Psyllid ID: psy4259

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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---
Protein Sequence
MGMLAHDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFFERVNPYGGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAGDRRNKNVLGT
Secondary Structure (PSIPRED)
ccccccEEEEEEEEccccEEEEEccccHHHHHHHHHHHHHccccccccEEEEEcccccccHHHHHHcccccccEEEEEEcccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccHHHccccHHHHHHHHHHHHccccHHHHHHHHHHccHHHHHHHHHcHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccHHHcHEEEccEEEcccccHHHcccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHHHcHHHHHHHHHHHHcccHHHHHHHHHcHHHHHHHHcccccccccccccccc
Coil and Loop (DISEMBL)
MGMLAHDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGkilsddqalseynideSKFIVVMLskpkptpapysgpsdptqpagqeseatrpatatsDSMLKVFFErvnpyggesedplaflrtqpqFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLnepvagdrrnknvlgt
Flexible Loop (DISEMBL)
mgmlahdisditqnqwqqTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAPYSGPSDPTQPAGQESEATrpatatsdSMLKVFFERVNPYGGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMlnepvagdrrnknvlgt
Low Complexity Region (SEG)
MGMLAHDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFFERVNPYGGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAGDRRNKNVLGT
Disordered region (IsUnstruct)
******************************************EYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML**************************************KVFFERVNPY********AFL**********TVVQ**PELLPTVLQQIGQSNPALLELISHNQEAFVRM*****************
Disordered Region (DISOPRED)
*****HD**DITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML********************************************VNPYGGESEDPLAFLRTQP***********NPE*************************AF********************
Disordered Region (DISEMBL)
MGMLAHDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK*****************************SDSMLKVFFERVNPYGGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAGDRRNKNVLGT
Disordered Region (DISPRO)
**MLAHDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP**************************************************DPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNE**************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGMLAHDISDITQNQWQQTVSxxxxxxxxxxxxxxxxxxxxxEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFFERVNPYGGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAGDRRNKNVLGT
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	203	2.2.26 [Sep-21-2011]
P54727	409	UV excision repair protei	yes	N/A	0.261	0.129	0.689	3e-17
Q4KMA2	415	UV excision repair protei	yes	N/A	0.270	0.132	0.689	3e-17
Q29RK4	408	UV excision repair protei	yes	N/A	0.261	0.129	0.689	3e-17
P54728	416	UV excision repair protei	yes	N/A	0.270	0.132	0.689	3e-17
O74803	368	UV excision repair protei	yes	N/A	0.330	0.182	0.536	3e-15
Q84L31	419	Putative DNA repair prote	yes	N/A	0.566	0.274	0.381	9e-14
A3KMV2	362	UV excision repair protei	no	N/A	0.472	0.265	0.464	1e-12
Q84L32	368	Putative DNA repair prote	no	N/A	0.556	0.307	0.382	4e-12
P54726	363	UV excision repair protei	no	N/A	0.482	0.269	0.418	1e-11
P54725	363	UV excision repair protei	no	N/A	0.403	0.225	0.468	1e-11

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

 Score = 88.6 bits (218), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 48/58 (82%)

Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEPV
Sbjct: 275 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 332

The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, XPA, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the XPC:RAD23B dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. XPC:RAD23B contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. XPC:RAD23B induces a bend in DNA upon binding. XPC:RAD23B stimulates the activity of DNA glycosylases TDG and SMUG1.
Homo sapiens (taxid: 9606)

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

 Score = 88.2 bits (217), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 48/58 (82%)

Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEPV
Sbjct: 275 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 332

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 = 88.2 bits (217), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 48/58 (82%)

Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEPV
Sbjct: 274 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 331

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

 Score = 88.2 bits (217), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 48/58 (82%)

Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEPV
Sbjct: 275 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 332

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|O74803|RHP23_SCHPO UV excision repair protein rhp23 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rhp23 PE=1 SV=1

 Score = 81.6 bits (200), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 37/69 (53%), Positives = 51/69 (73%)

Query: 126 PYGGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVR 185
           P     +DPL FLR+ PQFQQ+R +VQQNP++L T+LQQIGQ +PAL + I+ N EAF++
Sbjct: 238 PSNTVGDDPLGFLRSIPQFQQLRQIVQQNPQMLETILQQIGQGDPALAQAITQNPEAFLQ 297

Query: 186 MLNEPVAGD 194
           +L E   G+
Sbjct: 298 LLAEGAEGE 306

Protects ubiquitin chains against dissambly by deubiquitinating enzymes thereby promoting protein degradation.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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

 Score = 76.6 bits (187), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 69/118 (58%), Gaps = 3/118 (2%)

Query: 86  PAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFFERVNPYGGE-SEDPLAFLRTQPQF 144
           PA    P++P  PA  +  A  PA+  + + L +F + +   GG      L FLR   QF
Sbjct: 242 PASAGQPANP--PAQTQQPAAAPASGPNANPLDLFPQGLPNVGGNPGAGTLDFLRNSQQF 299

Query: 145 QQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAGDRRNKNVLG 202
           Q +R +VQ NP++L  +LQ++G+ NP L+ LI  +Q  F+R++NEPV G   + N+LG
Sbjct: 300 QALRAMVQANPQVLQPMLQELGKQNPNLMRLIQDHQADFLRLINEPVEGGGESGNLLG 357

May be involved in nucleotide excision repair.

Arabidopsis thaliana (taxid: 3702)

>sp|A3KMV2|RD23A_BOVIN UV excision repair protein RAD23 homolog A OS=Bos taurus GN=RAD23A PE=2 SV=1

 Score = 72.8 bits (177), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 62/99 (62%), Gaps = 3/99 (3%)

Query: 17  QQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKF 74
           QQT    ++  E VK LKEKI++EKG + +    QKLIYAGKILSDD  + +Y IDE  F
Sbjct: 12  QQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNF 71

Query: 75  IVVMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATATS 113
           +VVM++K K +P   S PS+ +  A  ES  + P+   S
Sbjct: 72  VVVMVTKAKTSPG-TSVPSEASPTATPESSTSFPSAPAS 109

Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, XPC:RAD23A dimer has NER activity. Can stabilize XPC.

Bos taurus (taxid: 9913)

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

 Score = 71.2 bits (173), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 47/123 (38%), Positives = 67/123 (54%), Gaps = 10/123 (8%)

Query: 89  YSG-PSDPTQPA--------GQESEATRPATATSDSMLKVF-FERVNPYGGESEDPLAFL 138
           YSG P   T PA        G+E  A  P+   + S L +F  E V+   G     L FL
Sbjct: 185 YSGIPETVTIPATNLSGVGSGRELTAPPPSGGPNSSPLDLFPQEAVSDAAGGDLGTLEFL 244

Query: 139 RTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAGDRRNK 198
           R   QFQQ+R++V  NP++L  +LQ++G+ NP LL LI  NQ  F+++LNEP  G   + 
Sbjct: 245 RGNDQFQQLRSMVNSNPQILQPMLQELGKQNPQLLRLIQENQAEFLQLLNEPYEGSDGDV 304

Query: 199 NVL 201
           ++ 
Sbjct: 305 DIF 307

May be involved in nucleotide excision repair.

Arabidopsis thaliana (taxid: 3702)

>sp|P54726|RD23A_MOUSE UV excision repair protein RAD23 homolog A OS=Mus musculus GN=Rad23a PE=1 SV=2

 Score = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 46/110 (41%), Positives = 61/110 (55%), Gaps = 12/110 (10%)

Query: 17  QQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKF 74
           QQT    ++  E VK LKEKI++EKG + +    QKLIYAGKILSDD  + EY+IDE  F
Sbjct: 12  QQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIKEYHIDEKNF 71

Query: 75  IVVMLSK----------PKPTPAPYSGPSDPTQPAGQESEATRPATATSD 114
           +VVM++K          P+ +P     PS P  P      +  P T+  D
Sbjct: 72  VVVMVTKAKAGQGIPAPPEASPTAVPEPSTPFPPVLASGMSHPPPTSRED 121

Involved in nucleotide excision repair and is thought to be functional equivalent for Rad23b in global genome nucleotide excision repair (GG-NER) by association with Xpc. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize Xpc. Reported differences to Rad23b in regard to NER activity and Xpc stabilization are probably due to differences in expression levels with Rad23a being much less expressed than Rad23b.

Mus musculus (taxid: 10090)

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

 Score = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 45/96 (46%), Positives = 56/96 (58%), Gaps = 14/96 (14%)

Query: 17  QQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKF 74
           QQT    ++  E VK LKEKI++EKG + +    QKLIYAGKILSDD  + +Y IDE  F
Sbjct: 12  QQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNF 71

Query: 75  IVVMLSKPK------------PTPAPYSGPSDPTQP 98
           +VVM++K K            PT AP S  S P  P
Sbjct: 72  VVVMVTKTKAGQGTSAPPEASPTAAPESSTSFPPAP 107

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	203
283945482	324	nuclear excision repair protein rad23 [B	0.906	0.567	0.418	3e-38
357621015	323	nuclear excision repair protein rad23 [D	0.862	0.541	0.441	5e-37
47205078	320	unnamed protein product [Tetraodon nigro	0.852	0.540	0.363	3e-24
170590706	354	UV excision repair protein Rad23 contain	0.857	0.491	0.356	3e-23
393911377	337	UV excision repair protein Rad23 [Loa lo	0.817	0.492	0.360	4e-22
345482490	377	PREDICTED: UV excision repair protein RA	0.290	0.156	0.822	1e-21
187117168	347	rad23 protein [Acyrthosiphon pisum] gi|8	0.300	0.175	0.836	2e-21
312095801	341	UV excision repair protein Rad23 contain	0.793	0.472	0.359	3e-21
345482494	367	PREDICTED: UV excision repair protein RA	0.290	0.160	0.806	4e-21
427787569	397	Putative nucleotide excision repair fact	0.206	0.105	0.793	5e-21

>gi|283945482|ref|NP_001164652.1| nuclear excision repair protein rad23 [Bombyx mori] gi|217331039|gb|ACK38234.1| nuclear excision repair protein Rad23 [Bombyx mori]

 Score =  163 bits (413), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 106/253 (41%), Positives = 134/253 (52%), Gaps = 69/253 (27%)

Query: 17  QQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFI 75
           QQT    +D +E VK LK KI+ EKG +++A++Q+LIYAGKIL DD  ++ YNIDE KFI
Sbjct: 10  QQTFQIEIDPEETVKALKLKIEVEKGKDFVADHQRLIYAGKILLDDNKINSYNIDEKKFI 69

Query: 76  VVMLSKPK-------PTPAPYSGPSDPTQPAGQE------SEATRPATA----------- 111
           V+M++KPK        T  P +G S  T     +       E  +P TA           
Sbjct: 70  VIMVTKPKVSESQPTSTSIPEAGESASTDSGDAKPKTVPPEEVVKPTTAETERVTETPNT 129

Query: 112 TSDSMLKVFFERVNPYG----------------------------------------GES 131
           TSD+ L+   + +   G                                           
Sbjct: 130 TSDAELEATIQSIMDMGYDRPQVEQALRASFNNRERAVEYLITGIPEELLHEQEAEESSD 189

Query: 132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           EDPLAFLR QPQFQQMR V+QQNP LL  VLQQIGQ+NPALL++IS +QEAFVRMLNEPV
Sbjct: 190 EDPLAFLRDQPQFQQMRAVIQQNPNLLNAVLQQIGQTNPALLQVISQHQEAFVRMLNEPV 249

Query: 192 ----AGDRRNKNV 200
               AG   ++NV
Sbjct: 250 NPSAAGVASDENV 262

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357621015|gb|EHJ73001.1| nuclear excision repair protein rad23 [Danaus plexippus]

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 106/240 (44%), Positives = 126/240 (52%), Gaps = 65/240 (27%)

Query: 17  QQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFI 75
           QQT    +D QE VK LK KI+ EKG +Y A+ Q+LIYAGKIL DD  L  YNIDE KFI
Sbjct: 10  QQTFQIEIDPQETVKALKLKIEVEKGKDYAADNQRLIYAGKILLDDNKLHTYNIDEKKFI 69

Query: 76  VVMLSKPK--------PTPAPYSGPSDPT----------------QPAGQESEATRPATA 111
           V+M++KPK         T AP +G S  T                QPA +   A+ P   
Sbjct: 70  VIMVTKPKTSDNQQASSTSAPEAGESASTESGDGKSKVVEEKPKPQPAAEPERASEPPVT 129

Query: 112 TSD---------------------SMLKVFF---ERVNPY----------------GGES 131
           +++                       L+  F   ER   Y                    
Sbjct: 130 SNEPDFESTVQSIMDMGYNRQQVEQALRASFNNRERAVEYLITGIPEELLQEQEAEESAD 189

Query: 132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           EDPL FLR QPQFQQMR V+QQNP LL TVLQQIGQ+NPALL+ IS +Q+AFVRMLNEPV
Sbjct: 190 EDPLGFLRDQPQFQQMRAVIQQNPNLLNTVLQQIGQTNPALLQAISQHQQAFVRMLNEPV 249

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|47205078|emb|CAF91196.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 119/245 (48%), Gaps = 72/245 (29%)

Query: 17  QQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKF 74
           QQT+   +D ++ VK LKEKI++E+G + +    QKLIYAGKIL DD  + EY IDE  F
Sbjct: 10  QQTIQIEIDPEQTVKALKEKIEAERGKDNFPVSGQKLIYAGKILQDDTPIKEYKIDERNF 69

Query: 75  IVVMLSK-------PKPT----PAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFF-- 121
           +VVM+SK        +PT    P  +   SD +Q  G ++ +     A  ++ML      
Sbjct: 70  VVVMVSKVGAGNQTHRPTVSSRPLAFCSSSDGSQ--GLDASSALVTGAEYEAMLTEIISM 127

Query: 122 ----ERV---------NPYGG--------------------------ESEDP-------- 134
               ERV         NP+                             +E P        
Sbjct: 128 GYERERVVAALRASFNNPHRAVEYLLTGIPSSPVQESNPPAQAPAPLPTESPASPAEGCF 187

Query: 135 --------LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRM 186
                   LAFLR QPQF  MR  +QQNP LL  +LQQ+GQ NP LL+ I+ +QE F++M
Sbjct: 188 PACPGENPLAFLRNQPQFLHMRQAIQQNPNLLSALLQQLGQENPQLLQQINQHQERFIQM 247

Query: 187 LNEPV 191
           LNEPV
Sbjct: 248 LNEPV 252

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|170590706|ref|XP_001900112.1| UV excision repair protein Rad23 containing protein [Brugia malayi] gi|158592262|gb|EDP30862.1| UV excision repair protein Rad23 containing protein [Brugia malayi]

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 112/247 (45%), Gaps = 73/247 (29%)

Query: 23  LDVQEEVKQLKEKIQSEKGS-EYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK 81
           LD    + ++K KI  EKG  EY  E QKLIY GK+L D Q + E  ID SKF+VVM+++
Sbjct: 39  LDPHLTIGEVKAKIAEEKGEVEYPTECQKLIYNGKVLDDAQTVEEVMIDPSKFVVVMIAR 98

Query: 82  PKPTPAPY--------------------------SGPSDPTQPAGQESEATRPATAT--- 112
            KP  AP                           SGPS P  P     E    A A    
Sbjct: 99  KKPIGAPVESTPQPSNLQIPAGAQVTTAPVSVADSGPSTPQNPDDLTPEQEETAQAIVAM 158

Query: 113 ---SDSMLKV----FF--ERVNPY-----------GGESEDP------------LAFLRT 140
               D +++     FF  +R   Y           GG  E              L FLR 
Sbjct: 159 GYPRDKVIRALRASFFNGDRAVEYLCSGIPEEEDLGGHQESAEHEEGERAQGLGLDFLRQ 218

Query: 141 QPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNE----------- 189
            PQF+Q+R +VQ NP +LP ++QQI QSNPAL+E I +NQE FV +LN            
Sbjct: 219 LPQFEQLRELVQSNPAILPQIIQQIAQSNPALMEAIQNNQEEFVNLLNNGSVSSGGGGVA 278

Query: 190 PVAGDRR 196
           P AG++R
Sbjct: 279 PSAGEQR 285

Source: Brugia malayi

Species: Brugia malayi

Genus: Brugia

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|393911377|gb|EFO15597.2| UV excision repair protein Rad23 [Loa loa]

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 109/230 (47%), Gaps = 64/230 (27%)

Query: 23  LDVQEEVKQLKEKIQSEKGS-EYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK 81
           LD    + ++K KI  EKG  EY  E QKLIY GK+L D Q + E  ID SKF+V+M+++
Sbjct: 17  LDPHLTIGEVKAKIAEEKGEVEYPIECQKLIYNGKVLDDAQTVEEVMIDPSKFVVIMIAR 76

Query: 82  PKP---TPAPYS-GPSDPTQPAGQESEATRPATATS------------------------ 113
            KP   TPA  +  PS+   PA  +     PA+ T                         
Sbjct: 77  KKPVGATPAESTPQPSNLQIPAAAQVTTVTPASVTDNSPAAPQNSDGLTPEQEETAQAIV 136

Query: 114 ------DSMLKV----FF--ERVNPY-----------GGESEDP------------LAFL 138
                 D +++     FF  +R   Y           GG  E              L FL
Sbjct: 137 AMGYSRDKVIRALRASFFNGDRAVEYLCSGIPEEEDLGGHQESAEHEEGERGQGLGLDFL 196

Query: 139 RTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLN 188
           R  PQF+Q+R +VQ NP LLP ++QQI QSNPAL+E I +NQE FV +LN
Sbjct: 197 RQLPQFEQLRELVQSNPALLPQIIQQIAQSNPALMEAIQNNQEEFVNLLN 246

Source: Loa loa

Species: Loa loa

Genus: Loa

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|345482490|ref|XP_003424606.1| PREDICTED: UV excision repair protein RAD23 homolog B-like isoform 2 [Nasonia vitripennis]

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 51/62 (82%), Positives = 56/62 (90%)

Query: 132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           +DPLAFLRTQPQFQQMR V+QQNP+LL  VLQQIGQ+NPALL+LIS NQEAFVRMLNEPV
Sbjct: 231 QDPLAFLRTQPQFQQMRQVIQQNPQLLNPVLQQIGQTNPALLQLISQNQEAFVRMLNEPV 290

Query: 192 AG 193
             
Sbjct: 291 GA 292

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|187117168|ref|NP_001119685.1| rad23 protein [Acyrthosiphon pisum] gi|89473754|gb|ABD72689.1| putative RAD23-like B [Acyrthosiphon pisum] gi|239788640|dbj|BAH70991.1| ACYPI000077 [Acyrthosiphon pisum]

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/61 (83%), Positives = 56/61 (91%)

Query: 133 DPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVA 192
           DPLAFLR QP FQQMRTVVQQNPELL +VLQQIGQ+NPALL++IS+NQEAFVRMLNEP  
Sbjct: 221 DPLAFLRNQPTFQQMRTVVQQNPELLNSVLQQIGQTNPALLQMISNNQEAFVRMLNEPNE 280

Query: 193 G 193
           G
Sbjct: 281 G 281

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312095801|ref|XP_003148472.1| UV excision repair protein Rad23 containing protein [Loa loa]

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 107/228 (46%), Gaps = 67/228 (29%)

Query: 28  EVKQLKEKIQSEKGS-EYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKP-- 84
           ++ ++K KI  EKG  EY  E QKLIY GK+L D Q + E  ID SKF+V+M+++ KP  
Sbjct: 33  KIGEVKAKIAEEKGEVEYPIECQKLIYNGKVLDDAQTVEEVMIDPSKFVVIMIARKKPVG 92

Query: 85  ------TPAPY----------------------------SGPSDPTQPAGQESEATRPAT 110
                 TP P                             SG SD   P  +E+     A 
Sbjct: 93  ATPAESTPQPSNLQIPAAAQVTTVTPASVTDNSPAAPQNSGISDGLTPEQEETAQAIVAM 152

Query: 111 ATS-DSMLKV----FF--ERVNPY-----------GGESEDP------------LAFLRT 140
             S D +++     FF  +R   Y           GG  E              L FLR 
Sbjct: 153 GYSRDKVIRALRASFFNGDRAVEYLCSGIPEEEDLGGHQESAEHEEGERGQGLGLDFLRQ 212

Query: 141 QPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLN 188
            PQF+Q+R +VQ NP LLP ++QQI QSNPAL+E I +NQE FV +LN
Sbjct: 213 LPQFEQLRELVQSNPALLPQIIQQIAQSNPALMEAIQNNQEEFVNLLN 260

Source: Loa loa

Species: Loa loa

Genus: Loa

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|345482494|ref|XP_003424607.1| PREDICTED: UV excision repair protein RAD23 homolog B-like isoform 3 [Nasonia vitripennis]

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           +DPLAFLRTQPQFQQMR V+QQNP+LL  VLQQIGQ+NPALL+LIS NQEAFVRMLNEP 
Sbjct: 231 QDPLAFLRTQPQFQQMRQVIQQNPQLLNPVLQQIGQTNPALLQLISQNQEAFVRMLNEPA 290

Query: 192 AG 193
           + 
Sbjct: 291 SA 292

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427787569|gb|JAA59236.1| Putative nucleotide excision repair factor nef2 rad23 component [Rhipicephalus pulchellus]

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 50/63 (79%), Positives = 55/63 (87%)

Query: 128 GGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRML 187
           GG  EDPLAFLR QPQFQQMR V+QQNP+LL  VLQQ+GQ+NP LL+LIS NQEAFVRML
Sbjct: 259 GGNPEDPLAFLRFQPQFQQMRQVIQQNPQLLNAVLQQLGQTNPQLLQLISRNQEAFVRML 318

Query: 188 NEP 190
           NEP
Sbjct: 319 NEP 321

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

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	203
ZFIN|ZDB-GENE-040808-59	362	rad23aa "RAD23 homolog Aa (S.	0.305	0.171	0.661	2.6e-37
UNIPROTKB|A3KMV2	362	RAD23A "UV excision repair pro	0.290	0.162	0.677	7.6e-36
UNIPROTKB|F1PTL1	362	RAD23A "Uncharacterized protei	0.300	0.168	0.666	1.9e-35
RGD|1309899	351	Rad23a "RAD23 homolog A (S. ce	0.290	0.168	0.677	4.8e-35
UNIPROTKB|P54725	363	RAD23A "UV excision repair pro	0.290	0.162	0.677	5.4e-35
UNIPROTKB|D4AD39	363	Rad23a "RAD23a homolog (S. cer	0.290	0.162	0.677	6.8e-35
MGI|MGI:105126	363	Rad23a "RAD23a homolog (S. cer	0.290	0.162	0.677	3.7e-34
POMBASE|SPBC2D10.12	368	rhp23 "Rad23 homolog Rhp23" [S	0.463	0.255	0.45	2e-33
UNIPROTKB|K7ESE3	308	RAD23A "UV excision repair pro	0.472	0.311	0.454	4.1e-30
UNIPROTKB|G4MUE8	401	MGG_01656 "UV excision repair	0.330	0.167	0.492	5.4e-25

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

 Score = 220 (82.5 bits), Expect = 2.6e-37, Sum P(2) = 2.6e-37
 Identities = 41/62 (66%), Positives = 50/62 (80%)

Query:   130 ESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNE 189
             E E+PL FLR+QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++MLN 
Sbjct:   223 EGENPLEFLRSQPQFQSMRQVIQQNPSLLPALLQQLGQENPELLQQISQHQELFIQMLNA 282

Query:   190 PV 191
             PV
Sbjct:   283 PV 284

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0003684 "damaged DNA binding" evidence=IEA

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

 Score = 214 (80.4 bits), Expect = 7.6e-36, Sum P(2) = 7.6e-36
 Identities = 40/59 (67%), Positives = 48/59 (81%)

Query:   132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
             E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++MLNEP
Sbjct:   228 ENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEP 286

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

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

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

GO:0003684 "damaged DNA binding" evidence=IEA

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

 Score = 215 (80.7 bits), Expect = 1.9e-35, Sum P(2) = 1.9e-35
 Identities = 42/63 (66%), Positives = 50/63 (79%)

Query:   128 GGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRML 187
             GGE+  PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++ML
Sbjct:   226 GGEN--PLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQML 283

Query:   188 NEP 190
             NEP
Sbjct:   284 NEP 286

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

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

GO:0031593 "polyubiquitin binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

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

 Score = 214 (80.4 bits), Expect = 4.8e-35, Sum P(2) = 4.8e-35
 Identities = 40/59 (67%), Positives = 48/59 (81%)

Query:   132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
             E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++MLNEP
Sbjct:   228 ENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEP 286

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

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

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

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

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

 Score = 214 (80.4 bits), Expect = 5.4e-35, Sum P(2) = 5.4e-35
 Identities = 40/59 (67%), Positives = 48/59 (81%)

Query:   132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
             E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++MLNEP
Sbjct:   229 ENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEP 287

GO:0003684 "damaged DNA binding" evidence=IEA

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

GO:0000502 "proteasome complex" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0031593 "polyubiquitin binding" evidence=IDA

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

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

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

GO:0005515 "protein binding" evidence=IPI

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

 Score = 214 (80.4 bits), Expect = 6.8e-35, Sum P(2) = 6.8e-35
 Identities = 40/59 (67%), Positives = 48/59 (81%)

Query:   132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
             E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++MLNEP
Sbjct:   229 ENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEP 287

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

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

 Score = 214 (80.4 bits), Expect = 3.7e-34, Sum P(2) = 3.7e-34
 Identities = 40/59 (67%), Positives = 48/59 (81%)

Query:   132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
             E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++MLNEP
Sbjct:   229 ENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEP 287

GO:0000502 "proteasome complex" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

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

GO:0031593 "polyubiquitin binding" evidence=ISO

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

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

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

POMBASE|SPBC2D10.12 rhp23 "Rad23 homolog Rhp23" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 204 (76.9 bits), Expect = 2.0e-33, Sum P(2) = 2.0e-33
 Identities = 45/100 (45%), Positives = 62/100 (62%)

Query:   101 QESEATRPATATSDSML---KVFFERVN---PYGGESEDPLAFLRTQPQFQQMRTVVQQN 154
             Q+SEA  P +    + L       E  N   P     +DPL FLR+ PQFQQ+R +VQQN
Sbjct:   207 QQSEALAPTSTGQPANLFEQAALSENENQEQPSNTVGDDPLGFLRSIPQFQQLRQIVQQN 266

Query:   155 PELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAGD 194
             P++L T+LQQIGQ +PAL + I+ N EAF+++L E   G+
Sbjct:   267 PQMLETILQQIGQGDPALAQAITQNPEAFLQLLAEGAEGE 306

GO:0003684 "damaged DNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005635 "nuclear envelope" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

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

GO:0007346 "regulation of mitotic cell cycle" evidence=TAS

GO:0016567 "protein ubiquitination" evidence=IMP

GO:0030433 "ER-associated protein catabolic process" evidence=ISO

GO:0031593 "polyubiquitin binding" evidence=TAS

GO:0042177 "negative regulation of protein catabolic process" evidence=IMP

GO:0043130 "ubiquitin binding" evidence=IDA

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

 Score = 187 (70.9 bits), Expect = 4.1e-30, Sum P(2) = 4.1e-30
 Identities = 45/99 (45%), Positives = 59/99 (59%)

Query:    17 QQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKF 74
             QQT    ++  E VK LKEKI++EKG + +    QKLIYAGKILSDD  + +Y IDE  F
Sbjct:    12 QQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNF 71

Query:    75 IVVMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATATS 113
             +VVM++K K      S P + +  A  ES  + P   TS
Sbjct:    72 VVVMVTKTKAGQGT-SAPPEASPTAAPESSTSFPPAPTS 109

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|G4MUE8 MGG_01656 "UV excision repair protein Rad23" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 163 (62.4 bits), Expect = 5.4e-25, Sum P(2) = 5.4e-25
 Identities = 33/67 (49%), Positives = 43/67 (64%)

Query:   128 GGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRML 187
             GG+S   L FLR   QFQQ+R VVQQ P++L  +LQQ+G  NP L +LI+ N E F+ +L
Sbjct:   273 GGQSLGNLDFLRNNTQFQQLRQVVQQQPQMLEPILQQLGAGNPQLAQLIAQNPEQFLALL 332

Query:   188 NEPVAGD 194
              E    D
Sbjct:   333 GEDADED 339

GO:0003674 "molecular_function" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	203
pfam09280	59	pfam09280, XPC-binding, XPC-binding domain	9e-26
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	1e-24
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	5e-23
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	2e-18
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	6e-13
smart00213	72	smart00213, UBQ, Ubiquitin homologues	6e-13
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	8e-13
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	6e-11
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	3e-04
smart00727	41	smart00727, STI1, Heat shock chaperonin-binding mo	3e-04
cd01803	76	cd01803, Ubiquitin, Ubiquitin	4e-04
pfam10302	90	pfam10302, DUF2407, DUF2407 ubiquitin-like domain	7e-04
cd01790	79	cd01790, Herp_N, Homocysteine-responsive endoplasm	0.003

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

 Score = 93.8 bits (234), Expect = 9e-26
 Identities = 41/59 (69%), Positives = 48/59 (81%)

Query: 135 LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAG 193
           LAFLR  PQFQQ+R +VQQNPELLP +LQQ+GQSNP LL+LI  NQE F+R+LNE   G
Sbjct: 1   LAFLRNNPQFQQLRQMVQQNPELLPPLLQQLGQSNPQLLQLIQQNQEEFLRLLNEGAEG 59

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

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

 Score = 91.6 bits (228), Expect = 1e-24
 Identities = 37/61 (60%), Positives = 45/61 (73%)

Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
          +D  + V +LKEKI+ EKG +Y  E QKLIY+GKIL DD  L EY IDE  F+VVM+SKP
Sbjct: 17 VDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSKP 76

Query: 83 K 83
          K
Sbjct: 77 K 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|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 94.2 bits (234), Expect = 5e-23
 Identities = 51/111 (45%), Positives = 63/111 (56%), Gaps = 9/111 (8%)

Query: 92  PSDPTQPAGQESEATRPATAT----SDSMLKVFFERVNPYGGESE-----DPLAFLRTQP 142
           P DP QP   +  A   A AT        +     +       +E     +PL FLR QP
Sbjct: 196 PEDPEQPEPVQQTAASTAAATTETPQHGSVFEQAAQGGTEQPATEAAQGGNPLEFLRNQP 255

Query: 143 QFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAG 193
           QFQQ+R VVQQNP+LLP +LQQIGQ NP LL+ IS + E F++MLNEPV  
Sbjct: 256 QFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGE 306

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|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 81.5 bits (201), Expect = 2e-18
 Identities = 51/114 (44%), Positives = 66/114 (57%), Gaps = 15/114 (13%)

Query: 15  QWQQTVSHLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESK 73
           Q Q+    ++  E VK+LKEKI++E+G + Y    QKLIY+GKILSDD+ + EY I E  
Sbjct: 9   QQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEYKIKEKD 68

Query: 74  FIVVMLSKPK------------PTPAPYSGPSDPTQPAGQESEATRPATATSDS 115
           F+VVM+SKPK            PT AP   PS P  PA   S A  PA+A  + 
Sbjct: 69  FVVVMVSKPKTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAA--PASAVEEK 120

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|215813 pfam00240, ubiquitin, Ubiquitin family

 Score = 61.1 bits (149), Expect = 6e-13
 Identities = 23/68 (33%), Positives = 41/68 (60%), Gaps = 3/68 (4%)

Query: 14 NQWQQTVSH-LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
              +T++  +D  + V +LKEKI+ ++G     + Q+LI++GK+L DD  LSEY I + 
Sbjct: 2  TLDGKTITLEVDPSDTVSELKEKIEDKEGIP--VDQQRLIFSGKVLEDDTTLSEYGIQDG 59

Query: 73 KFIVVMLS 80
            + ++L 
Sbjct: 60 STLHLVLR 67

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|214563 smart00213, UBQ, Ubiquitin homologues

 Score = 61.1 bits (149), Expect = 6e-13
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 14 NQWQQTVSH-LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
              +T++  +   + V +LKEKI    G     E Q+LIY GK+L DD+ L++Y I + 
Sbjct: 7  TLDGKTITLEVKPSDTVSELKEKIAELTGIP--PEQQRLIYKGKVLEDDRTLADYGIQDG 64

Query: 73 KFIVVMLS 80
            I ++L 
Sbjct: 65 STIHLVLR 72

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

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

 Score = 60.7 bits (148), Expect = 8e-13
 Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 2/58 (3%)

Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          +   + V +LK KI +++G     E Q+LIYAGKIL DD+ LS+Y I +   + ++L 
Sbjct: 14 VSPDDTVAELKAKIAAKEG--VPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVLR 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 = 55.7 bits (135), Expect = 6e-11
 Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 2/53 (3%)

Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFI 75
          ++ +  V  LKEKI  E G     E Q+LIY+G++L DD+ LSEY +++   I
Sbjct: 17 VEEEITVLDLKEKIAEEVGIP--VEQQRLIYSGRVLKDDETLSEYKVEDGHTI 67

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|176352 cd00196, UBQ, Ubiquitin-like proteins

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          V  LKEK+  + G     E Q+L+  GKIL D   L +Y + +   +V++ 
Sbjct: 20 VADLKEKLAKKLG--LPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP 68

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|128966 smart00727, STI1, Heat shock chaperonin-binding motif

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 5/45 (11%)

Query: 133 DPLAFLRTQ-PQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELI 176
           DP   LR Q PQ Q +   +QQNP++    L Q+ Q NP LL+LI
Sbjct: 1   DPEMALRLQNPQVQSLLQDMQQNPDM----LAQMLQENPQLLQLI 41

Length = 41

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 37.5 bits (87), Expect = 4e-04
 Identities = 19/51 (37%), Positives = 33/51 (64%), Gaps = 2/51 (3%)

Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L
Sbjct: 23 IENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71

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

>gnl|CDD|220681 pfam10302, DUF2407, DUF2407 ubiquitin-like domain

 Score = 36.9 bits (86), Expect = 7e-04
 Identities = 14/38 (36%), Positives = 21/38 (55%)

Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSE 66
          V  LK+ I+S    E      +LIYAG++L+D   L+ 
Sbjct: 26 VAWLKKLIRSRLPQELSNRRLRLIYAGRLLNDSSKLAS 63

This is a family of proteins found in fungi. The function is not known. This domain is related to the ubiquitin domain. Length = 90

>gnl|CDD|176385 cd01790, Herp_N, Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 13 QNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSE 66
          Q    QTVS   +   V +LK  +     S+ L + Q+LIY+GK+L D   L +
Sbjct: 11 QKYEDQTVS-CFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRD 63

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. Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	203
KOG0011|consensus	340		100.0
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	100.0
KOG0010|consensus	493		99.9
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.8
PF09280	59	XPC-binding: XPC-binding domain; InterPro: IPR0153	99.8
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.79
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.79
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.78
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.77
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.76
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.76
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.76
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.76
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.75
PTZ00044	76	ubiquitin; Provisional	99.75
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.74
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.73
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.73
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.73
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.72
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.71
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.71
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.7
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.68
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.65
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.61
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.6
KOG0005|consensus	70		99.59
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.56
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.53
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.53
KOG0003|consensus	128		99.46
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.43
KOG0004|consensus	156		99.42
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.42
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.32
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	99.31
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.29
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	99.17
KOG4248|consensus	1143		99.02
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	99.01
PLN02560	308	enoyl-CoA reductase	98.98
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.95
KOG0001|consensus	75		98.89
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	98.89
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.69
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.56
KOG1872|consensus	473		98.56
KOG0006|consensus	446		98.18
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.08
KOG3493|consensus	73		98.06
KOG4495|consensus	110		97.97
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	97.86
KOG1769|consensus	99		97.83
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.82
KOG0012|consensus	380		97.82
KOG4583|consensus	391		97.78
smart00727	41	STI1 Heat shock chaperonin-binding motif.	97.72
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	97.68
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.61
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	97.48
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.43
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	97.36
COG5417	81	Uncharacterized small protein [Function unknown]	97.34
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	97.34
KOG1639|consensus	297		97.24
KOG0013|consensus	231		97.05
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	97.01
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	96.73
KOG3206|consensus	234		96.73
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	96.66
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	96.53
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	96.24
PF13019	162	Telomere_Sde2: Telomere stability and silencing	95.85
KOG0010|consensus	493		95.49
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	93.59
PRK06437	67	hypothetical protein; Provisional	93.11
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	92.7
PRK08364	70	sulfur carrier protein ThiS; Provisional	92.64
PF12754	309	Blt1: Cell-cycle control medial ring component; In	92.15
KOG2086|consensus	380		91.72
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	91.48
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	91.36
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	91.08
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	90.74
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	89.71
KOG2507|consensus	506		89.24
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	88.82
PF14453	57	ThiS-like: ThiS-like ubiquitin	88.23
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	88.19
KOG2561|consensus	568		87.9
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	87.76
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	87.51
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	86.72
PRK07440	70	hypothetical protein; Provisional	86.41
KOG2982|consensus	418		85.53
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	84.76
PF11069	98	DUF2870: Protein of unknown function (DUF2870); In	84.57
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	84.16
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	83.76
PRK06488	65	sulfur carrier protein ThiS; Validated	83.69
PF10407	73	Cytokin_check_N: Cdc14 phosphatase binding protein	82.82
PRK05659	66	sulfur carrier protein ThiS; Validated	82.7
PRK05863	65	sulfur carrier protein ThiS; Provisional	82.56
PF00564	84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	82.55
smart00727	41	STI1 Heat shock chaperonin-binding motif.	82.46
TIGR02958	452	sec_mycoba_snm4 secretion protein snm4. Members of	82.24
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	82.07
PF08337	539	Plexin_cytopl: Plexin cytoplasmic RasGAP domain; I	81.37
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	80.29
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	80.22
KOG1364|consensus	356		80.01

>KOG0011|consensus

Probab=100.00  E-value=1.2e-41  Score=288.40  Aligned_cols=186  Identities=46%  Similarity=0.745  Sum_probs=153.2

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCCCCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTP   86 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~~~~   86 (203)
                      |+|+||+++|.+|+ ++.+++||.++|++|+...|.++|++.|||||+||+|+|+.|+.+|+|+++++|+||++|++.++
T Consensus         1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~k~~~   80 (340)
T KOG0011|consen    1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKDKSAS   80 (340)
T ss_pred             CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhccccCceEEEEEecCcccc
Confidence            78999999999999 99999999999999999999889999999999999999999999999999999999999987222


Q ss_pred             C---CCCCCCC--------CCC-CCCCCC--CCCC------------------CchhhHHHHHhCCcCCC----------
Q psy4259          87 A---PYSGPSD--------PTQ-PAGQES--EATR------------------PATATSDSMLKVFFERV----------  124 (203)
Q Consensus        87 ~---p~~~~~~--------p~~-~p~~~~--~~~~------------------~~~~~v~~~~~mG~~~~----------  124 (203)
                      +   |.+++..        |+. .....+  +++.                  ..+.+|.+||+|||+|+          
T Consensus        81 t~~ap~s~~~~~~p~~~~ap~~s~a~~~s~~~~~~~~~~~~~~~aas~Lv~G~~~e~~V~~Im~MGy~re~V~~AlRAaf  160 (340)
T KOG0011|consen   81 TQVAPQSSAATHLPKAAEAPPSSAAEDASPATPAQTSQEDTYEIAASTLVVGSEYEQTVQQIMEMGYDREEVERALRAAF  160 (340)
T ss_pred             cCCCCCCccccCCCccCCCCCccccccCCCCccccccccchhhhhhhhhhccchhHHHHHHHHHhCccHHHHHHHHHHhh
Confidence            2   1111100        100 000000  0000                  11679999999999998          


Q ss_pred             -CCC--------------------------CC------------------CCCChHHHhhCCHHHHHHHHHHHhCCCcHH
Q psy4259         125 -NPY--------------------------GG------------------ESEDPLAFLRTQPQFQQMRTVVQQNPELLP  159 (203)
Q Consensus       125 -np~--------------------------~~------------------~~~~pl~~l~~~P~~~~~r~~i~~nP~~l~  159 (203)
                       ||+                          +.                  .+.+|+++||++|+|++||++|++||++|+
T Consensus       161 NNPeRAVEYLl~GIP~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~~~~~~~~~l~fLr~~~qf~~lR~~iqqNP~ll~  240 (340)
T KOG0011|consen  161 NNPERAVEYLLNGIPEDAEVPEPEKSTAAAAELPANAQPLDLFPQGAVEASGGDPLEFLRNQPQFQQLRQMIQQNPELLH  240 (340)
T ss_pred             CChhhhHHHHhcCCcccccCCcccCCcccCCCCCCCCChhhcCCccchhhhcCCchhhhhccHHHHHHHHHHhhCHHHHH
Confidence             440                          01                  134679999999999999999999999999


Q ss_pred             HHHHHHhhcCHHHHHHHhhCHHHHHHHHcCCccc
Q psy4259         160 TVLQQIGQSNPALLELISHNQEAFVRMLNEPVAG  193 (203)
Q Consensus       160 ~il~~l~~~nP~l~~~i~~n~~~f~~ml~~p~~~  193 (203)
                      .+||+|++.||+|+++|++||++|++||++|.++
T Consensus       241 ~~Lqqlg~~nP~L~q~Iq~nqe~Fl~mlnep~~~  274 (340)
T KOG0011|consen  241 PLLQQLGKQNPQLLQLIQENQEAFLQLLNEPVEG  274 (340)
T ss_pred             HHHHHHhhhCHHHHHHHHHHHHHHHHHhhccccc
Confidence            9999999999999999999999999999999886

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=100.00  E-value=1.1e-40  Score=293.62  Aligned_cols=184  Identities=47%  Similarity=0.764  Sum_probs=147.3

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCC-CCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCCCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPT   85 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~-ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~~~   85 (203)
                      |+|+||+++|++|. +|++++||.+||++|+...|++ +++++|||||+||+|+|+++|++|+|+++++|+||++|++..
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            79999999999999 9999999999999999998733 899999999999999999999999999999999999887652


Q ss_pred             CC--------C----CCCCCC---C--------CCCC---------CCCCC--------CC-----CCc-------hhhH
Q psy4259          86 PA--------P----YSGPSD---P--------TQPA---------GQESE--------AT-----RPA-------TATS  113 (203)
Q Consensus        86 ~~--------p----~~~~~~---p--------~~~p---------~~~~~--------~~-----~~~-------~~~v  113 (203)
                      ++        |    +++++.   |        ++++         ++.++        +.     .++       +..|
T Consensus        81 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~~g~~~e~~I  160 (378)
T TIGR00601        81 TGKSAPPAATPTSAPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERETTI  160 (378)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCCccccccCCCcccccccchHHHHHH
Confidence            11        0    000000   0        0000         00000        00     011       5799


Q ss_pred             HHHHhCCcCCC-----------CC-----------C-----------C----------C-C-------------------
Q psy4259         114 DSMLKVFFERV-----------NP-----------Y-----------G----------G-E-------------------  130 (203)
Q Consensus       114 ~~~~~mG~~~~-----------np-----------~-----------~----------~-~-------------------  130 (203)
                      ++||+|||+|+           ||           .           .          . .                   
T Consensus       161 ~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~tGIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~lf~~a~~~~~~~~~~~  240 (378)
T TIGR00601       161 EEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAASTAAATTETPQHGSVFEQAAQGGTEQPATE  240 (378)
T ss_pred             HHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHHhCCCccccccccCCCcccccccccCCCCCCcchhhhhhcccccccccc
Confidence            99999999998           44           0           0          0 0                   


Q ss_pred             ---CCChHHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHHcCCc
Q psy4259         131 ---SEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV  191 (203)
Q Consensus       131 ---~~~pl~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml~~p~  191 (203)
                         +.++|++||++|+|++||++|++||++|++|||+|+++||+|+++|++||++|++||++|.
T Consensus       241 ~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLqql~~~nP~l~q~I~~n~e~Fl~ll~~~~  304 (378)
T TIGR00601       241 AAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPV  304 (378)
T ss_pred             cccCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHHHHHhhCHHHHHHHHHCHHHHHHHhcCcc
Confidence               1236899999999999999999999999999999999999999999999999999999985

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).

>KOG0010|consensus

Probab=99.90  E-value=2.8e-23  Score=184.71  Aligned_cols=75  Identities=27%  Similarity=0.379  Sum_probs=69.9

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      ..++|+||+.++ ++. .|..+.||.+||++|...++  +++++++|||+||+|+|++||..|||+||+|||+|++...
T Consensus        14 ~~irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~--a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~~   89 (493)
T KOG0010|consen   14 SLIRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFG--APPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQP   89 (493)
T ss_pred             ceeEEEEecCCc-ceeEecccchHHHHHHHHHHHhcC--CChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccCC
Confidence            469999999998 677 99999999999999999999  9999999999999999999999999999999999876543

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.80  E-value=1.7e-19  Score=124.85  Aligned_cols=71  Identities=24%  Similarity=0.352  Sum_probs=69.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      |+|+||+.+|+++. +|++++||++||++|+++.|  +++++|+|+|+||.|+|+.+|++|||+++++|+++++
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~g--i~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~   72 (74)
T cd01807           1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLN--VPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVR   72 (74)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--CCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEc
Confidence            78999999999999 99999999999999999999  9999999999999999999999999999999999875

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

>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array

Probab=99.80  E-value=1.3e-19  Score=119.74  Aligned_cols=59  Identities=66%  Similarity=1.103  Sum_probs=54.3

Q ss_pred             HHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHHcCCccc
Q psy4259         135 LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAG  193 (203)
Q Consensus       135 l~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml~~p~~~  193 (203)
                      |++|+++|+|++||++|++||++|+.+|++|+++||+|+++|++||++|++||++|.+|
T Consensus         1 L~~Lr~~Pqf~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~n~e~Fl~ll~~~~~~   59 (59)
T PF09280_consen    1 LEFLRNNPQFQQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQNPEEFLRLLNEPAEG   59 (59)
T ss_dssp             CGGGTTSHHHHHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHHTHHHHHHHHHSTS--
T ss_pred             ChHHHcChHHHHHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHHCHHHHHHHHcCCCCC
Confidence            46899999999999999999999999999999999999999999999999999998764

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 ....

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.79  E-value=4.2e-19  Score=123.34  Aligned_cols=74  Identities=53%  Similarity=0.750  Sum_probs=71.2

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCC--CCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEY--LAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~i--p~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      |+|+||+..|+.+. +|++++||.+||++|+..+|  +  ++++|+|+|+|+.|+|+.+|++|||++|++|++++++++
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            78999999999999 99999999999999999999  8  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).

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.79  E-value=3.7e-19  Score=123.01  Aligned_cols=70  Identities=19%  Similarity=0.264  Sum_probs=67.5

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      |+|+||+..|+.+. +|++++||++||++|++..|  +++++|||+|+|++|+|+++|++|||++|++||+..
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~--~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTG--TRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhC--CChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence            78999999999999 99999999999999999999  999999999999999999999999999999999853

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.

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

Probab=99.78  E-value=8.2e-19  Score=122.79  Aligned_cols=72  Identities=25%  Similarity=0.352  Sum_probs=68.1

Q ss_pred             eEEEEEeCCCCe-ee-e-cCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQT-VS-H-LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~-~~-~-v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+..|++ +. + +++++||++||++|++..|  +|+++|||+|+||.|+|+.+|++|||+++++|+++++.
T Consensus         1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~g--i~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~   75 (78)
T cd01797           1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFN--VEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQ   75 (78)
T ss_pred             CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhC--CCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            799999999997 66 5 8999999999999999999  99999999999999999999999999999999998864

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.

