNNLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      -..|..-+++|.+||   | +++..++||+++.+|.++|||||+.
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            457889999999999   9 8999999999999999999999983

>d2daha1 a.5.2.1 (A:8-48) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.49  E-value=9.3e-08  Score=61.39  Aligned_cols=38  Identities=29%  Similarity=0.439  Sum_probs=35.6

Q ss_pred             hHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          159 LEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      |+.-+++|-+||   | +++..++||+++.+|.++|||+|+.
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            677799999999   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=98.49  E-value=8.8e-08  Score=63.94  Aligned_cols=40  Identities=20%  Similarity=0.296  Sum_probs=37.7

Q ss_pred             ChHHHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHHhC
Q 022228          158 NLEGAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLYSG  200 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl~G  200 (300)
                      .|..-+++|-+||   | +++..++||+++.+|.++|||+|+.+
T Consensus         7 ry~~QL~qL~~MG---F~d~~~Ni~AL~~t~GdV~~Aie~Ll~~   47 (50)
T d2dnaa1           7 RFSKEMECLQAMG---FVNYNANLQALIATDGDTNAAIYKLKSS   47 (50)
T ss_dssp             HTHHHHHHHHHHT---CCCHHHHHHHHHHTTSCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcC---CCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            5778899999999   9 99999999999999999999999986

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NPL4-like protein 1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.41  E-value=2.3e-07  Score=69.32  Aligned_cols=70  Identities=21%  Similarity=0.168  Sum_probs=57.1

Q ss_pred             EEEEEcCCCcEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCCeEEEeC--------------CeecCCC-CchhhcccC
Q 022228            3 KIFVKTLKGTSFDVEVKP-EDTVFDVKMKIETVQGSDVYPAAQQMLIYQ--------------GKVLKDD-TTLEENKVA   66 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~-~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~--------------GkiL~D~-~tL~d~gI~   66 (300)
                      .|.||+.+| +..|+|+. +.||.+||.+|++..+   +|.++|.|..+              =..|.|+ .+|++|||.
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 67888864 7899999999999999   99999999543              2235554 579999999


Q ss_pred             CCcEEEEEEe
Q 022228           67 ENSFVVIMLT   76 (300)
Q Consensus        67 ~g~~I~v~v~   76 (300)
                      +|++|++...
T Consensus        78 hGsivyL~y~   87 (94)
T d1wf9a1          78 HGSMVYLAYE   87 (94)
T ss_dssp             TTCEEECCCS
T ss_pred             CceEEEEEee
Confidence            9999988654

>d3e46a1 a.5.2.1 (A:157-198) Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.69  E-value=3.2e-05  Score=47.50  Aligned_cols=40  Identities=28%  Similarity=0.398  Sum_probs=37.3

Q ss_pred             CCChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          156 GNNLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       156 g~~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      ..+|-..|.+|+.||   |+|.-|+.||.--..+.+.|-|.|+
T Consensus         3 speyt~kidklca~g---f~knavi~alsskswdvetatelll   42 (42)
T d3e46a1           3 SPEYTKKIENLCAAG---FDRNAVIVALSSKSWDVETATELLL   42 (42)
T ss_dssp             CHHHHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHcc---ccccceeeeeccCccchhhHHHhhC
Confidence            457889999999999   9999999999999999999999886

>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=97.63  E-value=4.6e-05  Score=45.53  Aligned_cols=37  Identities=32%  Similarity=0.494  Sum_probs=34.5

Q ss_pred             hHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          159 LEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       159 ~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      ++..|.+|++||   |+-=++.+||.|+.++.|-|..||+
T Consensus         2 lnskiaqlvsmg---fdpleaaqaldaangdldvaasfll   38 (38)
T d1z96a1           2 LNSKIAQLVSMG---FDPLEAAQALDAANGDLDVAASFLL   38 (38)
T ss_dssp             HHHHHHHHHHTT---CCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             cchHHHHHHHcC---CCHHHHHHHHhhhcCcHHHHHHhhC
Confidence            467899999999   9999999999999999999999985

>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=97.59  E-value=1e-05  Score=51.94  Aligned_cols=37  Identities=27%  Similarity=0.426  Sum_probs=35.4

