Psyllid ID: psy4260

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MIGAPAAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEEAPVAANEPQGNNIKQFSSVKEIEIPNLMQGDNKVYTLKYSN
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHHHccccccccccccccccccccccHHHHcccccccccccccccccccHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccHcHHHHHcccHHHHHHHHHHHHccccHHHHHHHHHHHHccHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHcHHHHHHHHcccccEEEEEEcc
Coil and Loop (DISEMBL)
migapaaatstpstpvsqagatatattpgnaestllmgdEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGipaavvgeeapvaanepqgnnikqfssvkeieipnlmqgdnkvytlkysn
Flexible Loop (DISEMBL)
migapaaatstpstpvsqagatatattpgnaeSTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEEAPVAanepqgnnikqfssvkeieipnlmqgdnkvytlkysn
Low Complexity Region (SEG)
MIGapaaatstpstpvsqagatatattPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIpaavvgeeapvaanepQGNNIKQFSSVKEIEIPNLMQGDNKVYTLKYSN
Disordered region (IsUnstruct)
**********************************LLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGE******************************************
Disordered Region (DISOPRED)
******************************************RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG********************************************TLKYS*
Disordered Region (DISEMBL)
***************************PGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEEAPVAANEPQGNNIKQFSSVKEIEIPNLMQGDNKVYTLKYSN
Disordered Region (DISPRO)
***********************************LMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVV******AANEPQGNNIKQFSSVKEIEIPNLMQGDNKVYTLKYSN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIGAPAAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEEAPVAANEPQGNNIKQFSSVKEIEIPNLMQGDNKVYTLKYSN
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	129	2.2.26 [Sep-21-2011]
O74803	368	UV excision repair protei	yes	N/A	0.581	0.203	0.506	4e-14
P54728	416	UV excision repair protei	yes	N/A	0.596	0.185	0.468	8e-14
Q4KMA2	415	UV excision repair protei	yes	N/A	0.573	0.178	0.493	1e-13
P54727	409	UV excision repair protei	yes	N/A	0.558	0.176	0.5	6e-13
A3KMV2	362	UV excision repair protei	yes	N/A	0.604	0.215	0.461	9e-13
P54725	363	UV excision repair protei	no	N/A	0.604	0.214	0.461	1e-12
P54726	363	UV excision repair protei	no	N/A	0.418	0.148	0.611	1e-12
Q29RK4	408	UV excision repair protei	no	N/A	0.403	0.127	0.634	1e-12
Q84L33	371	Putative DNA repair prote	yes	N/A	0.596	0.207	0.453	6e-12
Q84L32	368	Putative DNA repair prote	no	N/A	0.550	0.192	0.506	7e-12

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

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 42/83 (50%), Positives = 56/83 (67%), Gaps = 8/83 (9%)

Query: 6   AAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRAS 65
           AAA S P T       TAT+  P +A +TL +G +    V+N+V+MGYERS V  A+RA+
Sbjct: 120 AAAPSNPDT-------TATSEAPIDA-NTLAVGAQRNVAVENMVEMGYERSEVERAMRAA 171

Query: 66  FNNPDRAVEYLITGIPAAVVGEE 88
           FNNPDRAVEYL+TGIP  ++  +
Sbjct: 172 FNNPDRAVEYLLTGIPEDILNRQ 194

Protects ubiquitin chains against dissambly by deubiquitinating enzymes thereby promoting protein degradation.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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

 Score = 75.5 bits (184), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 44/94 (46%), Positives = 50/94 (53%), Gaps = 17/94 (18%)

Query: 4   APAAATSTPSTPVSQAGATATATTPGNAEST----------------LLMGDEYGRMVQN 47
           APA AT  P  P  +   T   T+P  A+ST                L+ G  Y  MV  
Sbjct: 138 APAGATQ-PEKPAEKPAQTPVLTSPAPADSTPGDSSRSNLFEDATSALVTGQSYENMVTE 196

Query: 48  IVDMGYERSAVTEALRASFNNPDRAVEYLITGIP 81
           I+ MGYER  V  ALRASFNNPDRAVEYL+ GIP
Sbjct: 197 IMSMGYEREQVIAALRASFNNPDRAVEYLLMGIP 230

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

Mus musculus (taxid: 10090)

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

 Score = 74.7 bits (182), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/81 (49%), Positives = 50/81 (61%), Gaps = 7/81 (8%)

Query: 1   MIGAPAAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTE 60
           ++ +PA A STP       G ++ +    +A S L+ G  Y  MV  I+ MGYER  V  
Sbjct: 157 VLTSPAPADSTP-------GDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIA 209

Query: 61  ALRASFNNPDRAVEYLITGIP 81
           ALRASFNNPDRAVEYL+ GIP
Sbjct: 210 ALRASFNNPDRAVEYLLMGIP 230

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

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 47/72 (65%)

Query: 10  STPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNP 69
           ++P+   S +G ++ +    +A S L+ G  Y  MV  I+ MGYER  V  ALRASFNNP
Sbjct: 159 TSPTATDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNP 218

Query: 70  DRAVEYLITGIP 81
           DRAVEYL+ GIP
Sbjct: 219 DRAVEYLLMGIP 230

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

 Score = 72.4 bits (176), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 50/78 (64%)

Query: 6   AAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRAS 65
           +A T++P +      ++ +     +A STL+ G EY  M+  I+ MGYER  V  ALRAS
Sbjct: 128 SAPTTSPESVSGSVPSSGSGGREEDAASTLVTGSEYETMLTEIMSMGYERERVVAALRAS 187

Query: 66  FNNPDRAVEYLITGIPAA 83
           +NNP RAVEYL+TGIP +
Sbjct: 188 YNNPHRAVEYLLTGIPGS 205

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

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 51/78 (65%)

Query: 6   AAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRAS 65
           +A T++P +      ++ ++    +A STL+ G EY  M+  I+ MGYER  V  ALRAS
Sbjct: 128 SAPTTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETMLTEIMSMGYERERVVAALRAS 187

Query: 66  FNNPDRAVEYLITGIPAA 83
           +NNP RAVEYL+TGIP +
Sbjct: 188 YNNPHRAVEYLLTGIPGS 205

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)

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

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/54 (61%), Positives = 40/54 (74%)

Query: 30  NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAA 83
           +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGIP +
Sbjct: 152 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPGS 205

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

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/52 (63%), Positives = 37/52 (71%)

Query: 30  NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIP 81
           +A S L+ G  Y  MV  I+ MGYER  V  ALRASFNNPDRAVEYL+ GIP
Sbjct: 179 DATSALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIP 230

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

 Score = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 39/86 (45%), Positives = 55/86 (63%), Gaps = 9/86 (10%)

Query: 5   PAAATSTPSTPV------SQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMG---YER 55
           PAA ++T S+PV      +Q    A   T G A STL+ G    +MVQ I++MG   +++
Sbjct: 106 PAAPSTTQSSPVPASPIPAQEQPAAQTDTYGQAASTLVSGSSLEQMVQQIMEMGGGSWDK 165

Query: 56  SAVTEALRASFNNPDRAVEYLITGIP 81
             VT ALRA++NNP+RAV+YL +GIP
Sbjct: 166 ETVTRALRAAYNNPERAVDYLYSGIP 191

May be involved in nucleotide excision repair.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 69.3 bits (168), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 51/75 (68%), Gaps = 4/75 (5%)

Query: 13  STPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMG---YERSAVTEALRASFNNP 69
           STPV Q   TA + T G A STL+ G    +MVQ I++MG   +++  VT ALRA++NNP
Sbjct: 119 STPV-QEQPTAQSDTYGQAASTLVSGSSIEQMVQQIMEMGGGSWDKETVTRALRAAYNNP 177

Query: 70  DRAVEYLITGIPAAV 84
           +RAV+YL +GIP  V
Sbjct: 178 ERAVDYLYSGIPETV 192

May be involved in nucleotide excision repair.

Arabidopsis thaliana (taxid: 3702)

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	129
345482492	358	PREDICTED: UV excision repair protein RA	0.697	0.251	0.586	5e-19
345482494	367	PREDICTED: UV excision repair protein RA	0.697	0.245	0.586	5e-19
345482490	377	PREDICTED: UV excision repair protein RA	0.689	0.236	0.593	7e-19
383860341	365	PREDICTED: UV excision repair protein RA	0.565	0.2	0.628	2e-18
307211720	357	UV excision repair protein RAD23-like pr	0.643	0.232	0.588	2e-18
340716523	337	PREDICTED: UV excision repair protein RA	0.635	0.243	0.595	4e-18
340716521	348	PREDICTED: UV excision repair protein RA	0.635	0.235	0.595	6e-18
350404552	365	PREDICTED: UV excision repair protein RA	0.581	0.205	0.636	7e-18
340716519	364	PREDICTED: UV excision repair protein RA	0.596	0.211	0.615	7e-18
340716525	357	PREDICTED: UV excision repair protein RA	0.635	0.229	0.595	8e-18

>gi|345482492|ref|XP_001608155.2| PREDICTED: UV excision repair protein RAD23 homolog B-like isoform 1 [Nasonia vitripennis]

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 54/92 (58%), Positives = 62/92 (67%), Gaps = 2/92 (2%)

Query: 7   AATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASF 66
           A T TP T   Q   T+ AT+    ES LLMG+EY  MV NI+DMGYER  V +ALRASF
Sbjct: 134 APTRTPETATQQPTPTSVATS-NPPESALLMGEEYNAMVNNIMDMGYERDQVEQALRASF 192

Query: 67  NNPDRAVEYLITGIPAAVVGEEAPVAANEPQG 98
           NNPDRAVEYL+TGIPA +  E+ P  A E Q 
Sbjct: 193 NNPDRAVEYLLTGIPAQLF-EDPPEEAAESQD 223

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 99.0 bits (245), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 54/92 (58%), Positives = 62/92 (67%), Gaps = 2/92 (2%)

Query: 7   AATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASF 66
           A T TP T   Q   T+ AT+    ES LLMG+EY  MV NI+DMGYER  V +ALRASF
Sbjct: 134 APTRTPETATQQPTPTSVATS-NPPESALLMGEEYNAMVNNIMDMGYERDQVEQALRASF 192

Query: 67  NNPDRAVEYLITGIPAAVVGEEAPVAANEPQG 98
           NNPDRAVEYL+TGIPA +  E+ P  A E Q 
Sbjct: 193 NNPDRAVEYLLTGIPAQLF-EDPPEEAAESQD 223

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 98.6 bits (244), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 54/91 (59%), Positives = 62/91 (68%), Gaps = 2/91 (2%)

Query: 7   AATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASF 66
           A T TP T   Q   T+ AT+    ES LLMG+EY  MV NI+DMGYER  V +ALRASF
Sbjct: 134 APTRTPETATQQPTPTSVATS-NPPESALLMGEEYNAMVNNIMDMGYERDQVEQALRASF 192

Query: 67  NNPDRAVEYLITGIPAAVVGEEAPVAANEPQ 97
           NNPDRAVEYL+TGIPA +  E+ P  A E Q
Sbjct: 193 NNPDRAVEYLLTGIPAQLF-EDPPEEAAESQ 222

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383860341|ref|XP_003705649.1| PREDICTED: UV excision repair protein RAD23 homolog B-like [Megachile rotundata]

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/78 (62%), Positives = 55/78 (70%), Gaps = 5/78 (6%)

Query: 13  STPVS-----QAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFN 67
           S PVS      A +TAT    G AES LLMG+ Y  MV NI+DMGYER  V +ALRASFN
Sbjct: 115 SNPVSTAQEQSAASTATECAGGQAESALLMGENYNTMVNNIMDMGYEREQVEQALRASFN 174