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

Probab=99.77  E-value=9.4e-19  Score=122.23  Aligned_cols=73  Identities=23%  Similarity=0.276  Sum_probs=65.3

Q ss_pred             ceEEEEEeCCCCeee---ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccc--cCCCCEEEEEe
Q psy4259           7 DISDITQNQWQQTVS---HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYN--IDESKFIVVML   79 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~---~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~g--I~~~~~i~v~~   79 (203)
                      .+.|+||+.+|++++   ++++++||++||++|+...+..+++++|||||+||+|+|+.||++|+  +.++.+||+++
T Consensus         1 ~i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~   78 (79)
T cd01790           1 PVTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC   78 (79)
T ss_pred             CeEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence            478999999999955   66899999999999999874325689999999999999999999996  99999999986

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

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.76  E-value=2.3e-18  Score=120.51  Aligned_cols=72  Identities=14%  Similarity=0.142  Sum_probs=68.5

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      .|+|+||+..|+.+. +|+++.||++||++|+++.+  +++++|||+|+||+|+|+ +|++|||++|++|+++..-
T Consensus         1 ~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~--~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~   73 (78)
T cd01804           1 PMNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLK--VPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTV   73 (78)
T ss_pred             CeEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhC--CChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeec
Confidence            489999999999999 99999999999999999999  999999999999999999 9999999999999998643

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

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.76  E-value=3.1e-18  Score=125.90  Aligned_cols=76  Identities=24%  Similarity=0.293  Sum_probs=72.3

Q ss_pred             CCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           4 LAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      .++.|+|+||+..|+++. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+.+|++|+|+++++|+++++-
T Consensus        24 ~~~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~g--ip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l  100 (103)
T cd01802          24 FYDTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEG--IPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAM  100 (103)
T ss_pred             cCCCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhC--CChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEec
Confidence            356799999999999999 99999999999999999999  99999999999999999999999999999999998764

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.

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

Probab=99.76  E-value=2.5e-18  Score=120.82  Aligned_cols=73  Identities=16%  Similarity=0.155  Sum_probs=70.3

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEE--EeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKL--IYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkL--i~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      |+|+||+..|+.+. +++++.||.+||++|+...+  +++++|||  +|+|++|+|+++|++|||++|++|+++++|-
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            89999999999999 99999999999999999999  99999999  9999999999999999999999999998763

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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.76  E-value=3e-18  Score=118.55  Aligned_cols=70  Identities=26%  Similarity=0.281  Sum_probs=66.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+  +++++ +|++++||++||.+|++..|  +|+++|+|+|+||.|+|+++|++|+|+++++||++++-
T Consensus         1 mqi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~g--ip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l   71 (74)
T cd01793           1 MQLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEG--IDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRL   71 (74)
T ss_pred             CEEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhC--CCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEec
Confidence            7899997  47888 99999999999999999999  99999999999999999999999999999999998753

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.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.75  E-value=2.5e-18  Score=117.92  Aligned_cols=68  Identities=24%  Similarity=0.367  Sum_probs=65.7

Q ss_pred             EEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259          10 DITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus        10 I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      ++||...|+++. +|++++||.+||.+|++..|  +|+++|+|+|+|++|+|+.+|++|+|+++++|||++
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~g--i~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~   69 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEG--VDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV   69 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhC--CCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence            478999999999 99999999999999999999  999999999999999999999999999999999986

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.

>PTZ00044 ubiquitin; Provisional

Probab=99.75  E-value=6.7e-18  Score=117.08  Aligned_cols=72  Identities=26%  Similarity=0.398  Sum_probs=69.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+.+|+++. +|++++||++||++|+...|  +|++.|||+|+|+.|+|+.+|++|+++++++||++++.
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~g--i~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (76)
T PTZ00044          1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEG--IDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQL   73 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--CCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEc
Confidence            78999999999999 99999999999999999999  99999999999999999999999999999999998864

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

Probab=99.74  E-value=6.7e-18  Score=115.50  Aligned_cols=69  Identities=20%  Similarity=0.375  Sum_probs=66.1

Q ss_pred             EEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259          10 DITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus        10 I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      |+||+..|+.+. +|++++||++||++|+++.|  +|+++|+|+|+|+.|+|+.+|++|||+++++||++.+
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            579999999999 99999999999999999999  9999999999999999999999999999999998753

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.

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

Probab=99.73  E-value=9.8e-18  Score=115.98  Aligned_cols=70  Identities=17%  Similarity=0.307  Sum_probs=67.1

Q ss_pred             EEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259          10 DITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        10 I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+||++.|+++. +|++++||.+||++|+...|  +|+++|+|+|+|+.|+|+++|++|||+++++|+++.+-
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g--i~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l   71 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRER--VQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRL   71 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhC--CCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEc
Confidence            689999999999 99999999999999999999  99999999999999999999999999999999998753

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.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.73  E-value=1.8e-17  Score=114.48  Aligned_cols=72  Identities=19%  Similarity=0.473  Sum_probs=69.5

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+.+|+.+. +|++++||.+||++|+...|  +|+++|+|+|+|+.|.|+++|++|++++|++||++++.
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g--~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~   73 (76)
T cd01806           1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLAL   73 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhC--CChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEc
Confidence            78999999999999 99999999999999999999  99999999999999999999999999999999998864

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.

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.73  E-value=1.8e-17  Score=113.40  Aligned_cols=71  Identities=35%  Similarity=0.501  Sum_probs=68.2

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      |+|+||+.+|+.+. ++++++||.+||++|+..+|  +++++|+|+|+|+.|+|+.+|++||+++|++||++.+
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            78999999999999 99999999999999999999  9999999999999999999999999999999998753

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.

>cd01803 Ubiquitin Ubiquitin

Probab=99.72  E-value=2.4e-17  Score=113.91  Aligned_cols=72  Identities=28%  Similarity=0.503  Sum_probs=69.4

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+.+|+.+. +|++++||++||++|+..+|  +|+++|+|+|+|+.|+|+.+|++||+++|++|+++++-
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g--~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~   73 (76)
T cd01803           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   73 (76)
T ss_pred             CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhC--CCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEc
Confidence            78999999999999 99999999999999999999  99999999999999999999999999999999998763

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

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

Probab=99.71  E-value=2.8e-17  Score=112.77  Aligned_cols=70  Identities=24%  Similarity=0.335  Sum_probs=65.9

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      ++|+||+..|+ +. ++++++||++||++|++..|  +++++|+|+|+|+.|+|+++|++||+++|++||++++
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            57999999997 58 99999999999999999999  9999999999999999999999999999999998763

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=99.71  E-value=3e-17  Score=111.55  Aligned_cols=67  Identities=36%  Similarity=0.568  Sum_probs=63.8

Q ss_pred             EeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259          13 QNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        13 k~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+.+|+.|. +|++++||.+||++|+..++  +|++.|+|+|+|+.|+|+.+|++|||++|++|+++++.
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~--~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~   68 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETG--IPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKP   68 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHT--STGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccc--cccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEec
Confidence            678999999 99999999999999999999  99999999999999999999999999999999988754

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=99.70  E-value=3.3e-17  Score=113.52  Aligned_cols=69  Identities=29%  Similarity=0.286  Sum_probs=65.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe---CCeecCCCCCccccccCCCCEEEEEe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY---AGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~---~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      |+|+|| +.|+.|. +|++++||++||++|++.++  +|+++|||+|   +|+.|+|+.+|++|+|++|++|++|.
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            578899 7899999 99999999999999999999  9999999997   99999999999999999999999986

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=99.68  E-value=1e-16  Score=110.18  Aligned_cols=66  Identities=27%  Similarity=0.432  Sum_probs=62.9

Q ss_pred             EEEEeC-CCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCC-CCccccccCCCCEEEE
Q psy4259          10 DITQNQ-WQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFIVV   77 (203)
Q Consensus        10 I~Vk~~-~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~-~tL~~~gI~~~~~i~v   77 (203)
                      |+||+. .|+++. +|++++||++||.+|+...|  +|+++|+|+|+||.|+|+ .+|++|||++|++||+
T Consensus         1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~g--ip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l   69 (71)
T cd01796           1 ITVYTARSETTFSLDVDPDLELENFKALCEAESG--IPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVL   69 (71)
T ss_pred             CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhC--CCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEE
Confidence            578999 899999 99999999999999999999  999999999999999998 6899999999999986

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=99.65  E-value=3e-16  Score=107.14  Aligned_cols=69  Identities=19%  Similarity=0.272  Sum_probs=65.4

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      |+|+||+. |+.+. ++++++||.+||++|+..+|  +++++|||+|+|+.|.|+++|++|||++|++|++++
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 88888 99999999999999999999  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).

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

Probab=99.61  E-value=1.7e-15  Score=105.34  Aligned_cols=66  Identities=32%  Similarity=0.445  Sum_probs=62.5

Q ss_pred             CCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259          15 QWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus        15 ~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ++|+++. +|++++||.+||++|+...|  +|+++|+|+|+|+.|+|+.+|++|+|.+|++|+|+++..
T Consensus         5 l~g~~~~l~v~~~~TV~~lK~~i~~~~g--ip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~   71 (76)
T cd01800           5 LNGQMLNFTLQLSDPVSVLKVKIHEETG--MPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKER   71 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHC--CCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecC
Confidence            4688999 99999999999999999999  999999999999999999999999999999999998654

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.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.60  E-value=2.2e-15  Score=110.84  Aligned_cols=78  Identities=22%  Similarity=0.209  Sum_probs=68.4

Q ss_pred             cceEEEEEeCCCCeee--ecCCCCcHHHHHHHHHhhhCCC-----CCCCceEEEeCCeecCCCCCccccc------cCCC
Q psy4259           6 HDISDITQNQWQQTVS--HLDVQEEVKQLKEKIQSEKGSE-----YLAEYQKLIYAGKILSDDQALSEYN------IDES   72 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~--~v~~~~TV~~LK~~I~~~~~~~-----ip~~~qkLi~~Gk~L~D~~tL~~~g------I~~~   72 (203)
                      +.+.|.||..+|..+-  .+.+++||.+||++|++.++.+     +++++|||||+||+|+|++||++|+      +...
T Consensus         3 ~~~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~   82 (113)
T cd01814           3 EQIEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGV   82 (113)
T ss_pred             ccEEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCc
Confidence            5689999999998887  8999999999999999887543     4599999999999999999999999      6667


Q ss_pred             CEEEEEeecCC
Q psy4259          73 KFIVVMLSKPK   83 (203)
Q Consensus        73 ~~i~v~~~k~~   83 (203)
                      .|+||+++.+.
T Consensus        83 ~TmHvvlr~~~   93 (113)
T cd01814          83 ITMHVVVQPPL   93 (113)
T ss_pred             eEEEEEecCCC
Confidence            89999886654

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

>KOG0005|consensus

Probab=99.59  E-value=9.7e-16  Score=99.64  Aligned_cols=69  Identities=22%  Similarity=0.456  Sum_probs=66.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |.|+||++.|+.+. +++++++|..+|++|+++.|  +|+.+|||||.||.+.|++|-++|++.-|+++|++
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            67999999999999 99999999999999999999  99999999999999999999999999999999974

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.56  E-value=4.3e-15  Score=102.55  Aligned_cols=58  Identities=28%  Similarity=0.335  Sum_probs=50.6

Q ss_pred             ecC-CCCcHHHHHHHHHhhhCCCC-CCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259          22 HLD-VQEEVKQLKEKIQSEKGSEY-LAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus        22 ~v~-~~~TV~~LK~~I~~~~~~~i-p~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      +|+ .++||.+||++|+++.+..+ ++++|||||+||+|+|++||++|||++|++||++.
T Consensus        15 ~~~~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          15 DVSPGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             CcCCccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            444 57999999999999963225 59999999999999999999999999999999874

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.

>smart00213 UBQ Ubiquitin homologues

Probab=99.53  E-value=2.3e-14  Score=95.23  Aligned_cols=63  Identities=37%  Similarity=0.570  Sum_probs=59.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESK   73 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~   73 (203)
                      |+|+||+.+ +.+. +|+++.||++||++|+..+|  +++++|+|+|+|+.|.|+++|++|||++|+
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            689999998 7888 99999999999999999999  999999999999999999999999999875

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

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.53  E-value=6.6e-14  Score=99.83  Aligned_cols=75  Identities=19%  Similarity=0.299  Sum_probs=71.2

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      +..|.|+|++.+|+.+. .|.+++|+..||+++++..|  +++++++|+|+|+.|+++.|+++|++.++++|+++++-
T Consensus         9 ~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~g--i~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l   84 (87)
T cd01763           9 SEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQG--LSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQ   84 (87)
T ss_pred             CCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhC--CCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEec
Confidence            44699999999999999 99999999999999999999  99999999999999999999999999999999998754

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.

>KOG0003|consensus

Probab=99.46  E-value=8.6e-15  Score=106.06  Aligned_cols=73  Identities=26%  Similarity=0.484  Sum_probs=68.6

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      |.++++++.|++++ ++++++||..||.+|..+.|  +|++.|+|+|+||+|+|..||++|+|.--++||++.+-.
T Consensus         1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~G--i~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~   74 (128)
T KOG0003|consen    1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
T ss_pred             CcEEEEEeeCceEEEEecccchHHHHHHHhccccC--CCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHh
Confidence            56889999999999 99999999999999999999  999999999999999999999999999999999876543

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.43  E-value=4.8e-13  Score=89.96  Aligned_cols=67  Identities=36%  Similarity=0.578  Sum_probs=62.9

Q ss_pred             EEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259          11 ITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus        11 ~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      +||..+|+.+. +++++.||++||++|+..+|  +++++|+|+|+|+.|+|+.+|.+|++.+++.|+++.
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            36777899999 99999999999999999999  999999999999999999999999999999999874

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.

>KOG0004|consensus

Probab=99.42  E-value=9.8e-14  Score=107.04  Aligned_cols=73  Identities=27%  Similarity=0.500  Sum_probs=69.5

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      |.|+|+++.++++. +|..++||..+|.+|+...|  ||+++|||||.|+.|+|..+|+||+|+.-++|++++.-.
T Consensus         1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~eg--Ip~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~   74 (156)
T KOG0004|consen    1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (156)
T ss_pred             CccchhhccccceeeeecccccHHHHHHhhhcccC--CCchhhhhhhhhcccccCCccccccccccceEEEEEEec
Confidence            68999999999999 99999999999999999999  999999999999999999999999999999999997543

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=99.42  E-value=5.5e-13  Score=92.56  Aligned_cols=67  Identities=19%  Similarity=0.241  Sum_probs=59.0

Q ss_pred             EEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecC-CCCCccccccC-CCCEEEEEe
Q psy4259          10 DITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILS-DDQALSEYNID-ESKFIVVML   79 (203)
Q Consensus        10 I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~-D~~tL~~~gI~-~~~~i~v~~   79 (203)
                      |.=|...|+++. +|++++||++||.+|+.+.|  +|+++|+| |+|+.|. |+.+|++||++ +|+++++.+
T Consensus         5 ~~~~~~~~~t~~l~v~~~~TV~~lK~kI~~~~g--ip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799           5 VEDAQSHTVTIWLTVRPDMTVAQLKDKVFLDYG--FPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             EeccccCCCeEEEEECCCCcHHHHHHHHHHHHC--cCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            333556788999 99999999999999999999  99999999 9999986 66899999998 789998753

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

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

Probab=99.32  E-value=5.6e-12  Score=86.27  Aligned_cols=70  Identities=24%  Similarity=0.345  Sum_probs=64.5

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCC-CceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLA-EYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~-~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      |+|+|++.+|+.+. .|.++++|..|++++++..+  ++. +.++|+|+|+.|.+++|+++||+.+|++|+|++
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            78999999999988 99999999999999999999  999 999999999999999999999999999999864

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 ....

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

Probab=99.31  E-value=1.8e-11  Score=91.03  Aligned_cols=76  Identities=24%  Similarity=0.311  Sum_probs=58.1

Q ss_pred             cceEEEEEeCCCC-eee-ecCCCCcHHHHHHHHHhhhCCC-----CCCCceEEEeCCeecCCCCCccccccCCCC-----
Q psy4259           6 HDISDITQNQWQQ-TVS-HLDVQEEVKQLKEKIQSEKGSE-----YLAEYQKLIYAGKILSDDQALSEYNIDESK-----   73 (203)
Q Consensus         6 ~~m~I~Vk~~~g~-~~~-~v~~~~TV~~LK~~I~~~~~~~-----ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~-----   73 (203)
                      +.+.|+|+..+|+ ... .+++++||++||+.|...|..+     ..++.+||||.||+|+|++||++|++..|+     
T Consensus         1 ~~i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~   80 (111)
T PF13881_consen    1 DKIELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGP   80 (111)
T ss_dssp             TSEEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--
T ss_pred             CeEEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCC
Confidence            3688999999999 445 9999999999999999988644     345688999999999999999999988777     


Q ss_pred             -EEEEEeec
Q psy4259          74 -FIVVMLSK   81 (203)
Q Consensus        74 -~i~v~~~k   81 (203)
                       ++||+++.
T Consensus        81 ~vmHlvvrp   89 (111)
T PF13881_consen   81 TVMHLVVRP   89 (111)
T ss_dssp             EEEEEEE-S
T ss_pred             EEEEEEecC
Confidence             45555543

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.29  E-value=1.4e-11  Score=88.63  Aligned_cols=62  Identities=26%  Similarity=0.306  Sum_probs=56.8

Q ss_pred             ee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCC-CCccccccCCCCEEEEEeecCC
Q psy4259          20 VS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus        20 ~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~-~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      .. +|++++||++||.+|...++  +++.+|+|+|.|+.|.|+ +||++|||..++.|++.+..|.
T Consensus        17 ~~L~V~~~~TVg~LK~lImQ~f~--V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~LlideP~   80 (107)
T cd01795          17 KALLVSANQTLKELKIQIMHAFS--VAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADEPI   80 (107)
T ss_pred             ceEEeCccccHHHHHHHHHHHhc--CCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecCCc
Confidence            44 89999999999999999999  999999999999999876 8999999999999999876543

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,

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

Probab=99.17  E-value=2.2e-10  Score=81.17  Aligned_cols=72  Identities=21%  Similarity=0.276  Sum_probs=58.7

Q ss_pred             eEEEEEeCCC-Ceee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEE-EeCCe-----ec-CCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQ-QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKL-IYAGK-----IL-SDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g-~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkL-i~~Gk-----~L-~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ++|.|+.... ...+ .+++++||.+||++++..+|  ++++.|+| +|.|+     .| +|+++|++||+++|..|||+
T Consensus         2 v~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G--~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVv   79 (84)
T cd01789           2 VTVNITSSADSFSFEKKYSRGLTIAELKKKLELVVG--TPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVI   79 (84)
T ss_pred             EEEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHC--CCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEE
Confidence            4566666443 2334 79999999999999999999  99999999 48887     46 56689999999999999987


Q ss_pred             eec
Q psy4259          79 LSK   81 (203)
Q Consensus        79 ~~k   81 (203)
                      -..
T Consensus        80 D~~   82 (84)
T cd01789          80 DVS   82 (84)
T ss_pred             eCC
Confidence            543

Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.

>KOG4248|consensus

Probab=99.02  E-value=3.8e-10  Score=108.25  Aligned_cols=70  Identities=27%  Similarity=0.464  Sum_probs=66.5

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      ..|+||+++.++.+ .|...+||.+||++|.++.+  |+.+.|||||.|++|.|+|++.+|+| +|.+|||+-+
T Consensus         3 ~~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~n--i~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlver   73 (1143)
T KOG4248|consen    3 PNVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVN--IPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVER   73 (1143)
T ss_pred             cceeeeecccceeEEEechHHHHHHHHHHHHHhcc--cccccceeeecceeeccchhhhhccC-CCeEEEeecc
Confidence            35899999999999 99999999999999999999  99999999999999999999999999 9999998755

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=99.01  E-value=9.5e-10  Score=76.49  Aligned_cols=68  Identities=18%  Similarity=0.249  Sum_probs=54.3

Q ss_pred             EEEEEeCCCCee-e-ec-CCCCcHHHHHHHHHhhhCCCCCCCceEE--EeCCeecCCCCCccccccCCCCEEEE
Q psy4259           9 SDITQNQWQQTV-S-HL-DVQEEVKQLKEKIQSEKGSEYLAEYQKL--IYAGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         9 ~I~Vk~~~g~~~-~-~v-~~~~TV~~LK~~I~~~~~~~ip~~~qkL--i~~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      +|.++..+.+.+ . ++ +++.||.+||+.|+..++. +++++|||  +++|++|.|+++|.+||+++|++|+|
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            456665552333 2 44 4889999999999999763 67899888  48899999999999999999999876

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.

>PLN02560 enoyl-CoA reductase

Probab=98.98  E-value=1.4e-09  Score=94.34  Aligned_cols=69  Identities=20%  Similarity=0.393  Sum_probs=60.8

Q ss_pred             eEEEEEeCCCCee---e-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC---C----eecCCCCCccccccCCCCEEE
Q psy4259           8 ISDITQNQWQQTV---S-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA---G----KILSDDQALSEYNIDESKFIV   76 (203)
Q Consensus         8 m~I~Vk~~~g~~~---~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~---G----k~L~D~~tL~~~gI~~~~~i~   76 (203)
                      |+|+|+..+|+.+   + +++++.||++||++|+++.+. .++++|||++.   |    +.|+|+++|+++|+++|++|+
T Consensus         1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~-~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy   79 (308)
T PLN02560          1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKK-YYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVV   79 (308)
T ss_pred             CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCC-CChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEE
Confidence            6889998888887   5 999999999999999999872 38999999982   3    488999999999999999987


Q ss_pred             E
Q psy4259          77 V   77 (203)
Q Consensus        77 v   77 (203)
                      +
T Consensus        80 ~   80 (308)
T PLN02560         80 F   80 (308)
T ss_pred             E
Confidence            6

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

Probab=98.95  E-value=4.3e-09  Score=74.80  Aligned_cols=73  Identities=22%  Similarity=0.307  Sum_probs=56.6

Q ss_pred             eEEEEEeCCC--Ceee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC----C---eec-CCCCCccccccCCCCEEE
Q psy4259           8 ISDITQNQWQ--QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA----G---KIL-SDDQALSEYNIDESKFIV   76 (203)
Q Consensus         8 m~I~Vk~~~g--~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~----G---k~L-~D~~tL~~~gI~~~~~i~   76 (203)
                      ++|.|.....  .... .++.++||.+||.+|+..+|  ++++.|+|.+.    |   ..+ +|+++|.+||+++|..||
T Consensus         2 v~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~G--i~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~   79 (87)
T PF14560_consen    2 VKLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTG--IPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIH   79 (87)
T ss_dssp             EEEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHT--S-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEE
T ss_pred             EEEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhC--CCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEE
Confidence            5677776554  3667 99999999999999999999  99999999875    2   234 456899999999999999


Q ss_pred             EEeecC
Q psy4259          77 VMLSKP   82 (203)
Q Consensus        77 v~~~k~   82 (203)
                      |.=..|
T Consensus        80 V~D~~p   85 (87)
T PF14560_consen   80 VVDTNP   85 (87)
T ss_dssp             EEE-T-
T ss_pred             EEeCCC
Confidence            875443

>KOG0001|consensus

Probab=98.89  E-value=1.4e-08  Score=67.77  Aligned_cols=70  Identities=27%  Similarity=0.475  Sum_probs=65.4

Q ss_pred             EEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259          10 DITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        10 I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      +.+++..|+.+. ++.+..+|..+|.+|+...+  ++.+.|++.|.|+.|.|+.+|.+|+|..++++++..+.
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~--~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~   72 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEG--IPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSL   72 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcC--CCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEec
Confidence            567788899999 99999999999999999999  99999999999999999999999999999999987654

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=98.89  E-value=6.2e-09  Score=76.70  Aligned_cols=71  Identities=14%  Similarity=0.165  Sum_probs=59.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCcccccc-------CCCCEEEEEe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-------DESKFIVVML   79 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI-------~~~~~i~v~~   79 (203)
                      |-|.||-.+ .++. ++.++.||.+||++|+....  .|+++|+|+..+.+|+|++||++||+       ....+|-+.+
T Consensus         3 vFlmIrR~K-TTiF~dakes~tVlelK~~iegI~k--~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~   79 (119)
T cd01788           3 VFLMIRRHK-TTIFTDAKESTTVYELKRIVEGILK--RPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAF   79 (119)
T ss_pred             eEEEEEecc-eEEEeecCCcccHHHHHHHHHHHhc--CChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEE
Confidence            556666333 3344 99999999999999999999  99999999977899999999999999       5577777777


Q ss_pred             ec
Q psy4259          80 SK   81 (203)
Q Consensus        80 ~k   81 (203)
                      ++
T Consensus        80 r~   81 (119)
T cd01788          80 RS   81 (119)
T ss_pred             ec
Confidence            65

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.

>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=98.69  E-value=3.4e-08  Score=69.31  Aligned_cols=71  Identities=18%  Similarity=0.178  Sum_probs=43.9

Q ss_pred             CcceEEEEEeCCCCeeeecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC---Ceec--CCCCCccccccCCCCEEEE
Q psy4259           5 AHDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA---GKIL--SDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~---Gk~L--~D~~tL~~~gI~~~~~i~v   77 (203)
                      ...|-|.||+.+|-...++++++|+.+||++|.+.++  ++...+.|..+   ...|  .++++|+++||++||.|++
T Consensus         2 ~~~milRvrS~dG~~Rie~~~~~t~~~L~~kI~~~l~--~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL   77 (80)
T PF11543_consen    2 ASSMILRVRSKDGMKRIEVSPSSTLSDLKEKISEQLS--IPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYL   77 (80)
T ss_dssp             ----EEEEE-SSEEEEEEE-TTSBHHHHHHHHHHHS-----TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE-
T ss_pred             CccEEEEEECCCCCEEEEcCCcccHHHHHHHHHHHcC--CCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEE
Confidence            3578999999888655599999999999999999999  99998888543   2345  4568999999999999976

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.

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.56  E-value=3.3e-07  Score=58.12  Aligned_cols=65  Identities=29%  Similarity=0.426  Sum_probs=58.1

Q ss_pred             EeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259          13 QNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus        13 k~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      +..++.... .+....||.+||++|..++|  ++++.++|+++|..+.+...+.++++.+++.|++..
T Consensus         3 ~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196           3 KLNDGKTVELLVPSGTTVADLKEKLAKKLG--LPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             EecCCCEEEEEcCCCCcHHHHHHHHHHHHC--cChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            334677777 88899999999999999999  999999999999999999888899999999998763

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.

>KOG1872|consensus

Probab=98.56  E-value=2.3e-07  Score=83.14  Aligned_cols=74  Identities=19%  Similarity=0.212  Sum_probs=67.5

Q ss_pred             ceEEEEEeCCCCeee-e-cCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           7 DISDITQNQWQQTVS-H-LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~-v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      ...|.|| +.|+.+. + ++.++|+..||.++...+|  ++|++||+.++|+.+.|+-.+..++|++|.+|++|.+.-.
T Consensus         3 ~~~v~VK-W~gk~y~v~~l~~d~t~~vlKaqlf~LTg--V~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e~   78 (473)
T KOG1872|consen    3 SDTVIVK-WGGKKYPVETLSTDETPSVLKAQLFALTG--VPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAEA   78 (473)
T ss_pred             cceEeee-ecCccccceeccCCCchHHHHHHHHHhcC--CCccceeEEEecccccccccccccccCCCCEEEeeccccc
Confidence            3467777 8899998 5 9999999999999999999  9999999999999999998999999999999999987654

>KOG0006|consensus

Probab=98.18  E-value=2.8e-06  Score=72.96  Aligned_cols=62  Identities=27%  Similarity=0.490  Sum_probs=56.0

Q ss_pred             eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259          19 TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus        19 ~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      .+. +|+.+.+|.+||+.++...|  +|+++.++||.||.|.|+.|+..+.+..-+.+|+|.-+|
T Consensus        15 ~l~v~v~~~t~I~~lke~Vak~~g--vp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~lRP   77 (446)
T KOG0006|consen   15 GLPVEVDSDTSIFQLKEVVAKRQG--VPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIMLLRP   77 (446)
T ss_pred             ceeEEEecCCCHHHHHHHHHHhhC--CChhheEEEEeccccccCceeecccccccchhhhhccCc
Confidence            356 89999999999999999999  999999999999999999999988888888888885444

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

Probab=98.08  E-value=2.4e-05  Score=53.57  Aligned_cols=71  Identities=20%  Similarity=0.329  Sum_probs=60.2

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC---C--eecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA---G--KILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~---G--k~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ++|+|+-+....++ .|+|..+|..+|++|...++  ++- .|||.|.   |  ..|.+.++|++|||=.+-.|.++-+-
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~--~~g-~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lleT~   77 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRN--CSG-LQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLETF   77 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhC--ccc-ceEEEeecCCcccccccccccHhhhcceeccEEEEEecC
Confidence            57999999999999 99999999999999999999  654 8999984   3  45788899999999777777666443

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

Probab=98.06  E-value=1.4e-06  Score=57.87  Aligned_cols=69  Identities=20%  Similarity=0.278  Sum_probs=58.8

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +++.+...-|++.. .+++++||+++|+.|+.++|  -.++...|---+.+++|.-+|++|.|++|-.+.+.
T Consensus         2 iev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtG--T~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely   71 (73)
T KOG3493|consen    2 IEVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG--TRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY   71 (73)
T ss_pred             ceehhhhhcCceEEEEeCCcccccCHHHHHHHhhC--CChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence            45677777799988 99999999999999999999  77777777655678899999999999999877653

>KOG4495|consensus

Probab=97.97  E-value=1.1e-05  Score=57.79  Aligned_cols=62  Identities=16%  Similarity=0.175  Sum_probs=49.6

Q ss_pred             ceEEEEEeCCCCeeeecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe-C-CeecCCCCCccccccC
Q psy4259           7 DISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY-A-GKILSDDQALSEYNID   70 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~-~-Gk~L~D~~tL~~~gI~   70 (203)
                      +|-|.||-.+-..|.+.+++.||-+||.+++....  -|++.|+|.. . ..+|+|.+||++||+.
T Consensus         2 ~~f~~VrR~kttif~da~es~tV~elK~~l~gi~~--~Pvn~qrL~kmd~eqlL~D~ktL~d~gft   65 (110)
T KOG4495|consen    2 DVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILK--RPVNEQRLYKMDTEQLLDDGKTLGDCGFT   65 (110)
T ss_pred             ceeeeeeecceeEEeecCccccHHHHHHHHHHHHh--CCCcchheeecCHHHHhhccchhhhcccc
Confidence            35566774433333399999999999999999998  8999999976 3 3789999999999864

>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=97.86  E-value=0.00015  Score=50.55  Aligned_cols=71  Identities=15%  Similarity=0.173  Sum_probs=59.9

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCc-eEEE--eCCeecCCC--CCccccccCCCCEEEE
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEY-QKLI--YAGKILSDD--QALSEYNIDESKFIVV   77 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~-qkLi--~~Gk~L~D~--~tL~~~gI~~~~~i~v   77 (203)
                      ....+|.||..+|+.+. .+..++||.+|.+.|.....  .+... .+|+  |-.+.|.++  +||+++|+..+.+|+|
T Consensus         4 ~~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~--~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    4 SDVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLF--SPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             SSEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHH--CTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred             CCEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcC--CCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence            35689999999999999 99999999999999998887  55554 7776  556888655  5999999999998876

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 ....

>KOG1769|consensus

Probab=97.83  E-value=0.00014  Score=52.48  Aligned_cols=73  Identities=12%  Similarity=0.236  Sum_probs=64.5

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      .-+.|+|+.-++.... .|..+.....|+...+...|  +.....|++|+|+.+.+.+|=++++..+++.|-++..
T Consensus        19 ~hi~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~G--l~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~   92 (99)
T KOG1769|consen   19 EHINLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQG--LSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQE   92 (99)
T ss_pred             ceEEEEEecCCCCEEEEEeecCChHHHHHHHHHHHcC--CccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEee
Confidence            3467777775566666 99999999999999999999  9999999999999999999999999999999988753

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

Probab=97.82  E-value=4.9e-05  Score=55.20  Aligned_cols=58  Identities=24%  Similarity=0.229  Sum_probs=44.3

Q ss_pred             EEEEeCC-CCeee-ecC--CCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCcccc
Q psy4259          10 DITQNQW-QQTVS-HLD--VQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEY   67 (203)
Q Consensus        10 I~Vk~~~-g~~~~-~v~--~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~   67 (203)
                      |+||..+ -..+. ++.  .+.||..||+.|....+....-.++||||+||.|.|...|...
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 LTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSE   64 (97)
T ss_pred             EEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhh
Confidence            4555554 22344 666  7899999999999999544667789999999999999777654

They contain a characteristic GFDRL sequence motif.

>KOG0012|consensus

Probab=97.82  E-value=4.9e-05  Score=66.41  Aligned_cols=60  Identities=15%  Similarity=0.335  Sum_probs=54.2

Q ss_pred             CCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCC--CCccccccCCCCEEEE
Q psy4259          16 WQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD--QALSEYNIDESKFIVV   77 (203)
Q Consensus        16 ~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~--~tL~~~gI~~~~~i~v   77 (203)
                      ..++|. +|..+-.+..|+..+...+|  ++.+..-|+|+++.|.++  ..|.+||+++++++.+
T Consensus        11 ~~~~~~i~v~~dg~L~nl~aL~~~d~g--~~~~~~~li~n~~~l~s~~s~~l~Q~g~~~~dsl~l   73 (380)
T KOG0012|consen   11 FEKKFPIPVTTDGELNNLAALCWKDTG--IVYDPSDLIYNPRPLVSNESQGLTQIGLKDGDSLAL   73 (380)
T ss_pred             ceeeeccccccccchhhHHHHHHHHhC--cccchhhcccCCCccccchhhhhhhcccccceeEec
Confidence            667788 99999999999999999999  999999999999999765  6799999999999965

>KOG4583|consensus

Probab=97.78  E-value=2.2e-06  Score=73.98  Aligned_cols=82  Identities=22%  Similarity=0.268  Sum_probs=63.0

Q ss_pred             CcceEEEEEeCCCCeee---ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccC--CCCEEEEEe
Q psy4259           5 AHDISDITQNQWQQTVS---HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNID--ESKFIVVML   79 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~---~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~--~~~~i~v~~   79 (203)
                      +.++++.||..+.+...   .++..+||++||.+++..+..+--..+|||||+||.|.|..+|+|.-+|  ..+++|+++
T Consensus         7 e~~v~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~qcl~d~lrkq~k~Hv~hlvc   86 (391)
T KOG4583|consen    7 EFPVTLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQCLTDWLRKQVKEHVKHLVC   86 (391)
T ss_pred             CcceEEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccchhHHHHHHHHHHHHHHHHhc
Confidence            34678889988765544   6678899999999999998754445689999999999999999987443  356788887


Q ss_pred             ecCCCCC
Q psy4259          80 SKPKPTP   86 (203)
Q Consensus        80 ~k~~~~~   86 (203)
                      ..+....
T Consensus        87 nsk~v~~   93 (391)
T KOG4583|consen   87 NSKEVVT   93 (391)
T ss_pred             CCCCCCC
Confidence            6665433

>smart00727 STI1 Heat shock chaperonin-binding motif

Probab=97.72  E-value=4.4e-05  Score=46.43  Aligned_cols=38  Identities=45%  Similarity=0.716  Sum_probs=31.4

Q ss_pred             HHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHH
Q psy4259         135 LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELI  176 (203)
Q Consensus       135 l~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i  176 (203)
                      +..++++|.|+++++.+++||++++.+++.    ||++++.|
T Consensus         4 ~~~~l~~P~~~~~l~~~~~nP~~~~~~~~~----nP~~~~~i   41 (41)
T smart00727        4 MALRLQNPQVQSLLQDMQQNPDMLAQMLQE----NPQLLQLI   41 (41)
T ss_pred             HHHHHcCHHHHHHHHHHHHCHHHHHHHHHh----CHHhHhhC
Confidence            456677999999999999999997777743    99998753

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

Probab=97.68  E-value=0.00011  Score=51.15  Aligned_cols=70  Identities=17%  Similarity=0.154  Sum_probs=49.5

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCC-CCCC---ceEEE-eCCeecCCCCCccccccCCCCEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAE---YQKLI-YAGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~-ip~~---~qkLi-~~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      ++|+|...+|+.+. .++.+.+|++|...|....+.. ....   ..+|. -+|..|+++++|+++||.+|+.+++
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            57788865568888 9999999999999999988721 1222   35666 6799999999999999999999986

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.

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.61  E-value=0.00044  Score=48.10  Aligned_cols=70  Identities=9%  Similarity=0.056  Sum_probs=57.5

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE--eCCeecCC---CCCccccccCCCCEEEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI--YAGKILSD---DQALSEYNIDESKFIVV   77 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi--~~Gk~L~D---~~tL~~~gI~~~~~i~v   77 (203)
                      ...+|.||..+|+.+. .+..++||.+|.+.|....+  ......+|+  |-.|.|.+   ++||.++|+..+.+|+|
T Consensus         3 ~~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~--~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v   78 (80)
T smart00166        3 DQCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALT--DGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL   78 (80)
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHccc--CCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence            4678999999999999 99999999999999966665  555667776  45678864   37999999988888865

Present in FAF1 and Shp1p.

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=97.48  E-value=0.00064  Score=47.45  Aligned_cols=66  Identities=18%  Similarity=0.185  Sum_probs=53.4

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE--eCCeecCC-CCCccccccCCCC
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI--YAGKILSD-DQALSEYNIDESK   73 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi--~~Gk~L~D-~~tL~~~gI~~~~   73 (203)
                      ..+|.||..+|+.+. .++.++||++|.+.|....+. .......|+  |-.|.|.| +.||+++|+.+..
T Consensus         4 ~t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~-~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s~   73 (79)
T cd01770           4 TTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPE-FAARPFTLMTAFPVKELSDESLTLKEANLLNAV   73 (79)
T ss_pred             eeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCC-CCCCCEEEecCCCCcccCCCCCcHHHCCCcCcE
Confidence            578999999999999 999999999999999987641 223556776  55788876 4899999998633

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.

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=97.43  E-value=0.0012  Score=45.57  Aligned_cols=67  Identities=12%  Similarity=0.178  Sum_probs=53.6

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecCC---CCCccccccCCCCEEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILSD---DQALSEYNIDESKFIVV   77 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~D---~~tL~~~gI~~~~~i~v   77 (203)
                      ..+|.||..+|+.+. .+..++||.+|.+.|.....   ......|+.  -.|.+.|   ++||.++|+.+ +.+.+
T Consensus         2 ~t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~---~~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~~-s~~~~   74 (77)
T cd01767           2 TTKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGP---PAEPFTLMTSFPRRVLTDLDYELTLQEAGLVN-EVVFQ   74 (77)
T ss_pred             cEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCC---CCCCEEEEeCCCCccCCCCCccCcHHHcCCcc-ceEEE
Confidence            468999999999999 99999999999999987754   245677764  4688865   58999999994 55544

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=97.36  E-value=0.0014  Score=45.66  Aligned_cols=68  Identities=13%  Similarity=0.242  Sum_probs=56.1

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE--eCCeecCC---CCCccccccCCCCEEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI--YAGKILSD---DQALSEYNIDESKFIVV   77 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi--~~Gk~L~D---~~tL~~~gI~~~~~i~v   77 (203)
                      ..+|.||..+|+.+. .++.++||.+|.+.|....+  . .....|+  |-.|.+.+   ++||.++|+.+..+|+|
T Consensus         4 ~~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~--~-~~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           4 ETRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTG--N-GGPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             EEEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCC--C-CCCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence            468999999999999 99999999999999987654  2 2557776  45788864   37999999999888875

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.

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.34  E-value=0.0014  Score=44.94  Aligned_cols=70  Identities=17%  Similarity=0.180  Sum_probs=57.1

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCC---CCCceEEEeCCeecCCCCCccccccCCCCEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEY---LAEYQKLIYAGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~i---p~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      ++|-++...|++|. .++.-.+|..|-..+.+.....+   .-..+|+.-++++|.++..|.+|+|.+|+.+.+
T Consensus         7 VTvD~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei   80 (81)
T COG5417           7 VTVDFTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI   80 (81)
T ss_pred             EEEEeEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence            44556778899999 99999999999888877665322   224568889999999999999999999999875

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=97.34  E-value=0.0016  Score=46.06  Aligned_cols=70  Identities=11%  Similarity=0.125  Sum_probs=58.1

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC--eecC--------CCCCccccccCCCC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG--KILS--------DDQALSEYNIDESK   73 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G--k~L~--------D~~tL~~~gI~~~~   73 (203)
                      .+.++|.||..+|+.+. .+..++||++|...|.. .+  ..++...|+++=  |.+.        .+.||++.|+....
T Consensus         2 ~~~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~--~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~   78 (85)
T cd01774           2 PDTVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LK--ETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSE   78 (85)
T ss_pred             CceEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CC--CCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCcc
Confidence            34689999999999999 99999999999999964 44  566788998764  7885        25799999999887


Q ss_pred             EEEE
Q psy4259          74 FIVV   77 (203)
Q Consensus        74 ~i~v   77 (203)
                      +|.|
T Consensus        79 ~L~V   82 (85)
T cd01774          79 VLFV   82 (85)
T ss_pred             EEEE
Confidence            7765

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.

>KOG1639|consensus

Probab=97.24  E-value=0.00057  Score=57.20  Aligned_cols=69  Identities=20%  Similarity=0.198  Sum_probs=52.3

Q ss_pred             eEEEEEeCCCC-eee--ecCCCCcHHHHHHHHHhhhCCCCCCCceEE----EeCCeecCCCCCccccccCCCCEEEE
Q psy4259           8 ISDITQNQWQQ-TVS--HLDVQEEVKQLKEKIQSEKGSEYLAEYQKL----IYAGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         8 m~I~Vk~~~g~-~~~--~v~~~~TV~~LK~~I~~~~~~~ip~~~qkL----i~~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      |+|++.+.++. ..+  +.+...||.|+++.|..+.-+ +.+.++|+    --+||.|.|+.+|++||..++++|+|
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            56777766553 333  778889999999888776654 66654544    34799999999999999999988865

>KOG0013|consensus

Probab=97.05  E-value=0.0013  Score=53.62  Aligned_cols=65  Identities=17%  Similarity=0.333  Sum_probs=54.7

Q ss_pred             CCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCC--EEEEEeecC
Q psy4259          16 WQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESK--FIVVMLSKP   82 (203)
Q Consensus        16 ~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~--~i~v~~~k~   82 (203)
                      .++.|. .+..-+||.++|.++..+.+  +.+..|++.|+|++|-|...|.+|+|..|.  +|.+.|...
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg--~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqviVlq~  222 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEG--VDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQVIVLQE  222 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhc--cchhhheeeccCCceeccccceeeeecCCCEEEEEEEeccC
Confidence            356666 77888999999999999999  788899999999999999999999999995  444444443

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=97.01  E-value=0.0052  Score=43.22  Aligned_cols=69  Identities=23%  Similarity=0.203  Sum_probs=58.7

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC--CeecC---CCCCccccccCCCCEEEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA--GKILS---DDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~--Gk~L~---D~~tL~~~gI~~~~~i~v~   78 (203)
                      .-+|.||..+|+... .+..++++.+|-..|.. .|  .+++..+|+.+  -|++.   .+.||.++|+....+|+|-
T Consensus         5 ~t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g--~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq   79 (82)
T cd01773           5 KARLMLRYPDGKREQIALPEQAKLLALVRHVQS-KG--YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ   79 (82)
T ss_pred             eeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cC--CCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEe
Confidence            468999999999999 99999999999999888 57  78888999844  67774   2479999999999998763

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.

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=96.73  E-value=0.013  Score=40.96  Aligned_cols=69  Identities=14%  Similarity=0.134  Sum_probs=57.8

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecC--C-CCCccccccCCCCEEEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILS--D-DQALSEYNIDESKFIVV   77 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~--D-~~tL~~~gI~~~~~i~v   77 (203)
                      ...+|.||..+|+.+. .+..++++.+|-..|... |  ++....+|+.  =-|.+.  | +.||.+.|+....+|.|
T Consensus         3 ~~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~--~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~V   77 (80)
T cd01771           3 PISKLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-G--YPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLIL   77 (80)
T ss_pred             CeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-C--CCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEE
Confidence            3578999999999999 999999999999999875 6  7777888874  467774  2 36999999998888876

Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>KOG3206|consensus

Probab=96.73  E-value=0.0069  Score=49.45  Aligned_cols=71  Identities=24%  Similarity=0.331  Sum_probs=54.8

Q ss_pred             eEEEEEeCCCC-eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE-eCC-----eecCCC-CCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQ-TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI-YAG-----KILSDD-QALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~-~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi-~~G-----k~L~D~-~tL~~~gI~~~~~i~v~   78 (203)
                      ++|.|.+...+ .+. .++.+.||.+||.+++..+|  .+++.++|- |.|     -.|+|+ ..|..|+..+|-.||++
T Consensus         2 v~v~Iss~~~~~~~Ekr~~~~ltl~q~K~KLe~~~G--~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihvi   79 (234)
T KOG3206|consen    2 VRVVISSSLNDFRTEKRLSNSLTLAQFKDKLELLTG--TEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVI   79 (234)
T ss_pred             eEEEEecccccchhhhhcCCcCcHHHHHhhhhhhhC--CCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEE
Confidence            45556544333 234 88899999999999999999  999999874 555     346655 78999999999999987


Q ss_pred             ee
Q psy4259          79 LS   80 (203)
Q Consensus        79 ~~   80 (203)
                      =.
T Consensus        80 D~   81 (234)
T KOG3206|consen   80 DS   81 (234)
T ss_pred             ec
Confidence            43

>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=96.66  E-value=0.007  Score=40.68  Aligned_cols=62  Identities=11%  Similarity=0.010  Sum_probs=44.8

Q ss_pred             eCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEE
Q psy4259          14 NQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus        14 ~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      ..+++.+. .|.++.++.++-+....+++  +.+++-.|.|++|.|+-+.++.-.|+.+|+.+.+
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            35677888 99999999999999999999  9999999999999999999999999999998864

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.