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .++|.+|++||   |+|+.|+.|--|.-.|-+-|..||++
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            67899999999   99999999999999999999999985

>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=97.53  E-value=0.00031  Score=50.78  Aligned_cols=70  Identities=14%  Similarity=0.214  Sum_probs=58.7

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC---CCCchhhcccCCCcEEEEE
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLK---DDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~---D~~tL~d~gI~~g~~I~v~   74 (300)
                      +.+|.||..+|+.+.-.+..++||.+|...|... +   .......|+  |-.|.|.   ++++|.++|+....+|+|-
T Consensus         5 ~~~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~-~---~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~vq   79 (82)
T d1h8ca_           5 VSKLRIRTPSGEFLERRFLASNKLQIVFDFVASK-G---FPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   79 (82)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-T---CCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHhc-C---CCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEEE
Confidence            3579999999999999999999999999999874 5   556778886  5788883   4679999999998888763

>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=97.42  E-value=0.00043  Score=49.57  Aligned_cols=71  Identities=17%  Similarity=0.196  Sum_probs=66.5

Q ss_pred             EEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCcEEEEEEec
Q 022228            4 IFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQGKVLKDDTTLEENKVAENSFVVIMLTK   77 (300)
Q Consensus         4 I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~GkiL~D~~tL~d~gI~~g~~I~v~v~k   77 (300)
                      |+|-+.+|+...|.|.|+.|+.++-+..+++.|   +.+++..|.|++|.|+-+..+.-.|+-+|..+-++-..
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~---~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~~s   73 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQD---FNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVS   73 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTT---CCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSS
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhC---CChhHceeeeCCEEcCccceeeecCCCCCCEEEEEEcc
Confidence            678888999999999999999999999999999   88999999999999999999999999999999988654

>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=97.01  E-value=0.0012  Score=48.80  Aligned_cols=69  Identities=10%  Similarity=0.086  Sum_probs=55.0

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecC--CCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY--QGKVLK--DDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~--~GkiL~--D~~tL~d~gI~~g~~I~v~   74 (300)
                      ++|.||..+|+.+...+..++||.+|...|....    ......+|+.  -.+.|.  +++||.++|+....+|+|-
T Consensus        17 ~~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~~----~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v~   89 (96)
T d2cr5a1          17 VTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVG----YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVE   89 (96)
T ss_dssp             EEEEEECTTSCEEEEEEESSSBTHHHHHHHHHHT----CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCcccHHHHHHHHHHhc----cCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEEe
Confidence            6899999999999999999999999999997653    3456777764  446663  3679999999988777653

>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=96.97  E-value=0.0015  Score=47.84  Aligned_cols=66  Identities=17%  Similarity=0.299  Sum_probs=53.9

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHh-CCCCCCCCCeEEEeC--CeecC-CCCchhhcccCCCcEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQ-GSDVYPAAQQMLIYQ--GKVLK-DDTTLEENKVAENSFV   71 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~-g~~~ip~~~qkLi~~--GkiL~-D~~tL~d~gI~~g~~I   71 (300)
                      .+|.||..+|+.+...+..++||.+|.+.|.... +   .......|+..  -|.|. ++.||.++|+.+ +.|
T Consensus        15 t~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~---~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~-s~v   84 (89)
T d1i42a_          15 TNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPA---MAATSFVLMTTFPNKELADENQTLKEANLLN-AVI   84 (89)
T ss_dssp             EEEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTT---TSSCCEEEEETTTTEECCCCSSCSGGGTTCC-SEE
T ss_pred             EEEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCcc---CCCCCEEEecCCCCcccCCCcCcHHHCCCcC-ceE
Confidence            4688999999999999999999999999998764 4   45667888864  67784 467999999985 444

>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=96.87  E-value=0.0013  Score=51.10  Aligned_cols=69  Identities=14%  Similarity=0.324  Sum_probs=56.5