Query: 68  NPDRAVEYLITGIPAAVV 85
           NPDRAVEYL+TGIPA + 
Sbjct: 175 NPDRAVEYLVTGIPAQLF 192

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307211720|gb|EFN87721.1| UV excision repair protein RAD23-like protein A [Harpegnathos saltator]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/85 (58%), Positives = 58/85 (68%), Gaps = 2/85 (2%)

Query: 13  STPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRA 72
           ST   Q  A   A   G AES LLMG++Y  MV+NI+DMGYER  V +ALRASFNNPDRA
Sbjct: 118 STVQEQIAAAVPAAGCGQAESALLMGEDYNTMVKNIMDMGYEREQVVQALRASFNNPDRA 177

Query: 73  VEYLITGIPAAVVGE--EAPVAANE 95
           VEYL+TGIPA +  +  E P  A E
Sbjct: 178 VEYLLTGIPAQLFEDPPEDPPEAQE 202

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340716523|ref|XP_003396747.1| PREDICTED: UV excision repair protein RAD23 homolog B-like isoform 3 [Bombus terrestris]

 Score = 95.9 bits (237), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 61/84 (72%), Gaps = 2/84 (2%)

Query: 8   ATSTPSTPVSQAGATATA-TTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASF 66
           A++  +T   Q+ A+ TA    G AES LLMG++Y  MV NIVDMGYER  V +ALRASF
Sbjct: 114 ASNPTNTAQEQSEASTTAGCVGGQAESALLMGEDYNTMVNNIVDMGYEREQVEQALRASF 173

Query: 67  NNPDRAVEYLITGIPAAVVGEEAP 90
           NNPDRAVEYL+TGIPA +  E+ P
Sbjct: 174 NNPDRAVEYLLTGIPAQLF-EDLP 196

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340716521|ref|XP_003396746.1| PREDICTED: UV excision repair protein RAD23 homolog B-like isoform 2 [Bombus terrestris]

 Score = 95.5 bits (236), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 61/84 (72%), Gaps = 2/84 (2%)

Query: 8   ATSTPSTPVSQAGATATA-TTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASF 66
           A++  +T   Q+ A+ TA    G AES LLMG++Y  MV NIVDMGYER  V +ALRASF
Sbjct: 114 ASNPTNTAQEQSEASTTAGCVGGQAESALLMGEDYNTMVNNIVDMGYEREQVEQALRASF 173

Query: 67  NNPDRAVEYLITGIPAAVVGEEAP 90
           NNPDRAVEYL+TGIPA +  E+ P
Sbjct: 174 NNPDRAVEYLLTGIPAQLF-EDLP 196

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350404552|ref|XP_003487142.1| PREDICTED: UV excision repair protein RAD23 homolog B-like [Bombus impatiens]

 Score = 95.5 bits (236), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 49/77 (63%), Positives = 57/77 (74%), Gaps = 2/77 (2%)

Query: 10  STPSTPVS-QAGATATA-TTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFN 67
           S P+  V  Q+ A+ TA    G AES LLMG++Y  MV NIVDMGYER  V +ALRASFN
Sbjct: 116 SNPTNTVQEQSEASTTAGCVGGQAESALLMGEDYNTMVNNIVDMGYEREQVEQALRASFN 175

Query: 68  NPDRAVEYLITGIPAAV 84
           NPDRAVEYL+TGIPA +
Sbjct: 176 NPDRAVEYLLTGIPAQL 192

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340716519|ref|XP_003396745.1| PREDICTED: UV excision repair protein RAD23 homolog B-like isoform 1 [Bombus terrestris]

 Score = 95.5 bits (236), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 48/78 (61%), Positives = 58/78 (74%), Gaps = 1/78 (1%)

Query: 8   ATSTPSTPVSQAGATATA-TTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASF 66
           A++  +T   Q+ A+ TA    G AES LLMG++Y  MV NIVDMGYER  V +ALRASF
Sbjct: 114 ASNPTNTAQEQSEASTTAGCVGGQAESALLMGEDYNTMVNNIVDMGYEREQVEQALRASF 173

Query: 67  NNPDRAVEYLITGIPAAV 84
           NNPDRAVEYL+TGIPA +
Sbjct: 174 NNPDRAVEYLLTGIPAQL 191

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340716525|ref|XP_003396748.1| PREDICTED: UV excision repair protein RAD23 homolog B-like isoform 4 [Bombus terrestris]

 Score = 95.1 bits (235), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 61/84 (72%), Gaps = 2/84 (2%)

Query: 8   ATSTPSTPVSQAGATATA-TTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASF 66
           A++  +T   Q+ A+ TA    G AES LLMG++Y  MV NIVDMGYER  V +ALRASF
Sbjct: 114 ASNPTNTAQEQSEASTTAGCVGGQAESALLMGEDYNTMVNNIVDMGYEREQVEQALRASF 173

Query: 67  NNPDRAVEYLITGIPAAVVGEEAP 90
           NNPDRAVEYL+TGIPA +  E+ P
Sbjct: 174 NNPDRAVEYLLTGIPAQLF-EDLP 196

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

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	129
FB|FBgn0026777	414	Rad23 "Rad23" [Drosophila mela	0.387	0.120	0.64	1.8e-11
UNIPROTKB|K7ESE3	308	RAD23A "UV excision repair pro	0.395	0.165	0.627	2.2e-11
RGD|1309899	351	Rad23a "RAD23 homolog A (S. ce	0.395	0.145	0.627	3.3e-11
UNIPROTKB|A3KMV2	362	RAD23A "UV excision repair pro	0.395	0.140	0.627	3.6e-11
UNIPROTKB|F1PTL1	362	RAD23A "Uncharacterized protei	0.395	0.140	0.627	3.6e-11
ZFIN|ZDB-GENE-040808-59	362	rad23aa "RAD23 homolog Aa (S.	0.395	0.140	0.607	3.6e-11
UNIPROTKB|P54725	363	RAD23A "UV excision repair pro	0.395	0.140	0.627	3.6e-11
MGI|MGI:105126	363	Rad23a "RAD23a homolog (S. cer	0.395	0.140	0.627	3.6e-11
UNIPROTKB|D4AD39	363	Rad23a "RAD23a homolog (S. cer	0.395	0.140	0.627	3.6e-11
UNIPROTKB|F1SD96	380	RAD23A "Uncharacterized protei	0.395	0.134	0.627	5.1e-11

FB|FBgn0026777 Rad23 "Rad23" [Drosophila melanogaster (taxid:7227)]

 Score = 164 (62.8 bits), Expect = 1.8e-11, P = 1.8e-11
 Identities = 32/50 (64%), Positives = 39/50 (78%)

Query:    31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             AES LLMGDEY + V ++V+MGY R  V  A+ AS+NNP+RAVEYLI GI
Sbjct:   149 AESNLLMGDEYNQTVLSMVEMGYPREQVERAMAASYNNPERAVEYLINGI 198

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

GO:0003684 "damaged DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

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

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

 Score = 160 (61.4 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 32/51 (62%), Positives = 38/51 (74%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct:   152 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 202

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

 Score = 160 (61.4 bits), Expect = 3.3e-11, P = 3.3e-11
 Identities = 32/51 (62%), Positives = 38/51 (74%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct:   152 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 202

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

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

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

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

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

 Score = 160 (61.4 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 32/51 (62%), Positives = 38/51 (74%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct:   152 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 202

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 = 160 (61.4 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 32/51 (62%), Positives = 38/51 (74%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct:   152 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 202

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

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

GO:0031593 "polyubiquitin binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

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

 Score = 160 (61.4 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 31/51 (60%), Positives = 38/51 (74%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+ NI+ MGYER  V  AL+AS+NNP RAVEYL+ GI
Sbjct:   150 DASSTLVTGQEYDAMLTNIMSMGYERDKVVAALKASYNNPHRAVEYLLNGI 200

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

 Score = 160 (61.4 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 32/51 (62%), Positives = 38/51 (74%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct:   152 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 202

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

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

 Score = 160 (61.4 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 32/51 (62%), Positives = 38/51 (74%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct:   152 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 202

GO:0000502 "proteasome complex" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

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

GO:0031593 "polyubiquitin binding" evidence=ISO

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

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

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

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

 Score = 160 (61.4 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 32/51 (62%), Positives = 38/51 (74%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct:   152 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 202

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

 Score = 159 (61.0 bits), Expect = 5.1e-11, P = 5.1e-11
 Identities = 32/51 (62%), Positives = 37/51 (72%)

Query:    30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
             +A STL+ G EY  M+  I  MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct:   169 DAASTLVTGSEYETMLTEITSMGYERERVVAALRASYNNPHRAVEYLLTGI 219

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

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

GO:0031593 "polyubiquitin binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O74803	RHP23_SCHPO	No assigned EC number	0.5060	0.5813	0.2038	yes	N/A
P32628	RAD23_YEAST	No assigned EC number	0.5166	0.4263	0.1381	yes	N/A

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	129
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	1e-20
pfam00627	37	pfam00627, UBA, UBA/TS-N domain	2e-09
cd00194	38	cd00194, UBA, Ubiquitin Associated domain	2e-09
smart00165	37	smart00165, UBA, Ubiquitin associated domain	7e-08

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

 Score = 84.9 bits (210), Expect = 1e-20
 Identities = 39/115 (33%), Positives = 55/115 (47%), Gaps = 17/115 (14%)

Query: 4   APAAATSTPSTPVSQAGATATATTP--------GNAESTLLMGDEYGRMVQNIVDMGYER 55
           A  A+     +P  ++       +P         +A STL++G E    ++ I++MGYER
Sbjct: 111 AAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERETTIEEIMEMGYER 170

Query: 56  SAVTEALRASFNNPDRAVEYLITGIP---------AAVVGEEAPVAANEPQGNNI 101
             V  ALRA+FNNPDRAVEYL+TGIP                A      PQ  ++
Sbjct: 171 EEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAASTAAATTETPQHGSV 225

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|201355 pfam00627, UBA, UBA/TS-N domain

 Score = 49.4 bits (119), Expect = 2e-09
 Identities = 14/33 (42%), Positives = 23/33 (69%)

Query: 44 MVQNIVDMGYERSAVTEALRASFNNPDRAVEYL 76
          +++ + +MG+ R    +ALRA+  N +RAVEYL
Sbjct: 5  LIKQLREMGFSREEAKKALRATNGNVERAVEYL 37

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

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

 Score = 49.0 bits (118), Expect = 2e-09
 Identities = 14/35 (40%), Positives = 25/35 (71%)

Query: 43 RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77
            ++ +++MG+ R    +ALRA+ NN +RAVE+L+
Sbjct: 3  EKLEQLLEMGFSREEARKALRATNNNVERAVEWLL 37

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

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

 Score = 45.2 bits (108), Expect = 7e-08
 Identities = 13/33 (39%), Positives = 22/33 (66%)

Query: 45 VQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77
          +  +++MG+ R    +ALRA+  N +RA EYL+
Sbjct: 5  IDQLLEMGFSREEALKALRAANGNVERAAEYLL 37