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

Probab=96.53  E-value=0.011  Score=41.99  Aligned_cols=69  Identities=14%  Similarity=0.225  Sum_probs=60.3

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +.+.|..-+|..+. .|..+.|...|.+..+...|  -.-+..|++|+|+.++-++|-.+++..+++.|.++
T Consensus        25 inLkvv~qd~telfFkiKktT~f~klm~af~~rqG--K~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav   94 (103)
T COG5227          25 INLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQG--KNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAV   94 (103)
T ss_pred             cceEEecCCCCEEEEEEeccchHHHHHHHHHHHhC--cCcceeEEEEcceecCCCCChhhcCCccchHHHHH
Confidence            55666666777777 99999999999999999999  67789999999999999999999999999987654

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

Probab=96.24  E-value=0.0089  Score=41.37  Aligned_cols=55  Identities=16%  Similarity=0.227  Sum_probs=45.9

Q ss_pred             cCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCcccc-ccCCCCEEEEE
Q psy4259          23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEY-NIDESKFIVVM   78 (203)
Q Consensus        23 v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~-gI~~~~~i~v~   78 (203)
                      |.++++|.++++.+...... ..-....|.|+|+.|+|...|+++ |+++|.++.++
T Consensus         1 v~~~d~v~dvrq~L~~~~~t-~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lv   56 (76)
T PF15044_consen    1 VSPTDTVQDVRQVLAESPET-CYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELV   56 (76)
T ss_pred             CChhhHHHHHHHHHHhCccc-cceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEE
Confidence            56889999999998877542 455677899999999888889888 68999999876

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=95.85  E-value=0.059  Score=42.57  Aligned_cols=62  Identities=23%  Similarity=0.170  Sum_probs=46.2

Q ss_pred             eEEEEEeCCC----Ceee-ecCCCCcHHHHHHHHHhhhCCCCCCCce-EEEe-CCeec--CCCCCccccccCC
Q psy4259           8 ISDITQNQWQ----QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQ-KLIY-AGKIL--SDDQALSEYNIDE   71 (203)
Q Consensus         8 m~I~Vk~~~g----~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~q-kLi~-~Gk~L--~D~~tL~~~gI~~   71 (203)
                      |.|.|++.+|    .++. .++.+.||.+|+.+|....+  ++...+ .|.+ .++.|  .++..+..+.-.+
T Consensus         1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~--~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~   71 (162)
T PF13019_consen    1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLP--IPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSS   71 (162)
T ss_pred             CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcC--CCccceeEEEEeCCCeeCCCccccHHhhccCc
Confidence            6799999999    4677 88899999999999999999  887774 4544 34444  3445567665433

>KOG0010|consensus

Probab=95.49  E-value=0.013  Score=53.38  Aligned_cols=47  Identities=30%  Similarity=0.585  Sum_probs=23.3

Q ss_pred             HHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHHcCC
Q psy4259         135 LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP  190 (203)
Q Consensus       135 l~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml~~p  190 (203)
                      +-.++.||.++.++    +||++++++|    ..||++.++|++|||- .+++++|
T Consensus       159 ~~~~m~nP~vq~ll----~Npd~mrq~I----~anPqmq~lm~~npei-~h~ln~p  205 (493)
T KOG0010|consen  159 LRQMMENPIVQSLL----NNPDLMRQLI----MANPQMQDLMQRNPEI-GHLLNNP  205 (493)
T ss_pred             HHHhhhChHHHHHh----cChHHHHHHH----hcCHHHHHHHhhCCcc-hhhhcCh
Confidence            45566666554443    4555533333    3455555555555432 4444444

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

Probab=93.59  E-value=0.41  Score=34.07  Aligned_cols=62  Identities=8%  Similarity=0.264  Sum_probs=41.3

Q ss_pred             CCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE--eC--C-eecCCC-CCccccccCCCCEEEEEeec
Q psy4259          17 QQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI--YA--G-KILSDD-QALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        17 g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi--~~--G-k~L~D~-~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ...++ .++..+||+.++..+.+.+.  + ....||-  |.  + -.|.+. .||.+.||.+|..|++=.+.
T Consensus        13 ~~~~t~~FSk~DTI~~v~~~~rklf~--i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn   81 (88)
T PF14836_consen   13 QSVLTKQFSKTDTIGFVEKEMRKLFN--I-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERN   81 (88)
T ss_dssp             CEEEEEEE-TTSBHHHHHHHHHHHCT----TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--
T ss_pred             ccHhHhhccccChHHHHHHHHHHHhC--C-CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeec
Confidence            34566 88999999999999999999  8 5667774  22  2 346555 79999999999988765543

>PRK06437 hypothetical protein; Provisional

Probab=93.11  E-value=0.79  Score=30.69  Aligned_cols=52  Identities=13%  Similarity=0.196  Sum_probs=41.2

Q ss_pred             CCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          16 WQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        16 ~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      .++... +++...||.+|=+.    .+  +++....+..+|+++.     .++-+++||.|.++
T Consensus         9 g~~~~~~~i~~~~tv~dLL~~----Lg--i~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv   61 (67)
T PRK06437          9 GHINKTIEIDHELTVNDIIKD----LG--LDEEEYVVIVNGSPVL-----EDHNVKKEDDVLIL   61 (67)
T ss_pred             CCcceEEEcCCCCcHHHHHHH----cC--CCCccEEEEECCEECC-----CceEcCCCCEEEEE
Confidence            445566 88888899888655    47  8888899999999997     56677889999876

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

Probab=92.70  E-value=0.75  Score=31.23  Aligned_cols=65  Identities=20%  Similarity=0.168  Sum_probs=48.6

Q ss_pred             EEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCC-CCceEEEe----CC--eecCCCCCccccccC--CCCEEEEE
Q psy4259          12 TQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYL-AEYQKLIY----AG--KILSDDQALSEYNID--ESKFIVVM   78 (203)
Q Consensus        12 Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip-~~~qkLi~----~G--k~L~D~~tL~~~gI~--~~~~i~v~   78 (203)
                      |+.++|...+ +|+.+.|+.+|=+.|....+  +. .+-.-|.|    +|  ..|+.+++|.++...  ...++++.
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~--l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~~~~~~~l~fr   75 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLG--LKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKKNNPPFTLYFR   75 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHT--TSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBTSSSSEEEEEE
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcC--CCCccEEEEEEeecCCCcceeccCcccHHHHcCCCCCCEEEEEE
Confidence            5778899888 99999999999999999999  54 34456777    23  457888999998776  33344443

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 ....

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=92.64  E-value=1.1  Score=30.24  Aligned_cols=59  Identities=12%  Similarity=0.186  Sum_probs=42.1

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |+|++... ..... +++...||.+|-+.+    +  ++.....+..+|.++..     +.-+++||.|.++
T Consensus         5 m~v~vng~-~~~~~~~~~~~~tv~~ll~~l----~--~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii   64 (70)
T PRK08364          5 IRVKVIGR-GIEKEIEWRKGMKVADILRAV----G--FNTESAIAKVNGKVALE-----DDPVKDGDYVEVI   64 (70)
T ss_pred             EEEEEecc-ccceEEEcCCCCcHHHHHHHc----C--CCCccEEEEECCEECCC-----CcCcCCCCEEEEE
Confidence            56666422 12445 778888999988765    6  77777788899999853     5557889998876

>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=92.15  E-value=0.042  Score=47.57  Aligned_cols=60  Identities=22%  Similarity=0.287  Sum_probs=0.0

Q ss_pred             ceEEEEEeCCCCeee----ecCC--CCcHHHHHHHHHh----------hhCCCCCCCceE-----EEeCCeecCCCCCcc
Q psy4259           7 DISDITQNQWQQTVS----HLDV--QEEVKQLKEKIQS----------EKGSEYLAEYQK-----LIYAGKILSDDQALS   65 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~----~v~~--~~TV~~LK~~I~~----------~~~~~ip~~~qk-----Li~~Gk~L~D~~tL~   65 (203)
                      .+.|++|....-.+.    .+.+  +.||.++|..++.          ..+  +|.+.+|     |+|+.|.+.|.+||.
T Consensus        78 sItV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~--vp~dKik~~~~~lL~~kkPv~~~ktl~  155 (309)
T PF12754_consen   78 SITVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETR--VPLDKIKNFRCRLLYKKKPVGDSKTLA  155 (309)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             eEEEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhccccccccccc--CCHHHhhhhhhhheecCccCCCcCcHH
Confidence            477888887766554    3323  6899999999999          778  9999999     999999999999988


Q ss_pred             ccc
Q psy4259          66 EYN   68 (203)
Q Consensus        66 ~~g   68 (203)
                      ++.
T Consensus       156 e~l  158 (309)
T PF12754_consen  156 EVL  158 (309)
T ss_dssp             ---
T ss_pred             HHH
Confidence            874

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.

>KOG2086|consensus

Probab=91.72  E-value=0.39  Score=42.78  Aligned_cols=67  Identities=24%  Similarity=0.210  Sum_probs=53.7

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC--CeecCCC-CCccccccCCCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA--GKILSDD-QALSEYNIDESK   73 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~--Gk~L~D~-~tL~~~gI~~~~   73 (203)
                      .+-.|.||..+|+... .++...||.+|+..|...... .+...+.|++.  -|.|.|+ .||++.|+.+..
T Consensus       304 PtTsIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~-~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsv  374 (380)
T KOG2086|consen  304 PTTSIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPG-DSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSV  374 (380)
T ss_pred             CcceEEEEecCCceeeeeccCcccHHHHHHHHHhcCCC-CcCCceeeeecCCCcccCCcchhHHhccchhhh
Confidence            3567899999999998 999999999999999988863 34445666644  5888776 899999998743

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=91.48  E-value=0.78  Score=31.60  Aligned_cols=65  Identities=5%  Similarity=-0.015  Sum_probs=42.7

Q ss_pred             eEEEEEeCC------CC-eee-ecCCCCcHHHHHHHHHhhhCCCCCC--CceEEEeCCeecCCCCCccccccCCCCEEEE
Q psy4259           8 ISDITQNQW------QQ-TVS-HLDVQEEVKQLKEKIQSEKGSEYLA--EYQKLIYAGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         8 m~I~Vk~~~------g~-~~~-~v~~~~TV~~LK~~I~~~~~~~ip~--~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      |+|+|+...      |. ... +++...||.+|++.+...... +..  ....+..+|+...+     +.-+++||.|.+
T Consensus         2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~-l~~~~~~~~vavN~~~v~~-----~~~l~dgDeVai   75 (82)
T PLN02799          2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPS-LEEVRSCCVLALNEEYTTE-----SAALKDGDELAI   75 (82)
T ss_pred             eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChh-HHHHhhCcEEEECCEEcCC-----CcCcCCCCEEEE
Confidence            667777642      43 344 777889999999999876531 211  12345678887643     345778999987


Q ss_pred             E
Q psy4259          78 M   78 (203)
Q Consensus        78 ~   78 (203)
                      +
T Consensus        76 ~   76 (82)
T PLN02799         76 I   76 (82)
T ss_pred             e
Confidence            6

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=91.36  E-value=1.1  Score=30.36  Aligned_cols=52  Identities=12%  Similarity=0.217  Sum_probs=38.5

Q ss_pred             ecCCCCcHHHHHHHHHhhhCC--CCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGS--EYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~--~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +++...||.+|.+.+...++.  ........+..+|+...     .+.-+++||.|.++
T Consensus        21 ~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~-----~~~~l~~gD~v~i~   74 (80)
T cd00754          21 ELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVR-----LDTPLKDGDEVAII   74 (80)
T ss_pred             ECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcC-----CCcccCCCCEEEEe
Confidence            777789999999999988651  01234556777898887     34568899999886

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.

>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis

Probab=91.08  E-value=0.9  Score=31.75  Aligned_cols=42  Identities=24%  Similarity=0.159  Sum_probs=35.9

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG   55 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G   55 (203)
                      ++|+++.    ++. .|.+..+..+|.++|.++.+  ++++..+|.|+-
T Consensus         5 vKV~f~~----tIaIrvp~~~~y~~L~~ki~~kLk--l~~e~i~LsYkd   47 (80)
T cd06406           5 VKVHFKY----TVAIQVARGLSYATLLQKISSKLE--LPAEHITLSYKS   47 (80)
T ss_pred             EEEEEEE----EEEEEcCCCCCHHHHHHHHHHHhC--CCchhcEEEecc
Confidence            4455552    777 99999999999999999999  999999999964

PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain

>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain

Probab=90.74  E-value=0.82  Score=32.41  Aligned_cols=43  Identities=16%  Similarity=0.132  Sum_probs=37.2

Q ss_pred             EEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCC---CceEEEe
Q psy4259           9 SDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLA---EYQKLIY   53 (203)
Q Consensus         9 ~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~---~~qkLi~   53 (203)
                      .+++|+.+|+.+- .+.+++.+.+|++.|.++.|  +..   ....|.|
T Consensus         2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~--~d~~~~~~~~L~Y   48 (86)
T cd06409           2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLG--DDDFETHLYALSY   48 (86)
T ss_pred             cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhC--CccccCCcccEEE
Confidence            4678899999999 99999999999999999999  665   4667777

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

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

Probab=89.71  E-value=1.2  Score=33.64  Aligned_cols=58  Identities=26%  Similarity=0.398  Sum_probs=42.7

Q ss_pred             ecCC-CCcHHHHHHHHHhhhCCC--------CCCCceEEEeC--C---------------eec---CCCCCccccccCCC
Q psy4259          22 HLDV-QEEVKQLKEKIQSEKGSE--------YLAEYQKLIYA--G---------------KIL---SDDQALSEYNIDES   72 (203)
Q Consensus        22 ~v~~-~~TV~~LK~~I~~~~~~~--------ip~~~qkLi~~--G---------------k~L---~D~~tL~~~gI~~~   72 (203)
                      .|+. +.||++|++.+.+.....        +.-+..||++.  |               .+|   +++++|.++||.+.
T Consensus        21 ~vdL~~~Tv~~l~~~v~~~I~t~~~~~Pfrn~~yDtlKIy~~AHg~Kt~nLvInle~De~~iL~~~~~~~tL~~~gv~nE  100 (122)
T PF10209_consen   21 NVDLKDTTVKDLKEQVKQDIKTRPGLPPFRNVKYDTLKIYTKAHGSKTNNLVINLEDDEDWILDVSDDDKTLKELGVENE  100 (122)
T ss_pred             cCCcccCcHHHHHHHHHHHHhcCCCCCCceeeecceEEEEecCCCCCcCCceeeccCCcceeeecCCCCCcHHHcCCCcc
Confidence            7887 999999999888765421        34456677653  1               467   67789999999998


Q ss_pred             CEEEEEe
Q psy4259          73 KFIVVML   79 (203)
Q Consensus        73 ~~i~v~~   79 (203)
                      ..|-+..
T Consensus       101 TEiSfF~  107 (122)
T PF10209_consen  101 TEISFFN  107 (122)
T ss_pred             ceeeeeC
Confidence            8887654

>KOG2507|consensus

Probab=89.24  E-value=0.87  Score=41.27  Aligned_cols=77  Identities=14%  Similarity=0.169  Sum_probs=61.8

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEE--EeCCeecCCC---CCccccccCCCCEEEEE
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKL--IYAGKILSDD---QALSEYNIDESKFIVVM   78 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkL--i~~Gk~L~D~---~tL~~~gI~~~~~i~v~   78 (203)
                      ++..+|.||..+|..|+ +++.++-+..+|+.|....+  +......|  -|--|+..|+   ++|.++.+-+...|+|+
T Consensus       312 ~d~~rLqiRLPdGssfte~Fps~~vL~~vr~yvrq~~~--i~~g~f~LatpyPRReft~eDy~KtllEl~L~psaalvvl  389 (506)
T KOG2507|consen  312 ADDVRLQIRLPDGSSFTEKFPSTSVLRMVRDYVRQNQT--IGLGAFDLATPYPRREFTDEDYDKTLLELRLFPSAALVVL  389 (506)
T ss_pred             cceeEEEEecCCccchhhcCCcchHHHHHHHHHHhccc--ccccceeeccccccccccchhhhhhHHHhccCCcceEEEE
Confidence            35789999999999999 99999999999999997777  66666655  4777777543   78999999998888776


Q ss_pred             eecCC
Q psy4259          79 LSKPK   83 (203)
Q Consensus        79 ~~k~~   83 (203)
                      -++..
T Consensus       390 pk~r~  394 (506)
T KOG2507|consen  390 PKKRA  394 (506)
T ss_pred             ecCCc
Confidence            55443

>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=88.82  E-value=1.2  Score=31.50  Aligned_cols=56  Identities=14%  Similarity=0.261  Sum_probs=39.6

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      .++=...+..||..++.+.+  +.-+.-.+......|+.+++|-+-||+-...+.+.+
T Consensus         8 ~mDI~epl~~Lk~lLe~Rl~--~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnv   63 (88)
T PF11620_consen    8 HMDIREPLSTLKKLLERRLG--ISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNV   63 (88)
T ss_dssp             EEESSSBGGGHHHHSHHHH---S--SS-EEEETTEE--TTSBTTTSS----SEEEEEE
T ss_pred             EEecCCcHHHHHHHHHHhhC--CCcCCCeEEeccceecCCccHHHhhccccCEEEEEE
Confidence            56667789999999999999  888888877788779999999999999888888765

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.

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=88.23  E-value=4  Score=26.64  Aligned_cols=45  Identities=11%  Similarity=0.216  Sum_probs=32.5

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      ++....|+.+||.++..        +.=-+||+|-..+++..     +++||.|+++-
T Consensus        11 ~~~~~~tl~~lr~~~k~--------~~DI~I~NGF~~~~d~~-----L~e~D~v~~Ik   55 (57)
T PF14453_consen   11 ETEENTTLFELRKESKP--------DADIVILNGFPTKEDIE-----LKEGDEVFLIK   55 (57)
T ss_pred             EcCCCcCHHHHHHhhCC--------CCCEEEEcCcccCCccc-----cCCCCEEEEEe
Confidence            66677899999987433        22267999988877654     55689998763

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

Probab=88.19  E-value=1.1  Score=30.12  Aligned_cols=58  Identities=12%  Similarity=0.172  Sum_probs=44.3

Q ss_pred             eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          19 TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        19 ~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ... .+....||.+|.+.+...++.........+..+|+...+  ...+.-+++||.|.++
T Consensus        13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~~v~~--~~~~~~l~~gD~V~i~   71 (77)
T PF02597_consen   13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGEIVPD--DGLDTPLKDGDEVAIL   71 (77)
T ss_dssp             EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEEEGG--GTTTSBEETTEEEEEE
T ss_pred             CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEEcCC--ccCCcCcCCCCEEEEE
Confidence            344 778899999999999888742112356788899999988  3666778899999886

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 ....

>KOG2561|consensus

Probab=87.90  E-value=0.15  Score=46.43  Aligned_cols=57  Identities=23%  Similarity=0.264  Sum_probs=50.2

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +++...|-.+|...|++++|  ++....|.|-+||+|.-.+||.+-|++....+.|++.
T Consensus        55 k~sL~i~Gselqa~iakklg--i~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~~  111 (568)
T KOG2561|consen   55 KCSLHITGSELQALIAKKLG--IKENHVKCIINGKILSCRKTLAEQGLKINQELMVAVG  111 (568)
T ss_pred             hcccccccHHHHHHHHHHcC--CchhhhheeeccceeecccchhhhhhhhhhHHHHHhc
Confidence            55667788899999999999  9999999999999999999999999998877766654

>smart00295 B41 Band 4

Probab=87.76  E-value=5.6  Score=31.43  Aligned_cols=71  Identities=14%  Similarity=0.114  Sum_probs=50.3

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCC-ceEEEeC---C---eecCCCCCccccccC-CCCEEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAE-YQKLIYA---G---KILSDDQALSEYNID-ESKFIV   76 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~-~qkLi~~---G---k~L~D~~tL~~~gI~-~~~~i~   76 (203)
                      ..+.|.|...+|.... .++.++||.++.+.|+.+.|  +... ..-|.+.   +   ..|+...+|.+...+ ....++
T Consensus         2 ~~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~--l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~l~   79 (207)
T smart00295        2 KPRVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLG--IRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVKSEPLTLY   79 (207)
T ss_pred             CcEEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhC--CCccceeEEEEEcCCCCcCeeCCCccCHHHhcCCCCCcEEE
Confidence            3578899999999999 99999999999999999999  6432 2244432   1   346666777776654 233444


Q ss_pred             EE
Q psy4259          77 VM   78 (203)
Q Consensus        77 v~   78 (203)
                      +.
T Consensus        80 fr   81 (207)
T smart00295       80 FR   81 (207)
T ss_pred             EE
Confidence            43

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.

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=87.51  E-value=2.8  Score=37.89  Aligned_cols=74  Identities=16%  Similarity=0.155  Sum_probs=59.2

Q ss_pred             eEEEEEeCCCCeeeecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC----Cee--cCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA----GKI--LSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~----Gk~--L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |-+.||+..|....+|.++++.+.|-.+|...+..++.+++..+.-+    |.+  +..++|+.++|++.|+.+++-.+.
T Consensus         1 Mi~rfRsk~G~~Rve~qe~d~lg~l~~kll~~~~~n~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~ysd   80 (571)
T COG5100           1 MIFRFRSKEGQRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEYSD   80 (571)
T ss_pred             CeEEEecCCCceeeeccccchhhhhhHHHHhhhccCCCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEecc
Confidence            56788888887666999999999999999888765578888887653    332  345689999999999999988743

>smart00666 PB1 PB1 domain

Probab=86.72  E-value=2.9  Score=28.39  Aligned_cols=45  Identities=13%  Similarity=0.101  Sum_probs=35.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG   55 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G   55 (203)
                      ++|+++. ++..+. .++...|..+|+.+|...++  ......+|-|..
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            4555654 556666 99999999999999999999  776778888863

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.

>PRK07440 hypothetical protein; Provisional

Probab=86.41  E-value=6.1  Score=26.59  Aligned_cols=62  Identities=15%  Similarity=0.221  Sum_probs=43.6

Q ss_pred             cceEEEEEeCCCCeeeecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           6 HDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ..|+|+|.   |+.+ ++....||.+|-+    ..+  +++...-+-++|.++.- ....++-+++||.|.++
T Consensus         3 ~~m~i~vN---G~~~-~~~~~~tl~~lL~----~l~--~~~~~vav~~N~~iv~r-~~w~~~~L~~gD~IEIv   64 (70)
T PRK07440          3 NPITLQVN---GETR-TCSSGTSLPDLLQ----QLG--FNPRLVAVEYNGEILHR-QFWEQTQVQPGDRLEIV   64 (70)
T ss_pred             CceEEEEC---CEEE-EcCCCCCHHHHHH----HcC--CCCCeEEEEECCEEeCH-HHcCceecCCCCEEEEE
Confidence            45666665   3322 6666788887764    356  77788888899999853 24566678899999876

>KOG2982|consensus

Probab=85.53  E-value=1.8  Score=38.02  Aligned_cols=55  Identities=15%  Similarity=0.213  Sum_probs=44.7

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe---CCeecC-----CCCCccccccCCCCEEEEE
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY---AGKILS-----DDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~---~Gk~L~-----D~~tL~~~gI~~~~~i~v~   78 (203)
                      -|.-.-||.|||.++..+.|  +-..++||.|   .||.-+     -++.|-.|+|.+|+.+.|-
T Consensus       353 ~I~~~~TV~D~~~~Ld~~VG--vk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~lvq  415 (418)
T KOG2982|consen  353 LICMTRTVLDFMKILDPKVG--VKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFLVQ  415 (418)
T ss_pred             EEEeehHHHHHHHHhccccc--cccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEeeee
Confidence            55667799999999999999  9999999987   455432     3367888999999998763

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

Probab=84.76  E-value=5.2  Score=27.25  Aligned_cols=57  Identities=14%  Similarity=0.143  Sum_probs=39.5

Q ss_pred             CCee-e-ecCCC-CcHHHHHHHHHhhhCCCCC-CCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          17 QQTV-S-HLDVQ-EEVKQLKEKIQSEKGSEYL-AEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        17 g~~~-~-~v~~~-~TV~~LK~~I~~~~~~~ip-~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |+.. . +++.. .||.+|++.+...++.... .....+..+|+...+     +.-+++|+.|.++
T Consensus        14 g~~~~~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~   74 (80)
T TIGR01682        14 GTDEETLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFI   74 (80)
T ss_pred             CCCeEEEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcCC-----CcCcCCCCEEEEe
Confidence            4443 4 77766 8999999999888652111 133456678888774     4578889999876

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

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

Probab=84.57  E-value=1.4  Score=31.83  Aligned_cols=33  Identities=39%  Similarity=0.563  Sum_probs=22.6

Q ss_pred             EEEeCCeecCCCCCcccc-ccCCCCEEEEEeecC
Q psy4259          50 KLIYAGKILSDDQALSEY-NIDESKFIVVMLSKP   82 (203)
Q Consensus        50 kLi~~Gk~L~D~~tL~~~-gI~~~~~i~v~~~k~   82 (203)
                      .|-|+||.|..+++|++| |-.+-..|+|-+.++
T Consensus         3 ~LW~aGK~l~~~k~l~dy~GkNEKtKiivKl~~~   36 (98)
T PF11069_consen    3 QLWWAGKELQRGKKLSDYIGKNEKTKIIVKLQKR   36 (98)
T ss_pred             eEEeccccccCCCcHHHhcCCCcceeEEEEeccC
Confidence            577999999999999999 333334444434343

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=84.16  E-value=5.5  Score=27.55  Aligned_cols=55  Identities=7%  Similarity=0.203  Sum_probs=38.1

Q ss_pred             ee-ecCCCCcHHHHHHHHHhhhCCC----CC-----CCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          20 VS-HLDVQEEVKQLKEKIQSEKGSE----YL-----AEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        20 ~~-~v~~~~TV~~LK~~I~~~~~~~----ip-----~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      .. +++ ..||.+|.+.+.++++..    +.     .....+..+|+..+++..   .-+++|+.|.++
T Consensus        18 ~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~   82 (88)
T TIGR01687        18 EEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIF   82 (88)
T ss_pred             EEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEe
Confidence            44 666 889999999999886520    11     123566678888765432   568899999876

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.

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=83.76  E-value=4.6  Score=26.46  Aligned_cols=50  Identities=12%  Similarity=0.238  Sum_probs=37.4

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +++...||.+|.+.+    +  ++.+...+.++|+++..+ ...++-+++||.|.++
T Consensus        10 ~~~~~~tv~~ll~~l----~--~~~~~i~V~vNg~~v~~~-~~~~~~L~~gD~V~ii   59 (65)
T cd00565          10 EVEEGATLAELLEEL----G--LDPRGVAVALNGEIVPRS-EWASTPLQDGDRIEIV   59 (65)
T ss_pred             EcCCCCCHHHHHHHc----C--CCCCcEEEEECCEEcCHH-HcCceecCCCCEEEEE
Confidence            555678999888764    5  667788889999988553 3445568899999876

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.

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=83.69  E-value=7.1  Score=25.55  Aligned_cols=54  Identities=13%  Similarity=0.287  Sum_probs=37.8

Q ss_pred             CCCeeeecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          16 WQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        16 ~g~~~~~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +|+.+. ++ ..||.+|.+.+    +  +......+-++|+++. .....+.-+++||.|.++
T Consensus         6 Ng~~~~-~~-~~tl~~Ll~~l----~--~~~~~vavavN~~iv~-~~~~~~~~L~dgD~Ieiv   59 (65)
T PRK06488          6 NGETLQ-TE-ATTLALLLAEL----D--YEGNWLATAVNGELVH-KEARAQFVLHEGDRIEIL   59 (65)
T ss_pred             CCeEEE-cC-cCcHHHHHHHc----C--CCCCeEEEEECCEEcC-HHHcCccccCCCCEEEEE
Confidence            344443 42 35888888764    5  6666677889999986 334667778999999876

>PF10407 Cytokin_check_N: Cdc14 phosphatase binding protein N-terminus ; InterPro: IPR018844 Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus

Probab=82.82  E-value=4.1  Score=27.95  Aligned_cols=62  Identities=23%  Similarity=0.281  Sum_probs=40.9

Q ss_pred             Ceee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe------CCeecCCCCCccccccCCCCEEEEEeec
Q psy4259          18 QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY------AGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        18 ~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~------~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ++|- =.+++.|+.+|+..|.+++.+-+|-+ ..+.-      .|=-|+.+-++++. +..++.|.|+++.
T Consensus         3 kKFLhlt~~~~tl~~L~~eI~~~f~kLYP~~-~~~~I~~LQD~~~cDLD~d~~V~DV-f~~~~~vrvi~~n   71 (73)
T PF10407_consen    3 KKFLHLTDPNNTLSQLKEEIEERFKKLYPNE-PELEILSLQDSDGCDLDPDFLVKDV-FNSNNVVRVILKN   71 (73)
T ss_pred             cEEEEEeCCCCcHHHHHHHHHHHHHHHCCCC-CCceEEEeecCCCCCCCcccEeeee-eccCCEEEEEecC
Confidence            4566 66789999999999999997634443 33321      23345555555554 4578888887754

This is the highly conserved N terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance [].

>PRK05659 sulfur carrier protein ThiS; Validated

Probab=82.70  E-value=8.9  Score=24.98  Aligned_cols=55  Identities=16%  Similarity=0.213  Sum_probs=38.5

Q ss_pred             CCCeeeecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          16 WQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        16 ~g~~~~~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +|+.+ ++....||.+|-..    .+  ++....-+.++|+++.-.. ..+.-+++||.|-++
T Consensus         6 NG~~~-~~~~~~tl~~lL~~----l~--~~~~~vav~vNg~iv~r~~-~~~~~l~~gD~vei~   60 (66)
T PRK05659          6 NGEPR-ELPDGESVAALLAR----EG--LAGRRVAVEVNGEIVPRSQ-HASTALREGDVVEIV   60 (66)
T ss_pred             CCeEE-EcCCCCCHHHHHHh----cC--CCCCeEEEEECCeEeCHHH-cCcccCCCCCEEEEE
Confidence            34433 55566788877654    57  8888888899998886442 444458899998876

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=82.56  E-value=7.5  Score=25.59  Aligned_cols=49  Identities=14%  Similarity=0.170  Sum_probs=36.3

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ++....||.+|=+.    .+  ++....-+.++|.++..+.. +.+ +++||.|-++
T Consensus        11 ~~~~~~tl~~ll~~----l~--~~~~~vav~~N~~iv~r~~~-~~~-L~~gD~ieIv   59 (65)
T PRK05863         11 EVDEQTTVAALLDS----LG--FPEKGIAVAVDWSVLPRSDW-ATK-LRDGARLEVV   59 (65)
T ss_pred             EcCCCCcHHHHHHH----cC--CCCCcEEEEECCcCcChhHh-hhh-cCCCCEEEEE
Confidence            45566787776554    57  88889999999998865432 345 8999999876

>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins

Probab=82.55  E-value=5.8  Score=26.94  Aligned_cols=46  Identities=20%  Similarity=0.175  Sum_probs=35.4

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG   55 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G   55 (203)
                      ++|+++..++.... .+....|..+|+.+|...++  .+....+|-|..
T Consensus         2 ~~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~--~~~~~~~l~Y~D   48 (84)
T PF00564_consen    2 VRVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFG--LLDEDFQLKYKD   48 (84)
T ss_dssp             EEEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHT--TSTSSEEEEEEE
T ss_pred             EEEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhC--CCCccEEEEeeC
Confidence            45666644444444 78888899999999999999  777888998853

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.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....

>smart00727 STI1 Heat shock chaperonin-binding motif

Probab=82.46  E-value=1.5  Score=26.02  Aligned_cols=25  Identities=36%  Similarity=0.700  Sum_probs=11.9

Q ss_pred             CCCcHHHHHHHHhhcCHHHHHHHhh-CH
Q psy4259         154 NPELLPTVLQQIGQSNPALLELISH-NQ  180 (203)
Q Consensus       154 nP~~l~~il~~l~~~nP~l~~~i~~-n~  180 (203)
                      ||.+ ..++++| .+||++.+.+.+ ||
T Consensus        10 ~P~~-~~~l~~~-~~nP~~~~~~~~~nP   35 (41)
T smart00727       10 NPQV-QSLLQDM-QQNPDMLAQMLQENP   35 (41)
T ss_pred             CHHH-HHHHHHH-HHCHHHHHHHHHhCH
Confidence            7754 3333332 346665544444 55

>TIGR02958 sec_mycoba_snm4 secretion protein snm4

Probab=82.24  E-value=9.9  Score=34.93  Aligned_cols=71  Identities=17%  Similarity=0.133  Sum_probs=53.6

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCC----CCCceEEE-eCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEY----LAEYQKLI-YAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~i----p~~~qkLi-~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      .+|+|...+ +..+ -++.+..|.+|-..|.+..+.+.    ....-.|. -+|..|+.+.||.+.||.||+.+++.-
T Consensus         3 ~RVtV~~~~-~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L~p   79 (452)
T TIGR02958         3 CRVTVLAGR-RAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVLVP   79 (452)
T ss_pred             EEEEEeeCC-eeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEEee
Confidence            467777543 4466 88899999999999998887421    22334444 368899999999999999999999863

Members of this family are the 12-transmembrane domain protein snm4, where snm stands for secretion in mycocbacteria. This system acts on Mycobacterium tuberculosis related pair of virulence factors ESAT-6 and CFP-10 and on other homologs. The system is conserved in many Actinobacteria, including the non-pathogenic Mycobacterium smegmatis.

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

Probab=82.07  E-value=7.2  Score=26.15  Aligned_cols=66  Identities=15%  Similarity=0.253  Sum_probs=48.6

Q ss_pred             CCCeee-ecCCCCcHHHHHHHHHhhhCCC-CCCCceEEE-eCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259          16 WQQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLI-YAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        16 ~g~~~~-~v~~~~TV~~LK~~I~~~~~~~-ip~~~qkLi-~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      +|+... +.+.+..+.-+..+..+..+.. -|++...|- -+|.+|+-++.++|||+.++-++.+.++.
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLKA   72 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLKA   72 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEeec
Confidence            455555 6677777777777766666522 567776665 36999999999999999999999887643

>PF08337 Plexin_cytopl: Plexin cytoplasmic RasGAP domain; InterPro: IPR013548 This domain is found at C terminus of various plexins (e

Probab=81.37  E-value=3.2  Score=38.92  Aligned_cols=75  Identities=19%  Similarity=0.275  Sum_probs=45.6

Q ss_pred             ceEEEEEeCC--CCeee-ecCCCCcHHHHHHHHHhhhCCC------CCCCceEEEe--C--Ce-ecCCC-----------
Q psy4259           7 DISDITQNQW--QQTVS-HLDVQEEVKQLKEKIQSEKGSE------YLAEYQKLIY--A--GK-ILSDD-----------   61 (203)
Q Consensus         7 ~m~I~Vk~~~--g~~~~-~v~~~~TV~~LK~~I~~~~~~~------ip~~~qkLi~--~--Gk-~L~D~-----------   61 (203)
                      ++.|.|-..+  ...+. .|-..+||.++|+||-...=++      ..+++.-|-|  +  |+ +|.|.           
T Consensus       189 ~ltl~v~~~~~~~~~i~VkVLdCDTItQVKeKiLDavyk~~p~S~rp~~~d~dLEwr~~~~~~~iL~D~D~ts~~~~~wk  268 (539)
T PF08337_consen  189 TLTLNVVPQEEGSEEIPVKVLDCDTITQVKEKILDAVYKNTPYSQRPRADDVDLEWRQGRGGRLILQDEDSTSKVEGGWK  268 (539)
T ss_dssp             EEEEEEECTTTSSTCEEEEEETTSBHHHHHHHHHHHHTTTS-GGGS--GGGEEEEEEETTSEEEEESSSSTTSEEETTEE
T ss_pred             EEEEEEEecCCCCceEEEEEEecCcccHHHHHHHHHHHcCCCCCCCCCccccceeeecCCCCcccccCCCCCcccCCCce
Confidence            3556654333  23355 7878899999999998765332      2344555544  2  23 56554           


Q ss_pred             --CCccccccCCCCEEEEEeec
Q psy4259          62 --QALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        62 --~tL~~~gI~~~~~i~v~~~k   81 (203)
                        .||+.|+|.+|++|.++.+.
T Consensus       269 rLNTL~HY~V~dga~vaLv~k~  290 (539)
T PF08337_consen  269 RLNTLAHYKVPDGATVALVPKQ  290 (539)
T ss_dssp             E--BHHHHT--TTEEEEEEES-
T ss_pred             EeccHhhcCCCCCceEEEeecc
Confidence              26788999999999877554

g. P51805 from SWISSPROT). Plexins are receptors for semaphorins, and plexin signalling is important in pathfinding and patterning of both neurons and developing blood vessels [, ]. The cytoplasmic region, which has been called a SEX domain [], and is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins []. ; PDB: 3H6N_A 4E71_A 4E74_A 3IG3_A 2REX_C 2JPH_A 2R2O_A 3HM6_X 3SU8_X 3SUA_E ....

>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium)

Probab=80.29  E-value=7.2  Score=27.20  Aligned_cols=62  Identities=21%  Similarity=0.219  Sum_probs=40.4

Q ss_pred             CCCeee-ecCCCCcHHHHHHHHHhhhCCCCCC-CceEEEeCC----e-ecCCCCCccc----cccCCCCEEEEEe
Q psy4259          16 WQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLA-EYQKLIYAG----K-ILSDDQALSE----YNIDESKFIVVML   79 (203)
Q Consensus        16 ~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~-~~qkLi~~G----k-~L~D~~tL~~----~gI~~~~~i~v~~   79 (203)
                      +|..+. .+.++.+..+|+++|...++  +.. ....|-|..    . .|..+.-|.+    |.....++|.+.+
T Consensus         8 ~~d~~r~~l~~~~~~~~L~~~i~~r~~--~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~~~~~~~~v~l~v   80 (82)
T cd06407           8 GEEKIRFRLPPSWGFTELKQEIAKRFK--LDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVYRSSGSHTIRLLV   80 (82)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhC--CCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHHHHCCCCeEEEEe
Confidence            445556 99999999999999999999  654 567777753    1 1233333444    3444455665554

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

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

Probab=80.22  E-value=8.9  Score=27.13  Aligned_cols=45  Identities=13%  Similarity=0.161  Sum_probs=34.4

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGK   56 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk   56 (203)
                      |+|+|. ..|..+. .|+++.+..+|.++|..+++  +. ...+|-|..-
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            445554 2566777 99999999999999999999  64 5667777653

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

>KOG1364|consensus

Probab=80.01  E-value=2.3  Score=37.52  Aligned_cols=65  Identities=20%  Similarity=0.018  Sum_probs=54.1

Q ss_pred             EEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC---eecCC--CCCccccccCCCCE
Q psy4259           9 SDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG---KILSD--DQALSEYNIDESKF   74 (203)
Q Consensus         9 ~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G---k~L~D--~~tL~~~gI~~~~~   74 (203)
                      .|.||..+|+.+. .+-.+++|.-|-..++..... .+-++.+|+++=   |.|.+  +.||.++||++..+
T Consensus       279 ~i~vR~pdG~R~qrkf~~sepv~ll~~~~~s~~dg-~~k~~FkLv~a~P~~k~l~~~~daT~~eaGL~nS~~  349 (356)
T KOG1364|consen  279 SIQVRFPDGRRKQRKFLKSEPVQLLWSFCYSHMDG-SDKKRFKLVQAIPASKTLDYGADATFKEAGLANSET  349 (356)
T ss_pred             EEEEecCCccHHHHhhccccHHHHHHHHHHHhhcc-cccccceeeecccchhhhhccccchHHHhccCcccc
Confidence            4999999999888 888999999998888877754 677888999876   66654  47999999998765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	203
1pve_A	72	Solution Structure Of Xpc Binding Domain Of Hhr23b		1e-17
2f4m_B	61	The Mouse Pngase-Hr23 Complex Reveals A Complete Re		2e-17
1uel_A	95	Solution Structure Of Ubiquitin-Like Domain Of Hhr2		3e-16
1p1a_A	85	Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Le		6e-15
1oqy_A	368	Structure Of The Dna Repair Protein Hhr23a Length =		6e-13
1oqy_A	368	Structure Of The Dna Repair Protein Hhr23a Length =		4e-12
1tp4_A	97	Solution Structure Of The Xpc Binding Domain Of Hhr		8e-12
2wyq_A	85	The Crystal Structure Of The Ubiquitin-Like (Ubl) D		1e-11
1p98_A	78	High-Resolution Nmr Structure Of The Ubl-Domain Of		5e-11

>pdb|1PVE|A Chain A, Solution Structure Of Xpc Binding Domain Of Hhr23b Length = 72

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/61 (67%), Positives = 49/61 (80%)
Query: 131 SEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
           S  PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEP
Sbjct: 2   SHMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEP 61
Query: 191 V 191
           V
Sbjct: 62  V 62

>pdb|2F4M|B Chain B, The Mouse Pngase-Hr23 Complex Reveals A Complete Remodulation Of The Protein-Protein Interface Compared To Its Yeast Orthologs Length = 61

Iteration: 1
 Score = 85.5 bits (210), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 48/60 (80%)
Query: 133 DPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVA 192
            PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEPV 
Sbjct: 2   HPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVG 61

>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 = 81.3 bits (199), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 46/85 (54%), Positives = 58/85 (68%), Gaps = 5/85 (5%)
Query: 11 ITQNQWQQTVSHLDV--QEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEY 67
          +T    QQ    +D+  +E VK LKEKI+SEKG + +    QKLIYAGKIL+DD AL EY
Sbjct: 3  VTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEY 62
Query: 68 NIDESKFIVVMLSKPKP--TPAPYS 90
           IDE  F+VVM++KPK   TPAP +
Sbjct: 63 KIDEKNFVVVMVTKPKAVSTPAPAT 87

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

Iteration: 1
 Score = 77.0 bits (188), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 52/76 (68%), Gaps = 3/76 (3%)
Query: 11 ITQNQWQQTVSHLDV--QEEVKQLKEKIQSEKGSEYL-AEYQKLIYAGKILSDDQALSEY 67
          +T    QQ    +D+  +E VK LKEKI+SEKG +      QKLIYAGKIL+DD AL EY
Sbjct: 6  VTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEY 65
Query: 68 NIDESKFIVVMLSKPK 83
           IDE  F+VVM++KPK
Sbjct: 66 KIDEKNFVVVMVTKPK 81

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 48/112 (42%), Positives = 60/112 (53%), Gaps = 15/112 (13%)
Query: 2   GMLAHDISDITQNQWQQTVSHLDVQ--EEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKIL 58
           G L      IT    QQ    + ++  E VK LKEKI++EKG + +    QKLIYAGKIL
Sbjct: 1   GPLGSSAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKIL 60
Query: 59  SDDQALSEYNIDESKFIVVMLSKPK------------PTPAPYSGPSDPTQP 98
           SDD  + +Y IDE  F+VVM++K K            PT AP S  S P  P
Sbjct: 61  SDDVPIRDYRIDEKNFVVVMVTKTKAGQGTSAPPEASPTAAPESSTSFPPAP 112

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 40/59 (67%), Positives = 48/59 (81%)
Query: 132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
           E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++MLNEP
Sbjct: 234 ENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEP 292

>pdb|1TP4|A Chain A, Solution Structure Of The Xpc Binding Domain Of Hhr23a Protein Length = 97

Iteration: 1
 Score = 66.6 bits (161), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 48/60 (80%)
Query: 131 SEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
            E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++MLNEP
Sbjct: 8   GENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEP 67

>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 = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 38/76 (50%), Positives = 50/76 (65%), Gaps = 3/76 (3%)
Query: 11 ITQNQWQQTVSHLDVQ--EEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEY 67
          IT    QQ    + ++  E VK LKEKI++EKG + +    QKLIYAGKILSDD  + +Y
Sbjct: 8  ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 67
Query: 68 NIDESKFIVVMLSKPK 83
           IDE  F+VVM++K 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 = 63.9 bits (154), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 48/74 (64%), Gaps = 3/74 (4%)
Query: 11 ITQNQWQQTVSHLDVQ--EEVKQLKEKIQSEKGSEYL-AEYQKLIYAGKILSDDQALSEY 67
          IT    QQ    + ++  E VK LKEKI++EKG +      QKLIYAGKILSDD  + +Y
Sbjct: 5  ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 64
Query: 68 NIDESKFIVVMLSK 81
           IDE  F+VVM++K
Sbjct: 65 RIDEKNFVVVMVTK 78

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	203
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	7e-25
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	3e-24
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	4e-23
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	7e-23
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	2e-21
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	1e-17
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	2e-17
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	3e-15
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	4e-13
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	4e-15
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	9e-15
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	2e-14
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	2e-14
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	5e-14
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	3e-13
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	7e-13
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	8e-13
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	6e-12
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	1e-11
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	2e-11
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	2e-11
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	5e-11
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	9e-11
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	9e-11
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	4e-10
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	9e-10
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	2e-09
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	3e-09
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	5e-09
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	6e-09
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	7e-09
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	7e-09
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	1e-08
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	1e-08
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	1e-08
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	2e-08
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	2e-08
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	3e-08
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	6e-08
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	6e-08
1we6_A	111	Splicing factor, putative; structural genomics, ub	7e-08
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	7e-08
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	7e-08
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	1e-07
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	1e-07
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	2e-07
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	2e-07
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	3e-07
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	3e-07
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	4e-07
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	8e-07
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	1e-06
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	1e-06
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	5e-05
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	3e-06
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	7e-06
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	4e-06
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	5e-06
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	2e-04
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	8e-06
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	8e-06
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	8e-06
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	9e-05

>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 = 91.5 bits (227), Expect = 7e-25
 Identities = 41/64 (64%), Positives = 49/64 (76%)

Query: 131 SEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
           S  PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEP
Sbjct: 2   SHMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEP 61

Query: 191 VAGD 194
           V   
Sbjct: 62  VQEA 65

>2f4m_B UV excision repair protein RAD23 homolog B; glycoproteins, ubiquitin-dependent protein degradation, NUCL excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: a.189.1.1 PDB: 2f4o_B* Length = 61

 Score = 89.5 bits (222), Expect = 3e-24
 Identities = 40/58 (68%), Positives = 48/58 (82%)

Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEPV
Sbjct: 3   PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 60

>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 = 87.8 bits (218), Expect = 4e-23
 Identities = 42/80 (52%), Positives = 51/80 (63%), Gaps = 3/80 (3%)

Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESK 73
          QQ    +D+  E  VK LKEKI+SEKG + +    QKLIYAGKIL+DD AL EY IDE  
Sbjct: 9  QQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKN 68

Query: 74 FIVVMLSKPKPTPAPYSGPS 93
          F+VVM++KPK    P     
Sbjct: 69 FVVVMVTKPKAVSTPAPATL 88

>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 = 87.5 bits (217), Expect = 7e-23
 Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 4/91 (4%)

Query: 17  QQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKF 74
           ++    LD++    + + K K+      E      KLIY+GK+L D + +SE  + +   
Sbjct: 10  KKEKVPLDLEPSNTILETKTKLAQSISCE--ESQIKLIYSGKVLQDSKTVSECGLKDGDQ 67

Query: 75  IVVMLSKPKPTPAPYSGPSDPTQPAGQESEA 105
           +V M+S+ K T    +     +    + + A
Sbjct: 68  VVFMVSQKKSTKTKVTERDPNSSSVDKLAAA 98

>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 = 83.1 bits (206), Expect = 2e-21
 Identities = 35/70 (50%), Positives = 48/70 (68%), Gaps = 3/70 (4%)

Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESK 73
          QQ    + ++ +  VK LKEKI++EKG + +    QKLIYAGKILSDD  + +Y IDE  
Sbjct: 14 QQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKN 73

Query: 74 FIVVMLSKPK 83
          F+VVM++K K
Sbjct: 74 FVVVMVTKTK 83

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

 Score = 72.8 bits (179), Expect = 2e-17
 Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 5/67 (7%)

Query: 22 HLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFIVVM 78
           ++V     V  LK+KI   +      +  +L Y+G  L+DD + L+EY I E   IVV 
Sbjct: 28 TVEVDRTETVSSLKDKIHIVEN--TPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVF 85

Query: 79 LSKPKPT 85
          L      
Sbjct: 86 LKSINRA 92

>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 = 71.9 bits (175), Expect = 3e-15
 Identities = 40/67 (59%), Positives = 48/67 (71%)

Query: 128 GGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRML 187
               E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++ML
Sbjct: 230 EAAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQML 289

Query: 188 NEPVAGD 194
           NEP    
Sbjct: 290 NEPPGEL 296

>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 = 66.2 bits (160), Expect = 4e-13
 Identities = 47/176 (26%), Positives = 74/176 (42%), Gaps = 3/176 (1%)

Query: 17  QQTVSHLDVQEE--VKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESK 73
           QQ    + ++ +  VK LKEKI++EKG + +    QKLIYAGKILSDD  + +Y IDE  
Sbjct: 16  QQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKN 75

Query: 74  FIVVMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFFERVNPYGGESED 133
           F+VVM++K K      + P      A + S +  PA  +  S              ES  
Sbjct: 76  FVVVMVTKTKAGQGTSAPPEASPTAAPESSTSFPPAPTSGMSHPPPAAREDKSPSEESAP 135

Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNE 189
             +            +  ++       V     ++    +  + + +E  V  L  
Sbjct: 136 TTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETMLTEIMSMGYERERVVAALRA 191

>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 = 66.9 bits (164), Expect = 4e-15
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
            V  +  VK+ KE I +       +E Q+LIY G++L DD+ L EYN+      +V  +
Sbjct: 20 FIVGAQMNVKEFKEHIAASVS--IPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERA 77

Query: 81 KPKPTPAPYS 90
           P+      +
Sbjct: 78 PPQTHLPSGA 87

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

 Score = 65.7 bits (161), Expect = 9e-15
 Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 5/67 (7%)

Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGK-ILSDDQALSEYNIDESK 73
            +   L+V     +  +K+KI+  +        Q LI  G  IL +D  + +  I  + 
Sbjct: 19 NGSSFELEVDYRDTLLVVKQKIERSQH--IPVSKQTLIVDGIVILREDLTVEQCQIVPTS 76

Query: 74 FIVVMLS 80
           I + +S
Sbjct: 77 DIQLEVS 83

>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 = 65.5 bits (160), Expect = 2e-14
 Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 29  VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAP 88
           ++QLKE+I     +    +   LI+AGKIL D  +L++  + +   + +++ +       
Sbjct: 39  IQQLKEEISQRFKAH--PDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRAMGN 96

Query: 89  YSGPSDPT 96
               S P+
Sbjct: 97  ECPASGPS 104

>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 = 64.5 bits (158), Expect = 2e-14
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          ++V  E  V Q KE I    G       Q+LIY+GKIL DDQ +  Y+I +   + ++ S
Sbjct: 18 VNVAPESTVLQFKEAINKANGIP--VANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 75

Query: 81 KP 82
          +P
Sbjct: 76 QP 77

>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 = 63.8 bits (155), Expect = 5e-14
 Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 2/78 (2%)

Query: 12 TQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEY-NID 70
           Q      +S  D    V  LK  +          E Q+LIY+GK+L D Q L +     
Sbjct: 16 NQRHRDLELS-GDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQ 74

Query: 71 ESKFIVVMLSKPKPTPAP 88
          E + ++ ++   K  P+ 
Sbjct: 75 EKRHVLHLVCNVKSGPSS 92

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score = 62.3 bits (152), Expect = 3e-13
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 23  LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
           ++V  E  V Q KE I    G       Q+LIY+GKIL DDQ +  Y+I +   + ++ S
Sbjct: 42  VNVAPESTVLQFKEAINKANGIP--VANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 99

Query: 81  KP 82
           +P
Sbjct: 100 QP 101

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

 Score = 61.8 bits (150), Expect = 7e-13
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 29  VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAP 88
           V+Q KE I     S+   +   LI+AGKIL D   L ++ I +   + +++ +   + + 
Sbjct: 54  VQQFKEAISKRFKSQ--TDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPNSSSV 111

Query: 89  YSGPSDPTQPA 99
               +      
Sbjct: 112 DKYAAALEHHH 122

>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 = 61.2 bits (149), Expect = 8e-13
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
            V +   ++QLKE+I     +    +   LI+AGKIL D  +L++  + +   + +++ 
Sbjct: 36 FSVTDTCTIQQLKEEISQRFKAH--PDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIK 93

Query: 81 KPKPT 85
          +    
Sbjct: 94 RQHRA 98

>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 = 59.0 bits (143), Expect = 6e-12
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 29  VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAP 88
           V  +K ++ + +G       Q+  ++G+ L+D     E  I +   + V++S+P   P P
Sbjct: 46  VFHMKRRLHAAEG--VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQNPTP 103

>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 = 59.1 bits (143), Expect = 1e-11
 Identities = 5/59 (8%), Positives = 18/59 (30%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
            V+E   V       +  + ++   E +          + +  S  +  + +  + + 
Sbjct: 15 EVVEEFTPVVLATPIPEEVQQAQ--TEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVA 71

>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 = 56.5 bits (137), Expect = 2e-11
 Identities = 15/60 (25%), Positives = 39/60 (65%), Gaps = 4/60 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          +D++    V+++KE+++ ++G     + Q+LIY+GK ++D++  ++Y I     + ++L+
Sbjct: 15 IDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLA 72

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 56.9 bits (138), Expect = 2e-11
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
            V  +  VK+ KE I +       +E Q+LIY G++L DD+ L EYN+   
Sbjct: 32 FIVGAQMNVKEFKEHIAASVS--IPSEKQRLIYQGRVLQDDKKLQEYNVGGK 81

>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 = 56.2 bits (136), Expect = 5e-11
 Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVVMLSKPKPTPA 87
          V++ K++I         A+   LI+ GKIL D   LS+  I D S   VV+ S   P+  
Sbjct: 39 VRRFKKQISKYLHCN--ADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSGPSSG 96

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

 Score = 55.0 bits (133), Expect = 9e-11
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          L V E+  V  LK+ +  +         Q+L++ GK L+D + LS+Y+I  +  + +++
Sbjct: 22 LQVPEDELVSTLKQLVSEKLN--VPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVV 78

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

 Score = 55.5 bits (134), Expect = 9e-11
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 23  LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVVML 79
             V E   V+Q KE+I     S    +   LI+AGKIL D   LS++ I D     +V+ 
Sbjct: 39  FAVPENSSVQQFKEEISKRFKSH--TDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIK 96

Query: 80  SKPKP 84
           ++ +P
Sbjct: 97  TQNRP 101

>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 = 53.5 bits (129), Expect = 4e-10
 Identities = 15/60 (25%), Positives = 39/60 (65%), Gaps = 4/60 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          +D++    V+++KE+++ ++G     + Q+LIY+GK ++D++  ++Y I     + ++L+
Sbjct: 15 IDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLA 72

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

 Score = 52.4 bits (126), Expect = 9e-10
 Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI     + ++L
Sbjct: 18 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLL 74

>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 = 51.5 bits (124), Expect = 2e-09
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK 81
          +     VK LK ++Q       L   QKLI+ GK+L +   L + ++     +++M S+
Sbjct: 28 VSPDCTVKDLKSQLQPITN--VLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMASQ 84

>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 = 51.5 bits (123), Expect = 3e-09
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 8   ISDITQNQWQQTVSHLDV--QEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QAL 64
           +  + ++  + T S L V    E+   +   + E G    AE  +++Y  ++L+DD  +L
Sbjct: 12  VYCVRRDLTEVTFS-LQVNPDFELSNFRVLCELESGVP--AEEAQIVYMEQLLTDDHCSL 68

Query: 65  SEYNIDESKFIVVMLSKPKPTPAPYSGPSDPT 96
             Y + +   +V++         P   PS P+
Sbjct: 69  GSYGLKDGDMVVLLQKDNVGLRTPGRTPSGPS 100

>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 = 50.5 bits (121), Expect = 5e-09
 Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 19 TVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DES 72
          T+  +  +  +++L+E++ +        E Q+L Y GK L +   L +Y++    
Sbjct: 22 TIEDVSRKATIEELRERVWALFDVR--PECQRLFYRGKQLENGYTLFDYDVGLND 74

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

 Score = 50.5 bits (121), Expect = 6e-09
 Identities = 15/59 (25%), Positives = 38/59 (64%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          +D++    V+++KE+++ ++G     + Q+LIY+GK ++D++  ++Y I     + ++L
Sbjct: 27 IDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVL 83

>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 = 50.0 bits (120), Expect = 7e-09
 Identities = 11/60 (18%), Positives = 30/60 (50%), Gaps = 4/60 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          ++V  +  + QLKE +  +      A+  ++I+AGK L +   +   ++++   + ++  
Sbjct: 15 VEVDSDTSILQLKEVVAKQ--QGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQR 72

>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 = 50.4 bits (120), Expect = 7e-09
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 17 QQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFI 75
           + ++    ++ V  LK K    + S+      KLIY G++L D  + LS  NI  +  I
Sbjct: 18 TEELAVARPEDTVGTLKSKYFPGQESQ-----MKLIYQGRLLQDPARTLSSLNITNNCVI 72

Query: 76 VVMLSKPKPTPAPYSGPSDPT 96
              S P    +  S  S P+
Sbjct: 73 HCHRSPPGAAVSGPSASSGPS 93

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

 Score = 49.9 bits (119), Expect = 1e-08
 Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 12 TQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEY 67
           Q    QT+S   +   V +LK  + +   S+ L + Q+L+Y+G++L D   L + 
Sbjct: 32 NQKYSDQTIS-CFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDI 86

>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 = 49.3 bits (118), Expect = 1e-08
 Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L
Sbjct: 18 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLL 74

>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 = 49.4 bits (118), Expect = 1e-08
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 10/83 (12%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML- 79
          L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L 
Sbjct: 16 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 73

Query: 80 -----SKPKPTPAPYSGPSDPTQ 97
                  +        P    Q
Sbjct: 74 LRGYADLREDPDRQDHHPGSGAQ 96

>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 = 48.9 bits (117), Expect = 2e-08
 Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
            +     +  LK++I+ +       + Q+L + G++L D   L  Y I +S  +++   
Sbjct: 22 YAINPNSFILGLKQQIEDQ--QGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKK 79

Query: 81 KPKPTPA 87
          K     +
Sbjct: 80 KGSGPSS 86

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

 Score = 48.9 bits (117), Expect = 2e-08
 Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          ++++    ++ LK KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L
Sbjct: 24 VEMEPSDTIENLKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 80

>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 = 48.5 bits (116), Expect = 3e-08
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 19 TVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM 78
          TV  L    +V++L+ KIQ     E     Q+L Y GK + D   L +Y +  +  I ++
Sbjct: 17 TVDSLSRLTKVEELRRKIQELFHVE--PGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLL 74

Query: 79 L 79
          +
Sbjct: 75 V 75

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

 Score = 48.5 bits (115), Expect = 6e-08
 Identities = 13/78 (16%), Positives = 25/78 (32%), Gaps = 6/78 (7%)

Query: 29  VKQLKEKIQSEKGSEY------LAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
              + + +      ++           +LIY G+ L  +  L    +   K  V+ L   
Sbjct: 40  ASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 99

Query: 83  KPTPAPYSGPSDPTQPAG 100
           +  P P S      +  G
Sbjct: 100 ETLPEPNSQGQRNREKTG 117

>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 = 48.5 bits (115), Expect = 6e-08
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 4/69 (5%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          L+V+    +  +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L 
Sbjct: 15 LEVESSDTIDNVKSKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

Query: 81 KPKPTPAPY 89
                 P 
Sbjct: 73 LRGGIIEPS 81

>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 = 47.9 bits (114), Expect = 7e-08
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 19  TVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM 78
            ++   + E V  LKEKI  E      A  QKL      L D+ +L+ YN+   + + + 
Sbjct: 44  EITVQSLSENVGSLKEKIAGEIQ--IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLS 101

Query: 79  L 79
           L
Sbjct: 102 L 102

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score = 47.5 bits (113), Expect = 7e-08
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)

Query: 23 LDV--QEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE 71
           +V  QE V Q+K  + S +G     E Q ++ AG  L D+  L +  ++ 
Sbjct: 32 FEVTGQETVAQIKAHVASLEG--IAPEDQVVLLAGAPLEDEATLGQCGVEA 80

>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 = 46.9 bits (112), Expect = 7e-08
 Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI     + ++L
Sbjct: 15 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVL 71

>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 = 1e-07
 Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 29  VKQLKEKIQSEKG-SEYLAEYQKLIYAGKILSDDQALSEYNIDESKFI-VVMLSKPKPTP 86
           +  LK+ I  +   S    E   LIY G+ L DDQ L  Y I     + V+  S   P+ 
Sbjct: 47  ISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKSWSGPSS 106

Query: 87  A 87
            
Sbjct: 107 G 107

>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 = 46.7 bits (111), Expect = 1e-07
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK 81
           + +     +LK+KI S  G       QK++Y G  + +D+ L E  +     I+V+ S 
Sbjct: 32 KVPLDSTGSELKQKIHSITG--LPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGST 88

Query: 82 PKPTPA 87
               +
Sbjct: 89 ISGPSS 94

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

 Score = 46.7 bits (111), Expect = 2e-07
 Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L
Sbjct: 15 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score = 46.8 bits (111), Expect = 2e-07
 Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 4/59 (6%)

Query: 23  LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
           L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L
Sbjct: 50  LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 106

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          L+V+    +  +K KIQ ++G     + Q+LI+AGK L D + LS+YNI     + ++L
Sbjct: 24 LEVESSDTIDNVKSKIQDKEG--IPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVL 80

>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 = 46.0 bits (109), Expect = 3e-07
 Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 3/74 (4%)

Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
          L+  E     K ++ +  G       QK++  G  L DD       +     +++M S  
Sbjct: 24 LNTDEPPMVFKAQLFALTG--VQPARQKVMVKGGTLKDDD-WGNIKMKNGMTVLMMGSAD 80

Query: 83 KPTPAPYSGPSDPT 96
               P +  S P+
Sbjct: 81 ALPEEPSAKTSGPS 94

>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 = 46.3 bits (110), Expect = 4e-07
 Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE 71
           L + ++V  +K KI    G    A  QKL Y G  + D  +L+ YN+  
Sbjct: 51 TLPLTDQVSVIKVKIHEATG--MPAGKQKLQYEGIFIKDSNSLAYYNMAS 98

>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 = 44.7 bits (106), Expect = 8e-07
 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
           +V+    V  LK+++   +      +   L + GK L D   L EY +     + + L
Sbjct: 19 YEVRLTQTVAHLKQQVSGLE--GVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNL 75

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

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
           +V+    V  LK+++          +   L + GK L D   L EY +     + + L
Sbjct: 19 YEVRLTQTVAHLKQQVSGL--EGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNL 75

>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 = 45.4 bits (107), Expect = 1e-06
 Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 4/86 (4%)

Query: 23  LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
           L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L 
Sbjct: 15  LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

Query: 81  KPKPTPAPYSGPSDPTQPAGQESEAT 106
                       +  T     E   T
Sbjct: 73  LRGGMQIFVKTLTGKTITLEVEPSDT 98

>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 = 40.8 bits (95), Expect = 5e-05
 Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 10  DITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
            +     +     ++  + ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI
Sbjct: 80  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNI 137

Query: 70  DESKFIVVML 79
            +   + ++L
Sbjct: 138 QKESTLHLVL 147

>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 = 44.6 bits (105), Expect = 3e-06
 Identities = 14/78 (17%), Positives = 25/78 (32%), Gaps = 4/78 (5%)

Query: 1   MGMLAHDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSD 60
                  I          T   + + + V  LK+++   +      +   L + GK L D
Sbjct: 77  KSDEPLSILVRNNKGRSSTY-EVRLTQTVAHLKQQVSGLE--GVQDDLFWLTFEGKPLED 133

Query: 61  DQALSEYNI-DESKFIVV 77
              L EY +   S   + 
Sbjct: 134 QLPLGEYGLKPLSTVFMN 151

>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 = 43.4 bits (102), Expect = 7e-06
 Identities = 18/111 (16%), Positives = 35/111 (31%), Gaps = 13/111 (11%)

Query: 1   MGMLAHDISDITQNQWQQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIY--AGK 56
           MG       D+T          + +     V +LK +I  + G    A  Q+L    +G 
Sbjct: 1   MGW------DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG--VHAFQQRLAVHPSGV 52

Query: 57  ILSDDQALSEYNIDESKFIVVMLSKPKPTPAPY-SGPSDPTQPAGQESEAT 106
            L D   L+   +     +++++ K     +         +         T
Sbjct: 53  ALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQT 103

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

 Score = 44.7 bits (105), Expect = 4e-06
 Identities = 7/49 (14%), Positives = 20/49 (40%), Gaps = 4/49 (8%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
            +++   V  LK +I  +    +  +   L+  G I  + + +++   
Sbjct: 15 YTLEQGTSVLDLKSQISQDM--GFEIDMMTLVNNGFIAPNTELVTDDVT 61

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 44.3 bits (104), Expect = 5e-06
 Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 4/86 (4%)

Query: 23  LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
           L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L 
Sbjct: 35  LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 92

Query: 81  KPKPTPAPYSGPSDPTQPAGQESEAT 106
                       +  T     E   T
Sbjct: 93  LRGGMQIFVKTLTGKTITLEVEPSDT 118

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 11  ITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI- 69
           +     +     ++  + ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI 
Sbjct: 101 VKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQ 158

Query: 70  DES 72
            ES
Sbjct: 159 KES 161

>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 = 42.4 bits (99), Expect = 8e-06
 Identities = 12/68 (17%), Positives = 23/68 (33%), Gaps = 6/68 (8%)

Query: 29  VKQLKEKIQSEKGSEY------LAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
              + + +      ++           +LIY G+ L  +  L    +   K  V+ L   
Sbjct: 39  ASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 98

Query: 83  KPTPAPYS 90
           +  P P S
Sbjct: 99  ETLPEPNS 106

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 43.8 bits (103), Expect = 8e-06
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 6   HDISDITQNQWQQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQA 63
           H    I           L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + 
Sbjct: 103 HYGGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRT 160

Query: 64  LSEYNIDESKFIVVML 79
           LS+YNI +   + ++L
Sbjct: 161 LSDYNIQKESTLHLVL 176

>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 = 44.4 bits (104), Expect = 8e-06
 Identities = 18/48 (37%), Positives = 31/48 (64%), Gaps = 2/48 (4%)

Query: 22  HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
            ++  + ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI
Sbjct: 249 EVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNI 294

>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 = 40.3 bits (94), Expect = 9e-05
 Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 3/51 (5%)

Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVVM 78
          +  +K KIQ ++G     + Q+LI+AGK L D + LS+YNI  ES   +V+
Sbjct: 23 IDNVKSKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	203
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	100.0
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.85
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.83
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.82
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.82
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.82
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	99.82
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.81
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	99.81
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.81
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.8
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.79
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.79
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.79
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.79
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.79
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.79
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.78
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.78
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.78
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.78
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.78
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.77
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.77
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.77
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.77
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.77
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.77
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.77
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.77
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.77
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.76
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.76
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.76
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.76
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.76
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.76
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.76
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.76
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.75
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.75
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.75
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.75
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.74
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.74
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.74
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.73
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.73
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.73
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.73
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.73
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.72
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.72
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	99.72
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.72
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.72
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.55
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.71
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.7
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.7
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.7
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.7
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.69
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.69
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.69
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.69
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.69
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.68
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.68
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.67
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.67
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.66
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.64
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.64
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.63
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.63
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.62
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.61
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.6
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.6
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.57
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.57
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.57
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.57
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.56
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.56
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.53
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.51
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.5
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.44
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.44
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.43
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.39
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.36
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.32
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	99.31
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.3
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.24
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.23
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	98.97
2pjh_A	80	Protein NPL4, nuclear protein localization protein	98.72
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.71
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	98.67
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	98.64
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	98.46
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	98.34
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.21
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	98.11
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	98.02
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	97.98
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	97.94
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	97.92
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	97.91
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	97.83
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.81
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	97.68
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	97.43
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	97.2
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	97.03
2lnm_A	62	Protein TIC 40, chloroplastic; translocon, import,	96.55
2llw_A	71	Heat shock protein STI1; DP domain, alpha helix, c	96.44
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	96.19
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	95.4
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	95.22
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	95.14
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	95.06
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	94.72
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	94.72
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	94.45
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	94.42
2llv_A	71	Heat shock protein STI1; DP domain, alpha helix, c	94.23
2llw_A	71	Heat shock protein STI1; DP domain, alpha helix, c	93.03
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	92.4
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	92.3
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	92.1
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	92.06
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	91.86
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	91.7
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	91.5
3onh_A	127	Ubiquitin-activating enzyme E1-like; ligase, SUMO	90.02
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	89.02
2lnm_A	62	Protein TIC 40, chloroplastic; translocon, import,	88.78
1wgy_A	104	RAP guanine nucleotide exchange factor 5; ubiquiti	88.49
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	87.17
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	87.07
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	85.69
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	85.62
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	85.58
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	84.52
2k9x_A	110	Tburm1, uncharacterized protein; unknown function;	84.14
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	84.03
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	83.65
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	83.33
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	83.27
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	82.92
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	82.11
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	81.71
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	81.55
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	80.9
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	80.49
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	80.21

>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=4e-40  Score=288.94  Aligned_cols=186  Identities=44%  Similarity=0.690  Sum_probs=146.7

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHh---hhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQS---EKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~---~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ..|+|+||+.+|++|. +|++++||.+||++|+.   +.|  +++++|||||+||+|+|+++|++|+|++|++|++++.|
T Consensus         6 ~~M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~g--ip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k   83 (368)
T 1oqy_A            6 SAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDA--FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTK   83 (368)
T ss_dssp             CCCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSS--CCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEEC
T ss_pred             ceEEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCC--CChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEec
Confidence            4699999999999999 99999999999999999   566  99999999999999999999999999999999667666


Q ss_pred             CCCCCC-CC--C-----CC----------C-CCCCC-C-C-------------CCCC--C--------C------CC---
Q psy4259          82 PKPTPA-PY--S-----GP----------S-DPTQP-A-G-------------QESE--A--------T------RP---  108 (203)
Q Consensus        82 ~~~~~~-p~--~-----~~----------~-~p~~~-p-~-------------~~~~--~--------~------~~---  108 (203)
                      .+..++ ++  +     ++          + .|+++ + +             +.++  +        .      .+   
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~s~l~  163 (368)
T 1oqy_A           84 TKAGQGTSAPPEASPTAAPESSTSFPPAPTSGMSHPPPAAREDKSPSEESAPTTSPESVSGSVPSSGSSGREEDAASTLV  163 (368)
T ss_dssp             CCSSSCCCCCSSCCCCCSSSCCCSCCCSSSCCCCCCCSSSSCCCCCSCSCCCCSSTTCSCCCSCSCCCSCCCCCCCTTTC
T ss_pred             CCCCCCCCCCcccCCCCCccccCCCCCCCCCCCCCCCccccccCCccccCCCCCCCCccccccccccccccccccccccc
Confidence            543211 10  0     00          0 00000 0 0             0000  0        0      01   


Q ss_pred             ----chhhHHHHHhCCcCCC-----------CCC--------------------------------CCCCCChHHHhhCC
Q psy4259         109 ----ATATSDSMLKVFFERV-----------NPY--------------------------------GGESEDPLAFLRTQ  141 (203)
Q Consensus       109 ----~~~~v~~~~~mG~~~~-----------np~--------------------------------~~~~~~pl~~l~~~  141 (203)
                          .++.|++|++|||+|+           |+.                                ++...+++++||++
T Consensus       164 ~g~~~~~~i~~l~~MGf~~~~~~~AL~a~~nn~~~A~e~L~~gip~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~Lr~~  243 (368)
T 1oqy_A          164 TGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLRDQ  243 (368)
T ss_dssp             CTTTHHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTTTTSSTTCSSCCCCCCCCCCSSCCCCSSCCSCCTTHHHHHS
T ss_pred             CCcchHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCcccccccCCccccccccccCccccccchHHHHhcC
Confidence                1578999999999998           331                                01234679999999


Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHHcCCccc
Q psy4259         142 PQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAG  193 (203)
Q Consensus       142 P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml~~p~~~  193 (203)
                      |+|++||++|++||++|++|||+|+++||+|+++|++||++|++||++|.++
T Consensus       244 pqf~~lR~~vq~nP~~l~~~lq~l~~~nP~l~~~I~~n~~~Fl~~l~e~~~~  295 (368)
T 1oqy_A          244 PQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQMLNEPPGE  295 (368)
T ss_dssp             HHHHHHHHSTTTCTTHHHHHHTTTTTTCHHHHHHHHHHHHHHHHHHHSCCCC
T ss_pred             hHHHHHHHHHHhChHHHHHHHHHHHhhCHHHHHHHHHCHHHHHHHHcCcccc
Confidence            9999999999999999999999999999999999999999999999998653

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

Probab=99.85  E-value=2.8e-21  Score=141.66  Aligned_cols=77  Identities=27%  Similarity=0.395  Sum_probs=69.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCCCCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTP   86 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~~~~   86 (203)
                      |+|+||+++|+.|. +|++++||.+||++|+..+|  +|+++|||+|+||.|+|+++|++|||++|++|+++++++++++
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~~~~~   79 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSIS--CEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQKKSTK   79 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTT--SCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC-----
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--CChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCCCCCC
Confidence            78999999999999 99999999999999999999  9999999999999999999999999999999999998876544

>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=99.83  E-value=1.9e-20  Score=132.75  Aligned_cols=78  Identities=32%  Similarity=0.477  Sum_probs=72.0

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      +..|+|+||+.+|+++. +|++++||.+||++|+..++  +++++|||+|+||.|+|+++|++|+| +|++||++++.+.
T Consensus         3 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g--ip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~~   79 (90)
T 4dwf_A            3 PDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS--IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAPP   79 (90)
T ss_dssp             CCEEEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCCC
T ss_pred             CcEEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhC--CCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCCC
Confidence            45799999999999999 99999999999999999999  99999999999999999999999999 8999999887655


Q ss_pred             CC
Q psy4259          84 PT   85 (203)
Q Consensus        84 ~~   85 (203)
                      .+
T Consensus        80 ~~   81 (90)
T 4dwf_A           80 QT   81 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.82  E-value=2.3e-20  Score=135.06  Aligned_cols=78  Identities=22%  Similarity=0.285  Sum_probs=70.1

Q ss_pred             CCCcceEEEEEeCCCCeee---ecCCCCcHHHHHHHH-HhhhCCCCCCCceEEEeCCeecCCCCCcccccc-CCCCEEEE
Q psy4259           3 MLAHDISDITQNQWQQTVS---HLDVQEEVKQLKEKI-QSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVV   77 (203)
Q Consensus         3 ~~~~~m~I~Vk~~~g~~~~---~v~~~~TV~~LK~~I-~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI-~~~~~i~v   77 (203)
                      +.+..|+|+||++.|++|.   +|++++||.+||++| +...|  +|+++|||||+||.|+|+.+|++|+| ++|++|++
T Consensus        15 ~~~~~m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~g--ip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~l   92 (98)
T 4a20_A           15 MDNAAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKA--SHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITV   92 (98)
T ss_dssp             ---CCEEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSC--SCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEE
T ss_pred             CCCCCEEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcC--CChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEE
Confidence            3456899999999999877   456999999999999 88888  99999999999999999999999999 99999999


Q ss_pred             EeecC
Q psy4259          78 MLSKP   82 (203)
Q Consensus        78 ~~~k~   82 (203)
                      ++++|
T Consensus        93 mvskp   97 (98)
T 4a20_A           93 MIKPN   97 (98)
T ss_dssp             EECCC
T ss_pred             EEeCC
Confidence            99875

>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=99.82  E-value=7.9e-20  Score=131.19  Aligned_cols=77  Identities=52%  Similarity=0.736  Sum_probs=72.2

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhh---hCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSE---KGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~---~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      |+|+||+..|+.+. +|++++||.+||++|+..   .|  +|+++|||+|+||.|+|+++|++|||++|++|+++++++.
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~g--ip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~~~   78 (95)
T 1uel_A            1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDA--FPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPK   78 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTT--CCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCC--CChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeCCC
Confidence            79999999999999 999999999999999999   67  9999999999999999999999999999999999998776


Q ss_pred             CCC
Q psy4259          84 PTP   86 (203)
Q Consensus        84 ~~~   86 (203)
                      +.+
T Consensus        79 ~~~   81 (95)
T 1uel_A           79 AVS   81 (95)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            443

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

Probab=99.82  E-value=5.9e-20  Score=127.01  Aligned_cols=74  Identities=20%  Similarity=0.344  Sum_probs=70.9

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +.+|+|+||+.+|+++. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+++|++|+|++|++|+++++
T Consensus         2 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g--ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~r   76 (79)
T 3phx_B            2 DEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG--VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLR   76 (79)
T ss_dssp             -CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             CCCEEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcC--CCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEe
Confidence            45799999999999999 99999999999999999999  9999999999999999999999999999999999875

>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=99.82  E-value=5e-21  Score=129.65  Aligned_cols=63  Identities=63%  Similarity=1.020  Sum_probs=60.2

Q ss_pred             CChHHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHHcCCcccc
Q psy4259         132 EDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAGD  194 (203)
Q Consensus       132 ~~pl~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml~~p~~~~  194 (203)
                      .+++++|+++|+|++||++|++||++|+++|++|+++||+|+++|++||++|++||++|.+++
T Consensus         3 ~~~l~~Lr~~Pqf~qlR~~vqqNP~lL~~lLqqL~~~NPqL~q~I~~n~e~Fl~ll~e~~~~~   65 (72)
T 1pve_A            3 HMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEA   65 (72)
T ss_dssp             TCTTGGGTTCTTTTTHHHHHTTCGGGHHHHHHHHHTTCHHHHHHHHTTHHHHHHHHHSCSCCG
T ss_pred             CchHHHHHcChHHHHHHHHHHHCHHHHHHHHHHHHhHCHHHHHHHHHCHHHHHHHHcCCccCC
Confidence            567899999999999999999999999999999999999999999999999999999998765

>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=99.81  E-value=1.3e-19  Score=126.85  Aligned_cols=77  Identities=45%  Similarity=0.656  Sum_probs=70.3

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhh---hCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSE---KGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~---~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +..|+|+||+.+|+.+. +|++++||.+||++|+..   .|  +|+++|||+|+|+.|+|+++|++|||++|++||++++
T Consensus         3 ~~~m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~g--ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~   80 (85)
T 2wyq_A            3 PMAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDA--FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT   80 (85)
T ss_dssp             -CCEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTT--CCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC
T ss_pred             CceEEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccC--CCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEc
Confidence            35799999999999999 999999999999999998   67  9999999999999999999999999999999999987


Q ss_pred             cCC
Q psy4259          81 KPK   83 (203)
Q Consensus        81 k~~   83 (203)
                      +++
T Consensus        81 ~~~   83 (85)
T 2wyq_A           81 KTK   83 (85)
T ss_dssp             ---
T ss_pred             CCC
Confidence            765

>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=99.81  E-value=6.8e-20  Score=120.53  Aligned_cols=59  Identities=68%  Similarity=1.113  Sum_probs=56.9

Q ss_pred             ChHHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHHcCCc
Q psy4259         133 DPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV  191 (203)
Q Consensus       133 ~pl~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml~~p~  191 (203)
                      +++++|+++|+|++||++|++||++|+++|++|+++||+|+++|++||++|++||++|.
T Consensus         2 ~~l~~Lr~~Pqf~~lR~~vq~NP~~L~~lLqql~~~nP~l~~~I~~n~e~Fl~ll~e~~   60 (61)
T 2f4m_B            2 HPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV   60 (61)
T ss_dssp             CGGGGGTTCHHHHHHHHHHHHCGGGHHHHHHHHHHHCHHHHHHHHHSHHHHHHHHTSCC
T ss_pred             chHHHHHcChHHHHHHHHHHHCHHHHHHHHHHHHhHCHHHHHHHHHCHHHHHHHHcccC
Confidence            56899999999999999999999999999999999999999999999999999999885

>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=99.81  E-value=1.3e-19  Score=129.18  Aligned_cols=73  Identities=16%  Similarity=0.274  Sum_probs=69.3

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      ++.|+|+||+..|+++. +|++++||++||++|+++.|  +|+++|||+|+|++|+|+.||++|+|++|++|++..
T Consensus        19 ~~mIqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~G--ip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~~   92 (93)
T 3plu_A           19 SHMIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIG--TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   92 (93)
T ss_dssp             -CEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEE
T ss_pred             CceEEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhC--CCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEEe
Confidence            35699999999999999 99999999999999999999  999999999999999999999999999999999853

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

Probab=99.80  E-value=3.4e-19  Score=126.71  Aligned_cols=74  Identities=26%  Similarity=0.469  Sum_probs=71.0

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      ...|+|+||+.+|+.+. +|++++||.+||++|+..+|  +|+++|||+|+|+.|+|+++|++|||++|++|+++++
T Consensus        15 ~~~m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r   89 (91)
T 3v6c_B           15 RGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR   89 (91)
T ss_dssp             CCSEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC--CCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECC
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhC--CChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEe
Confidence            34799999999999999 99999999999999999999  9999999999999999999999999999999999875

>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=4.2e-19  Score=125.64  Aligned_cols=74  Identities=19%  Similarity=0.417  Sum_probs=70.6

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      |+|+||+++|++|. +|++++||.+||++|+..+|  +|+++|||+|+|+.|+|+++|++|+|++|++|+++++-+.
T Consensus         1 M~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl~G   75 (88)
T 4fbj_B            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRG   75 (88)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBCC-
T ss_pred             CEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHC--cChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEECCC
Confidence            78999999999999 99999999999999999999  9999999999999999999999999999999999987654

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

Probab=99.79  E-value=2.3e-19  Score=126.16  Aligned_cols=73  Identities=19%  Similarity=0.260  Sum_probs=70.0

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCee-cCCCCCccccccCCCCEEEEEee
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKI-LSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~-L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +-|+|+||++.|+.+. +|++++||.+||++|+...|  +|+++|||+|+|+. |+|+++|++|+|++|++|+++++
T Consensus         9 ~~~~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            9 SHMKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQH--IPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVS   83 (84)
T ss_dssp             CCEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHT--CCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEEC
T ss_pred             CceEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHC--cChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEc
Confidence            3599999999999999 99999999999999999999  99999999999999 99999999999999999999864

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=1.3e-19  Score=128.32  Aligned_cols=73  Identities=23%  Similarity=0.311  Sum_probs=68.3

Q ss_pred             eEEEEEeCCCCeee-ecC--CCCcHHHHHHHH-HhhhCCCCCCCceEEEeCCeecCCCCCcccccc-CCCCEEEEEeecC
Q psy4259           8 ISDITQNQWQQTVS-HLD--VQEEVKQLKEKI-QSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVVMLSKP   82 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~--~~~TV~~LK~~I-~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI-~~~~~i~v~~~k~   82 (203)
                      |+|+||+.+|++|. +|+  +++||.+||++| +...|  +|+++|||||+||+|+|+.+|++|+| .+|++|+|++++.
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~g--ip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~~   79 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKA--SHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPN   79 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSC--SSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECCC
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcC--CChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCCC
Confidence            89999999999998 755  999999999999 99999  99999999999999999999999999 6999999998653

>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=99.79  E-value=3.6e-19  Score=130.32  Aligned_cols=78  Identities=15%  Similarity=0.276  Sum_probs=73.5

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKP   84 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~~   84 (203)
                      ..|+|+||+..|+.+. +|++++||.+||.+|+...|  +++++|||+|+|+.|+|+++|++|||++|++|||+++++..
T Consensus        22 ~~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           22 YECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG--VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQ   99 (106)
T ss_dssp             CSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTC--CCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSSC
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHC--cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            3599999999999999 99999999999999999999  99999999999999999999999999999999999887665


Q ss_pred             C
Q psy4259          85 T   85 (203)
Q Consensus        85 ~   85 (203)
                      .
T Consensus       100 ~  100 (106)
T 1ttn_A          100 N  100 (106)
T ss_dssp             C
T ss_pred             C
Confidence            3

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.79  E-value=4.6e-19  Score=125.03  Aligned_cols=73  Identities=32%  Similarity=0.469  Sum_probs=69.3

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +..|+|+||+.+|+.+. +|++++||.+||++|+..+|  +|+++|||+|+||.|+|+++|++||| +|++||++.+
T Consensus        15 ~~~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           15 PDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVS--IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVER   88 (88)
T ss_dssp             CCEEEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEEC
T ss_pred             CCeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhC--CCHHHEEEEECCEECCCCCcHHHcCC-CCcEEEEEEC
Confidence            45699999999999999 99999999999999999999  99999999999999999999999999 8999998864

>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=99.79  E-value=8.8e-19  Score=120.68  Aligned_cols=73  Identities=21%  Similarity=0.289  Sum_probs=69.5

Q ss_pred             ceEEEEEeCCCCee-e-e-cCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           7 DISDITQNQWQQTV-S-H-LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~-~-~-v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      .|+|+||+..|+.+ . + |++++||.+||++|+...|  +|+++|||+|+|+.|+|+++|++|||++|++||++++.
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            69999999999985 7 8 9999999999999999999  99999999999999999999999999999999998764

>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=99.78  E-value=7.5e-19  Score=123.55  Aligned_cols=75  Identities=19%  Similarity=0.413  Sum_probs=71.3

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ...|+|+||+.+|+.+. +|++++||.+||++|+..++  +|+++|||+|+|+.|+|+++|++|+|+++++|+++++-
T Consensus        10 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g--ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl   85 (88)
T 3dbh_I           10 GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRL   85 (88)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC--CCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCC
T ss_pred             CCcEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHC--cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            34699999999999999 99999999999999999999  99999999999999999999999999999999998764

>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=99.78  E-value=1.3e-18  Score=124.64  Aligned_cols=76  Identities=25%  Similarity=0.258  Sum_probs=69.6

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCC-CCccccccCCCCEEEEEeecC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~-~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ...|+|+||+..|+.+. +|++++||.+||++|+...     +++|||+|+||.|+|+ ++|++|+|++|++|||+++++
T Consensus         5 ~~~m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~-----~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~   79 (95)
T 1wia_A            5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ-----ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPP   79 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST-----TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCC
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC-----cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCC
Confidence            34699999999999999 9999999999999998875     7899999999999999 999999999999999998876


Q ss_pred             CCC
Q psy4259          83 KPT   85 (203)
Q Consensus        83 ~~~   85 (203)
                      ..+
T Consensus        80 ~~~   82 (95)
T 1wia_A           80 GAA   82 (95)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.78  E-value=1.4e-18  Score=124.28  Aligned_cols=74  Identities=27%  Similarity=0.481  Sum_probs=71.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      |+|+||+.+|+.+. +|++++||.+||++|+..++  +|+++|||+|+|+.|+|+++|++|+|++|++|+++++-..
T Consensus         2 m~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~g--ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~~g   76 (96)
T 3k9o_B            2 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   76 (96)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC
T ss_pred             cEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhC--CChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCC
Confidence            89999999999999 99999999999999999999  9999999999999999999999999999999999987654

>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=3.9e-19  Score=128.72  Aligned_cols=71  Identities=17%  Similarity=0.225  Sum_probs=68.4

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      .|+|+||++.|+++. +|++++||.+||++|+++.|  +|+++|||||.||+|+|+.||++|+|+++++|++..
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            499999999999999 99999999999999999999  999999999999999999999999999999999864

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

Probab=99.78  E-value=1.1e-18  Score=120.80  Aligned_cols=75  Identities=20%  Similarity=0.314  Sum_probs=71.0

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      +..|+|+||+.+|+.+. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+++|++|||++|++|+++++.
T Consensus         5 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~--i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A            5 SSGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLN--VPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             SSSEEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTC--CCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            45799999999999999 99999999999999999999  99999999999999999999999999999999998753

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.77  E-value=9.7e-19  Score=126.16  Aligned_cols=75  Identities=27%  Similarity=0.480  Sum_probs=71.0

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ..|+|+||+++|+.|. +|++++||.+||++|+..++  +|+++|||+|+||.|+|+++|++|+|++|++|+++++-.
T Consensus        21 ~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl~   96 (98)
T 4hcn_B           21 RPMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   96 (98)
T ss_dssp             -CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCS
T ss_pred             CeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhC--CChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            4699999999999999 99999999999999999999  999999999999999999999999999999999987643

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.77  E-value=1.9e-18  Score=126.35  Aligned_cols=76  Identities=21%  Similarity=0.302  Sum_probs=70.3

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKP   84 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~~   84 (203)
                      ..|+|+||+..|+ +. +|++++||.+||++|+..++  +++++|||+|+||.|+|+++|++|+|++|++|||+++.+..
T Consensus        16 ~~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           16 HLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK--AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   92 (106)
T ss_dssp             SEEEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHT--CCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCCCC
T ss_pred             ceEEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHC--cChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCCC
Confidence            4599999998886 78 99999999999999999999  99999999999999999999999999999999999876543

>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=99.77  E-value=1.2e-18  Score=121.69  Aligned_cols=76  Identities=26%  Similarity=0.478  Sum_probs=70.5

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      ++|+|+||+.+|+.+. +|++++||.+||++|++.++  +|+++|||+|+|+.|+|+++|++|+|+++++|+++++-..
T Consensus         2 s~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~--ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~G   78 (85)
T 3n3k_B            2 SHMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRG   78 (85)
T ss_dssp             --CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC-
T ss_pred             CeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--CCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccC
Confidence            4799999999999999 99999999999999999999  9999999999999999999999999999999999986543

>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=99.77  E-value=1.4e-18  Score=126.26  Aligned_cols=78  Identities=18%  Similarity=0.300  Sum_probs=70.2

Q ss_pred             CcceEEEEEeCCC----Ceee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCC-CCccccccCCCCEEEEE
Q psy4259           5 AHDISDITQNQWQ----QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFIVVM   78 (203)
Q Consensus         5 ~~~m~I~Vk~~~g----~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~-~tL~~~gI~~~~~i~v~   78 (203)
                      +..|+|+||+..+    +.|. +|++++||.+||++|+..+|  +++++|||+|+||.|+|+ ++|++|+|++|++|||+
T Consensus         5 ~~~m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~g--ip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~   82 (102)
T 1v5o_A            5 SSGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG--VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLL   82 (102)
T ss_dssp             SCCEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTC--CCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEEC
T ss_pred             CCeEEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHC--cChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEE
Confidence            3469999999754    6888 99999999999999999999  999999999999999988 79999999999999998


Q ss_pred             eecCCC
Q psy4259          79 LSKPKP   84 (203)
Q Consensus        79 ~~k~~~   84 (203)
                      .+.+..
T Consensus        83 ~~~~gg   88 (102)
T 1v5o_A           83 QKDNVG   88 (102)
T ss_dssp             BCCCCC
T ss_pred             ECCCCC
Confidence            766543

>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=99.77  E-value=2.1e-18  Score=117.61  Aligned_cols=72  Identities=19%  Similarity=0.438  Sum_probs=69.3

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+.+|+.+. +|++++||.+||++|+...+  +|+++|+|+|+|+.|+|+++|++|||++|++|+++++.
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~--i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~   73 (76)
T 1ndd_A            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL   73 (76)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             CEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHC--cChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            78999999999999 99999999999999999999  99999999999999999999999999999999998764

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.77  E-value=8.1e-19  Score=124.12  Aligned_cols=76  Identities=20%  Similarity=0.318  Sum_probs=70.5

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      ..|+|+||+..|+.+. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+++|++|+|++|++|+++++...
T Consensus         3 ~~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            3 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG--VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG   79 (88)
T ss_dssp             CEEEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTC--SCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC---
T ss_pred             ccEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhC--CChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCC
Confidence            4799999999999999 99999999999999999999  9999999999999999999999999999999999886543

>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=99.77  E-value=1.9e-18  Score=120.45  Aligned_cols=75  Identities=27%  Similarity=0.479  Sum_probs=71.1

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ++|+|+||+.+|+.+. +|++++||.+||++|++.++  +|+++|||+|+|+.|+|+++|++|+|+++++|+++++-.
T Consensus         2 s~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~--i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~   77 (85)
T 3mtn_B            2 SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLR   77 (85)
T ss_dssp             -CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC--CCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCC
T ss_pred             CeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHC--cChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECc
Confidence            4799999999999999 99999999999999999999  999999999999999999999999999999999987654

>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=99.77  E-value=1.5e-18  Score=124.92  Aligned_cols=75  Identities=17%  Similarity=0.209  Sum_probs=69.0

Q ss_pred             CcceEEEEEeCCCCee-e-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           5 AHDISDITQNQWQQTV-S-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~-~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ...|+|+|| +.|+.| . +|++++||.+||++|+..+|  +|+++|||+|+||.|+|+ +|++|+|++|++|+++++..
T Consensus         5 ~~~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            5 SSGYSVTVK-WGKEKFEGVELNTDEPPMVFKAQLFALTG--VQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             CCEEEEEEE-ETTEEEEEEEEESSSCHHHHHHHHHHHTC--CCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCC
T ss_pred             CcEEEEEEE-ECCEEEEEEEECCCCcHHHHHHHHHHHHC--cCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecch
Confidence            356999999 578999 7 99999999999999999999  999999999999999999 99999999999999987655


Q ss_pred             C
Q psy4259          83 K   83 (203)
Q Consensus        83 ~   83 (203)
                      .
T Consensus        81 ~   81 (96)
T 1wgg_A           81 A   81 (96)
T ss_dssp             C
T ss_pred             h
Confidence            3

>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=99.77  E-value=1.6e-18  Score=125.65  Aligned_cols=79  Identities=20%  Similarity=0.267  Sum_probs=72.6

Q ss_pred             CCCCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           2 GMLAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         2 ~~~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      ...+..|+|+||+..|+ +. +|++++||.+||++|+...|  +|+++|||+|+||.|+|+++|++|+|++|++|+|+++
T Consensus        17 ~~~~~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r   93 (100)
T 1yqb_A           17 RGSPHLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFK--AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIK   93 (100)
T ss_dssp             SCCTTEEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEEC
T ss_pred             CCCCCeEEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHC--cChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEc
Confidence            34566799999999886 78 99999999999999999999  9999999999999999999999999999999999887


Q ss_pred             cCC
Q psy4259          81 KPK   83 (203)
Q Consensus        81 k~~   83 (203)
                      .+.
T Consensus        94 ~~~   96 (100)
T 1yqb_A           94 RQH   96 (100)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.76  E-value=1.8e-18  Score=123.49  Aligned_cols=76  Identities=21%  Similarity=0.275  Sum_probs=69.4

Q ss_pred             cceEEEEEeCCCC--eee-ecCCCCcHHHHHHHHHhhh--CCCCCCCceEEEeCCeecCCCCCcccc--ccCCCCEEEEE
Q psy4259           6 HDISDITQNQWQQ--TVS-HLDVQEEVKQLKEKIQSEK--GSEYLAEYQKLIYAGKILSDDQALSEY--NIDESKFIVVM   78 (203)
Q Consensus         6 ~~m~I~Vk~~~g~--~~~-~v~~~~TV~~LK~~I~~~~--~~~ip~~~qkLi~~Gk~L~D~~tL~~~--gI~~~~~i~v~   78 (203)
                      ..|+|+||+.+++  .+. +|++++||.+||++|+..+  +  +++++|||||+||.|+|+++|++|  +|+++++||++
T Consensus         6 ~~m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~--i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv   83 (93)
T 1wgd_A            6 SGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPER--PRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLV   83 (93)
T ss_dssp             CCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTC--CCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEE
T ss_pred             cEEEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCC--CChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEE
Confidence            4699999999988  566 7779999999999999998  8  999999999999999999999999  99999999998


Q ss_pred             eecCC
Q psy4259          79 LSKPK   83 (203)
Q Consensus        79 ~~k~~   83 (203)
                      ++.+.
T Consensus        84 ~~~~g   88 (93)
T 1wgd_A           84 CNVKS   88 (93)
T ss_dssp             CCCCC
T ss_pred             eCCCC
Confidence            76544

>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=99.76  E-value=3.5e-18  Score=116.47  Aligned_cols=72  Identities=28%  Similarity=0.499  Sum_probs=69.2

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+.+|+.+. +|++++||.+||++|+..++  +|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++.
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~--i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~   73 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRL   73 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHC--cCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            78999999999999 99999999999999999999  99999999999999999999999999999999998764

>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=99.76  E-value=2.6e-18  Score=120.72  Aligned_cols=78  Identities=21%  Similarity=0.297  Sum_probs=73.0

Q ss_pred             CCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           4 LAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      .+..|+|+||+.+|+.+. +|++++||.+||++|+...+  +|+++|+|+|+|+.|+|+++|++|+|+++++|+++++..
T Consensus         4 ~~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g--i~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~   81 (87)
T 1wh3_A            4 GSSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG--LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKG   81 (87)
T ss_dssp             CSSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTC--CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSC
T ss_pred             CCCCEEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhC--CChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEecc
Confidence            456799999999999999 99999999999999999999  999999999999999999999999999999999988654


Q ss_pred             C
Q psy4259          83 K   83 (203)
Q Consensus        83 ~   83 (203)
                      .
T Consensus        82 G   82 (87)
T 1wh3_A           82 S   82 (87)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.76  E-value=3.5e-18  Score=117.07  Aligned_cols=71  Identities=30%  Similarity=0.446  Sum_probs=67.5

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      .|+|+||+ .|+.+. +|++++||.+||++|+...|  +|+++|+|+|+|+.|+|+++|++|||++|++|+++.+
T Consensus         4 ~m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~--i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~   75 (77)
T 2bwf_A            4 SLNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANG--IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   75 (77)
T ss_dssp             EEEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhC--CCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEc
Confidence            38999999 899999 99999999999999999999  9999999999999999999999999999999998764