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC---CCCchhhcccCCCcEEEEE
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--YQGKVLK---DDTTLEENKVAENSFVVIM   74 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~~GkiL~---D~~tL~d~gI~~g~~I~v~   74 (300)
                      .+|.||..+|+.+...+..++||.+|...|....    +.....+|+  |--|.|.   .+++|.++||....+|+|-
T Consensus        44 ~~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~~----~~~~~~~L~~~fPr~~l~~~d~~~TL~e~gL~P~~~L~ve  117 (124)
T d1wj4a_          44 AQLMLRYPDGKREQITLPEQAKLLALVKHVQSKG----YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHH----CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             eEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcc----cCCcceEEeecccccccccccccCcHHHcCCCCCCEEEEE
Confidence            4789999999999999999999999999997753    445677776  4567773   4679999999998888664

>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=96.85  E-value=0.00076  Score=49.56  Aligned_cols=45  Identities=29%  Similarity=0.554  Sum_probs=40.7

Q ss_pred             CCChHHHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 022228          156 GNNLEGAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLYSGIPE  203 (300)
Q Consensus       156 g~~~e~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl~GIP~  203 (300)
                      -.+++..|.+|||| |   -..++|.-||-=+.|+.+|||+|||-|-++
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            34678999999999 7   899999999999999999999999998654

>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=96.82  E-value=0.0011  Score=40.56  Aligned_cols=36  Identities=28%  Similarity=0.479  Sum_probs=32.6

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcC-ChHHHHHHHH
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYN-NPERAVEYLY  198 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafn-NpdrAvEyLl  198 (300)
                      .++++.|+.-|   |+.|-|+||||-..| |.+.|+||+.
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            46889999999   999999999998876 8999999984

>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=96.54  E-value=0.0018  Score=45.92  Aligned_cols=44  Identities=30%  Similarity=0.406  Sum_probs=38.8

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh-C--CCCccc
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS-G--IPEQAE  206 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~-G--IP~~~~  206 (300)
                      .+.|++|+-||   |+|+-++.|||.--+|..-|..-|.. |  +|..++
T Consensus        30 QesidqLvYMG---F~~~~Ae~ALRvfrGnVQlAaQtLahngG~LP~dLq   76 (83)
T d1vega_          30 QESINQLVYMG---FDTVVAEAALRVFGGNVQLAAQTLAHHGGSLPPDLQ   76 (83)
T ss_dssp             HHHHHHHHHHS---CCHHHHHHHHHHTTTCHHHHHHHHHHHTSSCCTTSS
T ss_pred             HHHHHHHHHhc---ccHHHHHHHHHHhcccHHHHHHHHHHcCCcCCcccc
Confidence            57899999999   99999999999999999999988764 3  887654

>d1vjka_ d.15.3.1 (A:) Molybdopterin synthase subunit MoaD {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.92  E-value=0.033  Score=39.72  Aligned_cols=68  Identities=18%  Similarity=0.217  Sum_probs=49.8

Q ss_pred             EEEEEEcCC------C-cEEEEEeCCCCCHHHHHHHHHHHhCCC--------CCCCCCeEEEeCCeecCCCCchhhcccC
Q 022228            2 MKIFVKTLK------G-TSFDVEVKPEDTVFDVKMKIETVQGSD--------VYPAAQQMLIYQGKVLKDDTTLEENKVA   66 (300)
Q Consensus         2 M~I~VKtl~------g-~~~~ieV~~~~TV~~LK~kI~~~~g~~--------~ip~~~qkLi~~GkiL~D~~tL~d~gI~   66 (300)
                      |+|+|+.+.      | ....+++....||.+|++.+..+++.-        .......++..+|+...++     +-|+
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            899999875      3 467889999999999999998875410        0112345666788877654     4578


Q ss_pred             CCcEEEEE
Q 022228           67 ENSFVVIM   74 (300)
Q Consensus        67 ~g~~I~v~   74 (300)
                      +||.|.++
T Consensus        77 ~gDevai~   84 (88)
T d1vjka_          77 DGDVVGVF   84 (88)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEe
Confidence            99999876

>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=95.38  E-value=0.0085  Score=40.52  Aligned_cols=37  Identities=27%  Similarity=0.420  Sum_probs=34.8

Q ss_pred             HHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          160 EGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       160 e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      |+.|+.|.+|  .   ++++-++.-|++.-+|.|+||+-||.
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            7789999999  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=95.10  E-value=0.017  Score=38.03  Aligned_cols=35  Identities=31%  Similarity=0.301  Sum_probs=31.2