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	129
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	99.93
KOG0011|consensus	340		99.9
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	99.47
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	99.4
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	99.38
KOG0944|consensus	763		98.62
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	98.24
KOG0418|consensus	200		97.95
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	97.92
KOG0011|consensus	340		97.78
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	97.71
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	97.66
smart00546	43	CUE Domain that may be involved in binding ubiquit	97.56
KOG0944|consensus	763		97.51
KOG2561|consensus	568		97.39
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	97.36
PF09288	55	UBA_3: Fungal ubiquitin-associated domain ; InterP	97.04
KOG2561|consensus	568		96.77
PRK06369	115	nac nascent polypeptide-associated complex protein	96.36
KOG0010|consensus	493		96.35
PF09280	59	XPC-binding: XPC-binding domain; InterPro: IPR0153	96.03
TIGR00264	116	alpha-NAC-related protein. This hypothetical prote	95.92
TIGR00116	290	tsf translation elongation factor Ts. This protein	95.91
PF07223	358	DUF1421: Protein of unknown function (DUF1421); In	95.85
PRK12332	198	tsf elongation factor Ts; Reviewed	95.84
PF11626	87	Rap1_C: TRF2-interacting telomeric protein/Rap1 -	95.82
PRK09377	290	tsf elongation factor Ts; Provisional	95.75
CHL00098	200	tsf elongation factor Ts	95.64
KOG2689|consensus	290		95.48
COG1308	122	EGD2 Transcription factor homologous to NACalpha-B	95.23
PF07499	47	RuvA_C: RuvA, C-terminal domain; InterPro: IPR0111	93.25
COG0264	296	Tsf Translation elongation factor Ts [Translation,	93.01
PF06972	60	DUF1296: Protein of unknown function (DUF1296); In	92.3
PF08938	79	HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This	90.75
PF11547	53	E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro	90.72
KOG1071|consensus	340		89.19
smart00804	63	TAP_C C-terminal domain of vertebrate Tap protein.	88.98
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	88.64
PF03943	51	TAP_C: TAP C-terminal domain; InterPro: IPR005637	87.55
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	85.1
PF03474	39	DMA: DMRTA motif; InterPro: IPR005173 This region	82.35
COG4008	153	Predicted metal-binding transcription factor [Tran	81.63

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=99.93  E-value=2.3e-26  Score=196.63  Aligned_cols=92  Identities=42%  Similarity=0.642  Sum_probs=77.0

Q ss_pred             CcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCCcCCCC----C----------C-c----
Q psy4260          31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEE----A----------P-V----   91 (129)
Q Consensus        31 ~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~~~~~~----~----------~-~----   91 (129)
                      +.|++++|+.+|+.|++||+|||+|++|++|||++|||+|||||||++|||+..+..+    +          + .    
T Consensus       146 ~~s~l~~g~~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~tGIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  225 (378)
T TIGR00601       146 AASTLVVGSERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAASTAAATTETPQHGSV  225 (378)
T ss_pred             cccccccchHHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHHhCCCccccccccCCCcccccccccCCCCCCcch
Confidence            5678999999999999999999999999999999999999999999999997632100    0          0 0    


Q ss_pred             -------------------cCCCCCCCCCCCccchhhhh------hhhhhhcCCce
Q psy4260          92 -------------------AANEPQGNNIKQFSSVKEIE------IPNLMQGDNKV  122 (129)
Q Consensus        92 -------------------a~~~~~~~n~PqF~~~r~~~------lp~llq~~~~~  122 (129)
                                         ...+.+||++|+|.+||++|      |+.|||++++-
T Consensus       226 f~~a~~~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLqql~~~  281 (378)
T TIGR00601       226 FEQAAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQE  281 (378)
T ss_pred             hhhhhcccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHHHHHhh
Confidence                               01236689999999999999      99999998764

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

>KOG0011|consensus

Probab=99.90  E-value=2.8e-24  Score=182.07  Aligned_cols=96  Identities=41%  Similarity=0.589  Sum_probs=81.3

Q ss_pred             CCCCcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCCcCCCC---------C-----Cc--
Q psy4260          28 PGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEE---------A-----PV--   91 (129)
Q Consensus        28 ~~~~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~~~~~~---------~-----~~--   91 (129)
                      .+.+.++++.|+.++..|.+||+|||+|++|++|||++|||+|||||||++|||++...+.         .     ++  
T Consensus       122 ~~~aas~Lv~G~~~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~GIP~~~~~~~~~~~~~~~~~~p~~~~p~~  201 (340)
T KOG0011|consen  122 YEIAASTLVVGSEYEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLNGIPEDAEVPEPEKSTAAAAELPANAQPLD  201 (340)
T ss_pred             hhhhhhhhhccchhHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhcCCcccccCCcccCCcccCCCCCCCCChhh
Confidence            3446788999999999999999999999999999999999999999999999999633211         1     11  


Q ss_pred             ---------cCC--CCCCCCCCCccchhhhh------hhhhhhcCCceE
Q psy4260          92 ---------AAN--EPQGNNIKQFSSVKEIE------IPNLMQGDNKVY  123 (129)
Q Consensus        92 ---------a~~--~~~~~n~PqF~~~r~~~------lp~llq~~~~~~  123 (129)
                               ..+  ..++||.|||.+||++|      |..|||++||.+
T Consensus       202 ~~~~~~~~~~~~~~l~fLr~~~qf~~lR~~iqqNP~ll~~~Lqqlg~~n  250 (340)
T KOG0011|consen  202 LFPQGAVEASGGDPLEFLRNQPQFQQLRQMIQQNPELLHPLLQQLGKQN  250 (340)
T ss_pred             cCCccchhhhcCCchhhhhccHHHHHHHHHHhhCHHHHHHHHHHHhhhC
Confidence                     022  56789999999999999      999999999875

>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []

Probab=99.47  E-value=8e-14  Score=83.38  Aligned_cols=36  Identities=42%  Similarity=0.654  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHH
Q psy4260          41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYL   76 (129)
Q Consensus        41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L   76 (129)
                      +++.|++|++|||++++|++||++++||+++|++||
T Consensus         2 ~~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    2 DEEKVQQLMEMGFSREQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence            678999999999999999999999999999999998

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

>cd00194 UBA Ubiquitin Associated domain

Probab=99.40  E-value=6.7e-13  Score=78.68  Aligned_cols=37  Identities=38%  Similarity=0.696  Sum_probs=35.3

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      ++.|++|++|||++++|++||++++||+++|++||++
T Consensus         2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~~   38 (38)
T cd00194           2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWLLE   38 (38)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            6789999999999999999999999999999999984

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

>smart00165 UBA Ubiquitin associated domain

Probab=99.38  E-value=7e-13  Score=78.35  Aligned_cols=37  Identities=35%  Similarity=0.636  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      +++.|++|++|||++++|++||++++||+++|++|||
T Consensus         1 ~~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L~   37 (37)
T smart00165        1 DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL   37 (37)
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence            3678999999999999999999999999999999996

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

>KOG0944|consensus

Probab=98.62  E-value=3.7e-08  Score=90.78  Aligned_cols=43  Identities=33%  Similarity=0.558  Sum_probs=41.0

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIP   81 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP   81 (129)
                      +..++.+..|++|||++.||++||++.+||+|||+||+|+++.
T Consensus       633 ~~~e~~v~si~smGf~~~qa~~aL~~~n~nveravDWif~h~d  675 (763)
T KOG0944|consen  633 EVDEESVASIVSMGFSRNQAIKALKATNNNVERAVDWIFSHMD  675 (763)
T ss_pred             CCChhHheeeeeecCcHHHHHHHHHhcCccHHHHHHHHHhccc
Confidence            5789999999999999999999999999999999999999965

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=98.24  E-value=1.3e-06  Score=75.48  Aligned_cols=42  Identities=24%  Similarity=0.408  Sum_probs=39.3

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ..+..+.|++|++|||+|+.|+.|-.+|+-|.|.|++|||++
T Consensus       334 T~eE~~AIeRL~~LGF~r~~viqaY~ACdKNEelAAn~Lf~~  375 (378)
T TIGR00601       334 TPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQ  375 (378)
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHhh
Confidence            556778999999999999999999999999999999999976

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

>KOG0418|consensus

Probab=97.95  E-value=1.1e-05  Score=65.01  Aligned_cols=45  Identities=24%  Similarity=0.260  Sum_probs=41.5

Q ss_pred             ccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          35 LLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        35 ~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ...+..+..+|+.|.+|||+|+.++.+|+..+||.++|.+.|++|
T Consensus       156 ~~~~~~~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~~~~s~  200 (200)
T KOG0418|consen  156 LPDDPWDKKKVDSLIEMGFSELEAILVLSGSDWNLADATEQLLSG  200 (200)
T ss_pred             CCCCchhHHHHHHHHHhcccHHHHHHHhhccccchhhhhHhhccC
Confidence            456677889999999999999999999999999999999999875

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

Probab=97.92  E-value=2.3e-05  Score=47.79  Aligned_cols=38  Identities=24%  Similarity=0.420  Sum_probs=34.6

Q ss_pred             HHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          42 GRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        42 ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ++.|++|.+|  .++++.++.+|++++||+|+|++.|+.+
T Consensus         2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~   41 (42)
T PF02845_consen    2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM   41 (42)
T ss_dssp             HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            6789999999  8999999999999999999999999864

CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.

>KOG0011|consensus

Probab=97.78  E-value=3.1e-05  Score=66.69  Aligned_cols=43  Identities=23%  Similarity=0.347  Sum_probs=39.5

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      ..+..+.|++|++|||+|.-|+.|.=+|+-|.|.|++|||++.
T Consensus       295 tpee~eAIeRL~alGF~ralViqayfACdKNEelAAN~Ll~~~  337 (340)
T KOG0011|consen  295 TPEEKEAIERLEALGFPRALVIQAYFACDKNEELAANYLLSHS  337 (340)
T ss_pred             CHHHHHHHHHHHHhCCcHHHHHHHHHhcCccHHHHHHHHHhhc
Confidence            4456778999999999999999999999999999999999884

>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A

Probab=97.71  E-value=0.00012  Score=44.91  Aligned_cols=38  Identities=13%  Similarity=0.212  Sum_probs=32.5

Q ss_pred             HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      +++|.++++. |.+++.|+.-|++++||+++||+..|..
T Consensus         1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~   39 (43)
T PF14555_consen    1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDD   39 (43)
T ss_dssp             HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHS
T ss_pred             CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            5788998887 9999999999999999999999987764

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

Probab=97.66  E-value=6.4e-05  Score=68.82  Aligned_cols=41  Identities=22%  Similarity=0.477  Sum_probs=37.8

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCCC
Q psy4260          42 GRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPA   82 (129)
Q Consensus        42 ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP~   82 (129)
                      +..|.||++|||..+.+.|||-..+| |.|-|.+|||.|+.+
T Consensus       559 qs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqHMdD  600 (749)
T COG5207         559 QSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQHMDD  600 (749)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhhccC
Confidence            56899999999999999999999988 999999999999654

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

Probab=97.56  E-value=0.00025  Score=43.17  Aligned_cols=38  Identities=18%  Similarity=0.420  Sum_probs=34.9

Q ss_pred             HHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          42 GRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        42 ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ++.|+.|.+|  .++++.+++.|++++||+|+|++-|+.+
T Consensus         3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~   42 (43)
T smart00546        3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG   42 (43)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            5679999999  6889999999999999999999999875

CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)

>KOG0944|consensus

Probab=97.51  E-value=0.00015  Score=67.46  Aligned_cols=43  Identities=19%  Similarity=0.363  Sum_probs=39.2

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHHHcCCCC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRAS-FNNPDRAVEYLITGIPA   82 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras-~~n~erAvE~L~~giP~   82 (129)
                      .++..|.+|++|||..+.++|||-.+ |.+.|.|.+||+.||.|
T Consensus       570 ~d~s~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl~~HMdD  613 (763)
T KOG0944|consen  570 ADRSVISQLVEMGFPEEACRRALYYTGNSGAEAASNWLMEHMDD  613 (763)
T ss_pred             hhHHHHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHHHHhccC
Confidence            56778999999999999999999999 66999999999999765

>KOG2561|consensus

Probab=97.39  E-value=0.00017  Score=64.93  Aligned_cols=39  Identities=31%  Similarity=0.476  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .++....+|+|||.+.+++.|||.|+||+|+||.|+.+.
T Consensus       303 ~d~~lsllv~mGfeesdaRlaLRsc~g~Vd~AvqfI~er  341 (568)
T KOG2561|consen  303 NDETLSLLVGMGFEESDARLALRSCNGDVDSAVQFIIER  341 (568)
T ss_pred             cchHHHHHHHcCCCchHHHHHHHhccccHHHHHHHHHHH
Confidence            356778899999999999999999999999999999764