>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=99.76  E-value=1.5e-18  Score=125.62  Aligned_cols=73  Identities=16%  Similarity=0.123  Sum_probs=65.2

Q ss_pred             EEEEEeCC----CCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           9 SDITQNQW----QQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         9 ~I~Vk~~~----g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      .|.|+..+    ++++. +|++++||.+||++|+.+.|  +|+++|||||+||+|+|++||++|+|++|++|+|++.+..
T Consensus        17 ti~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~g--ip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti~vl~lrg~   94 (100)
T 1wju_A           17 TIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG--LQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELKQS   94 (100)
T ss_dssp             EEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTT--CCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECCCCC
T ss_pred             EEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHC--cCHHHeEEEeCCeECCCCCcHHHcCCCCCCEEEEEEECCC
Confidence            45566665    77899 99999999999999999999  9999999999999999999999999999999977765543

>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=99.76  E-value=2.6e-18  Score=125.91  Aligned_cols=80  Identities=25%  Similarity=0.240  Sum_probs=72.0

Q ss_pred             CCCCcceEEEEEeCCC---Ceee-ec--------CC-CCcHHHHHHHHHhhh--CCCCCCCc-eEEEeCCeecCCCCCcc
Q psy4259           2 GMLAHDISDITQNQWQ---QTVS-HL--------DV-QEEVKQLKEKIQSEK--GSEYLAEY-QKLIYAGKILSDDQALS   65 (203)
Q Consensus         2 ~~~~~~m~I~Vk~~~g---~~~~-~v--------~~-~~TV~~LK~~I~~~~--~~~ip~~~-qkLi~~Gk~L~D~~tL~   65 (203)
                      +|....|+|+||+.++   ++|. +|        ++ ++||.+||++|+...  +  +++++ |||||+||.|+|+++|+
T Consensus         7 ~~~~~~~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~g--ip~~~~qrLi~~Gk~L~D~~tL~   84 (107)
T 1x1m_A            7 GMSLSDWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQES--VPDPELIDLIYCGRKLKDDQTLD   84 (107)
T ss_dssp             CCCCCSCCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTT--CCCSSSEEEEETTEECCTTCBHH
T ss_pred             CccCCceEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccC--CChhhcEEEEECCeECCCCCcHH
Confidence            5677789999999998   7888 84        44 499999999999999  8  99999 99999999999999999


Q ss_pred             ccccCCCCEEEEEeecCC
Q psy4259          66 EYNIDESKFIVVMLSKPK   83 (203)
Q Consensus        66 ~~gI~~~~~i~v~~~k~~   83 (203)
                      +|+|++|++||++++.+.
T Consensus        85 ~y~i~~g~~i~lv~~~~~  102 (107)
T 1x1m_A           85 FYGIQPGSTVHVLRKSWS  102 (107)
T ss_dssp             HHTCCTTCEEEEEESSCC
T ss_pred             HcCCCCCCEEEEEeCCCC
Confidence            999999999999886543

>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=4.2e-18  Score=120.22  Aligned_cols=77  Identities=17%  Similarity=0.286  Sum_probs=71.6

Q ss_pred             CcceEEEEEeCCC-Ceee-e-cCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           5 AHDISDITQNQWQ-QTVS-H-LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         5 ~~~m~I~Vk~~~g-~~~~-~-v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      +..|+|+||+..| +.+. + |++++||.+||++|+...+  +|+++|||+|+|+.|+|+++|++|+|+++++||++++.
T Consensus         5 ~~~m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~g--ip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   82 (89)
T 1wy8_A            5 SSGMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD--VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   82 (89)
T ss_dssp             SSCEEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSC--CCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             CCcEEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHC--cChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeC
Confidence            3579999999999 6888 7 9999999999999999999  99999999999999999999999999999999998865


Q ss_pred             CC
Q psy4259          82 PK   83 (203)
Q Consensus        82 ~~   83 (203)
                      ..
T Consensus        83 ~g   84 (89)
T 1wy8_A           83 DS   84 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.76  E-value=4e-18  Score=120.57  Aligned_cols=74  Identities=28%  Similarity=0.485  Sum_probs=68.7

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      .|+|+||+++|+.+. +|++++||.+||++|++..+  +|+++|||+|+|+.|+|+++|++|+|++|++|+++++..
T Consensus         9 ~~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r~~   83 (88)
T 1sif_A            9 GLQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   83 (88)
T ss_dssp             -CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHC--CCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC---
T ss_pred             ceEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHC--cChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            589999999999999 99999999999999999999  999999999999999999999999999999999987644

>2uyz_B Small ubiquitin-related modifier 1; sumoylation, cell division, nuclear protein, ubiquitin-like modifier, UBL conjugation pathway; 1.4A {Homo sapiens} SCOP: d.15.1.1 PDB: 2vrr_B 2iy0_B 2iy1_B 2g4d_B 2las_A 2io2_B 1z5s_B 3uip_B* 1tgz_B* 2bf8_B

Probab=99.75  E-value=2.2e-18  Score=119.06  Aligned_cols=75  Identities=17%  Similarity=0.285  Sum_probs=71.3

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      +.|+|+||+.+|+.+. +|++++||.+||++|+.+.|  +|+++|||+|+|+.|+|++||++|+|++|++|+++++..
T Consensus         2 ~~m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~g--i~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~   77 (79)
T 2uyz_B            2 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG--VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQT   77 (79)
T ss_dssp             CEEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT--CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCC
T ss_pred             CeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHC--CCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEecc
Confidence            3699999999999999 99999999999999999999  999999999999999999999999999999999987643

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

Probab=99.75  E-value=6.9e-18  Score=122.50  Aligned_cols=76  Identities=21%  Similarity=0.306  Sum_probs=70.9

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      +..|+|+||+. |+.+. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+++|++|||++|++|+|+++.+.
T Consensus        23 ~~~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           23 PKIMKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFK--SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQN   99 (101)
T ss_dssp             CCCEEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHT--CCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCSS
T ss_pred             CCeEEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHC--cChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCC
Confidence            35799999998 88899 99999999999999999999  9999999999999999999999999999999999886543

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

Probab=99.75  E-value=5.9e-18  Score=127.48  Aligned_cols=76  Identities=21%  Similarity=0.292  Sum_probs=69.8

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      +..|+|+||+. |+.+. +|++++||.+||++|+..++  +++++|||+|+||.|+|+++|++|+|++|++|+|+++...
T Consensus        30 ~~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~g  106 (125)
T 1j8c_A           30 PKIIKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFK--SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDP  106 (125)
T ss_dssp             CCCEEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHC--SCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC---
T ss_pred             CCcEEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHC--cCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            45799999998 89999 99999999999999999999  9999999999999999999999999999999999887654

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

Probab=99.75  E-value=4.8e-18  Score=121.80  Aligned_cols=76  Identities=30%  Similarity=0.374  Sum_probs=71.0

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCC-CCccccccCCCCEEEEEeecC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~-~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ...|+|+||+..| ++. +|++++||.+||++|+...|  +|+++|||+|+||.|+|+ ++|++|+|++|++|+|+++.+
T Consensus        13 ~~~~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~   89 (94)
T 2kan_A           13 VRKIHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVEN--TPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSI   89 (94)
T ss_dssp             SCCEEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSS--SCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCC
T ss_pred             CCCEEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHC--cCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCC
Confidence            4579999999888 888 99999999999999999999  999999999999999999 999999999999999988765


Q ss_pred             C
Q psy4259          83 K   83 (203)
Q Consensus        83 ~   83 (203)
                      .
T Consensus        90 g   90 (94)
T 2kan_A           90 N   90 (94)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=5.6e-18  Score=122.01  Aligned_cols=75  Identities=17%  Similarity=0.285  Sum_probs=71.3

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ..|+|+||+.+|+.+. +|.+++||.+||++|+.+.|  +|+++|||+|+|+.|+|++||++|+|++|++|+++++..
T Consensus        20 ~~m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~g--ip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~~   95 (97)
T 1wyw_B           20 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG--VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQT   95 (97)
T ss_dssp             CEEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT--CCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSS
T ss_pred             CcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--CChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecC
Confidence            3599999999999999 99999999999999999999  999999999999999999999999999999999988643

>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=99.74  E-value=3.2e-18  Score=122.71  Aligned_cols=75  Identities=24%  Similarity=0.286  Sum_probs=70.4

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      ..|+|+||+. |+.+. +|++++||.+||++|+...+  +++++|||+|+|+.|+|+++|++|+|++|++||++++...
T Consensus        16 ~~m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~g--ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~   91 (96)
T 1wx8_A           16 RIIRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLH--CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHS   91 (96)
T ss_dssp             CEEEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTC--SCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSS
T ss_pred             CcEEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhC--CCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCC
Confidence            4699999998 89999 99999999999999999999  9999999999999999999999999999999999876554

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.2e-17  Score=123.34  Aligned_cols=78  Identities=18%  Similarity=0.242  Sum_probs=70.8

Q ss_pred             CcceEEEEE-eCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           5 AHDISDITQ-NQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         5 ~~~m~I~Vk-~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      .+.+.|+|+ ...+..++ +++++.||++||++++...+  +|+++|+|||+||+|+|+.||++|||++|++||++++..
T Consensus        13 ~~~itvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~--iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~   90 (118)
T 2daf_A           13 DSLATVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLG--IPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFST   90 (118)
T ss_dssp             SSCEEEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHT--CCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEES
T ss_pred             CccEEEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhC--CChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecC
Confidence            446888887 55688899 99999999999999999999  999999999999999999999999999999999998775


Q ss_pred             CC
Q psy4259          83 KP   84 (203)
Q Consensus        83 ~~   84 (203)
                      .+
T Consensus        91 ~p   92 (118)
T 2daf_A           91 NP   92 (118)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=1.2e-17  Score=123.12  Aligned_cols=73  Identities=27%  Similarity=0.495  Sum_probs=70.6

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      .|+|+||+++|+.|. +|++++||.+||.+|+..++  +|+++|||+|+||.|+|+++|++|+|+++++|+++++-
T Consensus        35 ~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl  108 (111)
T 3vdz_A           35 AMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  108 (111)
T ss_dssp             CEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECC
T ss_pred             cEEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhC--CChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEec
Confidence            699999999999999 99999999999999999999  99999999999999999999999999999999998864

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

Probab=99.73  E-value=1.7e-17  Score=119.42  Aligned_cols=74  Identities=27%  Similarity=0.481  Sum_probs=70.5

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      |+|+||+.+|+.+. +|++++||.+||++|+...|  +|+++|+|+|+|+.|+|+++|++|||++|++|+++++...
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~g--i~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~g   75 (98)
T 1yx5_B            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (98)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTC--CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCC
Confidence            79999999999999 99999999999999999999  9999999999999999999999999999999999887653

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.73  E-value=4.2e-18  Score=123.69  Aligned_cols=72  Identities=29%  Similarity=0.447  Sum_probs=67.4

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      .|+|+||+ .|+.+. +|++++||.+||++|+..+|  +|+++|||+|+|+.|+|+++|++|||++|++|+++++.
T Consensus        28 ~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           28 SLNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANG--IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ  100 (101)
T ss_dssp             -CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHS--CCSTTCCEEETTEECCTTSBTTTTTCCTTEEEEECCCC
T ss_pred             EEEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHC--cChHHEEEEECCEECCCcCcHHHCCCCCCCEEEEEeCC
Confidence            47888997 889999 99999999999999999999  99999999999999999999999999999999998764

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.73  E-value=2.1e-17  Score=121.77  Aligned_cols=77  Identities=26%  Similarity=0.440  Sum_probs=72.2

Q ss_pred             CCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           4 LAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ....|+|+||+.+|+.+. +|++++||.+||++|+...+  +++++|||+|+||.|+|+++|++|+|++|++|+++++-.
T Consensus        32 ~~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~qrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~  109 (111)
T 2ojr_A           32 ELLAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  109 (111)
T ss_dssp             GSSCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHC--CCTTTEEEEETTEECCSSCBTTTTTCCTTCEEEEEECCC
T ss_pred             CCCeEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHC--cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            345799999999999999 99999999999999999999  999999999999999999999999999999999987643

>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=99.73  E-value=3.4e-17  Score=121.66  Aligned_cols=78  Identities=13%  Similarity=0.153  Sum_probs=66.4

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCC----C--CCCceEEEeCCeecCCCCCccccccCCCC--EE
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSE----Y--LAEYQKLIYAGKILSDDQALSEYNIDESK--FI   75 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~----i--p~~~qkLi~~Gk~L~D~~tL~~~gI~~~~--~i   75 (203)
                      .+.|.|+||++.|++++ +|++++||.+||++|+..++.+    +  ++++|||||+||+|+|+.||++|+|+.++  +|
T Consensus        14 ~~~m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tl   93 (116)
T 1wgh_A           14 ADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVM   93 (116)
T ss_dssp             SSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEE
T ss_pred             CCeEEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEE
Confidence            35699999999999999 9999999999999999954321    3  69999999999999999999999998775  56


Q ss_pred             EEEeecC
Q psy4259          76 VVMLSKP   82 (203)
Q Consensus        76 ~v~~~k~   82 (203)
                      |++++-.
T Consensus        94 hLvlr~~  100 (116)
T 1wgh_A           94 HLVARET  100 (116)
T ss_dssp             EEEECSS
T ss_pred             EEEccCC
Confidence            6665443

>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=99.72  E-value=4.2e-18  Score=124.45  Aligned_cols=77  Identities=17%  Similarity=0.148  Sum_probs=69.2

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCC---------------CceEEEeCCeecC-CCCCcccc
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLA---------------EYQKLIYAGKILS-DDQALSEY   67 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~---------------~~qkLi~~Gk~L~-D~~tL~~~   67 (203)
                      ...|+|+||+++|++|. +|++++||.+||++|+.+.+  +++               ++|+|||+||.|. |++||++|
T Consensus         5 ~~~M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~--i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dy   82 (105)
T 1v2y_A            5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ--LKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDY   82 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHH--HHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHH
T ss_pred             CCcEEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhC--CCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHc
Confidence            34699999999999999 99999999999999999998  777               4579999999997 56999999


Q ss_pred             ccCCCCEEEEEeecCC
Q psy4259          68 NIDESKFIVVMLSKPK   83 (203)
Q Consensus        68 gI~~~~~i~v~~~k~~   83 (203)
                      ||++|++|||+.+-+.
T Consensus        83 gI~~g~~l~lv~~lr~   98 (105)
T 1v2y_A           83 GIRNRDEVSFIKKLGQ   98 (105)
T ss_dssp             TCCSSEEEEEEECSCS
T ss_pred             CCCCCCEEEEEehhcc
Confidence            9999999999876543

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.72  E-value=1e-17  Score=119.69  Aligned_cols=73  Identities=22%  Similarity=0.264  Sum_probs=67.1

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ...|+|+||+  |+.+. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+++|++|+|++|++|+++++-
T Consensus        17 ~~~m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl   90 (93)
T 2l7r_A           17 RGSMQLFVRA--QELHTFEVTGQETVAQIKAHVASLEG--IAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRM   90 (93)
T ss_dssp             ---CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHT--CCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCC
T ss_pred             CCcEEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhC--cChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEec
Confidence            4569999997  88999 99999999999999999999  99999999999999999999999999999999998754

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

Probab=99.72  E-value=6.6e-18  Score=122.31  Aligned_cols=74  Identities=22%  Similarity=0.329  Sum_probs=64.0

Q ss_pred             CCcceEEEEEeCCCC--eee-ecCCCCcHHHHHHHHHhhh-CCCCCCCceEEEeCCeecCCCCCcccc--ccCCCCEEEE
Q psy4259           4 LAHDISDITQNQWQQ--TVS-HLDVQEEVKQLKEKIQSEK-GSEYLAEYQKLIYAGKILSDDQALSEY--NIDESKFIVV   77 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~--~~~-~v~~~~TV~~LK~~I~~~~-~~~ip~~~qkLi~~Gk~L~D~~tL~~~--gI~~~~~i~v   77 (203)
                      ....|+|+||+.+|+  .+. +|++++||.+||++|+.++ |. +++++|||||+||+|+|+++|++|  +|+++++|++
T Consensus        20 ~~~~m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~-pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~tihL   98 (99)
T 2kdb_A           20 QGHPVTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSK-PLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHL   98 (99)
T ss_dssp             ---CEEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTC-CCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEEEE
T ss_pred             CCCeEEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCC-CChhhEEEEECCEECCCCCCHHHHhcCCCCCCEEEe
Confidence            345799999999998  567 9999999999999999975 41 456999999999999999999999  9999999997


Q ss_pred             E
Q psy4259          78 M   78 (203)
Q Consensus        78 ~   78 (203)
                      +
T Consensus        99 v   99 (99)
T 2kdb_A           99 V   99 (99)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.72  E-value=2.7e-17  Score=116.99  Aligned_cols=76  Identities=21%  Similarity=0.346  Sum_probs=68.4

Q ss_pred             CcceEEEEEeCCCCeee-ecCCC-----CcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCC-CCCccccccCCCCEEEE
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQ-----EEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSD-DQALSEYNIDESKFIVV   77 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~-----~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D-~~tL~~~gI~~~~~i~v   77 (203)
                      +..|+|+||+ .|+.+. +|+++     +||.+||++|+..+|  +|+++|||+|+||.|+| +++|++|+|++|++|||
T Consensus         5 ~~~~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~g--ip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l   81 (92)
T 1wxv_A            5 SSGLTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIG--VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVML   81 (92)
T ss_dssp             CSSEEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTC--CCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEE
T ss_pred             CCeEEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHC--cCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEE
Confidence            3469999997 588889 99985     999999999999999  99999999999999998 56899999999999999


Q ss_pred             EeecCC
Q psy4259          78 MLSKPK   83 (203)
Q Consensus        78 ~~~k~~   83 (203)
                      +.+++.
T Consensus        82 ~~~~~~   87 (92)
T 1wxv_A           82 IGKKNS   87 (92)
T ss_dssp             ESCCSC
T ss_pred             EecCCC
Confidence            876544

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A

Probab=99.55  E-value=5.3e-19  Score=121.13  Aligned_cols=72  Identities=17%  Similarity=0.321  Sum_probs=69.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+.+|+.+. +|++++||.+||++|+...|  +|+++|+|+|+|+.|+|+++|++|||++|++|+++++-
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g--i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rl   73 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQG--VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRP   73 (76)
Confidence            78999999999999 99999999999999999999  99999999999999999999999999999999998754

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

Probab=99.71  E-value=3.4e-17  Score=123.22  Aligned_cols=77  Identities=12%  Similarity=0.144  Sum_probs=65.7

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCC----C--CCCceEEEeCCeecCCCCCccccccCCCC--EEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSE----Y--LAEYQKLIYAGKILSDDQALSEYNIDESK--FIV   76 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~----i--p~~~qkLi~~Gk~L~D~~tL~~~gI~~~~--~i~   76 (203)
                      ..|.|+||+..|++++ +|++++||.+||++|+..++.+    +  ++++|||||+||+|+|++||++|+|+.++  +||
T Consensus        16 ~~m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tlh   95 (125)
T 2gow_A           16 DMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMH   95 (125)
T ss_dssp             TCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEEE
T ss_pred             CeEEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEE
Confidence            4599999999999999 9999999999999999944311    5  58999999999999999999999999887  456


Q ss_pred             EEeecC
Q psy4259          77 VMLSKP   82 (203)
Q Consensus        77 v~~~k~   82 (203)
                      ++++-.
T Consensus        96 lv~r~~  101 (125)
T 2gow_A           96 LVARET  101 (125)
T ss_dssp             EEECSC
T ss_pred             EEecCC
Confidence            655443

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.70  E-value=6.9e-17  Score=127.57  Aligned_cols=74  Identities=27%  Similarity=0.482  Sum_probs=71.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      |+|+||+.+|+.+. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+++|++|+|++|++||++++-..
T Consensus         1 MqI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl~G   75 (169)
T 3l0w_B            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (169)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC--CCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCCC
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHC--cCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEecc
Confidence            79999999999999 99999999999999999999  9999999999999999999999999999999999987554

>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=99.70  E-value=7.7e-17  Score=125.30  Aligned_cols=76  Identities=20%  Similarity=0.322  Sum_probs=72.5

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      +..|+|+||+.+|+++. +|++++||.+||++|+...|  +|+++|+|+|+|+.|+|+.+|++|+|++|++||++++-.
T Consensus        79 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g--ip~~~q~L~~~G~~L~d~~tL~~y~i~~g~~l~l~~rl~  155 (159)
T 3rt3_B           79 DEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG--VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLR  155 (159)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHC--CCHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecC
Confidence            56799999999999999 99999999999999999999  999999999999999999999999999999999998654

>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=99.70  E-value=2.4e-17  Score=118.36  Aligned_cols=74  Identities=22%  Similarity=0.249  Sum_probs=67.0

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ...|+|+|| +.++.|. +|++++||.+||++|+..++  +|+++|||+|+||.| |+.+|++|+|+++++|||+.++.
T Consensus        15 ~~~~~i~Vk-~~g~~~~i~v~~~~TV~~LK~~I~~~tg--ip~~~QrL~~~Gk~L-dd~tL~~~~i~~g~~i~lv~~~~   89 (95)
T 1v86_A           15 KELVDLKII-WNKTKHDVKVPLDSTGSELKQKIHSITG--LPPAMQKVMYKGLVP-EDKTLREIKVTSGAKIMVVGSTI   89 (95)
T ss_dssp             CCCEEEEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHC--SCSTTCCCBSSSBCC-SSSBHHHHCCCTTEEEEECCSSC
T ss_pred             CceEEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHHC--cCHHHeEEEECCeeC-CcCcHHHCCCCCCCEEEEEeccc
Confidence            456899999 5788899 99999999999999999999  999999999999999 55699999999999999886553

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.70  E-value=1.2e-16  Score=118.35  Aligned_cols=75  Identities=27%  Similarity=0.476  Sum_probs=71.6

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      +.+|+||++.|+.+. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+++|++|+|++|++|+++++...
T Consensus         9 ~~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~G   84 (114)
T 2kdi_A            9 EFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEG--IPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRG   84 (114)
T ss_dssp             CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCS
T ss_pred             cEEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHC--cChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCC
Confidence            689999999999999 99999999999999999999  9999999999999999999999999999999999886654

>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=99.69  E-value=4.4e-17  Score=120.85  Aligned_cols=72  Identities=14%  Similarity=0.158  Sum_probs=65.8

Q ss_pred             eEEEEEeCCCC-eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCC-------CCEEEEE
Q psy4259           8 ISDITQNQWQQ-TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE-------SKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~-~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~-------~~~i~v~   78 (203)
                      |.|+|+...++ ++. +|++++||.+||++|+.+.|  +|+++|||||+||.|+|++||++|||++       +++||++
T Consensus         1 m~vFl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~g--iPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~Lv   78 (118)
T 4ajy_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK--RPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLA   78 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEEE
T ss_pred             CceEEEEecCCEEEEEEcCCCChHHHHHHHHHHHHC--CCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEEE
Confidence            45666666666 677 99999999999999999999  9999999999999999999999999999       9999999


Q ss_pred             eec
Q psy4259          79 LSK   81 (203)
Q Consensus        79 ~~k   81 (203)
                      ++.
T Consensus        79 lr~   81 (118)
T 4ajy_B           79 FRA   81 (118)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            876

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.69  E-value=7.4e-17  Score=113.44  Aligned_cols=69  Identities=25%  Similarity=0.376  Sum_probs=64.3

Q ss_pred             EEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259          10 DITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus        10 I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +.++++.|+.+. +|++++||.+||++|+...|  +|+++|||+|+||.|+|+++|++|||++|++|+|+++
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            445668899999 99999999999999999999  9999999999999999999999999999999998864

>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=99.69  E-value=1.1e-16  Score=117.98  Aligned_cols=77  Identities=25%  Similarity=0.264  Sum_probs=71.7

Q ss_pred             CcceEEEEEeC---CCCeee-ecCC-CCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           5 AHDISDITQNQ---WQQTVS-HLDV-QEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         5 ~~~m~I~Vk~~---~g~~~~-~v~~-~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      +..|+|+|++.   .|+.+. +|++ ++||.+||++|+..+|  +|+++|||+|+|+.|+|+++|++|+|++|++|+|++
T Consensus        25 ~~~i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~g--ip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~  102 (111)
T 1we6_A           25 PGPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQ--IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSL  102 (111)
T ss_dssp             CSCEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTT--CCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEEC
T ss_pred             CCcEEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHC--CCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEE
Confidence            34699999998   889999 9998 9999999999999999  999999999999999999999999999999999998


Q ss_pred             ecCC
Q psy4259          80 SKPK   83 (203)
Q Consensus        80 ~k~~   83 (203)
                      +...
T Consensus       103 r~~G  106 (111)
T 1we6_A          103 RERS  106 (111)
T ss_dssp             SSCC
T ss_pred             EcCC
Confidence            6543

>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=99.69  E-value=9.7e-17  Score=120.55  Aligned_cols=78  Identities=23%  Similarity=0.249  Sum_probs=66.5

Q ss_pred             CcceEEEEEeCCCCee-e-ecCCCCcHHHHHHHHHhhhCCC---CCC--CceEEEeCCeecCCCCCccccccCCC-----
Q psy4259           5 AHDISDITQNQWQQTV-S-HLDVQEEVKQLKEKIQSEKGSE---YLA--EYQKLIYAGKILSDDQALSEYNIDES-----   72 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~-~-~v~~~~TV~~LK~~I~~~~~~~---ip~--~~qkLi~~Gk~L~D~~tL~~~gI~~~-----   72 (203)
                      .+.|+|+||+.+|+.| . ++++++||.+||++|+..++.+   +|+  ++|||||+||+|+|++||++|+|..+     
T Consensus        14 ~~~~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~~~~~~~   93 (126)
T 1se9_A           14 HNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGA   93 (126)
T ss_dssp             CCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTC
T ss_pred             cccEEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcHHHcCCCcCCccCC
Confidence            3579999999999999 5 9999999999999997655311   775  79999999999999999999999998     


Q ss_pred             -CEEEEEeecC
Q psy4259          73 -KFIVVMLSKP   82 (203)
Q Consensus        73 -~~i~v~~~k~   82 (203)
                       .++|++++-+
T Consensus        94 v~tmhlVlrl~  104 (126)
T 1se9_A           94 VTTMHVIIQAP  104 (126)
T ss_dssp             CEEEEEEECCC
T ss_pred             cEEEEEEeccC
Confidence             4677776544

>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=99.69  E-value=9.5e-17  Score=114.00  Aligned_cols=75  Identities=25%  Similarity=0.305  Sum_probs=68.4

Q ss_pred             CcceEEEEEeCCCCeee--ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE---eCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           5 AHDISDITQNQWQQTVS--HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI---YAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~--~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi---~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      +..|+|+||. .|+.|.  +|++++||.+||++|++.+|  +|+++|||+   |+|+.|+|+.+|++|+|++|++|+++.
T Consensus         5 ~~~m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~g--ip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~   81 (90)
T 1v5t_A            5 SSGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTG--VLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMG   81 (90)
T ss_dssp             CCSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTC--CCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEEC
T ss_pred             CceEEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHC--cCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEe
Confidence            4569999995 777775  88999999999999999999  999999999   999999999999999999999999987


Q ss_pred             ecC
Q psy4259          80 SKP   82 (203)
Q Consensus        80 ~k~   82 (203)
                      +..
T Consensus        82 ~~~   84 (90)
T 1v5t_A           82 TRE   84 (90)
T ss_dssp             CCS
T ss_pred             cCc
Confidence            543

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A

Probab=99.68  E-value=4.2e-17  Score=121.22  Aligned_cols=71  Identities=15%  Similarity=0.165  Sum_probs=63.8

Q ss_pred             eEEEEEeCCCC-eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccC-------CCCEEEEE
Q psy4259           8 ISDITQNQWQQ-TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNID-------ESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~-~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~-------~~~~i~v~   78 (203)
                      |.++|+...++ ++. +|++++||.+||++|+.+.|  +|+++|||||+||.|+|++||++|||+       .+++||++
T Consensus         1 M~mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~eg--IP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L~   78 (118)
T 2fnj_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK--RPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLA   78 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEE
T ss_pred             CcEEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhC--CCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEEE
Confidence            44555555565 578 99999999999999999999  999999999999999999999999999       69999999


Q ss_pred             ee
Q psy4259          79 LS   80 (203)
Q Consensus        79 ~~   80 (203)
                      ++
T Consensus        79 lr   80 (118)
T 2fnj_B           79 FR   80 (118)
T ss_dssp             EB
T ss_pred             ec
Confidence            87

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.68  E-value=2e-16  Score=124.75  Aligned_cols=76  Identities=26%  Similarity=0.476  Sum_probs=71.8

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      +..|+|+||+++|+++. +|++++||.+||++|+..+|  +|+++|||+|+|+.|+|+.+|++|+|+++++|+++++.+
T Consensus        18 ~~~m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g--ip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~   94 (172)
T 3u30_A           18 GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   94 (172)
T ss_dssp             -CCEEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--cChHHEEEEECCccccccCCHhHcCCcccceeeeeeccc
Confidence            34699999999999999 99999999999999999999  999999999999999999999999999999999998654

>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=2.2e-16  Score=122.71  Aligned_cols=72  Identities=19%  Similarity=0.210  Sum_probs=69.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE-e-CCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI-Y-AGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi-~-~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+++|+.+. +|++++||.+||++|+..+|  +|+++|||+ | +|+.|+|+++|++|+|++|++|+++++.
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            89999999999999 99999999999999999999  999999999 9 7999999999999999999999999874

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.67  E-value=2.8e-16  Score=114.54  Aligned_cols=73  Identities=12%  Similarity=0.168  Sum_probs=67.3

Q ss_pred             ceEEEEEeCCC--Ceee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCcccccc-CCCCEEEEEeec
Q psy4259           7 DISDITQNQWQ--QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g--~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI-~~~~~i~v~~~k   81 (203)
                      .|+|+|++..+  .+++ +|++++||.+||++|++++|  +|+++|||+|+|+.++|++||.+||| .+|+++|+++-.
T Consensus        24 ~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           24 RLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYG--FPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLS  100 (105)
T ss_dssp             EEEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEECC
T ss_pred             EEEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhC--CCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEEe
Confidence            48899999875  5777 99999999999999999999  99999999999999999999999999 599999998754

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.66  E-value=1.8e-16  Score=127.12  Aligned_cols=74  Identities=27%  Similarity=0.455  Sum_probs=71.0

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      .|+|+||+.+|+++. +|++++||.+||++|+...+  +|+++|+|+|+|+.|+|+.+|++|+|+++++|+++++-.
T Consensus       105 eMqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~g--Ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~Lvlrlr  179 (189)
T 3q3f_A          105 GGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  179 (189)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC--CCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCC
T ss_pred             ceeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccC--CCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcC
Confidence            599999999999999 99999999999999999999  999999999999999999999999999999999987654

>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=99.64  E-value=9.6e-16  Score=117.50  Aligned_cols=73  Identities=27%  Similarity=0.492  Sum_probs=69.8

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      |+|+||+.+|+.+. +|++++||.+||++|+..+|  +|+++|+|+|+|+.|+|+.+|++|||++|++|+++.+.+
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g--ip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~   74 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCT
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHC--cChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeecc
Confidence            78999999999999 99999999999999999999  999999999999999999999999999999999987643

>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=99.64  E-value=1.4e-17  Score=125.77  Aligned_cols=74  Identities=27%  Similarity=0.482  Sum_probs=0.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      |+|+||+.+|+++. +|++++||.+||++|+..+|  +|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++...
T Consensus         1 M~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~~rl~G   75 (128)
T 3u5e_m            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (128)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhC--cChHHEEEEECCEECCCCCchhhhccCCCCEEEEEEEcCC
Confidence            78999999999999 99999999999999999999  9999999999999999999999999999999999987654

>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=99.63  E-value=9.3e-16  Score=113.61  Aligned_cols=77  Identities=27%  Similarity=0.339  Sum_probs=70.1

Q ss_pred             CcceEEEEEeCC----------CCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCC
Q psy4259           5 AHDISDITQNQW----------QQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESK   73 (203)
Q Consensus         5 ~~~m~I~Vk~~~----------g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~   73 (203)
                      +..++|+|+..+          |+.+. +|++++||.+||++|+...|  +|+++|||+|+|+.|+|+.+|++|+|++|+
T Consensus        23 ~~~i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~g--ip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~  100 (115)
T 1we7_A           23 KGPVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATG--MPAGKQKLQYEGIFIKDSNSLAYYNMASGA  100 (115)
T ss_dssp             CSCEEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSS--CCTTTEEEEETTEEECTTSBHHHHTCCSSC
T ss_pred             CCCEEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHC--CChHHEEEEECCEECCCCCCHHHCCCCCCC
Confidence            357889999864          67888 99999999999999999999  999999999999999999999999999999


Q ss_pred             EEEEEeecCC
Q psy4259          74 FIVVMLSKPK   83 (203)
Q Consensus        74 ~i~v~~~k~~   83 (203)
                      +||++++-..
T Consensus       101 ~i~lv~rl~G  110 (115)
T 1we7_A          101 VIHLALKERS  110 (115)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEEEcCC
Confidence            9999886543

>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=99.63  E-value=2.1e-15  Score=115.62  Aligned_cols=75  Identities=27%  Similarity=0.473  Sum_probs=71.1

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ..|+|+||+.+|+.+. +|++++||.+||++|+...|  +|+++|+|+|+|+.|+|+++|++|+|++|++|+++++.+
T Consensus        75 ~~~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g--i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~r~~  150 (152)
T 3b08_A           75 GGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  150 (152)
T ss_dssp             TCEEEEEEESSSCEEEEEECTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCC
T ss_pred             cccceeeeecCCCEEEEEeCCCCcHHHHHHHHHHHhC--cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            4589999999999999 99999999999999999999  999999999999999999999999999999999987654

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.62  E-value=1.1e-15  Score=120.40  Aligned_cols=75  Identities=27%  Similarity=0.475  Sum_probs=69.9

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ...|.|+||+.+|+++. +|++++||.+||++|+..+|  +|+++|+|+|+|+.|+|+++|++|+|++|++||++++-
T Consensus        94 ~gg~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g--ip~~~q~L~~~g~~L~D~~tL~~y~i~~g~tl~l~~rl  169 (172)
T 3u30_A           94 RGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  169 (172)
T ss_dssp             CCCEEEEEEESSCCEEEEEECTTCBHHHHHHHHHHHHC--CCGGGCCEEETTEECCTTSBSGGGTCCTTCEEEECC--
T ss_pred             cccccceeecccCcceeEEecCCCCHHHHHHHHHHHhC--CCceeEEEEECCccCCCCCcHHHhCCCCCCEEEEEEec
Confidence            34689999999999999 99999999999999999999  99999999999999999999999999999999998753

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=9.9e-16  Score=108.48  Aligned_cols=69  Identities=12%  Similarity=0.179  Sum_probs=62.9

Q ss_pred             ceEEEEEeCCCCee---e-ecCCCCcHHHHHHHHHhh-hCCCCCCCceEEEeC--CeecCCCCCccccccCCCCEEEE
Q psy4259           7 DISDITQNQWQQTV---S-HLDVQEEVKQLKEKIQSE-KGSEYLAEYQKLIYA--GKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~---~-~v~~~~TV~~LK~~I~~~-~~~~ip~~~qkLi~~--Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      .|+|+||++.|+.+   . +|++++||.+||++|+.. .+  +++++|||+|.  ||+|+|++||++|+|+++++|||
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            39999999998776   3 789999999999999995 67  99999999976  99999999999999999999875

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.60  E-value=1.6e-15  Score=106.93  Aligned_cols=73  Identities=16%  Similarity=0.247  Sum_probs=63.1

Q ss_pred             eEEEEEe--CCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe-------CCeecCCCCCccccccCCCCEEEE
Q psy4259           8 ISDITQN--QWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY-------AGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         8 m~I~Vk~--~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~-------~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      ++|.|..  .+.+.+. .+++++||.+||++|+..+|  +|+++|||||       .|+.|+|+++|++|+|++|++|||
T Consensus         3 V~v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~~G--ip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihl   80 (86)
T 4b6w_A            3 VKVSLTHSASRMRVPEKRYGLAQTIESIKENVFTHFA--TPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHV   80 (86)
T ss_dssp             EEEEEEETTCSCCEEEEEEETTSBHHHHHHHHHTTSC--CCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEE
T ss_pred             EEEEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHHHC--CCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEE
Confidence            4555543  3455667 99999999999999999999  9999999997       489999999999999999999999


Q ss_pred             EeecC
Q psy4259          78 MLSKP   82 (203)
Q Consensus        78 ~~~k~   82 (203)
                      +-+.|
T Consensus        81 vd~~P   85 (86)
T 4b6w_A           81 VDLQP   85 (86)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            87654

>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=99.60  E-value=7.6e-17  Score=125.23  Aligned_cols=73  Identities=27%  Similarity=0.494  Sum_probs=0.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      |+|+||+.+|+++. +|++++||.+||++|+...|  +|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++-.
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~   74 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (152)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhC--CCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeecc
Confidence            78999999999999 99999999999999999999  999999999999999999999999999999999997543

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.57  E-value=5.8e-15  Score=105.97  Aligned_cols=72  Identities=21%  Similarity=0.177  Sum_probs=63.9

Q ss_pred             CcceEEEEEeCCCC--eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC--Ce---ec-CCCCCccccccCCCCEE
Q psy4259           5 AHDISDITQNQWQQ--TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA--GK---IL-SDDQALSEYNIDESKFI   75 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~--~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~--Gk---~L-~D~~tL~~~gI~~~~~i   75 (203)
                      ++.++|+|+...++  .++ +|++++||.+||++|+..+|  +|+++|||+|.  |+   .| +|+++|++|+|++|++|
T Consensus        13 ~~~v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~G--iP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gsti   90 (95)
T 2kjr_A           13 SDFIKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTG--GCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRL   90 (95)
T ss_dssp             CCEEEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHC--SCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEE
T ss_pred             CCeEEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHC--cCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEE
Confidence            45689999987664  677 99999999999999999999  99999999998  55   34 88899999999999999


Q ss_pred             EEE
Q psy4259          76 VVM   78 (203)
Q Consensus        76 ~v~   78 (203)
                      +|+
T Consensus        91 hlv   93 (95)
T 2kjr_A           91 HVV   93 (95)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            985

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.57  E-value=4.8e-15  Score=108.52  Aligned_cols=73  Identities=15%  Similarity=0.089  Sum_probs=65.9

Q ss_pred             cceEEEEEeCCCCeee-ecC-CCCcHHHHHHHHHhhhCCCCCCCceEEEeCCe-----------e----cCCCCCccccc
Q psy4259           6 HDISDITQNQWQQTVS-HLD-VQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGK-----------I----LSDDQALSEYN   68 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~-~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk-----------~----L~D~~tL~~~g   68 (203)
                      ..|.|+||+.+|+. . +|+ +++||.+||++|+..++  +|+++|+|+|.|+           .    ++|+++|++||
T Consensus         6 ~~M~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~g--ip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~g   82 (107)
T 1wf9_A            6 SGTMLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQ--IPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLN   82 (107)
T ss_dssp             CCEEEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSC--CCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTC
T ss_pred             CeEEEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHhC--cCcccCEEEECCccccccCccccccccccCCCCCCHHHCC
Confidence            45999999999966 6 999 99999999999999999  9999999999998           4    57889999999


Q ss_pred             cCCCCEEEEEeec
Q psy4259          69 IDESKFIVVMLSK   81 (203)
Q Consensus        69 I~~~~~i~v~~~k   81 (203)
                      |++|++|||....
T Consensus        83 i~~G~~L~l~~~~   95 (107)
T 1wf9_A           83 LAHGSMVYLAYEG   95 (107)
T ss_dssp             CCTTCEEECCCSS
T ss_pred             CCCCCEEEEEeCC
Confidence            9999999987653

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.57  E-value=7.4e-15  Score=125.65  Aligned_cols=74  Identities=27%  Similarity=0.498  Sum_probs=70.3

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +..|+|+||+..|+.+. +|++++||.+||++|+...|  +|+++|||+|+||.|+|+++|++|+|+++++|+|+++
T Consensus       231 ~~~MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~G--Ip~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlR  305 (307)
T 3ai5_A          231 TGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR  305 (307)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHC--CCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC-
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC--cChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEe
Confidence            45799999999999999 99999999999999999999  9999999999999999999999999999999999875

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=3.6e-15  Score=108.02  Aligned_cols=72  Identities=15%  Similarity=0.201  Sum_probs=65.5

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      +|.++++.+.|+++. +|++++||.+||++|++++|  +|+++|||+|  .|+ |+|+.+|++|+|+.|++||++...
T Consensus         8 ~m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tg--Ipp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~~   82 (100)
T 2dzm_A            8 RMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQ--IPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTPD   82 (100)
T ss_dssp             CEEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHC--CCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCSS
T ss_pred             ceEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHC--CChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEecC
Confidence            588888889999999 99999999999999999999  9999999996  566 999999999999999999987643

>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=99.56  E-value=1.8e-14  Score=103.09  Aligned_cols=75  Identities=17%  Similarity=0.181  Sum_probs=65.0

Q ss_pred             ceEEEEEeCCCC-eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC---ee----cCCCCCccccccCCCCEEEE
Q psy4259           7 DISDITQNQWQQ-TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG---KI----LSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         7 ~m~I~Vk~~~g~-~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G---k~----L~D~~tL~~~gI~~~~~i~v   77 (203)
                      .+.|+|+..... .++ +|++++||.+||++|+..+|  +|+++|||+|.|   +.    ++|+++|++|||.+|++|||
T Consensus         7 ~v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~g--ip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v   84 (95)
T 1v6e_A            7 GVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVG--SPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHV   84 (95)
T ss_dssp             CEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTC--SCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEE
T ss_pred             EEEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHC--CCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEE
Confidence            588999876553 577 99999999999999999999  999999999986   54    58899999999999999998


Q ss_pred             EeecCC
Q psy4259          78 MLSKPK   83 (203)
Q Consensus        78 ~~~k~~   83 (203)
                      +-..|.
T Consensus        85 ~d~~P~   90 (95)
T 1v6e_A           85 IDHSGS   90 (95)
T ss_dssp             BCCSCC
T ss_pred             EECCcc
Confidence            765443

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.56  E-value=1.3e-14  Score=104.45  Aligned_cols=74  Identities=12%  Similarity=0.039  Sum_probs=64.4

Q ss_pred             CcceEEEEEeCCC--Ceee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC---ee----cCCCCCccccccCCCCE
Q psy4259           5 AHDISDITQNQWQ--QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG---KI----LSDDQALSEYNIDESKF   74 (203)
Q Consensus         5 ~~~m~I~Vk~~~g--~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G---k~----L~D~~tL~~~gI~~~~~   74 (203)
                      ++.+.|.|+....  +.++ +|++++||.+||++|+..+|  +|+++|||+|.|   +.    ++|+++|++|+|++|++
T Consensus        12 ~~~v~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~G--ip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~   89 (97)
T 2kj6_A           12 DDSVHLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCG--TSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFR   89 (97)
T ss_dssp             CCCEEEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHC--CCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCE
T ss_pred             CceEEEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHC--cCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCE
Confidence            4568888887554  4677 99999999999999999999  999999999988   33    58889999999999999


Q ss_pred             EEEEee
Q psy4259          75 IVVMLS   80 (203)
Q Consensus        75 i~v~~~   80 (203)
                      |+|+-.
T Consensus        90 Ihlvd~   95 (97)
T 2kj6_A           90 LHIIDL   95 (97)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            998754

>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=99.53  E-value=3.8e-14  Score=106.06  Aligned_cols=80  Identities=9%  Similarity=0.105  Sum_probs=67.5

Q ss_pred             CCCCcceEEEEEeCCCC-eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC---ee----cCCCCCccccccCCC
Q psy4259           2 GMLAHDISDITQNQWQQ-TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG---KI----LSDDQALSEYNIDES   72 (203)
Q Consensus         2 ~~~~~~m~I~Vk~~~g~-~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G---k~----L~D~~tL~~~gI~~~   72 (203)
                      |.++..|.|+|+...+. .+. +|++++||.+||.+|+..+|  +|+++|||+|.|   +.    ++|+++|++|||.+|
T Consensus         1 ~~m~~~v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~G--ip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g   78 (122)
T 1t0y_A            1 GSMTEVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVG--TTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDG   78 (122)
T ss_dssp             --CCCEEEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHC--CCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSS
T ss_pred             CCCCCEEEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhC--CCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCC
Confidence            34556799999986554 567 99999999999999999999  999999999987   43    478899999999999


Q ss_pred             CEEEEEeecCC
Q psy4259          73 KFIVVMLSKPK   83 (203)
Q Consensus        73 ~~i~v~~~k~~   83 (203)
                      ++|||+...|.
T Consensus        79 ~~ihvvd~~p~   89 (122)
T 1t0y_A           79 YRIHAVDVTGG   89 (122)
T ss_dssp             EEEEEEECTTC
T ss_pred             CEEEEEeCCCC
Confidence            99999875543

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.51  E-value=3.1e-14  Score=100.08  Aligned_cols=71  Identities=14%  Similarity=0.215  Sum_probs=63.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC--CeecC---CCCCccccccCCCCEEEEEee
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA--GKILS---DDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~--Gk~L~---D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      |+|.||+.+|+... ++++++||.+||++|+++.|  +++++|+|+|+  +|.|+   |+++|++|||++|++|||...
T Consensus         1 m~i~vr~~~G~~~v~~l~~~~Tv~~Lk~~I~~~~g--i~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~~   77 (86)
T 2kzr_A            1 WRVRCKAKGGTHLLQGLSSRTRLRELQGQIAAITG--IAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEED   77 (86)
T ss_dssp             CCEEEEETTEEEEECSCCTTCBHHHHHHHHHHHTC--CCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCCC
T ss_pred             CEEEEEcCCCCEEeeecCCCCCHHHHHHHHHHHhC--CCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEeC
Confidence            78999999996655 59999999999999999999  99999999997  48874   678999999999999987644

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.50  E-value=2.1e-14  Score=123.77  Aligned_cols=78  Identities=22%  Similarity=0.273  Sum_probs=67.9

Q ss_pred             CCCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE---eCCeecCCCCCccccccCCCCEEEEE
Q psy4259           3 MLAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI---YAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         3 ~~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi---~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |..+.|+|+|| +.|++|. +|++++||.+||++|++.+|  +|+++||||   |+||.|+|+.+|++|||++|++|+++
T Consensus         1 ~~~~~i~i~Vk-~~g~~~~v~v~~~~Tv~~lK~~I~~~tg--Vpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~   77 (320)
T 3shq_A            1 MEVKEVVVIVK-WSGKEYPVDLTDQDTVEVLRHEIFRKTQ--VRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMV   77 (320)
T ss_dssp             ---CEEEEEEE-ETTEEEEEEEETTSBHHHHHHHHHHHHC--CCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEE
T ss_pred             CCCceEEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHHC--cCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEE
Confidence            44567999999 5899999 99999999999999999999  999999999   89999999999999999999999998


Q ss_pred             eecCC
Q psy4259          79 LSKPK   83 (203)
Q Consensus        79 ~~k~~   83 (203)
                      ++...
T Consensus        78 gs~~~   82 (320)
T 3shq_A           78 GSTEA   82 (320)
T ss_dssp             CCCC-
T ss_pred             ccchh
Confidence            76543

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

Probab=99.44  E-value=8.5e-15  Score=117.05  Aligned_cols=67  Identities=16%  Similarity=0.211  Sum_probs=0.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+++|++|+ +|++++||.+||.+|+...|  +|+++|+|||+|+.|+|+.||+     ++++|||+++-
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keG--IP~~qQRLIf~GK~LeD~~TLs-----~~STLhLvlRL   68 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMG--FEIDMMTLVNNGFIAPNTELVT-----DDVTYYLSLKL   68 (189)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhC--cChhHEEEEecCeECCCCCccc-----CCCEEEEEEec
Confidence            78999999999999 99999999999999999999  9999999999999999999998     88999998753