Q ss_pred             HHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          161 GAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       161 ~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      +.|.+|-++ |   +.--+|..||..+.+|.|+|+|||-
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            467777776 8   8999999999999999999999994

>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=94.96  E-value=0.019  Score=38.35  Aligned_cols=36  Identities=14%  Similarity=0.193  Sum_probs=32.3

Q ss_pred             HHHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          160 EGAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       160 e~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      -+.|.+|-+. |   +.--+|..||..+.||.|.|+|||-
T Consensus         5 ~~lvk~LRe~Tg---a~~~dcKkAL~e~~gD~ekA~e~Lr   41 (56)
T d1xb2b1           5 KELLMKLRRKTG---YSFINCKKALETCGGDLKQAESWLH   41 (56)
T ss_dssp             HHHHHHHHHHHC---CCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            3578888887 8   8999999999999999999999995

>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=94.59  E-value=0.013  Score=38.72  Aligned_cols=23  Identities=26%  Similarity=0.567  Sum_probs=21.7

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHH
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRA  185 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrA  185 (300)
                      +..|.++++||   |+|+.|+.+||-
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   999999999986

>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=94.28  E-value=0.035  Score=36.72  Aligned_cols=35  Identities=20%  Similarity=0.228  Sum_probs=31.6

Q ss_pred             HHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 022228          161 GAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       161 ~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      +.|.+|-++ |   +.--+|..||..+.+|.|.|+|||-
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            568888887 7   8899999999999999999999994

>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=93.86  E-value=0.024  Score=37.57  Aligned_cols=40  Identities=20%  Similarity=0.224  Sum_probs=36.7

Q ss_pred             CChHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          157 NNLEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       157 ~~~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      .++++.+++|.+|  .   ++++=+..-|++.-+|.|+||+.||.
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            4678899999999  7   99999999999999999999999983

>d2dkla1 a.5.2.1 (A:8-79) Trinucleotide repeat containing 6c protein, TNRC6C {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Trinucleotide repeat containing 6c protein, TNRC6C
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.93  E-value=0.14  Score=35.20  Aligned_cols=37  Identities=30%  Similarity=0.456  Sum_probs=33.5

Q ss_pred             HHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHHHh
Q 022228          160 EGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYLYS  199 (300)
Q Consensus       160 e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyLl~  199 (300)
                      ...|.++..||   |.|+..+.||+..-.|.+-|+--|+-
T Consensus        15 np~~KQfsnMG---f~re~~e~~l~sN~m~L~~a~~~l~d   51 (72)
T d2dkla1          15 SRLIKQLTDMG---FPREPAEEALKSNNMNLDQAMSALLE   51 (72)
T ss_dssp             HHHHHHHHHHT---CCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             hHHHHHHhhcC---CcCCChHHhhhccCcchhhcccchhh
Confidence            45789999999   99999999999999999999987763

>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=91.86  E-value=0.046  Score=35.33  Aligned_cols=23  Identities=22%  Similarity=0.314  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHhCCCchHHHHhc
Q 022228          272 PQFQVLRAMVQANPQLFPCFKSW  294 (300)
Q Consensus       272 pqf~~lR~~vq~nP~~L~~~lq~  294 (300)
                      .++-+||++|..||+.|.+||+.
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            46789999999999999999874

>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=91.53  E-value=0.44  Score=33.77  Aligned_cols=72  Identities=18%  Similarity=0.220  Sum_probs=55.1

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--eecCCCCchhhcccCCCcEEEEEEe
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ---G--KVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~---G--kiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      |+|.|..+++ ++++.|+...+..+|=++|+...+.  ...+-.-|-|-   |  .-|+.++.|....++.+..+.+..+
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            7899999997 5899999999999999999999992  33455566553   3  2478889999887666665555443

>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=91.19  E-value=0.14  Score=31.43  Aligned_cols=35  Identities=26%  Similarity=0.422  Sum_probs=31.4