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

Probab=97.36  E-value=8.1e-05  Score=68.17  Aligned_cols=41  Identities=15%  Similarity=0.220  Sum_probs=39.1

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      +.+|++++.|++|||...++|+||...++|.+|+|+|.+++
T Consensus       619 eVdE~~~~Slle~Gln~n~~Rkal~~~n~d~~r~V~w~~N~  659 (749)
T COG5207         619 EVDESKARSLLENGLNPNLCRKALMDMNTDSKRRVVWCIND  659 (749)
T ss_pred             cccHHHHHHHHHcCCCHHHHHHHHHHccCCchheEEEEEeC
Confidence            45899999999999999999999999999999999999996

>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle

Probab=97.04  E-value=0.00067  Score=45.02  Aligned_cols=27  Identities=33%  Similarity=0.426  Sum_probs=21.2

Q ss_pred             hHHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260          41 YGRMVQNIVDMGYERSAVTEALRASFN   67 (129)
Q Consensus        41 ~ee~I~~L~eMGF~reqv~~ALras~~   67 (129)
                      ..+.|+++++|||++++|+.|||+-+-
T Consensus         9 ~~~lVd~F~~mGF~~dkVvevlrrlgi   35 (55)
T PF09288_consen    9 DKDLVDQFENMGFERDKVVEVLRRLGI   35 (55)
T ss_dssp             SHHHHHHHHHHT--HHHHHHHHHHS--
T ss_pred             CHHHHHHHHHcCCcHHHHHHHHHHhCC
Confidence            467899999999999999999998753

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

>KOG2561|consensus

Probab=96.77  E-value=0.0018  Score=58.48  Aligned_cols=46  Identities=28%  Similarity=0.333  Sum_probs=40.4

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCCcC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVV   85 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~~~   85 (129)
                      .++.+|.+|+.|||++-.++.||+..+||.+.|...|.-.++.+.+
T Consensus       428 vd~~~la~Lv~mGF~e~~A~~ALe~~gnn~~~a~~~L~~s~~n~~~  473 (568)
T KOG2561|consen  428 VDGISLAELVSMGFEEGKARSALEAGGNNEDTAQRLLSASVANEGE  473 (568)
T ss_pred             cchhhHHHHHHhccccchHHHHHHhcCCcHHHHHHHHHHhCCCCcc
Confidence            3577899999999999999999999999999999999876665533

>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed

Probab=96.36  E-value=0.009  Score=44.68  Aligned_cols=40  Identities=13%  Similarity=0.145  Sum_probs=36.1

Q ss_pred             CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      ...++.|+.+++- |-+++.|++||+.++||+-.|+-+|.+
T Consensus        74 ~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~  114 (115)
T PRK06369         74 EIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS  114 (115)
T ss_pred             CCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence            4678889999887 999999999999999999999988864

>KOG0010|consensus

Probab=96.35  E-value=0.0061  Score=55.00  Aligned_cols=39  Identities=36%  Similarity=0.551  Sum_probs=34.8

Q ss_pred             chHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          40 EYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        40 ~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      .+....++|-+||| +|+...+||++.+||+++|||-|+.
T Consensus       453 r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverll~  492 (493)
T KOG0010|consen  453 RYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERLLG  492 (493)
T ss_pred             HHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhc
Confidence            35667899999996 5999999999999999999999985

>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=96.03  E-value=0.00072  Score=44.92  Aligned_cols=26  Identities=23%  Similarity=0.339  Sum_probs=22.9

Q ss_pred             CCCCCCCCccchhhhh------hhhhhhcCCc
Q psy4260          96 PQGNNIKQFSSVKEIE------IPNLMQGDNK  121 (129)
Q Consensus        96 ~~~~n~PqF~~~r~~~------lp~llq~~~~  121 (129)
                      .++||+|+|+.||++|      ||.|||+.+.
T Consensus         2 ~~Lr~~Pqf~~lR~~vq~NP~lL~~lLqql~~   33 (59)
T PF09280_consen    2 EFLRNNPQFQQLRQLVQQNPQLLPPLLQQLGQ   33 (59)
T ss_dssp             GGGTTSHHHHHHHHHHHC-GGGHHHHHHHHHC
T ss_pred             hHHHcChHHHHHHHHHHHCHHHHHHHHHHHhc
Confidence            4689999999999999      9999998754

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 ....

>TIGR00264 alpha-NAC-related protein

Probab=95.92  E-value=0.016  Score=43.46  Aligned_cols=39  Identities=10%  Similarity=0.066  Sum_probs=35.1

Q ss_pred             CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      ...++.|+.+++- |-+|+.|++||++++||+-.|+-||.
T Consensus        76 ~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~  115 (116)
T TIGR00264        76 EITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLE  115 (116)
T ss_pred             CCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence            3678889999887 89999999999999999999998874

This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.

>TIGR00116 tsf translation elongation factor Ts

Probab=95.91  E-value=0.013  Score=49.41  Aligned_cols=72  Identities=15%  Similarity=0.152  Sum_probs=50.3

Q ss_pred             hHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc-CCCCCcC--C-CCCCc----------------cCCCCCCC
Q psy4260          41 YGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT-GIPAAVV--G-EEAPV----------------AANEPQGN   99 (129)
Q Consensus        41 ~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~-giP~~~~--~-~~~~~----------------a~~~~~~~   99 (129)
                      .-+.|.+|-++ |..--+|++||..++||.|.|++||-. |+-....  . .....                --.++++-
T Consensus         4 sa~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRkkG~akA~Kk~~R~a~EG~V~~~~~~~~~~ivElncETDFVA   83 (290)
T TIGR00116         4 TAQLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRESGIAKAAKKADRVAAEGVIVLKSDGNKAVIVEVNSETDFVA   83 (290)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhchhHHHHhcccccCCcEEEEEEcCCEEEEEEEecCCcccc
Confidence            34568999988 999999999999999999999999974 3211000  0 00000                14457777


Q ss_pred             CCCCccchhhhhh
Q psy4260         100 NIKQFSSVKEIEI  112 (129)
Q Consensus       100 n~PqF~~~r~~~l  112 (129)
                      ...+|..|-.-++
T Consensus        84 rne~F~~l~~~ia   96 (290)
T TIGR00116        84 KNAGFKEFANKLL   96 (290)
T ss_pred             CChHHHHHHHHHH
Confidence            8889988876663

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

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

Probab=95.85  E-value=0.017  Score=50.30  Aligned_cols=32  Identities=19%  Similarity=0.412  Sum_probs=25.4

Q ss_pred             ccccCCCchHHHHHHHHHcCCChHHHHHHHHH
Q psy4260          33 STLLMGDEYGRMVQNIVDMGYERSAVTEALRA   64 (129)
Q Consensus        33 s~~~~g~~~ee~I~~L~eMGF~reqv~~ALra   64 (129)
                      +.+......++.|++++.|||.||+|+...|+
T Consensus       313 ~~~~~~~p~ddvidKv~~MGf~rDqV~a~v~r  344 (358)
T PF07223_consen  313 PQSGNRHPYDDVIDKVASMGFRRDQVRATVRR  344 (358)
T ss_pred             ccccccCcHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            34455566899999999999999999875444

>PRK12332 tsf elongation factor Ts; Reviewed

Probab=95.84  E-value=0.016  Score=46.41  Aligned_cols=37  Identities=19%  Similarity=0.366  Sum_probs=33.6

Q ss_pred             HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      -+.|.+|-++ |..--+|.+||..++||.|.|++||-.
T Consensus         5 a~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~   42 (198)
T PRK12332          5 AKLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLRE   42 (198)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            4568888888 999999999999999999999999974

>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []

Probab=95.82  E-value=0.017  Score=40.15  Aligned_cols=35  Identities=29%  Similarity=0.519  Sum_probs=30.8

Q ss_pred             HHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          45 VQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        45 I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      |+.+.+.||+++.|..||.++.+|+..|..|++.+
T Consensus         1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~   35 (87)
T PF11626_consen    1 IKHYEELGYSREFVTHALYATSGDPELARRFVLNF   35 (87)
T ss_dssp             -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred             CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            56688999999999999999999999999988877

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

>PRK09377 tsf elongation factor Ts; Provisional

Probab=95.75  E-value=0.017  Score=48.80  Aligned_cols=77  Identities=14%  Similarity=0.166  Sum_probs=53.2

Q ss_pred             hHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc-CCCCCc---CCCCCCc----------------cCCCCCCC
Q psy4260          41 YGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT-GIPAAV---VGEEAPV----------------AANEPQGN   99 (129)
Q Consensus        41 ~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~-giP~~~---~~~~~~~----------------a~~~~~~~   99 (129)
                      .-..|.+|-++ |..--+|++||..++||.|.|++||-. |+-...   .-.....                --.++++-
T Consensus         5 s~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk~G~akA~Kk~~R~a~EG~I~~~~~~~~~~~vElncETDFVA   84 (290)
T PRK09377          5 TAALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRKKGLAKAAKKAGRVAAEGLVAAKVDGNKGVLVEVNSETDFVA   84 (290)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhchhhHHHhcCccccceEEEEEeCCCEEEEEEEecCCcccc
Confidence            34678999988 999999999999999999999999974 321100   0000000                14456777


Q ss_pred             CCCCccchhhhhhhhhhh
Q psy4260         100 NIKQFSSVKEIEIPNLMQ  117 (129)
Q Consensus       100 n~PqF~~~r~~~lp~llq  117 (129)
                      ....|..|-+-++-++|.
T Consensus        85 rne~F~~l~~~i~~~~l~  102 (290)
T PRK09377         85 KNEDFQALANEVAEAALA  102 (290)
T ss_pred             CChHHHHHHHHHHHHHHh
Confidence            888898887777544444

>CHL00098 tsf elongation factor Ts

Probab=95.64  E-value=0.021  Score=45.90  Aligned_cols=36  Identities=22%  Similarity=0.300  Sum_probs=32.9

Q ss_pred             HHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          43 RMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        43 e~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      +.|.+|-++ |..--+|++||..++||.|.|++||-.
T Consensus         3 ~~ik~LR~~Tgag~~dck~AL~e~~gd~~~A~~~Lr~   39 (200)
T CHL00098          3 ELVKELRDKTGAGMMDCKKALQEANGDFEKALESLRQ   39 (200)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            468888888 899999999999999999999999975

>KOG2689|consensus

Probab=95.48  E-value=0.022  Score=48.47  Aligned_cols=38  Identities=18%  Similarity=0.356  Sum_probs=32.5

Q ss_pred             HHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHH-HcCCCC
Q psy4260          45 VQNIVDMGYERSAVTEALRAS-FNNPDRAVEYL-ITGIPA   82 (129)
Q Consensus        45 I~~L~eMGF~reqv~~ALras-~~n~erAvE~L-~~giP~   82 (129)
                      ++.|++|||++..+.+||--. +-+.+.|++|| +.+..+
T Consensus         4 ~~~l~~mgfps~k~e~al~~~~n~~~e~al~wl~~d~~~d   43 (290)
T KOG2689|consen    4 AQSLEEMGFPSGKAEKALAVYGNRGIEQALDWLEMDHAGD   43 (290)
T ss_pred             HHHHHHhcCchhhhhhHhhhhccccHHHHHHHHHhcccCC
Confidence            389999999999999999877 66899999999 666433

>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]

Probab=95.23  E-value=0.045  Score=41.50  Aligned_cols=39  Identities=18%  Similarity=0.206  Sum_probs=34.1