>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=99.44  E-value=5.1e-13  Score=95.59  Aligned_cols=75  Identities=11%  Similarity=0.196  Sum_probs=71.0

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ..|+|+|++.+|+.+. .|.+++++..||++++++.|  ++++.+||+|.|+.|.+++|+++|++.+|++|+|+....
T Consensus         6 ~~i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~g--i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~   81 (94)
T 2io1_B            6 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG--LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT   81 (94)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHT--CCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCE
T ss_pred             CeEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhC--CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEecc
Confidence            4699999999999999 99999999999999999999  999999999999999999999999999999999987554

>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=99.43  E-value=7.3e-13  Score=94.25  Aligned_cols=78  Identities=12%  Similarity=0.200  Sum_probs=71.5

Q ss_pred             CCCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           3 MLAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         3 ~~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |....|.|+|++.+|+.+. .|.+++++..|++.++++.|  ++++.+||+|.|+.|.+++|.++|++.+|++|+|+...
T Consensus         1 ~~~~~i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~g--i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q   78 (91)
T 2io0_B            1 MANDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG--LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQ   78 (91)
T ss_dssp             ---CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTT--CCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             CCCCeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC--CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEec
Confidence            5567899999999999999 99999999999999999999  99999999999999999999999999999999998765


Q ss_pred             C
Q psy4259          82 P   82 (203)
Q Consensus        82 ~   82 (203)
                      .
T Consensus        79 ~   79 (91)
T 2io0_B           79 T   79 (91)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=99.39  E-value=1.8e-12  Score=88.09  Aligned_cols=69  Identities=12%  Similarity=0.208  Sum_probs=66.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |.|+|++.+|+.+. .|.+++++..|++.++++.|  ++++.+||+|.|+.|.+++|.++|++.+|++|+++
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~g--i~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   71 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG--LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHT--CCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC--CCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            78999999999999 99999999999999999999  99999999999999999999999999999999986

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.36  E-value=3.9e-12  Score=88.06  Aligned_cols=72  Identities=14%  Similarity=0.242  Sum_probs=68.2

Q ss_pred             CcceEEEEEeCCCC-eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           5 AHDISDITQNQWQQ-TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~-~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +..|.|+|++.+|+ .+. .|.+++++..|++.++++.|  ++++.+||+|.|+.|.+++|.++|++.+|++|+|+
T Consensus         5 ~~~i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~g--i~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A            5 SQELRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMG--LSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             CCCEEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHT--CTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             CCEEEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhC--CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            45799999999996 788 99999999999999999999  99999999999999999999999999999999986

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=99.32  E-value=7.5e-12  Score=89.28  Aligned_cols=74  Identities=11%  Similarity=0.198  Sum_probs=69.9

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ..|.|+|++.+|+.+. .|..++++..|+..++++.|  ++++.+||+|.|+.|.++.|.++|++.+|++|+|+...
T Consensus        16 ~~i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~g--i~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q   90 (93)
T 2d07_B           16 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG--LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQ   90 (93)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             CeEEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhC--CCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeec
Confidence            4699999999999888 99999999999999999999  99999999999999999999999999999999998754

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.31  E-value=1.2e-11  Score=88.64  Aligned_cols=79  Identities=20%  Similarity=0.209  Sum_probs=65.6

Q ss_pred             CCCCcceEEEEEe---CCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC------ee-c-CCCCCcccccc
Q psy4259           2 GMLAHDISDITQN---QWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG------KI-L-SDDQALSEYNI   69 (203)
Q Consensus         2 ~~~~~~m~I~Vk~---~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G------k~-L-~D~~tL~~~gI   69 (203)
                      |+.+..++|+|+.   ..|..+. .++.++||.+||.+|+..+|  +|+..|||.|.+      .. | +|+++|++|+|
T Consensus         4 ~~~~~~v~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~g--ip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i   81 (97)
T 1wjn_A            4 GSSGQLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLK--VPVSELLLSYESSKMPGREIELENDLQPLQFYSV   81 (97)
T ss_dssp             CSSSCEEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTT--CCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTC
T ss_pred             cccCccEEEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHC--CChhHeEEEEEcCCCCceeeccCCCcccHhhcCC
Confidence            3455568888876   3577788 99999999999999999999  999999999873      22 5 56689999999


Q ss_pred             CCCCEEEEEeecC
Q psy4259          70 DESKFIVVMLSKP   82 (203)
Q Consensus        70 ~~~~~i~v~~~k~   82 (203)
                      .+|++|||....|
T Consensus        82 ~~G~~I~V~d~~p   94 (97)
T 1wjn_A           82 ENGDCLLVRWSGP   94 (97)
T ss_dssp             CTTCEEEEECCSS
T ss_pred             CCCCEEEEEecCC
Confidence            9999999986543

>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=1.2e-11  Score=90.05  Aligned_cols=75  Identities=11%  Similarity=0.196  Sum_probs=70.5

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ..|.|+|++.+|+.+. .|..++++..|+..++++.|  ++++.+||+|.|+.|.+++|.++|++.+|++|+|+....
T Consensus        23 ~~I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~g--i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~   98 (104)
T 1wz0_A           23 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQG--LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT   98 (104)
T ss_dssp             CCEEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHT--CCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCC
T ss_pred             CeEEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhC--CCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEecc
Confidence            4699999999999888 99999999999999999999  999999999999999999999999999999999986543

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.24  E-value=1.3e-11  Score=90.58  Aligned_cols=74  Identities=11%  Similarity=0.223  Sum_probs=70.1

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ..|.|+|++.+|+.+. .|..++++..|++.++++.|  ++++.+||+|.|+.|.+++|.++|++.+|++|+|+...
T Consensus        25 ~~I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~g--i~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q   99 (110)
T 2k8h_A           25 ALVAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQG--ISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQ   99 (110)
T ss_dssp             CCEEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHT--CCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCC
T ss_pred             CeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC--CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcc
Confidence            4599999999999999 99999999999999999999  99999999999999999999999999999999998754

>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=99.23  E-value=3.5e-11  Score=87.80  Aligned_cols=73  Identities=12%  Similarity=0.256  Sum_probs=68.8

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ..|.|+|++ +|+.+. .|..++++..|++.++++.|  ++++.+||+|.|+.|.+++|.++|++.+|++|+|+...
T Consensus        30 ~~I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~g--i~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q  103 (106)
T 2eke_C           30 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG--KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ  103 (106)
T ss_dssp             SEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHT--CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             CeEEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhC--CCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeec
Confidence            359999999 999988 99999999999999999999  99999999999999999999999999999999998754

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=98.97  E-value=3.4e-09  Score=78.14  Aligned_cols=73  Identities=18%  Similarity=0.285  Sum_probs=68.8

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      ..|.|+|+..+|+.+. .|..++++..|+..++++.|  ++.+.+||+|.|+.|.++.|.+++++.+|++|.|+..
T Consensus        39 ~~I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~G--l~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~  112 (115)
T 3kyd_D           39 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG--VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQE  112 (115)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHT--CCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEEC
T ss_pred             CeEEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhC--CChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEee
Confidence            4589999998999888 99999999999999999999  9999999999999999999999999999999999864

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=98.72  E-value=9.7e-09  Score=71.02  Aligned_cols=70  Identities=13%  Similarity=0.135  Sum_probs=57.2

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCee---c--CCCCCccccccCCCCEEEEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKI---L--SDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~---L--~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ..|.|.||+.+| .+. +|++++||.+||++|++.++  ++++.+.|.++-..   |  .++.+|+++||++|+.|++.
T Consensus         3 ~~m~lRvrs~~G-~~Ri~v~~~~t~~~L~~~I~~~~~--i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A            3 ESIIIRVQSPDG-VKRITATKRETAATFLKKVAKEFG--FQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCCCEEECSSE-EEECCCCSSCCHHHHHHHHHHHTC--CCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             CcEEEEEECCCC-CEEEEcCCcChHHHHHHHHHHHcC--CCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            358999998887 455 99999999999999999999  88888776554332   3  36789999999999999863

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.71  E-value=5.5e-08  Score=78.26  Aligned_cols=75  Identities=12%  Similarity=0.227  Sum_probs=68.9

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      ..|.|+|+ .+|+.+. .|..++++..||..++++.|  ++.+.+|++|.|+.|.++.|.+++++.+|++|+++.....
T Consensus        28 ~~I~LkV~-~~g~~v~fkIk~~t~l~kL~~ay~er~G--i~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q~g  103 (200)
T 3pge_A           28 THINLKVS-DGSSEIFFKIKKTTPLRRLMEAFAKRQG--KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG  103 (200)
T ss_dssp             CCEEEEEE-CSSCEEEEEECTTSCTHHHHHHHHHHHS--SCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCSC
T ss_pred             CeEEEEEe-cCCCEEEEEEecCCHHHHHHHHHHHHhC--CChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCc
Confidence            34889997 4888888 99999999999999999999  9999999999999999999999999999999999876544

>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=98.67  E-value=4.1e-08  Score=78.14  Aligned_cols=74  Identities=12%  Similarity=0.218  Sum_probs=67.9

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      .|.|+|+ .+|+.+. .|..++++..|++.++++.|  +++..+|++|.|+.|.+++|.+++++.+||+|.|+.....
T Consensus        57 ~InLKVk-~dG~eV~FKIKrtTpL~KLmeAYcERqG--L~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~G  131 (207)
T 3tix_A           57 HINLKVS-DGSSEIFFKIKKTTPLRRLMEAFAKRQG--KEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIG  131 (207)
T ss_dssp             EEEEEEE-CSSCEEEEEEETTSCTHHHHHHHHHHTT--CCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCT
T ss_pred             cEEEEEe-cCCCEEEEEEccCChHHHHHHHHHHHhC--CCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            4888887 4888888 99999999999999999999  9999999999999999999999999999999999875543

>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=98.64  E-value=3.1e-07  Score=62.54  Aligned_cols=70  Identities=16%  Similarity=0.251  Sum_probs=65.5

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCC-ceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAE-YQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~-~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      +.+.+|+.+...+. .|..+.+|..|-+....+.+  ++++ .++|.|.|..|..+.++.+|++.+|+.|-+++
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            67788888888888 99999999999999999999  9999 99999999999999999999999999999875

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=98.46  E-value=7.4e-07  Score=63.71  Aligned_cols=71  Identities=15%  Similarity=0.249  Sum_probs=65.3

Q ss_pred             cceEEEEEeCCCC-eee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           6 HDISDITQNQWQQ-TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         6 ~~m~I~Vk~~~g~-~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ..+.|+|+..+|+ .+. .|..++++..|....+++.|  ++++..|++|.|..|..+.|.+++++.+|++|.|+
T Consensus        24 ~~I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g--~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           24 QQLQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMG--LSGRKLSFFFDGTKLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             SEEEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTT--CSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEEE
T ss_pred             CeEEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHC--CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            4588899988885 677 99999999999999999999  99999999999999999999999999999999875

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=98.34  E-value=5.9e-08  Score=78.22  Aligned_cols=74  Identities=12%  Similarity=0.234  Sum_probs=0.0

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      .|.|+| ..+|+.+. .|..++.+..|++.++++.|  ++++.+|++|+|+.|.+++|.+++++.+||+|.|+.....
T Consensus        21 ~InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqG--Ls~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~G   95 (227)
T 3v7o_A           21 HINLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQG--KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (227)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             eEEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhC--CCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccC
Confidence            578888 67888888 99999999999999999999  9999999999999999999999999999999999865543

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.21  E-value=9e-06  Score=57.53  Aligned_cols=72  Identities=11%  Similarity=0.119  Sum_probs=66.1

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      .+.|+|+. +|..+. .+..++-...|.+..+.+.|  +.++..+++|.|..+.++.|-+++++.++++|-+++.+
T Consensus        21 ~IniKV~~-~g~ev~FkIK~tt~l~KL~~aYc~r~g--v~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~~~   93 (95)
T 2l76_A           21 LFPLKIRC-RADLVRLPLRMSEPLQSVVDHMATHLG--VSPSRILLLFGETELSPTATPRTLKLGVADIIDCVVLT   93 (95)
T ss_dssp             CEEEEEEC-SSSEEEEEECSSSCTHHHHHHHHHHHT--SCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEECC
T ss_pred             eEEEEEEc-CCcEEEEEEecCChHHHHHHHHHhhcC--CChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEEec
Confidence            48899994 677777 99999999999999999999  99999999999999999999999999999999998765

>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=98.11  E-value=9.5e-06  Score=65.56  Aligned_cols=75  Identities=12%  Similarity=0.232  Sum_probs=68.1

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      +.+.|+|+. +++.+. .|..++++..||+..+++.|  ++.+.+|++|.|+.+.+++|-.++.+.++++|.+......
T Consensus        20 ~~i~ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g--~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~eq~G   95 (209)
T 3uf8_A           20 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG--KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (209)
T ss_dssp             SEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHT--CCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECSCTT
T ss_pred             CcEEEEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhC--CChheEEEEECCEeccCCCChHHhhhcccccchhhccccc
Confidence            458889987 777777 99999999999999999999  9999999999999999999999999999999998865544

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=98.02  E-value=1.4e-05  Score=55.09  Aligned_cols=70  Identities=13%  Similarity=0.148  Sum_probs=58.4

Q ss_pred             eEEEEEe--CCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCC---CceEEEeCCeecCCCCCccccccCCCCEEEE
Q psy4259           8 ISDITQN--QWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLA---EYQKLIYAGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         8 m~I~Vk~--~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~---~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      +.|++..  ..++.|. .++...||..|++.+.+.++...+.   ...|+.-+|.+|.++++|++|+|.+||.|.+
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 IDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEI   80 (81)
T ss_dssp             EEEEEECTTTTCCEEEEEEETTSBTTHHHHHHHHHSCCCSCCCTTCEEEEGGGTEEEETTSBTGGGTCCTTCEEEE
T ss_pred             EEEEEEeeccCCceEEEECCCchhHHHHHHHHHHHhCCCcCCCCCCEEEEecCCEEEcCCCEEeeCCcCCCCEEEE
Confidence            4566664  6789999 9999999999999999999833221   2457888999999999999999999999975

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=97.98  E-value=2.7e-05  Score=55.12  Aligned_cols=68  Identities=15%  Similarity=0.162  Sum_probs=50.1

Q ss_pred             EEEEEeCC-CCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecC--CCCCccccc-cCCCCEEEEE
Q psy4259           9 SDITQNQW-QQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILS--DDQALSEYN-IDESKFIVVM   78 (203)
Q Consensus         9 ~I~Vk~~~-g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~--D~~tL~~~g-I~~~~~i~v~   78 (203)
                      -|+|=... +..+. .+.+++||..||++|++++|  +++++|+|+|.||.|.  .+..-..|- -...+-|+++
T Consensus        14 vvHVf~~~~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           14 VIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTK--IISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVV   86 (94)
T ss_dssp             EEEEEETTTTEEEEEEEETTCBHHHHHHHHHHHHC--CCGGGEEEEETTEEECCCTTCBGGGSCCCBTTBCEEEE
T ss_pred             eEEEEEcccceEEEEEeccchHHHHHHHHHHHHhC--CCHHHHHHHhCCCccccCCCCccccCCCCCCCCCEEEE
Confidence            34554444 55566 99999999999999999999  9999999999997764  334445553 3444556544

>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=97.94  E-value=4.4e-05  Score=52.68  Aligned_cols=70  Identities=10%  Similarity=0.086  Sum_probs=59.2

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecC---CCCCccccccCCCCEEEEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILS---DDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~---D~~tL~~~gI~~~~~i~v~   78 (203)
                      ...+|.||..+|+.+. .+..++||.+|...|.. .+  .+....+|+.  -.|.|.   .++||+++|+.++++|+|-
T Consensus         6 ~~~~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            6 PVSKLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KG--FPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   81 (84)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TT--CCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEEE
T ss_pred             CeEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cC--CCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEEE
Confidence            3478999999999999 99999999999999988 56  6778889884  468884   3589999999998888764

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=97.92  E-value=1.4e-06  Score=75.75  Aligned_cols=74  Identities=12%  Similarity=0.240  Sum_probs=0.0

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ..+.|+|+. +|+.+. .|..++++..|++.++++.|  ++++.+|++|.|+.|.++.|.+++++.+|++|.++....
T Consensus        20 ~~I~LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G--~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q~   94 (360)
T 3ix6_A           20 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG--KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQI   94 (360)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             CeEEEEEec-CCcEEEEEEecCChHHHHHHHHHHHhC--CCcceEEEEECCeECCCCCChHHcCCCccchhhhhhccC
Confidence            357888886 677777 99999999999999999999  999999999999999999999999999999999987544

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=97.91  E-value=1.6e-05  Score=59.50  Aligned_cols=67  Identities=16%  Similarity=0.120  Sum_probs=56.7

Q ss_pred             EEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCC-------------------------------------ceE
Q psy4259           9 SDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAE-------------------------------------YQK   50 (203)
Q Consensus         9 ~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~-------------------------------------~qk   50 (203)
                      .|+|+.++|...+ .|+.+.||.+++..|+.+.|  ++..                                     .+|
T Consensus        13 ~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kig--I~n~~ey~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~k   90 (128)
T 2kc2_A           13 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIG--ITNHDEYSLVRELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQK   90 (128)
T ss_dssp             EEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHT--CCCCSSEEEEEECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCCS
T ss_pred             cEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhC--CCCcccccccccccccccccCchhhccccccccchhHHHHHHHH
Confidence            4899999999999 99999999999999999999  6633                                     445


Q ss_pred             EEe--CCeecCCCCCccccccCCCCEEEE
Q psy4259          51 LIY--AGKILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus        51 Li~--~Gk~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      |-.  .+..|+++.||.++||.++++|.+
T Consensus        91 L~~dd~~~WLD~srtL~EQGI~e~~tllL  119 (128)
T 2kc2_A           91 LHTDDELNWLDHGRTLREQGVEEHETLLL  119 (128)
T ss_dssp             CCCSSSEEEECSSSCHHHHTCCTTSEEEE
T ss_pred             hcccCCCCcccCCCcHHHcCCCCCCEEEE
Confidence            432  247888899999999999999765

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=97.83  E-value=8.7e-05  Score=51.97  Aligned_cols=76  Identities=7%  Similarity=-0.017  Sum_probs=67.4

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      +.-|.|+|-..+++.+. .|.++.++.++-+...+++|  +.+++-.|.|++|.|+-+..+.-.|+.+|+.+.++.++.
T Consensus         7 ~~~m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~g--l~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~s~   83 (90)
T 2al3_A            7 GGGSAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQD--FNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVSR   83 (90)
T ss_dssp             ---CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTT--CCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSSS
T ss_pred             CCccEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhC--CChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEccC
Confidence            34579999999999999 99999999999999999999  999999999999999888999999999999999875444

>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=97.81  E-value=0.00021  Score=51.84  Aligned_cols=72  Identities=8%  Similarity=0.050  Sum_probs=61.0

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecC--C-CCCccccccCCCCEEEEEee
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILS--D-DQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~--D-~~tL~~~gI~~~~~i~v~~~   80 (203)
                      ..+|.||..+|+.+. .+..++||.+|.+.|....+  .+.....|+.  --|.|.  | ++||+++|+.+..+|+|...
T Consensus        13 ~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~--~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~~   90 (109)
T 2dzk_A           13 IARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVG--NTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLPA   90 (109)
T ss_dssp             CEEEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHT--TSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEECC
T ss_pred             cEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccC--CCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEEC
Confidence            589999999999999 99999999999999999887  6667788874  468886  3 58999999999888876543

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=97.68  E-value=5.6e-06  Score=72.60  Aligned_cols=74  Identities=14%  Similarity=0.245  Sum_probs=0.0

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      .+.|+|+. ++..+. .|..++++..|++..+++.|  ++...++++|.|+.|.+++|.+++++.+|++|.++.....
T Consensus        30 ~i~lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g--~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~g  104 (389)
T 4da1_A           30 HINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG--KEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIG  104 (389)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             cEEEEEec-CCcEEEEEECCCChHHHHHHHHHHHhC--CCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeecccc
Confidence            47788876 667777 99999999999999999999  9999999999999999999999999999999999875543

>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=97.43  E-value=0.00043  Score=51.36  Aligned_cols=70  Identities=21%  Similarity=0.245  Sum_probs=59.5

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE--eCCeec--CC-CCCccccccCCCCEEEEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI--YAGKIL--SD-DQALSEYNIDESKFIVVM   78 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi--~~Gk~L--~D-~~tL~~~gI~~~~~i~v~   78 (203)
                      ...+|.||..+|+.+. .+..++||.+|...|... +  ++.....|+  |-.|.|  .| ++||.++|+.+...|+|.
T Consensus        42 ~~t~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~--~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~  117 (124)
T 1wj4_A           42 PKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSK-G--YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-H--CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             CcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C--CCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEE
Confidence            3589999999999999 999999999999999886 6  777788887  447888  34 589999999998888764

>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=97.20  E-value=0.0024  Score=46.14  Aligned_cols=69  Identities=12%  Similarity=0.110  Sum_probs=57.8

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecC-C-CCCccccccCCCCEEEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILS-D-DQALSEYNIDESKFIVVM   78 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~-D-~~tL~~~gI~~~~~i~v~   78 (203)
                      ..+|.||..+|+.+. .+..++||.+|...|... +  +.....+|+.  -.|.|. | ++||+++|+.+..+|+|.
T Consensus        23 ~~~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~--~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve   96 (109)
T 2cr5_A           23 VVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-G--YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVE   96 (109)
T ss_dssp             EEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-T--CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEE
T ss_pred             cEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-C--CCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEE
Confidence            589999999999999 999999999999999954 5  5667788874  478886 3 589999999998888664

>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=97.03  E-value=0.0017  Score=48.24  Aligned_cols=69  Identities=14%  Similarity=0.127  Sum_probs=55.3

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecCCC-CCccccccCCCCEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILSDD-QALSEYNIDESKFI   75 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~D~-~tL~~~gI~~~~~i   75 (203)
                      ...+|.||..+|+.+. .+..++||.+|.+.|...... +......|+.  -.|.|.|. +||.++|+.+...|
T Consensus        51 ~~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~-~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psavl  123 (127)
T 1s3s_G           51 PTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPA-MAATSFVLMTTFPNKELADENQTLKEANLLNAVIV  123 (127)
T ss_dssp             CCCCEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSG-GGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEEE
T ss_pred             CcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcC-CCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceEE
Confidence            3588999999999999 999999999999999986421 4456678874  47889764 89999999984443

>2lnm_A Protein TIC 40, chloroplastic; translocon, import, TIC40-NP, protein transport; NMR {Arabidopsis thaliana}

Probab=96.55  E-value=0.0032  Score=40.89  Aligned_cols=41  Identities=17%  Similarity=0.338  Sum_probs=35.2

Q ss_pred             CCh-HHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHh
Q psy4259         132 EDP-LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELIS  177 (203)
Q Consensus       132 ~~p-l~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~  177 (203)
                      .|| +..++++|.|.+.-+.+++||+.+..++     +||.+.+.|.
T Consensus        10 ~dPe~~~~m~dP~~~~~lq~i~~NP~~~~~~~-----~dP~v~~~~~   51 (62)
T 2lnm_A           10 ENPDVAMAFQNPRVQAALMECSENPMNIMKYQ-----NDKEVMDVFN   51 (62)
T ss_dssp             TSHHHHHHTTSHHHHHHHHHHTTCGGGHHHHT-----TCHHHHHHHH
T ss_pred             cChHHHHHcCCHHHHHHHHHHHHCHHHHHHHH-----hChHHHHHHH
Confidence            577 7889999999999999999999976654     5999998875

>2llw_A Heat shock protein STI1; DP domain, alpha helix, chaperone; NMR {Saccharomyces cerevisiae}

Probab=96.44  E-value=0.0031  Score=42.21  Aligned_cols=38  Identities=29%  Similarity=0.458  Sum_probs=23.3

Q ss_pred             HHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHh
Q psy4259         135 LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELIS  177 (203)
Q Consensus       135 l~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~  177 (203)
                      +..++++|.++++-+.+++||..+..++     +||.++..|+
T Consensus        22 i~~im~DP~~~~~lq~~~~NP~~~~k~~-----~nP~v~~~i~   59 (71)
T 2llw_A           22 VAAIMQDPVMQSILQQAQQNPAALQEHM-----KNPEVFKKIQ   59 (71)
T ss_dssp             HHHHHTCTHHHHHHHHHHHCHHHHHHHH-----HSHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHCHHHHHHHH-----hCHHHHHHHH
Confidence            5556666666666666666666655544     2666666553

>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=96.19  E-value=0.024  Score=39.00  Aligned_cols=75  Identities=12%  Similarity=0.090  Sum_probs=62.8

Q ss_pred             CCCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe---CCeecCCCCCccccccCCCCEEEEE
Q psy4259           3 MLAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY---AGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         3 ~~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~---~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |...++++.|.....++.. .|++..++.+|--.|.+++.  +.++..-|..   .+..|+=+++|.+|||++   ++.+
T Consensus         6 ~PE~TvRLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kce--fdp~~~~Ll~d~~~~e~LdLskSLndlgirE---Lya~   80 (91)
T 2daj_A            6 SGEKTVRVVINFKKTQKTIVRVSPHASLQELAPIICSKCE--FDPLHTLLLKDYQSQEPLDLTKSLNDLGLRE---LYAM   80 (91)
T ss_dssp             CCCSCEEEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTT--CCTTSEEEESCSSCCCBCCTTSCHHHHTCSE---EEEE
T ss_pred             CCccEEEEEEeecCcceeEEEeCCCCcHHHHHHHHhhccc--CChhhEEEecCCCCCcccchhcchhhhhhhh---hhee
Confidence            3455799999988877777 99999999999999999999  9999888875   367898899999999997   6665


Q ss_pred             eecC
Q psy4259          79 LSKP   82 (203)
Q Consensus        79 ~~k~   82 (203)
                      -.++
T Consensus        81 d~~~   84 (91)
T 2daj_A           81 DVNR   84 (91)
T ss_dssp             ECCC
T ss_pred             cccc
Confidence            4444

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=95.40  E-value=0.076  Score=38.37  Aligned_cols=72  Identities=19%  Similarity=0.208  Sum_probs=48.8

Q ss_pred             ceEEEEEeCC--CCeee-ecCCCCcHHHHHHHHHhhhCCCCC------CCceEEEeC----CeecCCC------------
Q psy4259           7 DISDITQNQW--QQTVS-HLDVQEEVKQLKEKIQSEKGSEYL------AEYQKLIYA----GKILSDD------------   61 (203)
Q Consensus         7 ~m~I~Vk~~~--g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip------~~~qkLi~~----Gk~L~D~------------   61 (203)
                      ++.|.+-...  +..+. .|-..+||.++|+||....-+..|      ++.+.|-|.    |++|.|.            
T Consensus        11 ~ltl~v~~~~~~~~~i~vkVLdCDTItQvKeKiLd~vyk~~pyS~rP~~~~~dLEwr~g~~~~iL~D~D~ts~~~~~wkr   90 (111)
T 4e71_A           11 PLTVSVIVQDEGVDAIPVKVLNCDTISQVKEKIIDQVYRGQPCSCWPRPDSVVLEWRPGSTAQILSDLDLTSQREGRWKR   90 (111)
T ss_dssp             EEEEEEEETTSCCCCEEEEEETTCBHHHHHHHHHHHHTC---------CCSEEEEEC--CCCEECCSSCTTSCC---CCC
T ss_pred             EEEEEEEecCCCCCceeeeeeccCcHHHHHHHHHHHHHcCCccccCCCCCceeeEEecCCCCccccccCccceecCcceE
Confidence            3556654433  34455 777899999999999977643322      456667762    5677662            


Q ss_pred             -CCccccccCCCCEEEEE
Q psy4259          62 -QALSEYNIDESKFIVVM   78 (203)
Q Consensus        62 -~tL~~~gI~~~~~i~v~   78 (203)
                       .||..|+|.+|++|.++
T Consensus        91 LNTL~HY~V~dgatl~l~  108 (111)
T 4e71_A           91 VNTLMHYNVRDGATLILS  108 (111)
T ss_dssp             CCBHHHHTCCTTCEEEEE
T ss_pred             ecchhhcCCCCCCEEEEE
Confidence             26778999999999875

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=95.22  E-value=0.062  Score=35.90  Aligned_cols=59  Identities=14%  Similarity=0.123  Sum_probs=44.6

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |+|+||........ +++...||.+|-+.    .+  ++++..-+..+|+++..+.      +.+||.|.++
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            78899977444344 99999999987654    77  9999887888999887655      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=95.14  E-value=0.11  Score=38.91  Aligned_cols=75  Identities=19%  Similarity=0.197  Sum_probs=50.8

Q ss_pred             ceEEEEEeCCC------Ceee-ecCCCCcHHHHHHHHHhhhCCCC------CCCceEEEe----CCe-ecCCC-------
Q psy4259           7 DISDITQNQWQ------QTVS-HLDVQEEVKQLKEKIQSEKGSEY------LAEYQKLIY----AGK-ILSDD-------   61 (203)
Q Consensus         7 ~m~I~Vk~~~g------~~~~-~v~~~~TV~~LK~~I~~~~~~~i------p~~~qkLi~----~Gk-~L~D~-------   61 (203)
                      ++.|.|-...+      ..+. .|-..+||.++|+||....-++.      .+++.-|-|    .|+ +|.|.       
T Consensus        24 ~ltl~v~~~~~~~~~~~~~i~VkVLdCDTItQvKeKiLDavYk~~PySqRP~~~d~dLEwr~g~~g~liL~D~D~tS~~~  103 (138)
T 2r2o_A           24 PLTLNALLAVGPGAGEAQGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQ  103 (138)
T ss_dssp             EEEEEEEEC-------CCCEEEEEETTCBHHHHHHHHHHHHTTTSCGGGCCCGGGEEEEEECSSSCEEEECSSSTTCCEE
T ss_pred             EEEEEEEccCCcccccCCceeEEEeccccHHHHHHHHHHHHHcCCccccCCCccceeEEEecCCcCceEeeccCCccccc
Confidence            45666544422      3455 77789999999999998876544      344556665    244 47664       


Q ss_pred             ------CCccccccCCCCEEEEEeec
Q psy4259          62 ------QALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        62 ------~tL~~~gI~~~~~i~v~~~k   81 (203)
                            .||+.|+|.+|++|.++-+.
T Consensus       104 ~~wkrLNTL~HY~V~Dga~l~l~~~~  129 (138)
T 2r2o_A          104 GLWRRLNTLQHYKVPDGATVALVPCL  129 (138)
T ss_dssp             TTEEECCBHHHHTCCTTCEEEEEEC-
T ss_pred             CCceeecchhccCCCCCCEEEEEECC
Confidence                  27899999999999876433

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=95.06  E-value=0.21  Score=32.67  Aligned_cols=60  Identities=13%  Similarity=0.133  Sum_probs=45.4

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      .|+|+|....++ .. ++....||.+|.+.+    +  ++.....+..+|..+..+.     -+++||.|.++
T Consensus         4 ~m~i~vNg~~~~-~~~~~~~~~tv~~Ll~~l----~--~~~~~v~vavN~~~v~~~~-----~L~~gD~V~ii   64 (70)
T 1ryj_A            4 GMKFTVITDDGK-KILESGAPRRIKDVLGEL----E--IPIETVVVKKNGQIVIDEE-----EIFDGDIIEVI   64 (70)
T ss_dssp             CEEEEEEETTEE-EEEEESSCCBHHHHHHHT----T--CCTTTEEEEETTEECCTTS-----BCCTTCEEEEE
T ss_pred             eEEEEEeCccCc-eeEECCCCCcHHHHHHHh----C--CCCCCEEEEECCEECCCcc-----cCCCCCEEEEE
Confidence            588888854433 34 777778999998875    5  6677778889999997654     57889999876

>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=94.72  E-value=0.2  Score=40.56  Aligned_cols=72  Identities=11%  Similarity=0.129  Sum_probs=53.8

Q ss_pred             eEEEEEeCCCC--eee-ecCCCCcHHHHHHHHHhhhCCCCCCC-ceEEEe-C----CeecCCC-CCccccccCCCCEEEE
Q psy4259           8 ISDITQNQWQQ--TVS-HLDVQEEVKQLKEKIQSEKGSEYLAE-YQKLIY-A----GKILSDD-QALSEYNIDESKFIVV   77 (203)
Q Consensus         8 m~I~Vk~~~g~--~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~-~qkLi~-~----Gk~L~D~-~tL~~~gI~~~~~i~v   77 (203)
                      +.+++......  .++ .++..+||.+|++.+...++  ++.+ ..||-. .    ...|.|. .||.++++.++..|.+
T Consensus       140 ~~l~l~~~~~~~~~~~~~~Sk~~ti~~l~~~~~~~~~--i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~ill  217 (231)
T 3jyu_A          140 LELKLCENSDPTNVLSCHFSKADTIATIEKEMRKLFN--IPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVI  217 (231)
T ss_dssp             EEEEEEETTEEEEEEEEEECTTCBHHHHHHHHHHHTT--CCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEE
T ss_pred             ceEEEEecCCCCceEEEEecccCcHHHHHHHHHHHhC--CCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEE
Confidence            44455433322  244 77999999999999999999  9887 588753 2    2457664 8999999999999987


Q ss_pred             Eeec
Q psy4259          78 MLSK   81 (203)
Q Consensus        78 ~~~k   81 (203)
                      =++.
T Consensus       218 E~r~  221 (231)
T 3jyu_A          218 EPQN  221 (231)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            7654

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=94.72  E-value=0.14  Score=41.03  Aligned_cols=73  Identities=10%  Similarity=0.148  Sum_probs=54.2

Q ss_pred             ceEEEEEeCCCC--eee-ecCCCCcHHHHHHHHHhhhCCCCCCC-ceEEE--e-CC--eecCCC-CCccccccCCCCEEE
Q psy4259           7 DISDITQNQWQQ--TVS-HLDVQEEVKQLKEKIQSEKGSEYLAE-YQKLI--Y-AG--KILSDD-QALSEYNIDESKFIV   76 (203)
Q Consensus         7 ~m~I~Vk~~~g~--~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~-~qkLi--~-~G--k~L~D~-~tL~~~gI~~~~~i~   76 (203)
                      ++.+++......  .++ .++..+||.+|++.+...++  ++.+ ..||-  | .+  ..|.|. +||.++++.++..|+
T Consensus       127 P~~l~l~~~~~~~~~~~~~~Sk~~ti~~l~~~~~~~~~--i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~il  204 (217)
T 4a3p_A          127 LTELKLCENGNMNNVVTRRFSKADTIDTIEKEIRKIFS--IPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLV  204 (217)
T ss_dssp             CEEEEEEETTEEEEEEEEEECTTSBHHHHHHHHHHHTT--CCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEE
T ss_pred             ccEEEEEecCCCCcceEEEEcccchHHHHHHHHHHHhC--CCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEE
Confidence            344555443322  245 88999999999999999999  9887 57874  3 22  456664 799999999999998


Q ss_pred             EEeec
Q psy4259          77 VMLSK   81 (203)
Q Consensus        77 v~~~k   81 (203)
                      +=++.
T Consensus       205 lE~r~  209 (217)
T 4a3p_A          205 IEQKN  209 (217)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            87654

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=94.45  E-value=0.41  Score=35.25  Aligned_cols=65  Identities=28%  Similarity=0.264  Sum_probs=45.8

Q ss_pred             CCCeee-ecCCCCcHHHHHHHHHhhhCCCCC------CCceEEEe-C---Ce-ecCCC-------------CCccccccC
Q psy4259          16 WQQTVS-HLDVQEEVKQLKEKIQSEKGSEYL------AEYQKLIY-A---GK-ILSDD-------------QALSEYNID   70 (203)
Q Consensus        16 ~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip------~~~qkLi~-~---Gk-~L~D~-------------~tL~~~gI~   70 (203)
                      ++..+. .|-..+||.++|++|....-+..|      ++.+.|-| .   |+ +|.|.             .||..|+|.
T Consensus        15 ~~~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~~krLNTL~HY~V~   94 (127)
T 3h6n_A           15 GMDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDGRKKLNTLAHYKIP   94 (127)
T ss_dssp             CCCCEEEEEETTSBHHHHHHHHHHHHSTTSCGGGSCCGGGEEEEEECSSSCEEECCSSSTTSCEETTEECCCBTTTTTCC
T ss_pred             CCCceeeeeeccCchhhhhHHHHHHHhccCCcccCCCCcccceEEecCCCCceEeecCCCcceecCceeEeccccccCCC
Confidence            344566 777889999999999987643333      45677776 2   33 36652             267889999


Q ss_pred             CCCEEEEEee
Q psy4259          71 ESKFIVVMLS   80 (203)
Q Consensus        71 ~~~~i~v~~~   80 (203)
                      +|++|.++.+
T Consensus        95 dgatv~l~~~  104 (127)
T 3h6n_A           95 EGASLAMSLI  104 (127)
T ss_dssp             TTCEEEEEEC
T ss_pred             CCCEEEEEEc
Confidence            9999987643

>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=94.42  E-value=0.11  Score=44.58  Aligned_cols=70  Identities=13%  Similarity=0.034  Sum_probs=54.4

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCC--CCCCceEEEe------CCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSE--YLAEYQKLIY------AGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~--ip~~~qkLi~------~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +.++|... +.+.+ .++++.||.++...|.++.+..  .+.++--|..      +|+.|++.+||+.|++.+|+.|...
T Consensus         4 ~~~~~~~~-~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~   82 (371)
T 3ivf_A            4 LSLKISIG-NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYR   82 (371)
T ss_dssp             EEEEEEET-TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEE
T ss_pred             EEEEEEec-ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeecc
Confidence            44555544 55556 9999999999999998887521  3566777776      5788999999999999999988764

>2llv_A Heat shock protein STI1; DP domain, alpha helix, chaperone; NMR {Saccharomyces cerevisiae}

Probab=94.23  E-value=0.023  Score=37.74  Aligned_cols=40  Identities=20%  Similarity=0.457  Sum_probs=29.8

Q ss_pred             Ch-HHHhhCCHHHHHHHHHHHhCCCcHHH-HHHHHhhcCHHHHHHHh
Q psy4259         133 DP-LAFLRTQPQFQQMRTVVQQNPELLPT-VLQQIGQSNPALLELIS  177 (203)
Q Consensus       133 ~p-l~~l~~~P~~~~~r~~i~~nP~~l~~-il~~l~~~nP~l~~~i~  177 (203)
                      || +..++.+|.|.++.+.+++||+.+.. .+     +||.+.+.|.
T Consensus        22 dP~t~~~~~DP~~~~~lq~i~~NP~~i~~~~~-----~dPrv~~~l~   63 (71)
T 2llv_A           22 NPKTSEMMKDPQLVAKLIGYKQNPQAIGQDLF-----TDPRLMTIMA   63 (71)
T ss_dssp             SSTTHHHHHSCTHHHHHHHHHHSCTTHHHHTT-----TCHHHHHHHH
T ss_pred             ChHHHHHhcCHHHHHHHHHHHHCHHHHHHHHh-----hCcHHHHHHH
Confidence            44 56677888888888888888888655 44     4888887764

>2llw_A Heat shock protein STI1; DP domain, alpha helix, chaperone; NMR {Saccharomyces cerevisiae}

Probab=93.03  E-value=0.27  Score=32.55  Aligned_cols=46  Identities=24%  Similarity=0.354  Sum_probs=30.2

Q ss_pred             HHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHH
Q psy4259         135 LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRML  187 (203)
Q Consensus       135 l~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml  187 (203)
                      +..++++|.++.+    ++||++.. +++++. +||...+-..+|| .++.++
T Consensus        13 ~~~~m~dPEi~~i----m~DP~~~~-~lq~~~-~NP~~~~k~~~nP-~v~~~i   58 (71)
T 2llw_A           13 YQRAMKDPEVAAI----MQDPVMQS-ILQQAQ-QNPAALQEHMKNP-EVFKKI   58 (71)
T ss_dssp             HHHHHHSHHHHHH----HTCTHHHH-HHHHHH-HCHHHHHHHHHSH-HHHHHH
T ss_pred             HHHHhcCHHHHHH----hCCHHHHH-HHHHHH-HCHHHHHHHHhCH-HHHHHH
Confidence            6678889975443    48997644 455544 5788776666776 566655

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=92.40  E-value=0.56  Score=34.08  Aligned_cols=74  Identities=19%  Similarity=0.255  Sum_probs=47.9

Q ss_pred             ceEEEEEeCC---CCeee-ecCCCCcHHHHHHHHHhhhCCCCC------CCceEEEe-CC---e-ecCCC----------
Q psy4259           7 DISDITQNQW---QQTVS-HLDVQEEVKQLKEKIQSEKGSEYL------AEYQKLIY-AG---K-ILSDD----------   61 (203)
Q Consensus         7 ~m~I~Vk~~~---g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip------~~~qkLi~-~G---k-~L~D~----------   61 (203)
                      ++.|.|-...   ...+. .|-..+||.++|++|....-+..|      ++.+.|-| .|   + +|.|.          
T Consensus        13 ~ltl~v~~~~~~~~~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~w   92 (117)
T 4e74_A           13 TLVLSCVSPDNANSPEVPVKILNCDTITQVKEKILDAIFKNVPCSHRPKAADMDLEWRQGSGARMILQDEDITTKIENDW   92 (117)
T ss_dssp             EEEEEECCC----CCCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECTTSCEEEECSSSTTCCC---C
T ss_pred             EEEEEEEccCCCCCCceEeeeecCCchHHHHHHHHHHHhcCCCcccCCCCCceeEEEecCCCCceEeecCCCccEecCcc
Confidence            3555554333   23355 777889999999999977643333      44566666 23   3 35541          


Q ss_pred             ---CCccccccCCCCEEEEEee
Q psy4259          62 ---QALSEYNIDESKFIVVMLS   80 (203)
Q Consensus        62 ---~tL~~~gI~~~~~i~v~~~   80 (203)
                         .||..|+|.+|++|.++-+
T Consensus        93 krLNTL~HY~V~dgatl~l~~~  114 (117)
T 4e74_A           93 KRLNTLAHYQVPDGSVVALVSK  114 (117)
T ss_dssp             CCCCBHHHHTCCTTCEEEEEEC
T ss_pred             eEeccccccCCCCCCEEEEEeC
Confidence               2577899999999987643

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=92.30  E-value=0.72  Score=30.21  Aligned_cols=64  Identities=8%  Similarity=0.154  Sum_probs=42.6

Q ss_pred             eEEEEEeCCCCe-ee-ecCCCCcHHHHHHHHHhhhCCCCCC--CceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQT-VS-HLDVQEEVKQLKEKIQSEKGSEYLA--EYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~-~~-~v~~~~TV~~LK~~I~~~~~~~ip~--~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |.|+||....-. -. ++ ...||.+|.+.+....+  +..  ....+..+|+.+.+    .+.-+++||.|.++
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            567777654321 23 66 56899999999986543  322  34566678877543    24568899999876

>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=92.10  E-value=0.41  Score=32.71  Aligned_cols=46  Identities=15%  Similarity=0.074  Sum_probs=39.0

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG   55 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G   55 (203)
                      ..++|+|...  -++. .|....+..+|.++|.++.+  ++++..+|.|+-
T Consensus         4 ~~~~VKV~~~--~tvairvp~~~~y~~L~~~l~~kL~--l~~~~~~LsYk~   50 (83)
T 1oey_A            4 MAYTLKVHYK--YTVVMKTQPGLPYSQVRDMVSKKLE--LRLEHTKLSYRP   50 (83)
T ss_dssp             SCEEEEEESS--SEEEEEECTTCCHHHHHHHHHHHTT--CCGGGCCEEECC
T ss_pred             CcEEEEEEEE--EEEEEECCCCCCHHHHHHHHHHHhC--CCcceeEEEeeC
Confidence            3466777654  5777 99999999999999999999  999999999964

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=92.06  E-value=0.5  Score=32.31  Aligned_cols=57  Identities=12%  Similarity=0.235  Sum_probs=49.6

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      .++-..++..||+.++.+.+  +.-+.-.+...+..|+++++|-+-+|+-...|.+.+-
T Consensus         8 hmDI~epL~~Lk~LLe~Rl~--i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvq   64 (89)
T 2juo_A            8 AIDINEPIGNLKKLLEPRLQ--CSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQ   64 (89)
T ss_dssp             EEESSSBGGGHHHHSHHHHC--SCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEE
T ss_pred             hccccCcHHHHHHHHHHHhc--CCcccCeEEeeccccCCCccHHHhhcccccEEEEEEE
Confidence            56667899999999999999  8888888888888899999999999998888877653

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1

Probab=91.86  E-value=1.6  Score=30.14  Aligned_cols=67  Identities=12%  Similarity=0.105  Sum_probs=46.5

Q ss_pred             ceEEEEEeCC------C-Ceee-ecCCCCcHHHHHHHHHhhhCCC---C------CCCceEEEeCCeecCCCCCcccccc
Q psy4259           7 DISDITQNQW------Q-QTVS-HLDVQEEVKQLKEKIQSEKGSE---Y------LAEYQKLIYAGKILSDDQALSEYNI   69 (203)
Q Consensus         7 ~m~I~Vk~~~------g-~~~~-~v~~~~TV~~LK~~I~~~~~~~---i------p~~~qkLi~~Gk~L~D~~tL~~~gI   69 (203)
                      .|+|+||...      | .... ++....||.+|.+.+...+..-   +      ......+..+|+....     +.-+
T Consensus         9 ~~~v~V~~FA~lre~~g~~~~~~e~~~~~Tv~~Ll~~L~~~~p~l~~~l~~~~g~~~~~v~v~VNg~~v~~-----~~~L   83 (98)
T 1vjk_A            9 SVKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSW-----DEEL   83 (98)
T ss_dssp             CEEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCT-----TCBC
T ss_pred             cEEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHhHChhHHHHhhccccccCCcEEEEECCEECCC-----CCCC
Confidence            5888888763      4 3445 7777889999999998764210   0      0234567778887753     5568


Q ss_pred             CCCCEEEEE
Q psy4259          70 DESKFIVVM   78 (203)
Q Consensus        70 ~~~~~i~v~   78 (203)
                      ++||.|.++
T Consensus        84 ~dGDeV~i~   92 (98)
T 1vjk_A           84 KDGDVVGVF   92 (98)
T ss_dssp             CTTCEEEEE
T ss_pred             CCCCEEEEE
Confidence            899999875

>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=91.70  E-value=0.39  Score=34.64  Aligned_cols=72  Identities=17%  Similarity=0.206  Sum_probs=43.4

Q ss_pred             CCCCcceEEEEEeCC------C--Ceee-ecCC---CCcHHHHHHHHHhhhCCCCCCCceEEEeC-Ce------ecCCCC
Q psy4259           2 GMLAHDISDITQNQW------Q--QTVS-HLDV---QEEVKQLKEKIQSEKGSEYLAEYQKLIYA-GK------ILSDDQ   62 (203)
Q Consensus         2 ~~~~~~m~I~Vk~~~------g--~~~~-~v~~---~~TV~~LK~~I~~~~~~~ip~~~qkLi~~-Gk------~L~D~~   62 (203)
                      +|. +.|+|+|+...      |  +.+. +++.   ..||.+|.+.+.+.+.    ..+-+|+.. |+      +|-|+.
T Consensus         7 ~~~-~~M~v~V~~~~~Lr~~~g~~~~~~vel~~~~~~~TV~~Ll~~L~~~~~----~~~~~lf~~~g~lr~~i~VlVN~~   81 (114)
T 1wgk_A            7 GMA-APLCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLL----KERPELFIQGDSVRPGILVLINDA   81 (114)
T ss_dssp             CCC-CCEEEEEEECTTTGGGTTTCSEEEEEECCCSSCCBHHHHHHHHTTTTC----CSCHHHHCCSSSCCSSEEEEESSS
T ss_pred             ccC-CCcEEEEEEchHHHHHhCCceEEEEEeCCCCCCCCHHHHHHHHHHHcc----chhHhhCccCCcccCCeEEEECCe
Confidence            444 67999999864      2  2445 6663   3699999999988863    112222211 21      233332