Q ss_pred             HHHHHHHhccCCCC-CHHHHHHHHHHhcCChHHHHHHHH
Q 022228          161 GAIQQILDMGGGTW-DRDTVVRALRAAYNNPERAVEYLY  198 (300)
Q Consensus       161 ~~I~~i~eMG~~~f-~r~qv~~ALrAafnNpdrAvEyLl  198 (300)
                      .+...|+|||   | +|.-=.+=|+-..||...+|.-|+
T Consensus         4 ~lM~~L~EMG---F~DR~lNq~LL~KH~~nl~~vV~eLl   39 (41)
T d2cp8a1           4 ALMAHLFEMG---FCDRQLNLRLLKKHNYNILQVVTELL   39 (41)
T ss_dssp             HHHHHHHHHT---CCCHHHHHHHHTTTTTCHHHHHHHHH
T ss_pred             HHHHHHHHhC---cchhHHHHHHHHHccCcHHHHHHHHH
Confidence            4678999999   9 999999999999999999997765

>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=89.85  E-value=0.2  Score=36.70  Aligned_cols=71  Identities=6%  Similarity=-0.000  Sum_probs=42.3

Q ss_pred             EEEEEEcCC--------CcEEEEEeC---CCCCHHHHHHHHHHHhCCC--CCCCC------CeEEEeCCeecCCCCch--
Q 022228            2 MKIFVKTLK--------GTSFDVEVK---PEDTVFDVKMKIETVQGSD--VYPAA------QQMLIYQGKVLKDDTTL--   60 (300)
Q Consensus         2 M~I~VKtl~--------g~~~~ieV~---~~~TV~~LK~kI~~~~g~~--~ip~~------~qkLi~~GkiL~D~~tL--   60 (300)
                      |+|+|+...        .+.+.+++.   ...||.+|-+.+.+++...  .+--+      ...++.+|+-..   .+  
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            789998743        245566664   3479999999999987621  00000      122233443221   11  


Q ss_pred             hhcccCCCcEEEEEE
Q 022228           61 EENKVAENSFVVIML   75 (300)
Q Consensus        61 ~d~gI~~g~~I~v~v   75 (300)
                      -++.|++||.|.++-
T Consensus        82 l~t~l~dgDeV~~~p   96 (101)
T d1xo3a_          82 LDYQLQDQDSILFIS   96 (101)
T ss_dssp             TSCCCCTTCEEEEEE
T ss_pred             CccCcCCCCEEEEeC
Confidence            256799999998873

>d1wgra_ d.15.1.5 (A:) Growth factor receptor-bound protein 7, GRB-7 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: Growth factor receptor-bound protein 7, GRB-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.01  E-value=0.93  Score=32.80  Aligned_cols=75  Identities=17%  Similarity=0.058  Sum_probs=47.4

Q ss_pred             EEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--e--CC--eecCCCCchhhccc--CCCcEEEEE
Q 022228            3 KIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLI--Y--QG--KVLKDDTTLEENKV--AENSFVVIM   74 (300)
Q Consensus         3 ~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi--~--~G--kiL~D~~tL~d~gI--~~g~~I~v~   74 (300)
                      .|.|-..+|.+..|.|+.++|+.+|-+.+.++.++. ..+ ..-|+  +  .|  +.|.|+..+-+.-.  ..++.-.++
T Consensus        11 vvkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~-~~~-~f~L~E~~~~~~leR~L~d~E~vl~v~~~W~~~~~~r~v   88 (100)
T d1wgra_          11 VVKVYSEDGACRSVEVAAGATARHVCEMLVQRAHAL-SDE-TWGLVECHPHLALERGLEDHESVVEVQAAWPVGGDSRFV   88 (100)
T ss_dssp             EEEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCC-CCC-CCCEEEEETTTTEEEEECSSSCHHHHHTTSCSSSCCEEE
T ss_pred             EEEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCC-CCC-CeEEEEecCCCcceeecCchHhHHHHHHcCCCCCCCEEE
Confidence            455556789999999999999999999999998842 111 22222  2  23  78888765544411  122333455


Q ss_pred             EecCC
Q 022228           75 LTKNK   79 (300)
Q Consensus        75 v~k~~   79 (300)
                      +||--
T Consensus        89 ~rkny   93 (100)
T d1wgra_          89 FRKNF   93 (100)
T ss_dssp             ECSCC
T ss_pred             EeecC
Confidence            56543

>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=88.02  E-value=1.5  Score=30.86  Aligned_cols=73  Identities=14%  Similarity=0.079  Sum_probs=54.4