Q ss_pred             CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      ...++-|..+++- |-+|++|++||+.++||+-.|+-.|.
T Consensus        82 ~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~  121 (122)
T COG1308          82 DISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT  121 (122)
T ss_pred             CCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence            4567889988887 99999999999999999999986663

>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction

Probab=93.25  E-value=0.081  Score=32.95  Aligned_cols=26  Identities=12%  Similarity=0.434  Sum_probs=22.4

Q ss_pred             hHHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260          41 YGRMVQNIVDMGYERSAVTEALRASF   66 (129)
Q Consensus        41 ~ee~I~~L~eMGF~reqv~~ALras~   66 (129)
                      .++.++-|+.+||++.++.+|++...
T Consensus         3 ~~d~~~AL~~LGy~~~e~~~av~~~~   28 (47)
T PF07499_consen    3 LEDALEALISLGYSKAEAQKAVSKLL   28 (47)
T ss_dssp             HHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence            46789999999999999999999884

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

>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]

Probab=93.01  E-value=0.18  Score=43.18  Aligned_cols=37  Identities=19%  Similarity=0.335  Sum_probs=32.8

Q ss_pred             HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      -..|+.|-++ |-.--+|.+||..++||.|.|+|||-.
T Consensus         6 a~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~   43 (296)
T COG0264           6 AALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLRE   43 (296)
T ss_pred             HHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            4568888888 888899999999999999999999964

>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function

Probab=92.30  E-value=0.48  Score=32.07  Aligned_cols=38  Identities=21%  Similarity=0.349  Sum_probs=31.8

Q ss_pred             HHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          42 GRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        42 ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ...|+.|-|.  +++++++-..|+.|+.|+|.|++-|++-
T Consensus         6 rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q   45 (60)
T PF06972_consen    6 RKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ   45 (60)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence            4456776666  3699999999999999999999999863

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

Probab=90.75  E-value=0.13  Score=35.17  Aligned_cols=26  Identities=23%  Similarity=0.495  Sum_probs=23.0

Q ss_pred             ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          54 ERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        54 ~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ++.+++.||-.+++|+++||+||++.
T Consensus        45 ~e~~i~eal~~~~fDvekAl~~Ll~~   70 (79)
T PF08938_consen   45 PEEQIKEALWHYYFDVEKALDYLLSK   70 (79)
T ss_dssp             -CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred             CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence            88999999999999999999999987

; PDB: 1UFZ_A 3IZQ_1.

>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin

Probab=90.72  E-value=0.87  Score=29.96  Aligned_cols=41  Identities=15%  Similarity=0.185  Sum_probs=32.4

Q ss_pred             CchHHHHHHHHH--cCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVD--MGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~e--MGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ...|+.|.+...  -|-+|+-+++-|+.++-|++.||+-|++.
T Consensus         7 ~vPedlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsR   49 (53)
T PF11547_consen    7 QVPEDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLSR   49 (53)
T ss_dssp             GS-HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhcc
Confidence            446788877544  49999999999999999999999999876

Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.

>KOG1071|consensus

Probab=89.19  E-value=0.93  Score=39.54  Aligned_cols=40  Identities=15%  Similarity=0.122  Sum_probs=35.2

Q ss_pred             chHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          40 EYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ..-+.|.+|-+- |++-..|++||..++||...|.+||..-
T Consensus        45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k~   85 (340)
T KOG1071|consen   45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHKK   85 (340)
T ss_pred             ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence            456778888776 9999999999999999999999999754

>smart00804 TAP_C C-terminal domain of vertebrate Tap protein

Probab=88.98  E-value=1.8  Score=29.02  Aligned_cols=36  Identities=22%  Similarity=0.204  Sum_probs=30.5

Q ss_pred             CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHH
Q psy4260          39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVE   74 (129)
Q Consensus        39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE   74 (129)
                      ...++.|.++... |-..+=++++|..++||.++|+.
T Consensus        10 ~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~   46 (63)
T smart00804       10 PEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALK   46 (63)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHH
Confidence            3456677777666 99999999999999999999995

The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=88.64  E-value=0.43  Score=28.79  Aligned_cols=24  Identities=25%  Similarity=0.398  Sum_probs=21.0

Q ss_pred             CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260          53 YERSAVTEALRASFNNPDRAVEYL   76 (129)
Q Consensus        53 F~reqv~~ALras~~n~erAvE~L   76 (129)
                      |+++-++.||+.++||..+|.+.|
T Consensus         5 ~E~~~i~~aL~~~~gn~~~aA~~L   28 (42)
T PF02954_consen    5 FEKQLIRQALERCGGNVSKAARLL   28 (42)
T ss_dssp             HHHHHHHHHHHHTTT-HHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHH
Confidence            678889999999999999999877

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1)

Probab=87.55  E-value=0.82  Score=29.20  Aligned_cols=33  Identities=21%  Similarity=0.238  Sum_probs=25.8

Q ss_pred             HHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHH
Q psy4260          43 RMVQNIVDM-GYERSAVTEALRASFNNPDRAVEY   75 (129)
Q Consensus        43 e~I~~L~eM-GF~reqv~~ALras~~n~erAvE~   75 (129)
                      +.|.++... |-..+-+.+.|..++||.++|+.-
T Consensus         2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~   35 (51)
T PF03943_consen    2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQN   35 (51)
T ss_dssp             HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            456666655 889999999999999999999963

Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=85.10  E-value=1.6  Score=34.40  Aligned_cols=27  Identities=19%  Similarity=0.443  Sum_probs=23.9

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASF   66 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~   66 (129)
                      ..++.++.|..+||++.+|.+|+++..
T Consensus       146 ~~~e~~~aL~~LGy~~~e~~~ai~~~~  172 (191)
T TIGR00084       146 ARDELFEALVSLGYKPQEIQQALKKIK  172 (191)
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence            357889999999999999999999874

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []

Probab=82.35  E-value=1.9  Score=26.84  Aligned_cols=25  Identities=20%  Similarity=0.243  Sum_probs=21.1

Q ss_pred             CChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          53 YERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        53 F~reqv~~ALras~~n~erAvE~L~   77 (129)
                      -.|......|+.|+||+-+|+|.++
T Consensus        15 ~kr~~Le~iL~~C~GDvv~AIE~~l   39 (39)
T PF03474_consen   15 QKRSVLELILQRCNGDVVQAIEQFL   39 (39)
T ss_pred             CChHHHHHHHHHcCCcHHHHHHHhC
Confidence            3467778899999999999999763

DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.

>COG4008 Predicted metal-binding transcription factor [Transcription]

Probab=81.63  E-value=4.1  Score=31.76  Aligned_cols=41  Identities=17%  Similarity=0.060  Sum_probs=35.7

Q ss_pred             CCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          37 MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      ......+.|.-+.+-|.+.+.|++||..++ |+-+|++.|..
T Consensus       110 ~s~~~~e~v~v~a~a~v~~eeAr~aleeag-Dl~~A~k~l~~  150 (153)
T COG4008         110 HSEPPVEEVEVLADAFVTPEEAREALEEAG-DLRTAMKILRM  150 (153)
T ss_pred             cCCCcHHHHHHHHHhcCCHHHHHHHHHHcC-CHHHHHHHHHH
Confidence            345567889999999999999999999998 99999998754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	129
1oqy_A	368	Structure Of The Dna Repair Protein Hhr23a Length =		8e-13
1ify_A	49	Solution Structure Of The Internal Uba Domain Of Hh		1e-11

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 38/51 (74%)
Query: 30  NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
           +A STL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct: 157 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 207

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/47 (63%), Positives = 35/47 (74%)
Query: 34 TLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
          TL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGI
Sbjct: 1  TLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 47

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	129
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	3e-21
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	6e-14
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	3e-07
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	3e-06
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	4e-06
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	1e-05
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	4e-06
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	2e-04
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	6e-04

>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} SCOP: a.5.2.1 Length = 49

 Score = 79.0 bits (195), Expect = 3e-21
 Identities = 31/49 (63%), Positives = 36/49 (73%)

Query: 34 TLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPA 82
          TL+ G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+TGIP 
Sbjct: 1  TLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPG 49

>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 = 65.8 bits (159), Expect = 6e-14
 Identities = 38/97 (39%), Positives = 55/97 (56%)

Query: 3   GAPAAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEAL 62
              +A T++P +      ++ ++    +A STL+ G EY  M+  I+ MGYER  V  AL
Sbjct: 130 SEESAPTTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETMLTEIMSMGYERERVVAAL 189

Query: 63  RASFNNPDRAVEYLITGIPAAVVGEEAPVAANEPQGN 99
           RAS+NNP RAVEYL+TGIP +   E   V  ++    
Sbjct: 190 RASYNNPHRAVEYLLTGIPGSPEPEHGSVQESQVSEQ 226

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 43.5 bits (103), Expect = 3e-07
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 44 MVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
           V  IV MG+ R    +ALRA+ N+ +RAV+++ +
Sbjct: 12 CVTTIVSMGFSRDQALKALRATNNSLERAVDWIFS 46

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

 Score = 42.6 bits (99), Expect = 3e-06
 Identities = 13/42 (30%), Positives = 25/42 (59%)

Query: 37  MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
                  +V  I  MG++R+   +ALRA+ NN +RA++++ +
Sbjct: 74  DNQPPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWIFS 115

>4ae4_A Ubiquitin-associated protein 1; protein transport, endosomal sorting, tetherin, VPU, HIV-1, monoubiquitin; HET: NHE; 1.65A {Homo sapiens} PDB: 4ae4_B* Length = 118

 Score = 41.9 bits (98), Expect = 4e-06
 Identities = 12/44 (27%), Positives = 23/44 (52%)

Query: 40  EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAA 83
           E+ +++    +MG+E   + E L    N+ D A+E L+    A+
Sbjct: 75  EFLQLMSKFKEMGFELKDIKEVLLLHNNDQDNALEDLMARAGAS 118

>4ae4_A Ubiquitin-associated protein 1; protein transport, endosomal sorting, tetherin, VPU, HIV-1, monoubiquitin; HET: NHE; 1.65A {Homo sapiens} PDB: 4ae4_B* Length = 118

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 37  MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI-------TGIPAAVVGEEA 89
           M     + V+ +V+MGY    V  A++A+  N ++ ++YL         G    +V EEA
Sbjct: 4   MSPSERQCVETVVNMGYSYECVLRAMKAAGANIEQILDYLFAHGQLCEKGFDPLLV-EEA 62

Query: 90  PVAANEPQGNNIKQFSSVKE 109
                  +   ++    + +
Sbjct: 63  LEMHQCSEEKMMEFLQLMSK 82

>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1 Length = 73

 Score = 41.0 bits (96), Expect = 4e-06
 Identities = 7/33 (21%), Positives = 18/33 (54%)

Query: 44 MVQNIVDMGYERSAVTEALRASFNNPDRAVEYL 76
           V  ++  G+      +AL+AS  + ++A +++
Sbjct: 32 SVDTLLSFGFAEDVARKALKASGGDIEKATDWV 64

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

 Score = 38.7 bits (89), Expect = 2e-04
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 22  TATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77
              ++ PG+  +      E    V  IV MG+ R    +ALRA+ N+ +RAV+++ 
Sbjct: 703 LPGSSGPGSTSAAADPPPED--CVTTIVSMGFSRDQALKALRATNNSLERAVDWIF 756

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

 Score = 35.6 bits (82), Expect = 6e-04
 Identities = 9/34 (26%), Positives = 22/34 (64%)