Q ss_pred             ---Cc--cccccCCCCEEEEE
Q psy4259          63 ---AL--SEYNIDESKFIVVM   78 (203)
Q Consensus        63 ---tL--~~~gI~~~~~i~v~   78 (203)
                         .|  .++-+++||.|.++
T Consensus        82 di~~l~gldt~L~dGDeV~ii  102 (114)
T 1wgk_A           82 DWELLGELDYQLQDQDSILFI  102 (114)
T ss_dssp             BHHHHCTTTCBCCSSEEEEEE
T ss_pred             eeeccCCcCcCCCCCCEEEEe
Confidence               22  34679999998875

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=91.50  E-value=0.65  Score=31.88  Aligned_cols=62  Identities=8%  Similarity=0.056  Sum_probs=42.3

Q ss_pred             cceEEEEEeCCCCeeeecCCC-CcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           6 HDISDITQNQWQQTVSHLDVQ-EEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~~v~~~-~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ..|+|+|.   |+.+ +++.. .||.+|.+.+    +  ++.....+..+|.++..+ ...+..+++||.|.++
T Consensus        19 ~~M~I~vN---Ge~~-el~~~~~Tv~dLL~~L----~--~~~~~vaVavNg~iV~~~-~~~~~~L~dGD~Vei~   81 (87)
T 1tyg_B           19 GRHMLQLN---GKDV-KWKKDTGTIQDLLASY----Q--LENKIVIVERNKEIIGKE-RYHEVELCDRDVIEIV   81 (87)
T ss_dssp             ---CEEET---TEEE-CCSSSCCBHHHHHHHT----T--CTTSCCEEEETTEEECGG-GTTTSBCCSSSEEEEE
T ss_pred             cceEEEEC---CEEE-ECCCCCCcHHHHHHHh----C--CCCCCEEEEECCEECChh-hcCCcCCCCCCEEEEE
Confidence            35666654   3322 55565 7999998865    5  667778888999988543 4555678999999876

>3onh_A Ubiquitin-activating enzyme E1-like; ligase, SUMO conjugation, UBC9; 1.60A {Saccharomyces cerevisiae} PDB: 3ong_A

Probab=90.02  E-value=0.78  Score=33.77  Aligned_cols=51  Identities=20%  Similarity=0.261  Sum_probs=36.3

Q ss_pred             CCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeec-----CCC--CCccccccCCCCEEEEEe
Q psy4259          26 QEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKIL-----SDD--QALSEYNIDESKFIVVML   79 (203)
Q Consensus        26 ~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L-----~D~--~tL~~~gI~~~~~i~v~~   79 (203)
                      ..|+.+|-+.|..++|  +.. ...++-  ..+.|     +|.  ++|+++||+.|++|.|+=
T Consensus        19 ~~TL~dLV~~l~~~~g--y~~-eiSV~~~~~~rLLyD~DfDDnl~k~L~dLgv~~gsfLtv~D   78 (127)
T 3onh_A           19 KMKLSDFVVLIREKYS--YPQ-DISLLDASNQRLLFDYDFEDLNDRTLSEINLGNGSIILFSD   78 (127)
T ss_dssp             HCBHHHHHHHHHHHHT--CCS-SEEEEETTTTEEEEETTBCTTTTSBTTTTTCCTTCEEEEEE
T ss_pred             ccCHHHHHHHHHHhcC--CCC-cEEEEecCCCCeEeCCCccccccCcHHHcCcCCCcEEEEEc
Confidence            4789998888888888  653 444432  22333     333  799999999999998763

>3hm6_X Plexin-B1; structural genomics consortium, SGC, membrane, transmembrane receptor, cell membrane, glycoprotein, phosphoprotein; 2.40A {Homo sapiens} PDB: 3sua_D* 3su8_X*

Probab=89.02  E-value=2.2  Score=39.38  Aligned_cols=75  Identities=17%  Similarity=0.192  Sum_probs=48.3

Q ss_pred             ceEEEEEeCCC------Ceee-ecCCCCcHHHHHHHHHhhhCCCCC------CCceEEEeC----Ce-ecCCCC------
Q psy4259           7 DISDITQNQWQ------QTVS-HLDVQEEVKQLKEKIQSEKGSEYL------AEYQKLIYA----GK-ILSDDQ------   62 (203)
Q Consensus         7 ~m~I~Vk~~~g------~~~~-~v~~~~TV~~LK~~I~~~~~~~ip------~~~qkLi~~----Gk-~L~D~~------   62 (203)
                      ++.|.|-...|      ..+. .|-..+||.++|++|....=+..|      ++.+-|-|.    |+ +|.|..      
T Consensus       257 ~ltL~v~~~~~~~~~~~~~i~VkVLdCDTItQVKeKiLDavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~  336 (644)
T 3hm6_X          257 PLTLNALLAVGPGAGEAQGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQ  336 (644)
T ss_dssp             EEEEEEECC-------CCCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECSSSCEEEECSSSTTCCEE
T ss_pred             eEEEEEeecCccccCCCCceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCCcceEEeeCCCCceeecccCccceec
Confidence            35666554332      2355 777899999999999966432222      455666662    33 466532      


Q ss_pred             -------CccccccCCCCEEEEEeec
Q psy4259          63 -------ALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        63 -------tL~~~gI~~~~~i~v~~~k   81 (203)
                             ||+.|+|.+|++|.++-+.
T Consensus       337 ~~wkrLNTL~HY~V~dga~v~L~p~~  362 (644)
T 3hm6_X          337 GLWRRLNTLQHYKVPDGATVALVPCL  362 (644)
T ss_dssp             TTEEECCBTTTTTCCTTCEEEEEEC-
T ss_pred             CcceeecchhhcCCCCCcEEEEEecc
Confidence                   7899999999999876433

>2lnm_A Protein TIC 40, chloroplastic; translocon, import, TIC40-NP, protein transport; NMR {Arabidopsis thaliana}

Probab=88.78  E-value=0.39  Score=30.73  Aligned_cols=46  Identities=15%  Similarity=0.302  Sum_probs=29.6

Q ss_pred             HHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHH
Q psy4259         135 LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRML  187 (203)
Q Consensus       135 l~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml  187 (203)
                      ++.+++||.+..+    ++||+++. +++++. +||...+-..+|| .++.++
T Consensus         5 ~~kl~~dPe~~~~----m~dP~~~~-~lq~i~-~NP~~~~~~~~dP-~v~~~~   50 (62)
T 2lnm_A            5 ISKIMENPDVAMA----FQNPRVQA-ALMECS-ENPMNIMKYQNDK-EVMDVF   50 (62)
T ss_dssp             HHHHTTSHHHHHH----TTSHHHHH-HHHHHT-TCGGGHHHHTTCH-HHHHHH
T ss_pred             HHHHHcChHHHHH----cCCHHHHH-HHHHHH-HCHHHHHHHHhCh-HHHHHH
Confidence            5678888974333    47888765 465554 5788666666776 454443

>1wgy_A RAP guanine nucleotide exchange factor 5; ubiquitin fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=88.49  E-value=4.2  Score=28.82  Aligned_cols=77  Identities=17%  Similarity=0.173  Sum_probs=54.5

Q ss_pred             CCCCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE---eCC--eecCCCCCccccccCCCCEE
Q psy4259           2 GMLAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI---YAG--KILSDDQALSEYNIDESKFI   75 (203)
Q Consensus         2 ~~~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi---~~G--k~L~D~~tL~~~gI~~~~~i   75 (203)
                      |..++++-..|-..+...++ .+..+.|+.+++..++.+.+  +..+.+.|.   ++|  .+|++++.--.-.+.-+..|
T Consensus         4 ~~~sD~i~~~Vy~~Dhsy~tvr~~v~~sa~eIl~~va~kl~--~~~e~l~Lv~v~ssGEk~~lqp~d~si~tsL~~NgRL   81 (104)
T 1wgy_A            4 GSSGEEIFCHVYITEHSYVSVKAKVSSIAQEILKVVAEKIQ--YAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRI   81 (104)
T ss_dssp             CCCSSCCCEEEECSSSCEEEECCCTTCBSHHHHHHHHHHHT--SCGGGEEEEEECSSCCCCBCCTTSBSSCCSSCSSCEE
T ss_pred             CCCCCceEEEEEeccCceEEEEEeccchHHHHHHHHHHHhc--CCccceEEEEEccCCcEeecCCcceEEEeeccccceE
Confidence            45667787888877777777 88899999999999999998  776677765   677  34565543222234446677


Q ss_pred             EEEee
Q psy4259          76 VVMLS   80 (203)
Q Consensus        76 ~v~~~   80 (203)
                      ++-.+
T Consensus        82 fvc~k   86 (104)
T 1wgy_A           82 YVYRK   86 (104)
T ss_dssp             EEEEC
T ss_pred             EEeeh
Confidence            65443

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=87.17  E-value=3.6  Score=37.89  Aligned_cols=75  Identities=16%  Similarity=0.236  Sum_probs=49.8

Q ss_pred             ceEEEEEeCCC---Ceee-ecCCCCcHHHHHHHHHhhhCCCC------CCCceEEEe----CCe-ecCCC----------
Q psy4259           7 DISDITQNQWQ---QTVS-HLDVQEEVKQLKEKIQSEKGSEY------LAEYQKLIY----AGK-ILSDD----------   61 (203)
Q Consensus         7 ~m~I~Vk~~~g---~~~~-~v~~~~TV~~LK~~I~~~~~~~i------p~~~qkLi~----~Gk-~L~D~----------   61 (203)
                      ++.|.|-...+   ..+. .|-..+||.++|++|....=+..      .++.+-|-|    .|+ +|.|.          
T Consensus       233 ~ltL~v~~~~~~~~~~i~vkVLdCDTItQVKeKiLdavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~w  312 (627)
T 3ig3_A          233 TLTLHCVCPESEGSAQVPVKVLNCDSITQAKDKLLDTVYKGIPYSQRPKAEDMDLEWRQGRMARIILQDEDITTKIECDW  312 (627)
T ss_dssp             EEEEEEECTTTC--CEEEEEEETTCBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEESCSSCEEEECSSSTTCCEETTE
T ss_pred             eEEEEEeccCCCCCCceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCccceeEeeCCCCceeeccCCccccccCce
Confidence            35666654432   3455 77789999999999997753322      345666665    233 35542          


Q ss_pred             ---CCccccccCCCCEEEEEeec
Q psy4259          62 ---QALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus        62 ---~tL~~~gI~~~~~i~v~~~k   81 (203)
                         .||..|+|.+|++|.++-+.
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               26889999999999876544

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=87.07  E-value=4.8  Score=26.85  Aligned_cols=55  Identities=9%  Similarity=0.089  Sum_probs=38.7

Q ss_pred             Ceee-ecCCCCcHHHHHHHHHhhhCCCC-----CC-----CceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          18 QTVS-HLDVQEEVKQLKEKIQSEKGSEY-----LA-----EYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        18 ~~~~-~v~~~~TV~~LK~~I~~~~~~~i-----p~-----~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      +... +++...||.+|.+.+...+.. +     ..     ....+..+|+....     +.-+++||.|.++
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~-~~~~~l~~~g~l~~~~~v~VN~~~v~~-----~~~l~~gDeV~i~   83 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPA-LESRVFGDDGELYDHINVLRNGEAAAL-----GEATAAGDELALF   83 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGG-GHHHHBCTTSCBCTTSEEEETTEECCT-----TSBCCTTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcH-HHHHHhccCCcccccEEEEECCEECCC-----CcccCCCCEEEEE
Confidence            4455 777788999999999877531 1     00     12566778888764     4568889999876

>2juj_A E3 ubiquitin-protein ligase CBL; alpha helix, UBA domain, calcium, cytoplasm, metal- binding, phosphorylation, proto-oncogene, SH2 domain; NMR {Homo sapiens}

Probab=85.69  E-value=0.12  Score=32.43  Aligned_cols=15  Identities=0%  Similarity=0.120  Sum_probs=13.5

Q ss_pred             hhhHHHHHhCCcCCC
Q psy4259         110 TATSDSMLKVFFERV  124 (203)
Q Consensus       110 ~~~v~~~~~mG~~~~  124 (203)
                      +..|+.||+|||.|+
T Consensus         8 e~~Ia~L~smGfsr~   22 (56)
T 2juj_A            8 SSEIENLMSQGYSYQ   22 (56)
T ss_dssp             HHHHHHHHTTTCCHH
T ss_pred             hHHHHHHHHcCCCHH
Confidence            789999999999764

>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=85.62  E-value=5.3  Score=32.62  Aligned_cols=72  Identities=14%  Similarity=0.170  Sum_probs=52.8

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCC-ceEEEe---CC--eecCCCCCccccccCCCCEEEEEe
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAE-YQKLIY---AG--KILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~-~qkLi~---~G--k~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      +|.|.|...+| ++. .|+.++|+.+|=+.|....|  +... -.-|.|   +|  ..|+.++++.+.+++.+..+.+..
T Consensus         1 ~i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~--L~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l~f   77 (294)
T 1ef1_A            1 TISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIG--LREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKF   77 (294)
T ss_dssp             CEEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHT--CCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEE
T ss_pred             CEEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcC--CCCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEEEE
Confidence            47889999988 678 99999999999999999999  5443 335554   34  347777888887766655554444


Q ss_pred             ec
Q psy4259          80 SK   81 (203)
Q Consensus        80 ~k   81 (203)
                      ++
T Consensus        78 r~   79 (294)
T 1ef1_A           78 RA   79 (294)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>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=85.58  E-value=4.9  Score=27.59  Aligned_cols=49  Identities=8%  Similarity=0.091  Sum_probs=38.4

Q ss_pred             CCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCc-eEEEeCC
Q psy4259           4 LAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEY-QKLIYAG   55 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~-qkLi~~G   55 (203)
                      ++..|+|++. ..|..+. .++++.+..+|.++|...++  +..++ ..|-|..
T Consensus         3 ~~~~vkvK~~-~~gdi~~~~v~~~i~~~~L~~kv~~~~~--~~~~~~f~lky~D   53 (89)
T 1vd2_A            3 LGSQVRVKAY-YRGDIMITHFEPSISFEGLCNEVRDMCS--FDNEQLFTMKWID   53 (89)
T ss_dssp             CSSCEEEEEE-SSSCEEEEEECTTCCHHHHHHHHHHHTT--CCSSCCEEEEECC
T ss_pred             CCCeEEEEEE-eCCeEEEEECCCCCCHHHHHHHHHHHhC--CCCCCeEEEEEEC
Confidence            4456777777 3466777 99999999999999999999  76544 6888864

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=84.52  E-value=7.4  Score=28.44  Aligned_cols=60  Identities=25%  Similarity=0.218  Sum_probs=38.6

Q ss_pred             eee-ecCCCCcHHHHHHHHHhhhC--CCCC----CCceEEEeC-C---eecCC----------C----CCccccccCCCC
Q psy4259          19 TVS-HLDVQEEVKQLKEKIQSEKG--SEYL----AEYQKLIYA-G---KILSD----------D----QALSEYNIDESK   73 (203)
Q Consensus        19 ~~~-~v~~~~TV~~LK~~I~~~~~--~~ip----~~~qkLi~~-G---k~L~D----------~----~tL~~~gI~~~~   73 (203)
                      .+. .|-..+||.++|++|....-  +.+|    ++.+.|-|. |   .+|.|          .    .||..|+|.+|+
T Consensus        40 ~v~VkVLdCDTItQVKEKILdavYk~k~~pys~r~~d~dLEwr~g~~~~~L~D~D~tS~~~e~~wkrLNTL~HY~V~Dga  119 (126)
T 3kuz_A           40 NISVNVLDCDTIGQAKEKIFQAFLSKNGSPYGLQLNEIGLELQMGTRQKELLDIDSSSVILEDGITKLNTIGHYEISNGS  119 (126)
T ss_dssp             EEEEEEETTCBHHHHHHHHHHHHHHHHSSCCSSCGGGEEEEEEETTEEEEECSSCTTCCBCTTSCBCCCBTGGGTCCTTC
T ss_pred             ceEeeeecCCcHHHHHHHHHHHHhccCCCcCCCCccccceEEecCCCcceeeccCCcceEecCCeeEeccccccCCCCCC
Confidence            355 77788999999999976531  1133    344555551 2   33333          1    256779999999


Q ss_pred             EEEEE
Q psy4259          74 FIVVM   78 (203)
Q Consensus        74 ~i~v~   78 (203)
                      +|-++
T Consensus       120 tlal~  124 (126)
T 3kuz_A          120 TIKVF  124 (126)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            99764

>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei}

Probab=84.14  E-value=0.72  Score=33.03  Aligned_cols=68  Identities=13%  Similarity=0.155  Sum_probs=40.5

Q ss_pred             ceEEEEEeCC------CCeee-ecCC----CCcHHHHHHHHHhhhCCCCCCCceEEEe-CC--e------ecCCCCCc--
Q psy4259           7 DISDITQNQW------QQTVS-HLDV----QEEVKQLKEKIQSEKGSEYLAEYQKLIY-AG--K------ILSDDQAL--   64 (203)
Q Consensus         7 ~m~I~Vk~~~------g~~~~-~v~~----~~TV~~LK~~I~~~~~~~ip~~~qkLi~-~G--k------~L~D~~tL--   64 (203)
                      .|+|+|+...      |+... +++.    ..||.+|-..+.+.+.    ..+-+|+. +|  .      +|-|+..+  
T Consensus         4 ~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            4 HNHITVQFAGGCELLFAKQTSLQLDGVVPTGTNLNGLVQLLKTNYV----KERPDLLVDQTGQTLRPGILVLVNSCDAEV   79 (110)
T ss_dssp             SSCCEEEEESSCGGGTTSCSEECCCCSCGGGCCHHHHHHHHTTTTC----CSCHHHHBCSSSSSBCTTEEEEESSSBHHH
T ss_pred             ccEEEEEEEecHHHHhCCeEEEEeCCcCCCCccHHHHHHHHHHHcc----ccchhhEecCCCcccCCCeEEEECCeeeec
Confidence            5788887754      34444 6652    2599998888887754    22333321 23  1      34444332  


Q ss_pred             ---cccccCCCCEEEEE
Q psy4259          65 ---SEYNIDESKFIVVM   78 (203)
Q Consensus        65 ---~~~gI~~~~~i~v~   78 (203)
                         .+|-+++||.|.++
T Consensus        80 l~gldt~L~dgD~V~fi   96 (110)
T 2k9x_A           80 VGGMDYVLNDGDTVEFI   96 (110)
T ss_dssp             HTSSCCCCCSSCEEEEE
T ss_pred             cCCcccCCCCcCEEEEe
Confidence               24679999998775

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=84.03  E-value=1.8  Score=27.52  Aligned_cols=50  Identities=12%  Similarity=0.198  Sum_probs=36.6

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ++....||.+|.+.+    +  ++.....+..+|+.+..+ ...+.-+++||.|.++
T Consensus        11 ~~~~~~tv~~ll~~l----~--~~~~~v~vavN~~~v~~~-~~~~~~L~~gD~v~i~   60 (66)
T 1f0z_A           11 QCAAGQTVHELLEQL----D--QRQAGAALAINQQIVPRE-QWAQHIVQDGDQILLF   60 (66)
T ss_dssp             CCCTTCCHHHHHHHH----T--CCCSSEEEEETTEEECHH-HHTTCCCCTTEEECEE
T ss_pred             EcCCCCcHHHHHHHc----C--CCCCCEEEEECCEECCch-hcCCcCCCCCCEEEEE
Confidence            555668999998876    5  667777888899888542 2334568889999876

>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=83.65  E-value=5.5  Score=33.85  Aligned_cols=72  Identities=13%  Similarity=0.061  Sum_probs=53.5

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCC---------eecCCCCCccccccCCCCEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAG---------KILSDDQALSEYNIDESKFIV   76 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~G---------k~L~D~~tL~~~gI~~~~~i~   76 (203)
                      .+.+.|..++|.... .|+.+.|+.+|=+.|....|. ...+-.-|.+..         ..|+-++++.+.++....+++
T Consensus        85 ~~~~~V~l~dg~~~~~~vd~~tt~~el~~~v~~~l~L-~e~~~FgL~~~~~~~~~~~~~~wL~~~k~l~~q~~~~~~~l~  163 (371)
T 3ivf_A           85 QRPLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGI-TNHDEYSLVRELMEEKKDDELNWLDHGRTLREQGVEEHETLL  163 (371)
T ss_dssp             EEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHTTC-SCGGGEEEECCC----------CCCTTSBTGGGTCCTTCEEE
T ss_pred             eeEEEEECcCCCEEEEEECCCCCHHHHHHHHHHHcCC-CCccccEEEEEecccccchHHHHHhcCchhHhhCCCCCceEE
Confidence            477889999999999 999999999999999999993 234445665532         346666777777766666766


Q ss_pred             EEe
Q psy4259          77 VML   79 (203)
Q Consensus        77 v~~   79 (203)
                      +.+
T Consensus       164 frv  166 (371)
T 3ivf_A          164 LRR  166 (371)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            643

>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=83.33  E-value=0.4  Score=31.88  Aligned_cols=9  Identities=44%  Similarity=0.770  Sum_probs=4.5

Q ss_pred             HHhCCCcHH
Q psy4259         151 VQQNPELLP  159 (203)
Q Consensus       151 i~~nP~~l~  159 (203)
                      -.+||++++
T Consensus        37 ~~~NPqL~q   45 (72)
T 1pve_A           37 GRENPQLLQ   45 (72)
T ss_dssp             HTTCHHHHH
T ss_pred             HhHCHHHHH
Confidence            345666543

>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=83.27  E-value=6.4  Score=26.51  Aligned_cols=69  Identities=4%  Similarity=0.028  Sum_probs=41.9

Q ss_pred             eEEEEEeCC------CCeee-ecCCCCcHHHHHHHHHhhhCCC---C-C-------CCceEEEeCCeecCCCCCcccccc
Q psy4259           8 ISDITQNQW------QQTVS-HLDVQEEVKQLKEKIQSEKGSE---Y-L-------AEYQKLIYAGKILSDDQALSEYNI   69 (203)
Q Consensus         8 m~I~Vk~~~------g~~~~-~v~~~~TV~~LK~~I~~~~~~~---i-p-------~~~qkLi~~Gk~L~D~~tL~~~gI   69 (203)
                      |+|+|+...      |+... ++ ...||.+|.+.+...++.-   + .       .....+..+|+...+...+ +.-+
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            556666542      33334 54 3579999999998875310   0 1       0135666788877643222 3468


Q ss_pred             CCCCEEEEE
Q psy4259          70 DESKFIVVM   78 (203)
Q Consensus        70 ~~~~~i~v~   78 (203)
                      ++||.|.++
T Consensus        79 ~~gDeV~i~   87 (93)
T 3dwg_C           79 ADGDSVTIL   87 (93)
T ss_dssp             CTTCEEEEE
T ss_pred             CCCCEEEEE
Confidence            999999876

>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=82.92  E-value=0.34  Score=28.50  Aligned_cols=15  Identities=7%  Similarity=0.096  Sum_probs=12.9

Q ss_pred             hhhHHHHHhCCcCCC
Q psy4259         110 TATSDSMLKVFFERV  124 (203)
Q Consensus       110 ~~~v~~~~~mG~~~~  124 (203)
                      ++.|+.|++|||+++
T Consensus         5 e~~i~~L~~MGF~~~   19 (43)
T 2g3q_A            5 SLAVEELSGMGFTEE   19 (43)
T ss_dssp             HHHHHHHHTTTSCHH
T ss_pred             HHHHHHHHHcCCCHH
Confidence            678999999999754

>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=82.11  E-value=1.7  Score=28.76  Aligned_cols=15  Identities=13%  Similarity=0.315  Sum_probs=13.4

Q ss_pred             hhhHHHHHhCCcCCC
Q psy4259         110 TATSDSMLKVFFERV  124 (203)
Q Consensus       110 ~~~v~~~~~mG~~~~  124 (203)
                      ++.|+.|++|||+++
T Consensus        30 ee~I~~L~eMGF~r~   44 (73)
T 1vg5_A           30 EEQIQKLVAMGFDRT   44 (73)
T ss_dssp             HHHHHHHHTTTCCHH
T ss_pred             HHHHHHHHHcCCCHH
Confidence            789999999999764

>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=81.71  E-value=6.6  Score=32.43  Aligned_cols=73  Identities=10%  Similarity=0.077  Sum_probs=53.6

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCC-CceEEEe--CC--eecCCCCCccccccCCCCEEEEEe
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLA-EYQKLIY--AG--KILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~-~~qkLi~--~G--k~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      ..+.+.|...+| ++. .|+.++|+.+|=+.|....|  +.. +-.-|.|  +|  ..|+.+++|.+.+++.+..+.+..
T Consensus        21 ~~~~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~--L~e~~~FgL~~~~~~~~~wL~~~~~i~~q~~~~~~~~~l~f   97 (314)
T 1h4r_A           21 KTFTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLG--LRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHF   97 (314)
T ss_dssp             CEEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHT--CCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEE
T ss_pred             CeeEEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhC--CCCCccceEEEEeCCcCeeCCCccCHHHcCCCCCCCEEEEE
Confidence            357889999998 788 99999999999999999999  544 3334544  44  347778888887766555544443


Q ss_pred             ec
Q psy4259          80 SK   81 (203)
Q Consensus        80 ~k   81 (203)
                      ++
T Consensus        98 r~   99 (314)
T 1h4r_A           98 LA   99 (314)
T ss_dssp             EE
T ss_pred             EE
Confidence            33

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=80.90  E-value=4.5  Score=26.14  Aligned_cols=52  Identities=8%  Similarity=0.119  Sum_probs=37.6

Q ss_pred             eee-ecCCCCcHHHHHHHHHhhhCCCCCCCce--EEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259          19 TVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQ--KLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus        19 ~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~q--kLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ... ++....||.+|.+.+...++.   ....  .+..+|+....+     .-+++||.|.++
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~p~---~~~v~~~v~vNg~~v~~~-----~~L~~gD~V~i~   71 (77)
T 2q5w_D           17 QEDIVLEQALTVQQFEDLLFERYPQ---INNKKFQVAVNEEFVQKS-----DFIQPNDTVALI   71 (77)
T ss_dssp             EEECCCSSCEEHHHHHHHHHHHCGG---GTTCCCEEEETTEEECTT-----SEECTTCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCcc---hhcceEEEEECCEECCCC-----CCcCCCCEEEEE
Confidence            345 777778999999998876431   1233  677899888653     568899999875

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=80.49  E-value=1.4  Score=32.50  Aligned_cols=30  Identities=7%  Similarity=0.166  Sum_probs=26.8

Q ss_pred             ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe
Q psy4259          22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY   53 (203)
Q Consensus        22 ~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~   53 (203)
                      .|..+.|+.+||..|+..+|  ++++++||-+
T Consensus        61 rv~k~~~~~~~~~~va~~lg--~~~~~~RlW~   90 (130)
T 2kvr_A           61 KVLKNSSLAEFVQSLSQTMG--FPQDQIRLWP   90 (130)
T ss_dssp             ECCTTSBHHHHHHHHHHHHC--CCGGGCEEEE
T ss_pred             EEeccCcHHHHHHHHHHHhC--CCcccEEEEE
Confidence            55678999999999999999  9999999854

>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=80.21  E-value=7.3  Score=35.52  Aligned_cols=74  Identities=9%  Similarity=0.109  Sum_probs=54.4

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCC-CceEEEeC---C--eecCCCCCccccccCCCCEEEE
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLA-EYQKLIYA---G--KILSDDQALSEYNIDESKFIVV   77 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~-~~qkLi~~---G--k~L~D~~tL~~~gI~~~~~i~v   77 (203)
                      +..+.|.|..++| ++. .|+.++|+.+|=..|+...|  +.. +-.-|.|.   |  ..|+.+++|.+.+++.+..+.+
T Consensus         2 ~k~i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~Lg--L~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L   78 (575)
T 2i1j_A            2 PKSMNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIG--LREVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQF   78 (575)
T ss_dssp             -CEEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHT--CCCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEE
T ss_pred             CceEEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcC--CCCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEE
Confidence            3468899999998 678 99999999999999999999  543 34455552   2  4577778888877766665554


Q ss_pred             Eeec
Q psy4259          78 MLSK   81 (203)
Q Consensus        78 ~~~k   81 (203)
                      ..++
T Consensus        79 ~FRv   82 (575)
T 2i1j_A           79 KFRA   82 (575)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            4443

---

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	203
d2f4mb1	58	a.189.1.1 (B:275-332) XPC-binding domain of Rad23	5e-26
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	8e-14
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	2e-12
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	2e-11
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	2e-11
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	3e-10
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	2e-09
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	2e-08
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	3e-08
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	4e-08
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	8e-08
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	1e-07
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	1e-07
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	1e-07
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	1e-07
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	2e-07
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	3e-07
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	3e-07
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	7e-07
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	9e-07
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	1e-06
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	2e-06
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	3e-06
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	4e-06
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	4e-06
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	2e-05
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	3e-05
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	5e-05
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	1e-04
d1x3zb1	57	a.189.1.1 (B:253-309) Rad23 STI1 domain {Baker's y	1e-04
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	2e-04
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	8e-04
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	0.001

>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 = 92.8 bits (231), Expect = 5e-26
 Identities = 40/58 (68%), Positives = 48/58 (82%)

Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
           PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEPV
Sbjct: 1   PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 58

>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 = 62.6 bits (152), Expect = 8e-14
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 12 TQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI- 69
          + NQ  + +    D    V  LK  +          E Q+LIY+GK+L D Q L +    
Sbjct: 14 SPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPK 73

Query: 70 DESKFIVVMLSKPKPTPA 87
           E + ++ ++   K  P+
Sbjct: 74 QEKRHVLHLVCNVKSGPS 91

>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 = 57.9 bits (140), Expect = 2e-12
 Identities = 31/61 (50%), Positives = 44/61 (72%), Gaps = 3/61 (4%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          + ++ +  VK LKEKI++EKG + +    QKLIYAGKILSDD  + +Y IDE  F+VVM+
Sbjct: 17 IRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMV 76

Query: 80 S 80
          +
Sbjct: 77 T 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 = 56.2 bits (135), Expect = 2e-11
 Identities = 40/78 (51%), Positives = 50/78 (64%), Gaps = 1/78 (1%)

Query: 22 HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
           +D +E VK LKEKI+SEKG + +    QKLIYAGKIL+DD AL EY IDE  F+VVM++
Sbjct: 16 DIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVT 75

Query: 81 KPKPTPAPYSGPSDPTQP 98
          KPK    P     +    
Sbjct: 76 KPKAVSTPAPATLEHHHH 93

>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 = 56.1 bits (135), Expect = 2e-11
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 17 QQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKIL-SDDQALSEYNIDESKFI 75
           + ++    ++ V  LK K    + S+      KLIY G++L    + LS  NI  +  I
Sbjct: 18 TEELAVARPEDTVGTLKSKYFPGQESQ-----MKLIYQGRLLQDPARTLSSLNITNNCVI 72

Query: 76 VVMLSKPKPTPAPYSGPSDPT 96
              S P    +  S  S P+
Sbjct: 73 HCHRSPPGAAVSGPSASSGPS 93

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 116

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.4 bits (128), Expect = 3e-10
 Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 6/78 (7%)

Query: 29  VKQLKEKIQSEKGSE------YLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
              + + +      +            +LIY G+ L  +  L    +   K  V+ L   
Sbjct: 39  ASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 98

Query: 83  KPTPAPYSGPSDPTQPAG 100
           +  P P S        +G
Sbjct: 99  ETLPEPNSQGQRSGPSSG 116

>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 = 50.7 bits (121), Expect = 2e-09
 Identities = 14/87 (16%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 2  GMLAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSD 60
          G+   ++    + +  +       +    ++L+ KI    G +    Y K++   K L  
Sbjct: 14 GIATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQ--ENYIKIVINKKQLQL 71

Query: 61 DQALSEYNIDESKFIVVMLSKPKPTPA 87
           + L E  +  +   +V+  K    P+
Sbjct: 72 GKTLEEQGVAHNVKAMVLELKQSSGPS 98

>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 = 48.1 bits (114), Expect = 2e-08
 Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 7/98 (7%)

Query: 2   GMLAHDISDITQNQWQQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILS 59
           GML   +  + ++  + T S L V  +  +   +   + E G     E  +++Y  ++L+
Sbjct: 7   GMLIT-VYCVRRDLTEVTFS-LQVNPDFELSNFRVLCELESGVPA--EEAQIVYMEQLLT 62

Query: 60  D-DQALSEYNIDESKFIVVMLSKPKPTPAPYSGPSDPT 96
           D   +L  Y + +   +V++         P   PS P+
Sbjct: 63  DDHCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTPSGPS 100

>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 = 46.7 bits (111), Expect = 3e-08
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 4/61 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          ++V  E  V Q KE I    G       Q+LIY+GKIL DDQ +  Y+I +   + ++ S
Sbjct: 15 VNVAPESTVLQFKEAINKANG--IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 72

Query: 81 K 81
          +
Sbjct: 73 Q 73

>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 = 47.2 bits (112), Expect = 4e-08
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 9  SDITQNQWQ---QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQAL 64
          +   + +W+   Q +   L + ++V  +K KI         A  QKL Y G  + D  +L
Sbjct: 10 NMQDKTEWKLNGQVLVFTLPLTDQVSVIKVKIHEAT--GMPAGKQKLQYEGIFIKDSNSL 67

Query: 65 SEYNIDESKFIVVML 79
          + YN+     I + L
Sbjct: 68 AYYNMANGAVIHLAL 82

>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 = 45.6 bits (108), Expect = 8e-08
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
            V  +  VK+ KE I +       +E Q+LIY G++L DD+ L EYN+      +V   
Sbjct: 15 FIVGAQMNVKEFKEHIAASVSIP--SEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLV-ER 71

Query: 81 KP 82
           P
Sbjct: 72 AP 73

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.0 bits (109), Expect = 1e-07
 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 27 EEVKQLKEKIQSE-KGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
            +  LK+ I  + + S    E   LIY G+ L DDQ L  Y I     + V+ 
Sbjct: 38 YSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLR 91

>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 = 45.3 bits (107), Expect = 1e-07
 Identities = 15/65 (23%), Positives = 34/65 (52%), Gaps = 4/65 (6%)

Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKF 74
           +T +  DV  +  +++L+E++ +        E Q+L Y GK L +   L +Y++  +  
Sbjct: 11 SKTCTIEDVSRKATIEELRERVWALFD--VRPECQRLFYRGKQLENGYTLFDYDVGLNDI 68

Query: 75 IVVML 79
          I +++
Sbjct: 69 IQLLV 73

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.4 bits (107), Expect = 1e-07
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 17 QQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY---AGKILSDDQALSEYNIDESK 73
          + +V+ L   + V  LK+ +++  G     E QKL+     GK   +D  L    +  + 
Sbjct: 18 EYSVTTLSEDDTVLDLKQFLKTLTGVL--PERQKLLGLKVKGKPAENDVKLGALKLKPNT 75

Query: 74 FIVVMLSKPKPTPAPYSG 91
           I++M ++      P SG
Sbjct: 76 KIMMMGTRES---GPSSG 90

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.3 bits (107), Expect = 1e-07
 Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          L V+    V  +K ++ + +G       Q+  ++G+ L+D     E  I +   + V++S
Sbjct: 18 LVVRSTDTVFHMKRRLHAAEG--VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVS 75

Query: 81 KPKP 84
          +P  
Sbjct: 76 QPVQ 79

>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 = 45.6 bits (108), Expect = 2e-07
 Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 4/60 (6%)

Query: 15 QWQQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
          +  +T    D +E   V +LK  ++         + Q+L    ++L D + L E      
Sbjct: 7  RRHKTTIFTDAKESSTVFELKRIVEGILK--RPPDEQRLYKDDQLLDDGKTLGECGFTSQ 64

>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 = 44.9 bits (106), Expect = 3e-07
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 9/69 (13%)

Query: 29 VKQLKEKIQSE-----KGSEYLAEYQKLIYAGKILSDDQALSEYNID----ESKFIVVML 79
          V  LKE + SE     +      +  KLI AGK+L + + + +Y             + +
Sbjct: 31 VSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHV 90

Query: 80 SKPKPTPAP 88
              P    
Sbjct: 91 IIQAPVTEK 99

>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 = 44.1 bits (104), Expect = 3e-07
 Identities = 21/60 (35%), Positives = 37/60 (61%), Gaps = 4/60 (6%)

Query: 22 HLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
           L+V+    ++ +K KIQ ++G     + Q+LI+AGK L D + LS+YNI +   + ++L
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71

>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 = 43.3 bits (102), Expect = 7e-07
 Identities = 12/63 (19%), Positives = 26/63 (41%), Gaps = 6/63 (9%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIY--AGKILSDDQALSEYNIDESKFIVVM 78
          + +     V +LK +I  +      A  Q+L    +G  L D   L+   +     ++++
Sbjct: 15 VSLSSSMSVSELKAQITQKI--GVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLV 72

Query: 79 LSK 81
          + K
Sbjct: 73 VDK 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 = 43.0 bits (101), Expect = 9e-07
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 4/69 (5%)

Query: 15 QWQQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
            +QT +   +     V++L+ KIQ           Q+L Y GK + D   L +Y +  +
Sbjct: 9  DGRQTHTVDSLSRLTKVEELRRKIQELFH--VEPGLQRLFYRGKQMEDGHTLFDYEVRLN 66

Query: 73 KFIVVMLSK 81
            I +++ +
Sbjct: 67 DTIQLLVRQ 75

>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 = 42.5 bits (100), Expect = 1e-06
 Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 3/64 (4%)

Query: 19 TVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILS-DDQALSEYNIDESKFIVV 77
          T      +  V+ L + ++   G      +QKLI+ GK L   +  LS   I +   +++
Sbjct: 18 TSQQGSSEPVVQDLAQVVEEVIG--VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVML 75

Query: 78 MLSK 81
          +  K
Sbjct: 76 IGKK 79

>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 = 41.8 bits (98), Expect = 2e-06
 Identities = 18/60 (30%), Positives = 38/60 (63%), Gaps = 4/60 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
          +D++    + ++KE+++ ++G       Q+LIYAGK L+DD+   +YNI+    + ++L+
Sbjct: 15 IDIEPTDTIDRIKERVEEKEGIP--PVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLA 72

>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 = 41.4 bits (97), Expect = 3e-06
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 4/60 (6%)

Query: 22 HLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
            +V+    V  LK+++   +      +   L + GK L D   L EY +     + + L
Sbjct: 17 TYEVRLTQTVAHLKQQVSGLE--GVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNL 74

>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 = 41.8 bits (98), Expect = 4e-06
 Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 12/76 (15%)

Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGK-------ILSDDQALSEYNIDESKFI 75
                + + K K++   GS   A   +L   G        +  +D  L  Y +D+   I
Sbjct: 25 YSRSLTIAEFKCKLELVVGSP--ASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRI 82

Query: 76 VVMLSKPKPTPAPYSG 91
           V+         P SG
Sbjct: 83 HVIDHSG---SGPSSG 95

>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 = 41.5 bits (97), Expect = 4e-06
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 7/71 (9%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
            +     +  LK++I+ ++G     + Q+L + G++L D   L  Y I +S  +++   
Sbjct: 22 YAINPNSFILGLKQQIEDQQGLP--KKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKK 79

Query: 81 KPKPTPAPYSG 91
          K      P SG
Sbjct: 80 KGS---GPSSG 87

>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 = 39.1 bits (91), Expect = 2e-05
 Identities = 12/59 (20%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          ++V  +  + QLKE +   +G    A+  ++I+AGK L +   +   ++++   + ++ 
Sbjct: 17 VEVDSDTSILQLKEVVAKRQGVP--ADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQ 73

>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 = 39.1 bits (91), Expect = 3e-05
 Identities = 12/70 (17%), Positives = 23/70 (32%), Gaps = 10/70 (14%)

Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGK--------ILSDDQALSEYNIDESKF 74
          L     V+++K  +              L Y           + +D Q L  Y+++    
Sbjct: 29 LPDSMTVQKVKGLLSRLLKVP--VSELLLSYESSKMPGREIELENDLQPLQFYSVENGDC 86

Query: 75 IVVMLSKPKP 84
          ++V  S P  
Sbjct: 87 LLVRWSGPSS 96

>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 = 38.3 bits (89), Expect = 5e-05
 Identities = 9/51 (17%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
          +++L E     +G E   +  + +Y G  +  DQ   + +++++  I    
Sbjct: 26 LRRLMEAFAKRQGKEM--DSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHR 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 = 37.5 bits (87), Expect = 1e-04
 Identities = 7/63 (11%), Positives = 21/63 (33%), Gaps = 10/63 (15%)

Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGK-------ILSDDQALSEYNI-DESKF 74
                +  LK+K++   G+    +  ++            +    ++L +  + D  + 
Sbjct: 22 YPAGMSLNDLKKKLELVVGTT--VDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRI 79

Query: 75 IVV 77
            V
Sbjct: 80 HAV 82

>d1x3zb1 a.189.1.1 (B:253-309) Rad23 STI1 domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 57

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]

 Score = 36.5 bits (84), Expect = 1e-04
 Identities = 21/46 (45%), Positives = 24/46 (52%)

Query: 146 QMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
            +R VV  NPE L  +L+ I    P L E I  N E FV ML E V
Sbjct: 12  SLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEAV 57

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 19/86 (22%), Positives = 30/86 (34%), Gaps = 17/86 (19%)

Query: 22  HLDVQEE--VKQLKEKIQSEKG-------------SEYLAEYQKLIYAGKILSDDQ-ALS 65
            + V +   V  LK+ IQ                   Y+     L  AG+ L++D+  L 
Sbjct: 21  PVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLR 80

Query: 66  EYNIDESKFIVVMLSKPKPTPAPYSG 91
           +Y I     +  +  K      P SG
Sbjct: 81  DYGIRNRDEVSFIK-KLGQKSGPSSG 105

>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 = 35.0 bits (80), Expect = 8e-04
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 10/69 (14%)

Query: 19 TVSHLDVQEE--------VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNID 70
          +V       E        V++ K++I         A+   LI+ GKIL D   LS+  I 
Sbjct: 14 SVKTPQDCHEFFLAENSNVRRFKKQISKYLHCN--ADRLVLIFTGKILRDQDILSQRGIL 71

Query: 71 ESKFIVVML 79
          +   + V++
Sbjct: 72 DGSTVHVVV 80

>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 = 34.6 bits (79), Expect = 0.001
 Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 4/49 (8%)

Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
          +    +  +  LK+ I ++ G+ +      L     I  D  +L +Y I
Sbjct: 43 VKCNTDDTIGDLKKLIAAQTGTRW--NKIVLKKWYTIFKDHVSLGDYEI 89

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	203
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.86
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.85
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.85
d2f4mb1	58	XPC-binding domain of Rad23 homolog B (Hhr23b) {Hu	99.85
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.85
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.84
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.84
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.83
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.83
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.82
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.82
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.82
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.82
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.82
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.82
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.81
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.81
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.8
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.8
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.78
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.78
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.77
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.76
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.75
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.75
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.75
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.73
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.73
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.73
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.7
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.69
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.68
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.61
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.61
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.55
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.54
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.47
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.39
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.36
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	98.8
d1x3zb1	57	Rad23 STI1 domain {Baker's yeast (Saccharomyces ce	98.78
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.65
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.68
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.51
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	97.28
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	97.27
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	97.23
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	95.06
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	91.12
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	90.01
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	89.34
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	87.74
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	83.3
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	80.73
d2f4mb1	58	XPC-binding domain of Rad23 homolog B (Hhr23b) {Hu	80.7

>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=1e-21  Score=139.57  Aligned_cols=79  Identities=53%  Similarity=0.767  Sum_probs=72.7

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCC-CCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCCCC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPT   85 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~-ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~~~   85 (203)
                      |+|+||+++|++|. +|++++||.+||++|+++.|.. +|+++|||||+||.|+|+++|++|||++|++|++++++++..
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~~~   80 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAV   80 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCCCC
Confidence            89999999999999 9999999999999999987632 789999999999999999999999999999999999877654


Q ss_pred             C
Q psy4259          86 P   86 (203)
Q Consensus        86 ~   86 (203)
                      +
T Consensus        81 ~   81 (95)
T d1uela_          81 S   81 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.85  E-value=1.2e-21  Score=137.18  Aligned_cols=78  Identities=21%  Similarity=0.297  Sum_probs=74.0

Q ss_pred             CCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           4 LAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      .++.|+|+||+++|+++. +|++++||.+||++|+.+.|  +|+++|||+|+||.|+|++||++|+|+++++||++.+.+
T Consensus         4 ~s~~mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g--ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~   81 (87)
T d1wh3a_           4 GSSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQG--LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKG   81 (87)
T ss_dssp             CSSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTC--CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSC
T ss_pred             CCCcEEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHC--cChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCC
Confidence            456899999999999999 99999999999999999999  999999999999999999999999999999999988766


Q ss_pred             C
Q psy4259          83 K   83 (203)
Q Consensus        83 ~   83 (203)
                      .
T Consensus        82 ~   82 (87)
T d1wh3a_          82 S   82 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.85  E-value=1.5e-21  Score=132.23  Aligned_cols=71  Identities=24%  Similarity=0.489  Sum_probs=69.2

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      |+|+||+++|++|+ +|++++||.+||++|+.+.|  +|+++|||+|+||.|+|+.||++|||++|++||++++
T Consensus         1 M~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~g--i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlr   72 (73)
T d1bt0a_           1 MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEG--IPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLA   72 (73)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhC--CChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEee
Confidence            89999999999999 99999999999999999999  9999999999999999999999999999999999875

>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=99.85  E-value=7.1e-22  Score=126.36  Aligned_cols=58  Identities=69%  Similarity=1.130  Sum_probs=56.5

Q ss_pred             hHHHhhCCHHHHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHHcCCc
Q psy4259         134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV  191 (203)
Q Consensus       134 pl~~l~~~P~~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml~~p~  191 (203)
                      |+++||++|+|++||++|++||++|+++|++|+++||+|+++|++|+++|++||++|.
T Consensus         1 pL~~Lr~~PqFq~lR~~vq~nP~~L~~lLqql~~~NP~L~q~I~~nqe~Fl~llnep~   58 (58)
T d2f4mb1           1 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV   58 (58)
T ss_dssp             GGGGGTTCHHHHHHHHHHHHCGGGHHHHHHHHHHHCHHHHHHHHHSHHHHHHHHTSCC
T ss_pred             CcHHHhcChHHHHHHHHHHHCHHHHHHHHHHHHhhCHHHHHHHHHCHHHHHHHHcCCC
Confidence            6899999999999999999999999999999999999999999999999999999984

>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=99.85  E-value=1.5e-21  Score=134.51  Aligned_cols=76  Identities=16%  Similarity=0.282  Sum_probs=73.3

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      .+++|+||+.+|+++. +|++++||.+||++|+.+.|  +|+++|||+|+||.|+|+.||++|+|++|++||+++++|.
T Consensus         2 ~e~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~--ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~p~   78 (80)
T d1ttna1           2 YECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEG--VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPV   78 (80)
T ss_dssp             CSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTC--CCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSS
T ss_pred             CeEEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhC--CCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecCCC
Confidence            5799999999999999 99999999999999999999  9999999999999999999999999999999999988765

>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=99.84  E-value=5.9e-21  Score=130.20  Aligned_cols=73  Identities=21%  Similarity=0.350  Sum_probs=70.6

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +.|+|+||+.+|++++ +|++++||.+||++|+.+.|  +|+++|+|+|+||.|+|++||++|||++|++||++++
T Consensus         2 ~~~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~g--i~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lR   75 (76)
T d1z2ma2           2 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEG--VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLR   75 (76)
T ss_dssp             CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             CCEEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhc--CChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEe
Confidence            5799999999999999 99999999999999999999  9999999999999999999999999999999999875