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe--CC--eecCCCCchhhcccCCCcEEEEEEe
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY--QG--KVLKDDTTLEENKVAENSFVVIMLT   76 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~--~G--kiL~D~~tL~d~gI~~g~~I~v~v~   76 (300)
                      +|.|.|..+++. +++.|+...+..+|=..|+...+.  ...+-.-|.|  +|  .-|+.++.|..+.++.+..+++..+
T Consensus         2 ~~~v~V~lLD~~-le~~v~~~a~G~~L~d~Vc~~L~L--~E~~YFGL~y~~~~~~~WLd~~k~l~kq~~~~~~~~~~~F~   78 (84)
T d1h4ra3           2 TFTVRIVTMDAE-MEFNCEMKWKGKDLFDLVCRTLGL--RETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   78 (84)
T ss_dssp             EEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTC--CCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             eEEEEEEEcCCc-EEEEEcCCChHHHHHHHHHHHcCC--cccccceEEEecCCceEEccCCCchhhhccCCCCCEEEEEE
Confidence            378999999984 799999999999999999999982  2334444544  44  3478889998887776665555443

>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=87.86  E-value=0.98  Score=31.61  Aligned_cols=60  Identities=13%  Similarity=0.081  Sum_probs=45.7

Q ss_pred             EEEEEEcCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe---CC--eecCCCCchhhc
Q 022228            2 MKIFVKTLKGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIY---QG--KVLKDDTTLEEN   63 (300)
Q Consensus         2 M~I~VKtl~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~---~G--kiL~D~~tL~d~   63 (300)
                      |+.+|..++|..+.+.|+...+..+|=++|....+.  ...+-.-|-|   +|  .-|+.++.|...
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            678999999999999999999999999999999982  2233333333   23  246777877765

>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=87.67  E-value=0.59  Score=29.37  Aligned_cols=38  Identities=16%  Similarity=0.185  Sum_probs=33.0

Q ss_pred             CChHHHHHHHHhc-cCCCCCHHHHHHHHHHhcCChHHHHHHH
Q 022228          157 NNLEGAIQQILDM-GGGTWDRDTVVRALRAAYNNPERAVEYL  197 (300)
Q Consensus       157 ~~~e~~I~~i~eM-G~~~f~r~qv~~ALrAafnNpdrAvEyL  197 (300)
                      ++.++.|++.|++ |   =++++++.=|.++.+|.++||.--
T Consensus         3 ~~~~~lI~qF~~iTg---~~~~~A~~~Le~~~w~Le~Ai~~y   41 (46)
T d1v92a_           3 EERQDALREFVAVTG---AEEDRARFFLESAGWDLQIALASF   41 (46)
T ss_dssp             THHHHHHHHHHHHTC---CCHHHHHHHHHHTTSCSHHHHHHH
T ss_pred             ccHHHHHHHHHHHHC---cCHHHHHHHHHHcCCcHHHHHHHH
Confidence            3567899999998 6   699999999999999999999643

>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=87.19  E-value=0.74  Score=30.94  Aligned_cols=49  Identities=16%  Similarity=0.325  Sum_probs=37.1

Q ss_pred             cCCChHHHHHHHHhc--cCCCCCHHHHHHHHHHhcCChHHHHHHHHhC-CCCccc
Q 022228          155 AGNNLEGAIQQILDM--GGGTWDRDTVVRALRAAYNNPERAVEYLYSG-IPEQAE  206 (300)
Q Consensus       155 ~g~~~e~~I~~i~eM--G~~~f~r~qv~~ALrAafnNpdrAvEyLl~G-IP~~~~  206 (300)
                      .|-+.+..|.++-++  =   +...-|.++|..-.+|+|+.|..|+.| +|.++.
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            467888899998875  2   335557788877445999999999999 777653

>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=84.19  E-value=1.3  Score=31.21  Aligned_cols=42  Identities=19%  Similarity=0.164  Sum_probs=33.8