Query: 44 MVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77
           ++ + +MG+  +  T+AL+ +  +  +A+E+LI
Sbjct: 32 ALRQLTEMGFPENRATKALQLNHMSVPQAMEWLI 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	129
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	99.91
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	99.78
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	99.65
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	99.64
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	99.61
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	99.6
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	99.59
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	99.59
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.58
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	99.56
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	99.55
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	99.55
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	99.55
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	99.55
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	99.53
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	99.53
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	99.53
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	99.52
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	99.52
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	99.49
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	99.48
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	99.48
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	99.44
2dna_A	67	Unnamed protein product; ubiquitin associated doma	99.44
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	99.44
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	99.41
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	99.36
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	99.3
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	99.21
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	99.2
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	99.17
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	99.12
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	99.06
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	99.04
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	99.01
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	98.97
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	98.96
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	98.92
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	98.86
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	98.85
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	98.73
2cos_A	54	Serine/threonine protein kinase LATS2; UBA domain,	98.59
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	98.12
2pwq_A	216	Ubiquitin conjugating enzyme; structural genomics	98.06
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	97.76
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	97.62
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	97.54
2dhy_A	67	CUE domain-containing protein 1; structural genomi	97.38
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	97.32
1tte_A	215	Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiq	97.22
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	97.13
1v92_A	46	NSFL1 cofactor P47; 3-helix bundle, recombination;	96.94
1q02_A	52	Sequestosome 1; helical bundle, protein binding; N	96.84
1pve_A	72	HHR23B, UV excision repair protein RAD23 homolog B	96.68
2dal_A	62	Protein KIAA0794; FAS associted factor 1, UBA-like	96.6
2dam_A	67	ETEA protein; KIAA0887, UBA-like domain, structura	96.21
2f4m_B	61	UV excision repair protein RAD23 homolog B; glycop	96.12
2dzl_A	66	Protein FAM100B; UBA-like domain, structural genom	96.11
4dbg_B	162	Ring finger protein 31; ubiquitin fold, ubiquitina	95.94
1xb2_B	291	EF-TS, elongation factor TS, mitochondrial, EF-TSM	95.89
1tr8_A	102	Conserved protein (MTH177); chaperones, nascent po	95.82
1aip_C	196	EF-TS, elongation factor TS; nucleotide exchange,	95.71
3e21_A	45	HFAF1, FAS-associated factor 1; UBA, alternative s	95.18
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	94.85
1p3q_Q	54	VPS9P, vacuolar protein sorting-associated protein	93.67
1ixs_A	62	Holliday junction DNA helicase RUVA; heterodimeric	92.65
2qho_B	53	E3 ubiquitin-protein ligase EDD1; protein-protein	92.0
1oai_A	59	Nuclear RNA export factor; nuclear transport, nucl	90.64
1vdl_A	80	Ubiquitin carboxyl-terminal hydrolase 25; UBA doma	90.35
1ufz_A	83	Hypothetical protein BAB28515; HBS1-like domain, s	88.55
3bq3_A	270	Defective in cullin neddylation protein 1; ubiquit	86.22
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	84.48
2jp7_A	57	MRNA export factor MEX67; solution MEX67, UBA, tra	83.15
3avx_A	1289	Elongation factor TS, elongation factor TU, linke	81.69
2ekf_A	61	Ancient ubiquitous protein 1; CUE, ubiquitin ligas	81.29
2ejs_A	58	Autocrine motility factor receptor, isoform 2; CUE	80.83

>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=99.91  E-value=1.3e-25  Score=189.55  Aligned_cols=92  Identities=42%  Similarity=0.641  Sum_probs=78.0

Q ss_pred             CcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCCcCCCCCC---------------ccCCC
Q psy4260          31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEEAP---------------VAANE   95 (129)
Q Consensus        31 ~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~~~~~~~~---------------~a~~~   95 (129)
                      +.|++++|+.+++.|++|++|||+|++|++|||+++||+|||+||||+|||+..+...+.               .....
T Consensus       158 ~~s~l~~g~~~~~~i~~l~~MGf~~~~~~~AL~a~~nn~~~A~e~L~~gip~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  237 (368)
T 1oqy_A          158 AASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPL  237 (368)
T ss_dssp             CCTTTCCTTTHHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTTTTSSTTCSSCCCCCCCCCCSSCCCCSSCCSCCTT
T ss_pred             ccccccCCcchHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCcccccccCCccccccccccCccccccchH
Confidence            468899999999999999999999999999999999999999999999999864421110               01233


Q ss_pred             CCCCCCCCccchhhhh------hhhhhhcCCce
Q psy4260          96 PQGNNIKQFSSVKEIE------IPNLMQGDNKV  122 (129)
Q Consensus        96 ~~~~n~PqF~~~r~~~------lp~llq~~~~~  122 (129)
                      .++||+|||++||++|      |+.|||+.++-
T Consensus       238 ~~Lr~~pqf~~lR~~vq~nP~~l~~~lq~l~~~  270 (368)
T 1oqy_A          238 EFLRDQPQFQNMRQVIQQNPALLPALLQQLGQE  270 (368)
T ss_dssp             HHHHHSHHHHHHHHSTTTCTTHHHHHHTTTTTT
T ss_pred             HHHhcChHHHHHHHHHHhChHHHHHHHHHHHhh
Confidence            4578999999999999      99999999863

>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.78  E-value=1.5e-19  Score=114.12  Aligned_cols=49  Identities=63%  Similarity=1.051  Sum_probs=46.4

Q ss_pred             cccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCC
Q psy4260          34 TLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPA   82 (129)
Q Consensus        34 ~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~   82 (129)
                      ++++++.++++|++|++|||+|++|++||++++||+|+|+|||++|||+
T Consensus         1 ~~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~e~L~~gip~   49 (49)
T 1ify_A            1 TLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPG   49 (49)
T ss_dssp             CCCCSHHHHHHHHHHHHTTCCHHHHHHHHHTTTSCSHHHHHHHHHCCCC
T ss_pred             CCCCCccCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHhCCCC
Confidence            4678899999999999999999999999999999999999999999884

>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.65  E-value=1.4e-16  Score=97.07  Aligned_cols=41  Identities=17%  Similarity=0.299  Sum_probs=38.7

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      .+++.|++|++|||+|++|++||++++||+++|++|||+||
T Consensus         3 p~e~~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~L~~~~   43 (43)
T 2g3q_A            3 PKSLAVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDSA   43 (43)
T ss_dssp             HHHHHHHHHHTTTSCHHHHHHHHHHHTSCHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHhCcCHHHHHHHHHcCC
Confidence            46789999999999999999999999999999999999885

>1vej_A Riken cDNA 4931431F19; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.64  E-value=6e-16  Score=105.96  Aligned_cols=50  Identities=22%  Similarity=0.375  Sum_probs=44.5

Q ss_pred             cccCCCchHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcCCCCC
Q psy4260          34 TLLMGDEYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITGIPAA   83 (129)
Q Consensus        34 ~~~~g~~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~giP~~   83 (129)
                      +......++++|++|++||| +|+++++||++++||+++||||||+|+|..
T Consensus        22 ~~~pe~~ye~qi~qL~eMGF~dr~~~~~AL~~t~Gnve~Ave~L~~~~~~~   72 (74)
T 1vej_A           22 SLFTEGRYQQELEELKALGFANRDANLQALVATDGDIHAAIEMLLGASGPS   72 (74)
T ss_dssp             GGGTTTTSHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHTCCCCC
T ss_pred             CCCchHHHHHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHhCCCCC
Confidence            34456778999999999999 689999999999999999999999997754

>1vg5_A RSGI RUH-014, rhomboid family protein; UBA domain, cDNA, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=99.61  E-value=3e-15  Score=102.11  Aligned_cols=44  Identities=30%  Similarity=0.371  Sum_probs=41.2

Q ss_pred             CCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          37 MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      ....++++|++|++|||+|++|++||++++||+|+|+||||+|.
T Consensus        25 ~~~~~ee~I~~L~eMGF~r~~a~~AL~~~~~nve~Ave~Ll~~~   68 (73)
T 1vg5_A           25 RVAASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQS   68 (73)
T ss_dssp             CSCCCHHHHHHHHTTTCCHHHHHHHHHHHTSCHHHHHHHHHTCS
T ss_pred             CCcccHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHCC
Confidence            45668999999999999999999999999999999999999984

>1wji_A Tudor domain containing protein 3; UBA domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.60  E-value=1.5e-15  Score=100.52  Aligned_cols=43  Identities=26%  Similarity=0.370  Sum_probs=40.0

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIP   81 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP   81 (129)
                      ..++++|++|++|||+|++|++||++++||+++|+||||++..
T Consensus         7 ~~~~~~I~~L~~MGF~~~~a~~AL~~~~~nve~A~e~L~~~~~   49 (63)
T 1wji_A            7 GVDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNK   49 (63)
T ss_dssp             SSCHHHHHHHHTTTCCHHHHHHHHHHTTSCHHHHHHHHHHHSS
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHCCC
Confidence            3578999999999999999999999999999999999999843

>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.59  E-value=5e-16  Score=103.96  Aligned_cols=43  Identities=23%  Similarity=0.420  Sum_probs=39.5

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      .+..++.|++|++|||+++||++|||+++||+|||+||||+|+
T Consensus        16 s~se~e~V~~LvsMGFs~~qA~kALKat~~NvErAaDWLFSH~   58 (63)
T 1wgn_A           16 SPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHS   58 (63)
T ss_dssp             CHHHHHHHHHHHHHHCCHHHHHHHHHHHCSCHHHHHHHHHHHS
T ss_pred             CcchHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence            3456778999999999999999999999999999999999993

>2jy5_A Ubiquilin-1; UBA, alternative splicing, cytoplasm, nucleus, phosphoprotein, proteasome, signaling protein; NMR {Homo sapiens} PDB: 2jy6_B

Probab=99.59  E-value=2.6e-15  Score=95.75  Aligned_cols=43  Identities=23%  Similarity=0.348  Sum_probs=40.5

Q ss_pred             CCCchHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          37 MGDEYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ....++++|++|++||| +|+.+++||++++||+++|+||||+|
T Consensus         8 p~~~~~~~l~~L~~MGF~~~~~~~~AL~~t~gn~e~A~e~L~~~   51 (52)
T 2jy5_A            8 PEVRFQQQLEQLSAMGFLNREANLQALIATGGDINAAIERLLGS   51 (52)
T ss_dssp             TTTTTHHHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHTTC
T ss_pred             chhHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            35678999999999999 99999999999999999999999987

>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=9.1e-16  Score=100.72  Aligned_cols=44  Identities=34%  Similarity=0.521  Sum_probs=41.0

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPA   82 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~   82 (129)
                      ..++++|++|++|||+|++|++||++++||+|+|++|||+|+++
T Consensus         7 ~~~~~~v~~L~~MGF~~~~a~~AL~~t~~nve~A~e~L~~~~~d   50 (63)
T 2dak_A            7 GPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDD   50 (63)
T ss_dssp             CCCHHHHHHHHHHTCCHHHHHHHHHHTTSCSHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence            45789999999999999999999999999999999999999654

>2knz_A Ubiquilin-4; cytoplasm, endoplasmic reticulum, nucleus, phosphoprotein, protein binding; NMR {Mus musculus}

Probab=99.56  E-value=4e-15  Score=95.09  Aligned_cols=44  Identities=23%  Similarity=0.323  Sum_probs=40.4

Q ss_pred             CCchHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260          38 GDEYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITGIP   81 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~giP   81 (129)
                      ...++++|++|++||| +|+.+++||++++||+++|+||||+|.+
T Consensus         8 e~~~~~~l~~L~~MGF~~~~~~~~AL~~t~gnve~Ave~L~~~~~   52 (53)
T 2knz_A            8 EVRFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLLGSQL   52 (53)
T ss_dssp             HHHHHHHHHHHHTTTCCCHHHHHHHHHHHTSCHHHHHHHHHHCCC
T ss_pred             hhHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHcCC
Confidence            3567889999999999 9999999999999999999999999853

>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=99.55  E-value=6.4e-15  Score=99.84  Aligned_cols=42  Identities=19%  Similarity=0.374  Sum_probs=39.9