>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=99.84  E-value=8.2e-21  Score=129.51  Aligned_cols=73  Identities=27%  Similarity=0.492  Sum_probs=70.4

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      |+|+||+++|++|. +|++++||.+||++|+.+.|  +|++.|||+|+||.|+|+.||++|||++|++|+++++-+
T Consensus         1 MqI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~g--i~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~rlr   74 (76)
T d1ogwa_           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECTT
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcC--CChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEecC
Confidence            79999999999999 99999999999999999999  999999999999999999999999999999999988643

>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=8.9e-21  Score=130.06  Aligned_cols=73  Identities=16%  Similarity=0.311  Sum_probs=70.0

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      -|.|+||+.+|++|+ +|++++||.+||++|+++.|  +|++.|+|+|+||.|+|+++|++|+|+++++||++.+-
T Consensus         2 ~M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~g--ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~   75 (78)
T d2zeqa1           2 GMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQG--VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRP   75 (78)
T ss_dssp             CEEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHT--CCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESS
T ss_pred             ceEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHC--cChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEecc
Confidence            389999999999999 99999999999999999999  99999999999999999999999999999999997654

>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=99.83  E-value=1.5e-20  Score=128.38  Aligned_cols=72  Identities=22%  Similarity=0.290  Sum_probs=68.4

Q ss_pred             eEEEEEeCCCC-eee--ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQ-TVS--HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~-~~~--~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      |+|+||+++|+ +++  .+++++||++||++|+.+.|  +|+++|||+|+||.|+|+.+|++|||++|++||+++++
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 676  59999999999999999999  99999999999999999999999999999999999875

>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=1e-20  Score=129.36  Aligned_cols=75  Identities=47%  Similarity=0.698  Sum_probs=70.1

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCC-CCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~-ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      +.|+|+||+.+|++|. +|++++||.+||++|+.+.|.. +|+++|||+|+||.|+|++||++|||++|++|++|++
T Consensus         1 s~~~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           1 SAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT   77 (77)
T ss_dssp             CCCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEE
T ss_pred             CcEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEEC
Confidence            3689999999999999 9999999999999999988732 8999999999999999999999999999999999874

>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=99.82  E-value=1.2e-20  Score=134.37  Aligned_cols=82  Identities=17%  Similarity=0.170  Sum_probs=72.9

Q ss_pred             CCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           4 LAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      .++.|+|+||..+++.+. +|++++||.+||++|+..++  +|+++|||+|+|+.|+|+ +|++|||++|++|+|++++.
T Consensus         4 ~s~~~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~g--vp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~t~~   80 (96)
T d1wgga_           4 GSSGYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTG--VQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             CCCEEEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTC--CCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCC
T ss_pred             CCCceEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcC--ccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEeeCC
Confidence            345799999998888888 99999999999999999999  999999999999999986 79999999999999987766


Q ss_pred             CCCCCC
Q psy4259          83 KPTPAP   88 (203)
Q Consensus        83 ~~~~~p   88 (203)
                      ....+|
T Consensus        81 ~~~~~p   86 (96)
T d1wgga_          81 ALPEEP   86 (96)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            544333

>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=99.82  E-value=3.4e-21  Score=130.54  Aligned_cols=72  Identities=33%  Similarity=0.504  Sum_probs=68.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      |+|+||+.+|++|. +|++++||.+||++|+.+.|  +|+++|||+|+||.|+|+++|++|+| ++++||++.+.|
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            79999999999999 99999999999999999999  99999999999999999999999999 579999876653

>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=99.82  E-value=3e-20  Score=131.94  Aligned_cols=78  Identities=23%  Similarity=0.169  Sum_probs=69.4

Q ss_pred             CCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecC-CCCCccccccCCCCEEEEEeec
Q psy4259           4 LAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILS-DDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~-D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      .+..|+|+||+++|+.+. +|++++||.+||++|+   .  +++++|||||+||.|. |.++|++|+|.+|++||+++++
T Consensus         4 ~~s~m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~---~--~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~   78 (95)
T d1wiaa_           4 GSSGINVRLKFLNDTEELAVARPEDTVGTLKSKYF---P--GQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSP   78 (95)
T ss_dssp             CCCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHS---S--STTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCC
T ss_pred             CCCcEEEEEEcCCCCEEEEEECCcCcHHHHHHHHh---c--CCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcC
Confidence            456899999999999999 9999999999999985   4  6779999999999997 5589999999999999999888


Q ss_pred             CCCCC
Q psy4259          82 PKPTP   86 (203)
Q Consensus        82 ~~~~~   86 (203)
                      +..++
T Consensus        79 ~~~~~   83 (95)
T d1wiaa_          79 PGAAV   83 (95)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.82  E-value=2.6e-20  Score=127.07  Aligned_cols=72  Identities=19%  Similarity=0.215  Sum_probs=69.3

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ..|+||+++|+.|. +|++++||.+||.+|+.+.|  +|+++|||+|  +||.|+|+.+|++|||++|++||+++++
T Consensus         1 ~~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~g--ip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1           1 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG--VHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             CEEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHC--CCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhc--cCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            36999999999999 99999999999999999999  9999999999  7999999999999999999999999876

>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=99.82  E-value=1.8e-20  Score=134.77  Aligned_cols=79  Identities=16%  Similarity=0.295  Sum_probs=70.5

Q ss_pred             CcceEEEE----EeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecC-CCCCccccccCCCCEEEEE
Q psy4259           5 AHDISDIT----QNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILS-DDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         5 ~~~m~I~V----k~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~-D~~tL~~~gI~~~~~i~v~   78 (203)
                      +..|+|+|    |..++.+|. +|++++||.+||++|+.+.+  +|+++|+|+|+||.|. |.+||++|||++|++|+|+
T Consensus         5 ~~~m~itV~~~~~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~g--ip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~   82 (102)
T d1v5oa_           5 SSGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESG--VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLL   82 (102)
T ss_dssp             SCCEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTC--CCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEEC
T ss_pred             cCCEEEEEEecccCCCCCEEEEEECCcccHHHHHHHHHHHhC--CCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEE
Confidence            34699999    778899999 99999999999999999999  9999999999999996 5579999999999999987


Q ss_pred             eecCCCC
Q psy4259          79 LSKPKPT   85 (203)
Q Consensus        79 ~~k~~~~   85 (203)
                      .++....
T Consensus        83 ~r~~~~~   89 (102)
T d1v5oa_          83 QKDNVGL   89 (102)
T ss_dssp             BCCCCCC
T ss_pred             ECCCCCC
Confidence            6655443

>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=99.81  E-value=5.1e-20  Score=125.65  Aligned_cols=71  Identities=18%  Similarity=0.305  Sum_probs=67.3

Q ss_pred             eEEEEEeCCCC-eee--ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           8 ISDITQNQWQQ-TVS--HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         8 m~I~Vk~~~g~-~~~--~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      |+|+||+++|+ +++  +|++++||.+||.+|+.+.|  +|+++|||+|+|+.|+|+.||++|||++|++||++++
T Consensus         1 M~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~g--ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~r   74 (76)
T d1wy8a1           1 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFD--VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR   74 (76)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSC--CCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEEC
T ss_pred             CEEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHC--CCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEc
Confidence            89999999994 566  59999999999999999999  9999999999999999999999999999999999875

>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=99.81  E-value=6.8e-20  Score=123.99  Aligned_cols=72  Identities=29%  Similarity=0.461  Sum_probs=67.1

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      +|+|+||+. +++|. +|++++||.+||++|+...|  +|+++|+|+|+||.|+|+.+|++|||++|++||++.++
T Consensus         1 si~I~Vk~~-~~~~~i~v~~~~tV~~lK~~I~~~~g--ip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~~   73 (73)
T d2bwfa1           1 SLNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANG--IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ   73 (73)
T ss_dssp             EEEEEEEET-TEEEEEEECTTCBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEEeC-CeEEEEEECCCChHHHHHHHHHHHHC--cChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEeeC
Confidence            489999975 56788 99999999999999999999  99999999999999999999999999999999998754

>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=99.80  E-value=5.7e-20  Score=127.67  Aligned_cols=76  Identities=21%  Similarity=0.301  Sum_probs=70.0

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      +..|+|+||+.++ ++. +|++++||.+||++|+++.|  +++++|+|+|+||.|+|+.+|++|||++|++||++++++.
T Consensus         5 ~~~i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~g--i~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~   81 (84)
T d1yqba1           5 PHLIKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFK--AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   81 (84)
T ss_dssp             TTEEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHT--CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCC
T ss_pred             CCEEEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHC--cCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCC
Confidence            3469999999755 578 99999999999999999999  9999999999999999999999999999999999887654

>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=99.80  E-value=7.6e-20  Score=123.80  Aligned_cols=69  Identities=16%  Similarity=0.286  Sum_probs=67.3

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      |+|+||+..|+++. +|++++||.+||++|+.+.|  +|+++|+|+|+||.|+|+.||++|||++|++|++.
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~--i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~   71 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIG--TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   71 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHC--CTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhc--ccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEE
Confidence            78999999999999 99999999999999999999  99999999999999999999999999999999985

>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=99.78  E-value=6.9e-19  Score=125.68  Aligned_cols=81  Identities=22%  Similarity=0.245  Sum_probs=70.8

Q ss_pred             CCcceEEEEEeCCCCeee--ecCCCCcHHHHHHHHHhhhCCC---CC--CCceEEEeCCeecCCCCCccccccCCCC---
Q psy4259           4 LAHDISDITQNQWQQTVS--HLDVQEEVKQLKEKIQSEKGSE---YL--AEYQKLIYAGKILSDDQALSEYNIDESK---   73 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~--~v~~~~TV~~LK~~I~~~~~~~---ip--~~~qkLi~~Gk~L~D~~tL~~~gI~~~~---   73 (203)
                      ..++|.|+||+.+|+.+.  .|++++||.+||++|+..++.+   +|  +++|||||+||+|+|++||++|+|..|+   
T Consensus         4 ~~~~i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~   83 (101)
T d1se9a_           4 VHNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAG   83 (101)
T ss_dssp             SCCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTT
T ss_pred             ccceEEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCC
Confidence            356899999999999874  9999999999999999875321   66  7899999999999999999999999998   


Q ss_pred             ---EEEEEeecCCC
Q psy4259          74 ---FIVVMLSKPKP   84 (203)
Q Consensus        74 ---~i~v~~~k~~~   84 (203)
                         ++|++++.+.+
T Consensus        84 ~~~tmHlVvrpp~~   97 (101)
T d1se9a_          84 AVTTMHVIIQAPVT   97 (101)
T ss_dssp             CCEEEEEEECCCSS
T ss_pred             CceEEEEEeCCCCC
Confidence               99998876543

>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=99.78  E-value=7.7e-19  Score=128.80  Aligned_cols=74  Identities=16%  Similarity=0.165  Sum_probs=66.3

Q ss_pred             CCCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHh--------hhCCCCCCCceEEEeCCeecCCCCCccccccCCCC
Q psy4259           3 MLAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQS--------EKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESK   73 (203)
Q Consensus         3 ~~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~--------~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~   73 (203)
                      +..+.|+|+|++++|+++. +|++++||.+||++|+.        +.+  +++++|||||.||+|+|+.+|++|+|.+|+
T Consensus        12 ~~~~~i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~--~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~   89 (116)
T d1wgha_          12 VPADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQV--SSPNILRLIYQGRFLHGNVTLGALKLPFGK   89 (116)
T ss_dssp             CCSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCC--CCTTTEEEEETTEEECSSCBTTTTTCCSSC
T ss_pred             CCCCeEEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccC--CChHHeEEEECCEEecCCCCHHHcCCCCCC
Confidence            4556799999999999999 99999999999999964        445  899999999999999999999999999999


Q ss_pred             EEEEE
Q psy4259          74 FIVVM   78 (203)
Q Consensus        74 ~i~v~   78 (203)
                      +++|+
T Consensus        90 ~~~lh   94 (116)
T d1wgha_          90 TTVMH   94 (116)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            75443

>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=99.77  E-value=7.9e-19  Score=126.26  Aligned_cols=71  Identities=23%  Similarity=0.279  Sum_probs=67.0

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      .|+|+||+.++ ++. +|++++||.+||++|+..+|  +++++|||+|+||.|+|+++|++|||++|++||++++
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 578 99999999999999999999  9999999999999999999999999999999999874

>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=99.76  E-value=2.3e-19  Score=124.23  Aligned_cols=75  Identities=23%  Similarity=0.262  Sum_probs=68.8

Q ss_pred             CCcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           4 LAHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      .+..|+|+||+.++ .+. +|++++||.+||++|++.++  +|+++|||+|+||.|+|+++|++|||++|++||+++++
T Consensus         7 ~~~~i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~--v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1           7 SSRIIRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLH--CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             CSCEEEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTC--SCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             CCCeEEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhC--CChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEeC
Confidence            34569999998755 568 99999999999999999999  99999999999999999999999999999999998764

>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=8.6e-19  Score=125.36  Aligned_cols=70  Identities=17%  Similarity=0.243  Sum_probs=68.0

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      |+|+||+..|+++. +|++++||.+||++|+.++|  +|+++|||+|+||+|+|+.||++|||++|++|++..
T Consensus        29 i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~g--ip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI~L~~   99 (100)
T d1uh6a_          29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG--TRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHC--CCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHC--CCcceEEEEEEeecccCcCCHHHcCCCCCCEEEEEE
Confidence            79999999999999 99999999999999999999  999999999999999999999999999999999864

>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=99.75  E-value=2.3e-18  Score=119.94  Aligned_cols=66  Identities=29%  Similarity=0.409  Sum_probs=63.1

Q ss_pred             CCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259          15 QWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus        15 ~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      ++|+++. +|++++||.+||++|+.+.|  +|+++|+|+|+|+.|+|+.||++|||++|++||++++++
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~--ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~R   85 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATG--MPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKER   85 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTC--CCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhc--CChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecC
Confidence            5788999 99999999999999999999  999999999999999999999999999999999998764

>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=99.75  E-value=9.1e-19  Score=125.33  Aligned_cols=76  Identities=17%  Similarity=0.178  Sum_probs=69.1

Q ss_pred             ceEEEE--EeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           7 DISDIT--QNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         7 ~m~I~V--k~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      +|+|+|  |...|++|. +|.+++||.+||++|+...+  +++++|||||+||+|+|++||++|+|+++++|+|+..+..
T Consensus        17 ti~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~g--i~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~~~~   94 (100)
T d1wjua_          17 TIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFG--LQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELKQS   94 (100)
T ss_dssp             EEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTT--CCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECCCCC
T ss_pred             EEEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHC--CCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEcCCC
Confidence            566766  667799999 99999999999999999999  9999999999999999999999999999999998876654


Q ss_pred             C
Q psy4259          84 P   84 (203)
Q Consensus        84 ~   84 (203)
                      +
T Consensus        95 ~   95 (100)
T d1wjua_          95 S   95 (100)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.73  E-value=8.4e-19  Score=126.59  Aligned_cols=77  Identities=18%  Similarity=0.183  Sum_probs=70.9

Q ss_pred             CcceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceE---------------EEeCCeecCCC-CCcccc
Q psy4259           5 AHDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQK---------------LIYAGKILSDD-QALSEY   67 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qk---------------Li~~Gk~L~D~-~tL~~~   67 (203)
                      ++.|+|+||+.+|+.|. +|++++||.+||++|+...+  +|+++||               |+|+|+.|.|+ .||++|
T Consensus         5 ss~M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~--ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~   82 (105)
T d1v2ya_           5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQ--LKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDY   82 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHH--HHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHH
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHC--cCHHHhcccccccccccccceEEEECCEECcccCCCHHHc
Confidence            45799999999999999 99999999999999999999  9999997               99999999776 589999


Q ss_pred             ccCCCCEEEEEeecCC
Q psy4259          68 NIDESKFIVVMLSKPK   83 (203)
Q Consensus        68 gI~~~~~i~v~~~k~~   83 (203)
                      ||++|++||++.+.++
T Consensus        83 gI~~g~~l~lv~r~~~   98 (105)
T d1v2ya_          83 GIRNRDEVSFIKKLGQ   98 (105)
T ss_dssp             TCCSSEEEEEEECSCS
T ss_pred             CCCCCCEEEEEEecCC
Confidence            9999999999876543

>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=99.73  E-value=8.3e-18  Score=118.73  Aligned_cols=77  Identities=21%  Similarity=0.252  Sum_probs=65.8

Q ss_pred             CcceEEEEEeCCCCe--ee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCC--CEEEEEe
Q psy4259           5 AHDISDITQNQWQQT--VS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES--KFIVVML   79 (203)
Q Consensus         5 ~~~m~I~Vk~~~g~~--~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~--~~i~v~~   79 (203)
                      +..|+|+||+.+++.  +. +|++++||.+||++|++.++..+++++|||||+||+|+|+.+|++|..+.+  .+||+++
T Consensus         5 s~~i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~   84 (93)
T d1wgda_           5 SSGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVC   84 (93)
T ss_dssp             SCCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEEC
T ss_pred             CCcEEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEe
Confidence            457999999998764  77 999999999999999999764489999999999999999999999976544  4888875


Q ss_pred             ec
Q psy4259          80 SK   81 (203)
Q Consensus        80 ~k   81 (203)
                      +.
T Consensus        85 ~~   86 (93)
T d1wgda_          85 NV   86 (93)
T ss_dssp             CC
T ss_pred             cC
Confidence            44

>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=99.73  E-value=4.5e-18  Score=119.33  Aligned_cols=77  Identities=25%  Similarity=0.278  Sum_probs=68.3

Q ss_pred             CCcceEEEEEeCCCCeee--ecCCCCcHHHHHHHHHhhhCCCCCCCceEEE---eCCeecCCCCCccccccCCCCEEEEE
Q psy4259           4 LAHDISDITQNQWQQTVS--HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI---YAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         4 ~~~~m~I~Vk~~~g~~~~--~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi---~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      .+..|+|+||. .|+.+.  +|++++||.+||++|+.+++  +|+++||||   |+|+.|+|+.+|++|+|++|++|+++
T Consensus         4 ~s~~~~i~Vk~-~~~~~~i~~v~~~~tV~~LK~~i~~~t~--vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv   80 (90)
T d1v5ta_           4 GSSGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTG--VLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMM   80 (90)
T ss_dssp             CCCSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTC--CCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEE
T ss_pred             CCCcEEEEEEE-CCeEEEEEEeCCCCcHHHHHHHHHHHHc--CCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEE
Confidence            45679999996 555555  89999999999999999999  999999999   58999999999999999999999998


Q ss_pred             eecCC
Q psy4259          79 LSKPK   83 (203)
Q Consensus        79 ~~k~~   83 (203)
                      +++..
T Consensus        81 ~s~~~   85 (90)
T d1v5ta_          81 GTRES   85 (90)
T ss_dssp             CCCSS
T ss_pred             eeCCC
Confidence            76543

>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=99.70  E-value=1.3e-17  Score=118.14  Aligned_cols=73  Identities=22%  Similarity=0.261  Sum_probs=67.3

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecC
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP   82 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~   82 (203)
                      +.|+|+|+ +++++|. +|++++||.+||++|+..++  +|+++|||+|+|+ |+|+.+|++|+|++|++|+|+.+..
T Consensus        16 ~~i~v~V~-~~~k~~~i~v~~~~TV~~LK~~I~~~tg--vp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~~   89 (95)
T d1v86a_          16 ELVDLKII-WNKTKHDVKVPLDSTGSELKQKIHSITG--LPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGSTI   89 (95)
T ss_dssp             CCEEEEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHC--SCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSSC
T ss_pred             cEEEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHhC--CChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecCC
Confidence            35899998 6888999 99999999999999999999  9999999999997 9999999999999999999886543

>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=99.69  E-value=2.8e-17  Score=113.11  Aligned_cols=72  Identities=21%  Similarity=0.331  Sum_probs=63.6

Q ss_pred             eEEEEEeCCCCeee-ec-----CCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecC-CCCCccccccCCCCEEEEEee
Q psy4259           8 ISDITQNQWQQTVS-HL-----DVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILS-DDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v-----~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~-D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      |+|+|+ ..+..+. +|     ++++||++||++|+..+|  +|+++|+|+|+|+.|. |+.+|++|||++|++|+++++
T Consensus         2 i~i~V~-~~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tg--vp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~~   78 (81)
T d1wxva1           2 LTVTVT-HSNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIG--VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGK   78 (81)
T ss_dssp             EEEEEE-CSSSEEEEEECCCSSSSSCBHHHHHHHHHHHTC--CCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESC
T ss_pred             EEEEEE-ECCeeEEEEEecCCCCCccHHHHHHHHHHHHHC--cCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEEe
Confidence            788887 4666666 66     578999999999999999  9999999999999996 558999999999999999987


Q ss_pred             cC
Q psy4259          81 KP   82 (203)
Q Consensus        81 k~   82 (203)
                      +.
T Consensus        79 ~~   80 (81)
T d1wxva1          79 KN   80 (81)
T ss_dssp             CS
T ss_pred             cC
Confidence            64

>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=99.68  E-value=4.1e-17  Score=118.62  Aligned_cols=74  Identities=28%  Similarity=0.324  Sum_probs=65.9

Q ss_pred             eEEEEEeC-CCCeee-ecCC-CCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeecCC
Q psy4259           8 ISDITQNQ-WQQTVS-HLDV-QEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPK   83 (203)
Q Consensus         8 m~I~Vk~~-~g~~~~-~v~~-~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k~~   83 (203)
                      ++|.|++. +|++++ +|.+ ++||.+||++|+.+.|  +|++.|||+|+||.|+|+.||++|+|++|++||++++-+.
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            44444443 588999 9986 8999999999999999  9999999999999999999999999999999999987665

>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=99.61  E-value=1.1e-15  Score=108.10  Aligned_cols=77  Identities=16%  Similarity=0.146  Sum_probs=68.1

Q ss_pred             CcceEEEEEeC-CCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCe-------ecCCCCCccccccCCCCEE
Q psy4259           5 AHDISDITQNQ-WQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGK-------ILSDDQALSEYNIDESKFI   75 (203)
Q Consensus         5 ~~~m~I~Vk~~-~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk-------~L~D~~tL~~~gI~~~~~i   75 (203)
                      ++.|.|+|++. ++..++ .+++++||.+||++|+..+|  +|++.|||+|.|+       .++|+++|++|+|.+|++|
T Consensus         5 ss~v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tG--ip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~i   82 (95)
T d1v6ea_           5 SSGVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVG--SPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRI   82 (95)
T ss_dssp             CCCEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTC--SCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEE
T ss_pred             CCcEEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhC--cCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEE
Confidence            56799999984 455567 89999999999999999999  9999999999887       5788899999999999999


Q ss_pred             EEEeecCC
Q psy4259          76 VVMLSKPK   83 (203)
Q Consensus        76 ~v~~~k~~   83 (203)
                      ||+.+.+.
T Consensus        83 hlvd~~p~   90 (95)
T d1v6ea_          83 HVIDHSGS   90 (95)
T ss_dssp             EEBCCSCC
T ss_pred             EEEeCCCC
Confidence            99876654

>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=99.61  E-value=1.1e-15  Score=109.38  Aligned_cols=70  Identities=14%  Similarity=0.142  Sum_probs=58.7

Q ss_pred             EEEEeCCC-Ceee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCC-------EEEEEee
Q psy4259          10 DITQNQWQ-QTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESK-------FIVVMLS   80 (203)
Q Consensus        10 I~Vk~~~g-~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~-------~i~v~~~   80 (203)
                      |+|+...+ .++. +|++++||.+||++|+.+.|  +++++|||||+||.|+|++||++|||.+++       ++++..+
T Consensus         2 ifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~g--ip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~~~~~~~~~~~l~~~   79 (103)
T d2c9wb1           2 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILK--RPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   79 (103)
T ss_dssp             EEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHC--CCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEE
T ss_pred             EEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhC--CCcccEEEEECCEEcCCCCCHHHcCCCcccccccCCcEEEEEEe
Confidence            44444444 4677 99999999999999999999  999999999999999999999999996554       6666654


Q ss_pred             c
Q psy4259          81 K   81 (203)
Q Consensus        81 k   81 (203)
                      .
T Consensus        80 ~   80 (103)
T d2c9wb1          80 A   80 (103)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=99.55  E-value=9.8e-15  Score=103.42  Aligned_cols=80  Identities=19%  Similarity=0.175  Sum_probs=67.8

Q ss_pred             CCCCcceEEEEEeC---CCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCee-------cC-CCCCcccccc
Q psy4259           2 GMLAHDISDITQNQ---WQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKI-------LS-DDQALSEYNI   69 (203)
Q Consensus         2 ~~~~~~m~I~Vk~~---~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~-------L~-D~~tL~~~gI   69 (203)
                      |+...-++|+|+..   +++.++ .|+.++||.+||.+|+..+|  +|++.|+|+|.|+.       |+ |+++|.+|||
T Consensus         4 ~ss~~~iti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~g--ip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI   81 (97)
T d1wjna_           4 GSSGQLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLK--VPVSELLLSYESSKMPGREIELENDLQPLQFYSV   81 (97)
T ss_dssp             CSSSCEEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTT--CCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTC
T ss_pred             CcCCCeEEEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHC--cChHHeEEEecCCCCCcccceecCCCcCHhhccC
Confidence            45555688888864   467788 99999999999999999999  99999999998872       54 6699999999


Q ss_pred             CCCCEEEEEeecCC
Q psy4259          70 DESKFIVVMLSKPK   83 (203)
Q Consensus        70 ~~~~~i~v~~~k~~   83 (203)
                      .+|++|+|..++|+
T Consensus        82 ~dg~~I~V~~~~P~   95 (97)
T d1wjna_          82 ENGDCLLVRWSGPS   95 (97)
T ss_dssp             CTTCEEEEECCSSC
T ss_pred             CCCCEEEEEeCCCC
Confidence            99999998766554

>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=99.54  E-value=1.2e-14  Score=102.09  Aligned_cols=57  Identities=28%  Similarity=0.316  Sum_probs=50.3

Q ss_pred             CCCCcHHHHHHHHHhhhCCCC-CCCceEEEeCCeecCCCCCccccccCCCCEEEEEee
Q psy4259          24 DVQEEVKQLKEKIQSEKGSEY-LAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS   80 (203)
Q Consensus        24 ~~~~TV~~LK~~I~~~~~~~i-p~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~   80 (203)
                      ..++||.+||++|+.++.... .+++|||||+||.|+|+++|++|+|++|++||++.+
T Consensus        35 ~~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r   92 (94)
T d1x1ma1          35 LGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK   92 (94)
T ss_dssp             CCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEES
T ss_pred             CCccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEe
Confidence            347899999999999876334 468999999999999999999999999999999865

>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=99.47  E-value=9.9e-14  Score=94.46  Aligned_cols=73  Identities=12%  Similarity=0.256  Sum_probs=67.1

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      ..+.|+|+. +|+.+. .|..++++..||+.++++.+  +++++++|+|+|+.|++++|+++|+|++|++|+++++.
T Consensus         3 ~~I~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~--i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q   76 (79)
T d1euvb_           3 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQG--KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   76 (79)
T ss_dssp             SEEEEEEES-SSCEEEEEEETTSCTHHHHHHHHHHTT--CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             cEEEEEECC-CCeEEEEEECCCCcHHHHHHHHHHHhC--CChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEec
Confidence            457788875 677788 99999999999999999999  99999999999999999999999999999999998764

>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=99.39  E-value=4.7e-13  Score=90.60  Aligned_cols=74  Identities=18%  Similarity=0.288  Sum_probs=70.1

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEeec
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK   81 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~~k   81 (203)
                      +.|+|+|++.+|+.+. .|..+.++..||..+++..+  +++++++|+|+|+.|.++.|+++|++.+|++|+|+.+.
T Consensus         1 e~I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~--~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q   75 (77)
T d2uyzb1           1 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG--VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ   75 (77)
T ss_dssp             CEEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHT--CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECC
T ss_pred             CEEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhC--CChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            3589999999999999 99999999999999999999  99999999999999999999999999999999998754

>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=99.36  E-value=1.6e-12  Score=90.55  Aligned_cols=75  Identities=8%  Similarity=0.065  Sum_probs=61.7

Q ss_pred             CcceEEEEEeCC-CCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCe-------ecCCCCCccccccCCCCEE
Q psy4259           5 AHDISDITQNQW-QQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGK-------ILSDDQALSEYNIDESKFI   75 (203)
Q Consensus         5 ~~~m~I~Vk~~~-g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk-------~L~D~~tL~~~gI~~~~~i   75 (203)
                      ++-+.|.|.+.. +..+. .++.++||.+||.+|+..+|  +|++.|+|+|.|+       .++|+++|.+|||.+|++|
T Consensus         2 s~~~~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~G--ip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~I   79 (90)
T d1t0ya_           2 TEVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVG--TTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRI   79 (90)
T ss_dssp             CCEEEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHC--CCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEE
T ss_pred             CcEEEEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHC--CChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEE
Confidence            344577777522 34456 88999999999999999999  9999999999886       4567799999999999999


Q ss_pred             EEEeec
Q psy4259          76 VVMLSK   81 (203)
Q Consensus        76 ~v~~~k   81 (203)
                      ||+-..
T Consensus        80 hvvd~~   85 (90)
T d1t0ya_          80 HAVDVT   85 (90)
T ss_dssp             EEEECT
T ss_pred             EEEeCC
Confidence            987544

>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=1.5e-08  Score=67.04  Aligned_cols=69  Identities=12%  Similarity=0.208  Sum_probs=65.1

Q ss_pred             eEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEE
Q psy4259           8 ISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM   78 (203)
Q Consensus         8 m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~   78 (203)
                      ++|+|+..+|+.+. .|..+.++..|....+...+  ++++..+++|+|..|..+.|.+++++.+|++|.|.
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            67899988999999 99999999999999999999  99999999999999999999999999999999863

>d1x3zb1 a.189.1.1 (B:253-309) Rad23 STI1 domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: XPC-binding domain
superfamily: XPC-binding domain
family: XPC-binding domain
domain: Rad23 STI1 domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.78  E-value=5.9e-09  Score=62.94  Aligned_cols=46  Identities=43%  Similarity=0.596  Sum_probs=43.4

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHHhhcCHHHHHHHhhCHHHHHHHHcC
Q psy4259         144 FQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNE  189 (203)
Q Consensus       144 ~~~~r~~i~~nP~~l~~il~~l~~~nP~l~~~i~~n~~~f~~ml~~  189 (203)
                      +-++|+.+..||+.|.++++.|..+.|+|++.|.+||+.|+.|+.+
T Consensus        10 l~~lr~vvsg~peal~plle~ls~ryp~lre~im~npe~fismlle   55 (57)
T d1x3zb1          10 LLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLE   55 (57)
T ss_dssp             HHHHHHHHHHCGGGHHHHHHHHHTTCHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHhcCChHHHHHHHHHHHHhhHHHHHHHHhCHHHHHHHHHh
Confidence            4579999999999999999999999999999999999999999864

>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=98.65  E-value=2.2e-08  Score=68.56  Aligned_cols=70  Identities=17%  Similarity=0.086  Sum_probs=57.3

Q ss_pred             EEEEeCCCCeeeecC-CCCcHHHHHHHHHhhhCCCCCCCceEEEeC--------------CeecCCC-CCccccccCCCC
Q psy4259          10 DITQNQWQQTVSHLD-VQEEVKQLKEKIQSEKGSEYLAEYQKLIYA--------------GKILSDD-QALSEYNIDESK   73 (203)
Q Consensus        10 I~Vk~~~g~~~~~v~-~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~--------------Gk~L~D~-~tL~~~gI~~~~   73 (203)
                      |.||+.+|....+|+ .+.||.+||.+|++..+  +|.+.|.|..+              -..|.|+ .+|++|||.+|+
T Consensus         3 iRiRsrdG~eRv~v~~~~~Tl~~LK~~Ie~~L~--VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGs   80 (94)
T d1wf9a1           3 LRVRSRDGLERVSVDGPHITVSQLKTLIQDQLQ--IPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGS   80 (94)
T ss_dssp             EEEECSSCEEEEEECCTTSBHHHHHHHHHHHSC--CCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTC
T ss_pred             EEEEecCCceEEEecCCCCcHHHHHHHHHHHhC--CCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCce
Confidence            678888887666885 47899999999999999  99999999543              2346666 679999999999


Q ss_pred             EEEEEeec
Q psy4259          74 FIVVMLSK   81 (203)
Q Consensus        74 ~i~v~~~k   81 (203)
                      +|++...-
T Consensus        81 ivyL~y~~   88 (94)
T d1wf9a1          81 MVYLAYEG   88 (94)
T ss_dssp             EEECCCSS
T ss_pred             EEEEEeee
Confidence            99987543

>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=97.68  E-value=9.5e-05  Score=49.13  Aligned_cols=68  Identities=9%  Similarity=0.094  Sum_probs=57.5

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecC---CCCCccccccCCCCEEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILS---DDQALSEYNIDESKFIVV   77 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~---D~~tL~~~gI~~~~~i~v   77 (203)
                      -.+|.||..+|+.+. .+..++||.+|...|... +  .+.....|+.  -.+.|.   +++||.++|+....+|+|
T Consensus         5 ~~~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~-~--~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~v   78 (82)
T d1h8ca_           5 VSKLRIRTPSGEFLERRFLASNKLQIVFDFVASK-G--FPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFL   78 (82)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-T--CCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHhc-C--CCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEE
Confidence            467999999999999 999999999999999874 6  6677788874  578884   357999999998888875

>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=97.51  E-value=0.00027  Score=47.61  Aligned_cols=68  Identities=18%  Similarity=0.153  Sum_probs=55.4

Q ss_pred             cceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhh-CCCCCCCceEEEeC--CeecCCC-CCccccccCCCCEEE
Q psy4259           6 HDISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEK-GSEYLAEYQKLIYA--GKILSDD-QALSEYNIDESKFIV   76 (203)
Q Consensus         6 ~~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~-~~~ip~~~qkLi~~--Gk~L~D~-~tL~~~gI~~~~~i~   76 (203)
                      ...+|.||..+|+.+. .+..++||.+|.+.|.... +  .......|+..  -|.|.|. +||.++|+.+ +.|+
T Consensus        13 p~t~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~--~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~-s~vl   85 (89)
T d1i42a_          13 PTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPA--MAATSFVLMTTFPNKELADENQTLKEANLLN-AVIV   85 (89)
T ss_dssp             CCEEEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTT--TSSCCEEEEETTTTEECCCCSSCSGGGTTCC-SEEE
T ss_pred             CcEEEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCcc--CCCCCEEEecCCCCcccCCCcCcHHHCCCcC-ceEE
Confidence            3578999999999999 9999999999999998764 4  56667888866  5778654 8999999985 4543

>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=97.28  E-value=0.00074  Score=44.08  Aligned_cols=69  Identities=7%  Similarity=0.003  Sum_probs=64.0

Q ss_pred             EEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeCCeecCCCCCccccccCCCCEEEEEe
Q psy4259           9 SDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML   79 (203)
Q Consensus         9 ~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~Gk~L~D~~tL~~~gI~~~~~i~v~~   79 (203)
                      .|+|-..+|+..+ .|.|+.|+.++-+....++|  +.+++-.|.|++|.|+-+..+.-.|+.+|..+.++-
T Consensus         2 ~V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~--~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~   71 (76)
T d2al3a1           2 AVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQD--FNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVP   71 (76)
T ss_dssp             CEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTT--CCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEEC
T ss_pred             cEEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhC--CChhHceeeeCCEEcCccceeeecCCCCCCEEEEEE
Confidence            3677788999999 99999999999999999999  999999999999999999999999999999999874

>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=97.27  E-value=0.00042  Score=47.09  Aligned_cols=68  Identities=12%  Similarity=0.125  Sum_probs=55.3

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEeC--CeecC-C-CCCccccccCCCCEEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYA--GKILS-D-DQALSEYNIDESKFIVV   77 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~~--Gk~L~-D-~~tL~~~gI~~~~~i~v   77 (203)
                      .++|.||..+|+.+. .+..++||.+|...|... +  ......+|+..  .+.+. | ++||.++|+....+|+|
T Consensus        16 ~~~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~-~--~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v   88 (96)
T d2cr5a1          16 VVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-G--YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNV   88 (96)
T ss_dssp             EEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-T--CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEE
T ss_pred             eEEEEEECCCCCEEEEEECCcccHHHHHHHHHHh-c--cCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEE
Confidence            489999999999999 999999999999998765 4  45567787754  46664 3 58999999998877765

>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=97.23  E-value=0.00055  Score=48.89  Aligned_cols=69  Identities=23%  Similarity=0.240  Sum_probs=56.6

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCceEEEe--CCeecC--C-CCCccccccCCCCEEEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIY--AGKILS--D-DQALSEYNIDESKFIVVM   78 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~qkLi~--~Gk~L~--D-~~tL~~~gI~~~~~i~v~   78 (203)
                      ..+|.||..+|+.+. .+..++||.+|...|... +  +.....+|+.  --+.|.  | ++||.++|+.+..+|+|-
T Consensus        43 ~~~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~-~--~~~~~~~L~~~fPr~~l~~~d~~~TL~e~gL~P~~~L~ve  117 (124)
T d1wj4a_          43 KAQLMLRYPDGKREQITLPEQAKLLALVKHVQSK-G--YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-H--CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             ceEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-c--cCCcceEEeecccccccccccccCcHHHcCCCCCCEEEEE
Confidence            478999999999999 999999999999999775 4  5566777764  357774  3 589999999998888653

>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=95.06  E-value=0.1  Score=33.81  Aligned_cols=67  Identities=13%  Similarity=0.094  Sum_probs=46.6

Q ss_pred             ceEEEEEeCC------CC-eee-ecCCCCcHHHHHHHHHhhhCCC---------CCCCceEEEeCCeecCCCCCcccccc
Q psy4259           7 DISDITQNQW------QQ-TVS-HLDVQEEVKQLKEKIQSEKGSE---------YLAEYQKLIYAGKILSDDQALSEYNI   69 (203)
Q Consensus         7 ~m~I~Vk~~~------g~-~~~-~v~~~~TV~~LK~~I~~~~~~~---------ip~~~qkLi~~Gk~L~D~~tL~~~gI   69 (203)
                      +|+|+|+...      |+ ... ++....||.+|++.+..+++..         ......++..+|+...++     +-+
T Consensus         1 smkI~v~~Fa~lre~~G~~~~~~~~~~~~Tv~~l~~~L~~~~~~~~~~l~~~~~~~~~~i~iavN~~~~~~d-----~~L   75 (88)
T d1vjka_           1 SVKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWD-----EEL   75 (88)
T ss_dssp             CEEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTT-----CBC
T ss_pred             CeEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHChHHHHHhhhccccccccEEEEEcceEcCCC-----cCc
Confidence            5899998864      44 445 8888899999999999876520         011234566677776543     457


Q ss_pred             CCCCEEEEE
Q psy4259          70 DESKFIVVM   78 (203)
Q Consensus        70 ~~~~~i~v~   78 (203)
                      ++||.|.++
T Consensus        76 ~~gDevai~   84 (88)
T d1vjka_          76 KDGDVVGVF   84 (88)
T ss_dssp             CTTCEEEEE
T ss_pred             CCCCEEEEe
Confidence            789999876

>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=91.12  E-value=0.033  Score=31.60  Aligned_cols=15  Identities=13%  Similarity=0.253  Sum_probs=13.3

Q ss_pred             hhhHHHHHhCCcCCC
Q psy4259         110 TATSDSMLKVFFERV  124 (203)
Q Consensus       110 ~~~v~~~~~mG~~~~  124 (203)
                      ++.|++|++|||+++
T Consensus         5 e~~i~~L~~MGF~~~   19 (41)
T d1oqya1           5 ETMLTEIMSMGYERE   19 (41)
T ss_dssp             HHHHHHHHTTTCCSH
T ss_pred             HHHHHHHHHcCCCHH
Confidence            578999999999875

>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=90.01  E-value=0.19  Score=31.84  Aligned_cols=16  Identities=13%  Similarity=0.318  Sum_probs=13.9

Q ss_pred             chhhHHHHHhCCcCCC
Q psy4259         109 ATATSDSMLKVFFERV  124 (203)
Q Consensus       109 ~~~~v~~~~~mG~~~~  124 (203)
                      .++.|+.|++|||+++
T Consensus        29 ~ee~i~~L~~MGF~~~   44 (73)
T d1vg5a_          29 SEEQIQKLVAMGFDRT   44 (73)
T ss_dssp             CHHHHHHHHTTTCCHH
T ss_pred             CHHHHHHHHHhCCCHH
Confidence            4889999999999764

>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=89.34  E-value=0.5  Score=31.39  Aligned_cols=69  Identities=10%  Similarity=0.044  Sum_probs=42.7

Q ss_pred             CcceEEEEEeCCC--------Ceee-ecC---CCCcHHHHHHHHHhhhCCCCCCCc-----------eEEEeCCeecCCC
Q psy4259           5 AHDISDITQNQWQ--------QTVS-HLD---VQEEVKQLKEKIQSEKGSEYLAEY-----------QKLIYAGKILSDD   61 (203)
Q Consensus         5 ~~~m~I~Vk~~~g--------~~~~-~v~---~~~TV~~LK~~I~~~~~~~ip~~~-----------qkLi~~Gk~L~D~   61 (203)
                      .++|+|+|+...|        +... +++   ...||.+|-+.+.+.++.  ...+           ..+..+|....  
T Consensus         2 ~~~m~V~V~F~g~L~~lf~~~r~~~v~l~~~~~~~TV~dll~~L~~~~p~--~~~~l~~~~~~lr~~v~v~vN~~di~--   77 (101)
T d1xo3a_           2 AAPLCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLK--ERPELFIQGDSVRPGILVLINDADWE--   77 (101)
T ss_dssp             CSSCEEEEEECSSGGGGGTTCCCEEEECCSSSCCCCHHHHHHHHHHHHCC--SCGGGSCCTTSCCSSEEEEETTEEHH--
T ss_pred             CCCeEEEEEEechHHHHhCCcceEEEEcCCCCCCcCHHHHHHHHHHhCCc--chhhhhccCcCeeeeEEEEEcCccee--
Confidence            4689999998553        2333 443   347999999999998873  1111           12223343221  


Q ss_pred             CCcc--ccccCCCCEEEEE
Q psy4259          62 QALS--EYNIDESKFIVVM   78 (203)
Q Consensus        62 ~tL~--~~gI~~~~~i~v~   78 (203)
                       .+.  ++.|++||.|.++
T Consensus        78 -~l~gl~t~l~dgDeV~~~   95 (101)
T d1xo3a_          78 -LLGELDYQLQDQDSILFI   95 (101)
T ss_dssp             -HHTTTSCCCCTTCEEEEE
T ss_pred             -ccCCCccCcCCCCEEEEe
Confidence             122  5679999999886

>d1wgra_ d.15.1.5 (A:) Growth factor receptor-bound protein 7, GRB-7 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: Growth factor receptor-bound protein 7, GRB-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.74  E-value=1.4  Score=29.07  Aligned_cols=76  Identities=11%  Similarity=0.002  Sum_probs=49.6

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCCCCc-eEEE--e-C-C--eecCCCCCcccccc--CCCCEEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYLAEY-QKLI--Y-A-G--KILSDDQALSEYNI--DESKFIV   76 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip~~~-qkLi--~-~-G--k~L~D~~tL~~~gI--~~~~~i~   76 (203)
                      +.-|.|-..+|.+.. .|+.++|+.+|-+.+..+.+  +..+. .-|+  + . |  +.|.|...+-+.-.  ..++.-.
T Consensus         9 ~~vvkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~--~~~~~~f~L~E~~~~~~leR~L~d~E~vl~v~~~W~~~~~~r   86 (100)
T d1wgra_           9 PHVVKVYSEDGACRSVEVAAGATARHVCEMLVQRAH--ALSDETWGLVECHPHLALERGLEDHESVVEVQAAWPVGGDSR   86 (100)
T ss_dssp             CEEEEEEETTSCEEEEEECTTCCHHHHHHHHHCSSS--CCCCCCCCEEEEETTTTEEEEECSSSCHHHHHTTSCSSSCCE
T ss_pred             ceEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHhC--CCCCCCeEEEEecCCCcceeecCchHhHHHHHHcCCCCCCCE
Confidence            566777778898888 99999999999999999998  54433 2232  2 2 3  78888765443311  1223334


Q ss_pred             EEeecCCC
Q psy4259          77 VMLSKPKP   84 (203)
Q Consensus        77 v~~~k~~~   84 (203)
                      ++.+|--+
T Consensus        87 ~v~rknya   94 (100)
T d1wgra_          87 FVFRKNFA   94 (100)
T ss_dssp             EEECSCCS
T ss_pred             EEEeecCC
Confidence            45566543

>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=83.30  E-value=0.11  Score=29.35  Aligned_cols=15  Identities=7%  Similarity=0.096  Sum_probs=12.9

Q ss_pred             hhhHHHHHhCCcCCC
Q psy4259         110 TATSDSMLKVFFERV  124 (203)
Q Consensus       110 ~~~v~~~~~mG~~~~  124 (203)
                      +.+|++|++|||.++
T Consensus         5 ~~ai~eL~~MGF~e~   19 (43)
T d2g3qa1           5 SLAVEELSGMGFTEE   19 (43)
T ss_dssp             HHHHHHHHTTTSCHH
T ss_pred             HHHHHHHHhcCCCHH
Confidence            578999999999764

>d1ef1a3 d.15.1.4 (A:4-87) Moesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Moesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.73  E-value=4.9  Score=25.41  Aligned_cols=66  Identities=15%  Similarity=0.165  Sum_probs=50.0

Q ss_pred             ceEEEEEeCCCCeee-ecCCCCcHHHHHHHHHhhhCCCCC-CCceEEEeC---C--eecCCCCCccccccCCCCEE
Q psy4259           7 DISDITQNQWQQTVS-HLDVQEEVKQLKEKIQSEKGSEYL-AEYQKLIYA---G--KILSDDQALSEYNIDESKFI   75 (203)
Q Consensus         7 ~m~I~Vk~~~g~~~~-~v~~~~TV~~LK~~I~~~~~~~ip-~~~qkLi~~---G--k~L~D~~tL~~~gI~~~~~i   75 (203)
                      +|+|.|.++++ .+. .++...+..+|=+.|....+  +. .+-.=|-|-   |  .-|+.++.|....++.+..+
T Consensus         1 t~~v~V~~LD~-~~~~~v~~~a~G~~l~~~Vc~~l~--L~E~dYFGL~y~d~~~~~~WLd~~k~l~kq~~~~~~~~   73 (84)
T d1ef1a3           1 TISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIG--LREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPL   73 (84)
T ss_dssp             CEEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHT--CCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSE
T ss_pred             CEEEEEEEcCC-EEEEEEcCCChHHHHHHHHHHHcC--CcccccceEEEECCCCCeEeccCCCchhhhccCCCCCE
Confidence            58899999997 588 99999999999999999999  54 333345443   3  34788888888766555533

>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=80.70  E-value=0.2  Score=30.35  Aligned_cols=21  Identities=38%  Similarity=0.668  Sum_probs=10.6

Q ss_pred             HhCCCcHHHHHHHHhhcCHHHHH
Q psy4259         152 QQNPELLPTVLQQIGQSNPALLE  174 (203)
Q Consensus       152 ~~nP~~l~~il~~l~~~nP~l~~  174 (203)
                      ++||++  +.|.++-++||++.+
T Consensus         6 r~~PqF--q~lR~~vq~nP~~L~   26 (58)
T d2f4mb1           6 RNQPQF--QQMRQIIQQNPSLLP   26 (58)
T ss_dssp             TTCHHH--HHHHHHHHHCGGGHH
T ss_pred             hcChHH--HHHHHHHHHCHHHHH
Confidence            455654  124445556666554