Q ss_pred             EEEEcC-CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC
Q 022228            4 IFVKTL-KGTSFDVEVKPEDTVFDVKMKIETVQGSDVYPAAQQMLIYQ   50 (300)
Q Consensus         4 I~VKtl-~g~~~~ieV~~~~TV~~LK~kI~~~~g~~~ip~~~qkLi~~   50 (300)
                      |+||.. ++..+.+.|.++.+..+|+++|..+.+     ....+|-|.
T Consensus        13 ikVKv~~~~D~~~~~l~~~it~~dL~~kI~~rf~-----~~~~~lkY~   55 (85)
T d1ip9a_          13 TKIKFYYKDDIFALMLKGDTTYKELRSKIAPRID-----TDNFKLQTK   55 (85)
T ss_dssp             EEEEECBTTCCEEEEECSCCCHHHHHHHHHHHHT-----SSCEEEEEC
T ss_pred             EEEEEEECCcEEEEEeCCCCCHHHHHHHHHHHhC-----CCceEEEEE
Confidence            444433 667889999999999999999999987     356888775

>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=82.94  E-value=0.31  Score=31.09  Aligned_cols=36  Identities=17%  Similarity=0.371  Sum_probs=28.4

Q ss_pred             ChHHHHHHHHhccCCCCCHHHHHHHHHHhcCChHHHHHHH
Q 022228          158 NLEGAIQQILDMGGGTWDRDTVVRALRAAYNNPERAVEYL  197 (300)
Q Consensus       158 ~~e~~I~~i~eMG~~~f~r~qv~~ALrAafnNpdrAvEyL  197 (300)
                      ..+++|.-|+..|   |.+.++.+|++...+ ++.-+|=|
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            4578999999999   999999999988754 44444443

>d1t3qa2 d.15.4.2 (A:7-87) Quinoline 2-oxidoreductase small subunit QorS, N-domain {Pseudomonas putida [TaxId: 303]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: 2Fe-2S ferredoxin-like
family: 2Fe-2S ferredoxin domains from multidomain proteins
domain: Quinoline 2-oxidoreductase small subunit QorS, N-domain
species: Pseudomonas putida [TaxId: 303]

Probab=82.66  E-value=0.64  Score=32.77  Aligned_cols=28  Identities=21%  Similarity=0.275  Sum_probs=25.1

Q ss_pred             CEEEEEEcCCCcEEEEEeCCCCCHHHHHH
Q 022228            1 MMKIFVKTLKGTSFDVEVKPEDTVFDVKM   29 (300)
Q Consensus         1 mM~I~VKtl~g~~~~ieV~~~~TV~~LK~   29 (300)
                      ||+|++. ++|+.+.++++++.++.++-.
T Consensus         3 ~~~i~~~-vNG~~~~~~~~~~~~Ll~~LR   30 (81)
T d1t3qa2           3 LMRISAT-INGKPRVFYVEPRMHLADALR   30 (81)
T ss_dssp             CEEEEEE-ETTEEEEEEECTTSBHHHHHH
T ss_pred             eEEEEEE-ECCEEEEEecCCCCCHHHHHh
Confidence            7999997 799999999999999988764

>d2k0bx1 a.5.2.1 (X:1-52) Sequestosome 1 (Sqstm1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Sequestosome 1 (Sqstm1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.27  E-value=0.57  Score=30.13  Aligned_cols=38  Identities=21%  Similarity=0.389  Sum_probs=30.5

Q ss_pred             CChHHHHHHHHhccCCCCCHHH--HHHHHHHhcCChHHHHHHH
Q 022228          157 NNLEGAIQQILDMGGGTWDRDT--VVRALRAAYNNPERAVEYL  197 (300)
Q Consensus       157 ~~~e~~I~~i~eMG~~~f~r~q--v~~ALrAafnNpdrAvEyL  197 (300)
                      +.++++|.+|+.||   |+-|-  ..+=|.+-.+|..+|++-|
T Consensus         8 p~l~~al~qM~aMG---FsneGGWLt~LL~skn~dI~~aLD~i   47 (52)
T d2k0bx1           8 PRLIESLSQMLSMG---FSDEGGWLTRLLQTKNYDIGAALDTI   47 (52)
T ss_dssp             TTHHHHHHHHHHHT---CCCSSSCHHHHHHHTTSCHHHHHHHT
T ss_pred             hHHHHHHHHHHHcC---CCCcchHHHHHHHHcCCCHHHHHHHH
Confidence            35789999999999   96553  5667788888888888866