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      ...+++|++|++|||+|++|++||++++||+++|+||||+|.
T Consensus        27 ~~~~~~v~~L~~MGF~~~~a~~AL~~t~~nve~Ave~L~~~~   68 (73)
T 1wiv_A           27 DIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNS   68 (73)
T ss_dssp             SSCHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence            467899999999999999999999999999999999999993

>1veg_A NEDD8 ultimate buster-1; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.55  E-value=6.2e-15  Score=102.94  Aligned_cols=41  Identities=22%  Similarity=0.243  Sum_probs=38.9

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ..++++|++|++|||+|++|++||++++||+++|+||||+|
T Consensus        27 ~~~ee~I~~Lv~MGF~~~~A~~AL~~t~gdve~A~e~L~sh   67 (83)
T 1veg_A           27 SPSQESINQLVYMGFDTVVAEAALRVFGGNVQLAAQTLAHH   67 (83)
T ss_dssp             CCCHHHHHHHHHHSCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            44789999999999999999999999999999999999996

>2cpw_A CBL-interacting protein STS-1 variant; ubiquitin associated domain, UBA, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.55  E-value=8.7e-15  Score=96.89  Aligned_cols=42  Identities=19%  Similarity=0.371  Sum_probs=39.2

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIP   81 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP   81 (129)
                      ..++.|++|++|||++++|++||++++| |+|+|+||||+|+.
T Consensus        18 ~~e~~i~~L~~MGF~~~~a~~AL~~t~~~nve~A~ewL~~~~~   60 (64)
T 2cpw_A           18 KHGSALDVLLSMGFPRARAQKALASTGGRSVQTACDWLFSHSG   60 (64)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHTTTSCHHHHHHHHHSCCS
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCC
Confidence            5678899999999999999999999999 99999999999943

>2bwb_A Ubiquitin-like protein DSK2; UBA, signaling protein; 2.3A {Saccharomyces cerevisiae} SCOP: a.5.2.1 PDB: 2bwe_A

Probab=99.55  E-value=6.8e-15  Score=92.04  Aligned_cols=41  Identities=27%  Similarity=0.472  Sum_probs=37.4

Q ss_pred             CchHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ..++++|++|++||| +|+.+++||++++||+++||||||+|
T Consensus         5 ~~~~~~i~~L~~MGF~d~~~~~~AL~~~~gnv~~Ave~L~~~   46 (46)
T 2bwb_A            5 ERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG   46 (46)
T ss_dssp             HHTHHHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHcc
Confidence            357889999999999 57788999999999999999999986

>2dag_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5 (USP 5), UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1e-14  Score=99.01  Aligned_cols=45  Identities=16%  Similarity=0.312  Sum_probs=41.1

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPAA   83 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP~~   83 (129)
                      ...++.|++|++|||+|++|++||++++| |+|+|+||||+|+++.
T Consensus         7 ~~~e~~v~~L~~MGF~~~~a~~AL~~t~n~~ve~A~ewL~~~~~d~   52 (74)
T 2dag_A            7 GLDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDP   52 (74)
T ss_dssp             SSCHHHHHHHHHHSCCHHHHHHHHHHHTSCCHHHHHHHHHHHTTST
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHhCCCCc
Confidence            45789999999999999999999999997 8999999999996653

>2crn_A Ubash3A protein; compact three-helix bundle, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.53  E-value=9.5e-15  Score=96.91  Aligned_cols=46  Identities=15%  Similarity=0.250  Sum_probs=41.6

Q ss_pred             CCCchHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCCC
Q psy4260          37 MGDEYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPA   82 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP~   82 (129)
                      .+..+++.|++|++|||+|++|++||++++| |+++|++|||+|+++
T Consensus         5 ~~~~~e~~v~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~wL~~h~~d   51 (64)
T 2crn_A            5 SSGSSPSLLEPLLAMGFPVHTALKALAATGRKTAEEALAWLHDHCND   51 (64)
T ss_dssp             SCCCSCSSHHHHHHTSCCHHHHHHHHHHHTSCCHHHHHHHHHHHSSS
T ss_pred             CCCCCHHHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHhCCCC
Confidence            3556788899999999999999999999988 999999999999654

>1whc_A RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain, structural genomics, riken structural genomics/proteomics initiative, unknown function; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.53  E-value=7.4e-15  Score=97.12  Aligned_cols=44  Identities=16%  Similarity=0.320  Sum_probs=40.0

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHHHcCCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRAS-FNNPDRAVEYLITGIPA   82 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras-~~n~erAvE~L~~giP~   82 (129)
                      ..+++.|++|++|||+|++|++||+++ +||+++|++|||+|+++
T Consensus         7 ~~~~~~v~~L~~MGF~~~~a~~AL~~t~~~nve~A~ewLl~~~~d   51 (64)
T 1whc_A            7 GAELTALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDD   51 (64)
T ss_dssp             CCCCCHHHHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHhcCCCHHHHHHHHHhCCCC
Confidence            346778999999999999999999999 69999999999999654

>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} SCOP: a.5.2.1

Probab=99.52  E-value=1.4e-14  Score=85.94  Aligned_cols=39  Identities=23%  Similarity=0.427  Sum_probs=36.2

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      +..++.|++|++|||++++|++||++++||+++|++|||
T Consensus         2 ~~~~~~i~~L~~mGf~~~~a~~AL~~~~~n~e~A~~~L~   40 (40)
T 1z96_A            2 PGLNSKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL   40 (40)
T ss_dssp             -CHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             chHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHC
Confidence            356889999999999999999999999999999999996

>1wr1_B Ubiquitin-like protein DSK2; UBA domain, UBA-ubiquitin complex, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1

Probab=99.52  E-value=1e-14  Score=95.51  Aligned_cols=43  Identities=26%  Similarity=0.426  Sum_probs=39.2

Q ss_pred             CCCchHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          37 MGDEYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ....++++|++|++||| +|+.+++||++++||+++||||||+|
T Consensus        13 pe~~~~~qi~~L~~MGF~d~~~~~~AL~~~~gnve~Ave~L~~~   56 (58)
T 1wr1_B           13 PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG   56 (58)
T ss_dssp             HHHHTHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            34567889999999999 58888999999999999999999998

>2ekk_A UBA domain from E3 ubiquitin-protein ligase HUWE1; ubiquitin associated domain, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=2.9e-14  Score=88.52  Aligned_cols=40  Identities=33%  Similarity=0.503  Sum_probs=37.5

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ..+++.|++|++|||++++|++||++++ |+|+|+||||+|
T Consensus         7 ~~~~~~v~~L~~MGF~~~~a~~AL~~~~-n~e~A~~~L~~h   46 (47)
T 2ekk_A            7 GVNQQQLQQLMDMGFTREHAMEALLNTS-TMEQATEYLLTH   46 (47)
T ss_dssp             SSCHHHHHHHHHHHCCHHHHHHHHHHSC-SHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHcC-CHHHHHHHHHcC
Confidence            4578999999999999999999999995 999999999987

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

Probab=99.48  E-value=3.3e-14  Score=98.68  Aligned_cols=43  Identities=21%  Similarity=0.346  Sum_probs=40.2

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPA   82 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~   82 (129)
                      .+++.|++|++|||++++|++||++++||+++|++|||+|+++
T Consensus        28 ~~e~~i~~L~~MGF~~~~a~~AL~~t~~nve~A~ewL~~~~~d   70 (83)
T 2dai_A           28 VDEAALRQLTEMGFPENRATKALQLNHMSVPQAMEWLIEHAED   70 (83)
T ss_dssp             CCHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHHGGGC
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHCCCC
Confidence            4789999999999999999999999999999999999999543

>1dv0_A DNA repair protein HHR23A; helical bundle, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.5.2.1 PDB: 1f4i_A

Probab=99.48  E-value=7.5e-15  Score=92.09  Aligned_cols=43  Identities=19%  Similarity=0.273  Sum_probs=39.7

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIP   81 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP   81 (129)
                      ++.+++|++|++|||+|.+|++||.+++||+++|++|||+|+.
T Consensus         2 ~~e~eaI~rL~~mGF~~~~a~~Al~a~~~n~e~A~~~Lf~~~~   44 (47)
T 1dv0_A            2 SQEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQNF   44 (47)
T ss_dssp             -CCHHHHTTTTTTTCCHHHHHHHHTTTTSCHHHHHHHTTSCCC
T ss_pred             cchHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCcC
Confidence            4578899999999999999999999999999999999999954

>1vek_A UBP14, ubiquitin-specific protease 14, putative; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.5.2.1

Probab=99.44  E-value=1.2e-13  Score=95.91  Aligned_cols=44  Identities=16%  Similarity=0.308  Sum_probs=40.2

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhC-CCHHHHHHHHHcCCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASF-NNPDRAVEYLITGIPA   82 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~-~n~erAvE~L~~giP~   82 (129)
                      ..+++.|++|++|||+|++|++||++++ ||+++|++|||+|+++
T Consensus        27 ~~~e~~v~~L~~MGF~~~~a~~AL~~t~n~n~e~A~ewL~~h~~d   71 (84)
T 1vek_A           27 VANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDD   71 (84)
T ss_dssp             CCCHHHHHHHHHHTCCHHHHHHHHHHTTTCCHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            4578999999999999999999999996 6999999999999654

>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.44  E-value=1.1e-13  Score=93.35  Aligned_cols=45  Identities=18%  Similarity=0.192  Sum_probs=39.2

Q ss_pred             CCchHHHHHHHHHcCCC-hHHHHHHHHHhCCCHHHHHHHHHcCCCC
Q psy4260          38 GDEYGRMVQNIVDMGYE-RSAVTEALRASFNNPDRAVEYLITGIPA   82 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~-reqv~~ALras~~n~erAvE~L~~giP~   82 (129)
                      ...+++.|++|++|||. ++.+++||++++||+++||||||+++++
T Consensus        16 e~~y~~ql~qL~~MGF~d~~an~~AL~at~Gnve~Ave~L~~~~~~   61 (67)
T 2dna_A           16 EVRFSKEMECLQAMGFVNYNANLQALIATDGDTNAAIYKLKSSQGF   61 (67)
T ss_dssp             HHHTHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHHCCSS
T ss_pred             HHHHHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            44578899999999985 5555999999999999999999999665

>2dah_A Ubiquilin-3; UBA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.44  E-value=1.3e-13  Score=88.85  Aligned_cols=42  Identities=26%  Similarity=0.288  Sum_probs=37.5

Q ss_pred             CchHHHHHHHHHcCCChH-HHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          39 DEYGRMVQNIVDMGYERS-AVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~re-qv~~ALras~~n~erAvE~L~~gi   80 (129)
                      ..++++|++|++|||.++ .+++||++++||+++||||||++.
T Consensus         7 ~~~~~~l~~L~~MGF~d~~~n~~AL~~~~Gdv~~Ave~L~~~~   49 (54)
T 2dah_A            7 GHFQVQLEQLRSMGFLNREANLQALIATGGDVDAAVEKLRQSS   49 (54)
T ss_dssp             CSSHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHHHS
T ss_pred             hhHHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence            467899999999999655 579999999999999999999983

>2dkl_A Trinucleotide repeat containing 6C protein; TNRC6C, KIAA1582 protein, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=99.41  E-value=2.9e-13  Score=94.36  Aligned_cols=40  Identities=30%  Similarity=0.532  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      .+++|++|++|||+|++|++||+.++||+|+|++|||+|.
T Consensus        21 n~~~I~qL~~MGF~~~~a~~AL~~~n~n~e~A~ewL~~h~   60 (85)
T 2dkl_A           21 MSRLIKQLTDMGFPREPAEEALKSNNMNLDQAMSALLEKK   60 (85)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHTTS
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHCc
Confidence            4889999999999999999999999999999999999993

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

Probab=99.36  E-value=8.7e-13  Score=95.70  Aligned_cols=42  Identities=31%  Similarity=0.510  Sum_probs=40.3

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIP   81 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP   81 (129)
                      ..++.|++|++|||++++|++||++++||+++|++|||+|++
T Consensus        77 ~~e~~v~~L~~MGF~~~~a~~AL~~~~~~~e~A~e~L~~~~~  118 (126)
T 2lbc_A           77 PPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWIFSHPE  118 (126)
T ss_dssp             CCHHHHHHHHHHTSCHHHHHHHHHHHTSCHHHHHHHHHTCCS
T ss_pred             cCHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            578999999999999999999999999999999999999966

>2cwb_A Chimera of immunoglobulin G binding protein G and ubiquitin-like protein SB132; helical bundle, protein binding; NMR {Streptococcus SP} PDB: 2den_A

Probab=99.30  E-value=3.1e-12  Score=92.96  Aligned_cols=43  Identities=26%  Similarity=0.401  Sum_probs=39.1

Q ss_pred             CCchHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          38 GDEYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      ...++++|++|.+||| +|+++++||++++||+++||||||++.
T Consensus        63 e~~~~~qL~qL~eMGF~d~~~ni~AL~~t~Gdve~AVe~L~~~~  106 (108)
T 2cwb_A           63 GSQWQPQLQQLRDMGIQDDELSLRALQATGGDIQAALELIFAGG  106 (108)
T ss_dssp             CCTTHHHHHHHHTTTCCCHHHHHHHHHHHTSCHHHHHHHHHHTS
T ss_pred             ccchHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Confidence            3467899999999999 578999999999999999999999983

>2ooa_A E3 ubiquitin-protein ligase CBL-B; alpha-helical domain; 1.56A {Homo sapiens} PDB: 2oob_A 2jnh_A 2do6_A

Probab=99.21  E-value=1.8e-11  Score=79.28  Aligned_cols=39  Identities=23%  Similarity=0.273  Sum_probs=35.7

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      ..++.|++||+|||+|++|++||+.++||+|.|..+|++
T Consensus        10 ~~~~~Ia~Lm~mGFsr~~ai~AL~~a~nnve~AaniLle   48 (52)
T 2ooa_A           10 NVDAKIAKLMGEGYAFEEVKRALEIAQNNVEVARSILRE   48 (52)
T ss_dssp             -CHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             ChHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            445899999999999999999999999999999999874

>4ae4_A Ubiquitin-associated protein 1; protein transport, endosomal sorting, tetherin, VPU, HIV-1, monoubiquitin; HET: NHE; 1.65A {Homo sapiens} PDB: 4ae4_B*

Probab=99.20  E-value=1.5e-11  Score=89.85  Aligned_cols=39  Identities=26%  Similarity=0.453  Sum_probs=36.6

Q ss_pred             hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      +.+.|.+|++|||++++|++||+.++||.|||+||||.+
T Consensus        76 ~~~~v~~L~eMGF~~~~a~~AL~~~~nd~erAlewL~~~  114 (118)
T 4ae4_A           76 FLQLMSKFKEMGFELKDIKEVLLLHNNDQDNALEDLMAR  114 (118)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence            456799999999999999999999999999999999975

>2d9s_A CBL E3 ubiquitin protein ligase; UBA domain, dimer, protein binding, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.17  E-value=4.3e-11  Score=77.69  Aligned_cols=41  Identities=20%  Similarity=0.276  Sum_probs=37.1

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      +..+..|++||+|||+|++|++||+.++||+|.|.+.|++-
T Consensus         7 ~~~e~~I~~L~~lGF~r~~ai~AL~~a~nnve~Aa~iL~ef   47 (53)
T 2d9s_A            7 GQLSSEIERLMSQGYSYQDIQKALVIAHNNIEMAKNILREF   47 (53)
T ss_dssp             SCSHHHHHHHHHHTCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHcCCCHHHHHHHHHHhcCCHHHHHHHHHHh
Confidence            34567799999999999999999999999999999999754

>3k9o_A Ubiquitin-conjugating enzyme E2 K; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 3k9p_A 1yla_A 2o25_A

Probab=99.12  E-value=4.8e-11  Score=92.30  Aligned_cols=42  Identities=31%  Similarity=0.545  Sum_probs=39.1

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      +..++++|++|++|||+|++|+.||++++||+++|+||||++
T Consensus       160 ~~~~eekV~~l~~MGf~~~~a~~AL~~~~wd~~~A~e~L~~~  201 (201)
T 3k9o_A          160 SPEYTKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLSN  201 (201)
T ss_dssp             CHHHHHHHHHHHTTTCCHHHHHHHHHHTTTCHHHHHHHHHHC
T ss_pred             cchhHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence            446799999999999999999999999999999999999974

>2juj_A E3 ubiquitin-protein ligase CBL; alpha helix, UBA domain, calcium, cytoplasm, metal- binding, phosphorylation, proto-oncogene, SH2 domain; NMR {Homo sapiens}

Probab=99.06  E-value=1.4e-10  Score=75.91  Aligned_cols=42  Identities=21%  Similarity=0.275  Sum_probs=38.5

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ....|+.|.+||+|||+|+.|++||..++||+|.|.+.|++-
T Consensus         4 ~~p~e~~Ia~L~smGfsr~da~~AL~ia~Ndv~~AtNiLlEf   45 (56)
T 2juj_A            4 SPQLSSEIENLMSQGYSYQDIQKALVIAQNNIEMAKNILREF   45 (56)
T ss_dssp             CHHHHHHHHHHHTTTCCHHHHHHHHHHTTTCSHHHHHHHHHS
T ss_pred             CCCChHHHHHHHHcCCCHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            345788999999999999999999999999999999999864

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

Probab=99.04  E-value=1.5e-10  Score=83.87  Aligned_cols=43  Identities=19%  Similarity=0.267  Sum_probs=38.9

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCCC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPA   82 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP~   82 (129)
                      ..++.+++|++|||++..|++||+.++| |++.|++||+.|.++
T Consensus         2 ~d~~~l~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~wL~~~~~d   45 (126)
T 2lbc_A            2 IDESSVMQLAEMGFPLEACRKAVYFTGNMGAEVAFNWIIVHMEE   45 (126)
T ss_dssp             CCTHHHHHHHTTSSCCHHHHHHHHHHTSCCHHHHHHHHHHGGGC
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHcCCCCHHHHHHHHHHhccc
Confidence            3567899999999999999999999977 999999999999554

>1wj7_A Hypothetical protein (RSGI RUH-015); UBA domain, ubiquitin associated domain, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: a.5.2.1

Probab=99.01  E-value=4.5e-10  Score=81.36  Aligned_cols=42  Identities=24%  Similarity=0.510  Sum_probs=39.7

Q ss_pred             chHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260          40 EYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITGIP   81 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~giP   81 (129)
                      ..++.|++|++| ||++++|+.||..++||+++|+++||+|.+
T Consensus        38 d~eekVk~L~EmtG~seeeAr~AL~~~ngDl~~AI~~Lleg~~   80 (104)
T 1wj7_A           38 DFEEKVKQLIDITGKNQDECVIALHDCNGDVNRAINVLLEGNP   80 (104)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHTCSS
T ss_pred             cHHHHHHHHHHhhCCCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            458899999999 999999999999999999999999999965

>2oo9_A E3 ubiquitin-protein ligase CBL; alpha-helical domain, homodimer; 2.10A {Homo sapiens}

Probab=98.97  E-value=1e-09  Score=69.44  Aligned_cols=42  Identities=24%  Similarity=0.333  Sum_probs=38.4

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      |...|+.|..|++|||+++.|++||-.+.||+|.|.+.|++-
T Consensus         1 ~~~~e~~I~~L~s~Gf~~~~~~rAL~ia~Nnie~A~nIL~ef   42 (46)
T 2oo9_A            1 GSQLSSEIENLMSQGYSYQDIQKALVIAQNNIEMAKNILREF   42 (46)
T ss_dssp             CCHHHHHHHHHHHTTBCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHcCCCHHHHHHHHHHhhccHHHHHHHHHHh
Confidence            456789999999999999999999999999999999998753

>4ae4_A Ubiquitin-associated protein 1; protein transport, endosomal sorting, tetherin, VPU, HIV-1, monoubiquitin; HET: NHE; 1.65A {Homo sapiens} PDB: 4ae4_B*

Probab=98.96  E-value=4.4e-10  Score=82.09  Aligned_cols=42  Identities=26%  Similarity=0.464  Sum_probs=39.0

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      +++..+.|++|++|||+++.|++||+++++|+++|+||||.+
T Consensus         5 ~~~e~~~v~~l~~MGFp~~~~~kAl~~~g~~~e~amewL~~h   46 (118)
T 4ae4_A            5 SPSERQCVETVVNMGYSYECVLRAMKAAGANIEQILDYLFAH   46 (118)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHCcCHHHHHHHHHHh
Confidence            445677899999999999999999999999999999999987

>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=98.92  E-value=1.9e-10  Score=97.11  Aligned_cols=42  Identities=19%  Similarity=0.300  Sum_probs=39.6

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      .+++++|++|++|||+|++|++||++|+||+++|++|||+|.
T Consensus       323 ~ee~eaI~rL~~mGF~~~~a~~al~a~~~n~e~A~~~L~~~~  364 (368)
T 1oqy_A          323 PQEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQN  364 (368)
T ss_dssp             TTTHHHHHHHHHHTCCSHHHHHHTSSSSSCSSHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHhhCc
Confidence            457889999999999999999999999999999999999984

>2cp8_A NEXT to BRCA1 gene 1 protein; UBA domain, structural genomics, human, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.5.2.1

Probab=98.85  E-value=3.3e-09  Score=68.89  Aligned_cols=44  Identities=16%  Similarity=0.206  Sum_probs=39.9

Q ss_pred             cCCCchHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          36 LMGDEYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        36 ~~g~~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ++...+..++++|.|||| +++.-++||++.+||+++||+.|+..
T Consensus         4 ~~ee~~a~~L~~L~eMGF~D~~~N~~aL~~~~gnv~~aI~~Ll~~   48 (54)
T 2cp8_A            4 GSSGQTAALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELLQL   48 (54)
T ss_dssp             SSCTTHHHHHHHHHHHTCCCHHHHHHHHTTTTTCHHHHHHHHHHH
T ss_pred             CHHHhhHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            345667889999999999 89999999999999999999999976

>3e46_A Ubiquitin-conjugating enzyme E2-25 kDa; huntington interacting, ligase, alternative splicing, cytoplasm, UBL conjugation, UBL conjugation pathway; 1.86A {Homo sapiens} SCOP: a.5.2.1 d.20.1.1 PDB: 3f92_A*

Probab=98.73  E-value=1e-08  Score=82.76  Aligned_cols=41  Identities=29%  Similarity=0.515  Sum_probs=38.6

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      ...++++|++|++|||+|++|+.||+..+||.++|+|+||+
T Consensus       212 ~~~~~~~v~~l~~mgf~~~~~~~al~~~nWd~~~A~e~L~~  252 (253)
T 3e46_A          212 SPEYTKKIENLCAAGFDRNAVIVALSSKSWDVETATELLLS  252 (253)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            44678999999999999999999999999999999999996

>2cos_A Serine/threonine protein kinase LATS2; UBA domain, structure genomics, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1

Probab=98.59  E-value=7.3e-08  Score=62.71  Aligned_cols=40  Identities=23%  Similarity=0.394  Sum_probs=36.0

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHc
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLIT   78 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~   78 (129)
                      ......+++|++|||+++.|.+||++++| .++.|+|||..
T Consensus         7 ~vn~qmlq~L~eMGFd~erae~Alk~Tg~~Gle~AmewL~k   47 (54)
T 2cos_A            7 GVNRQMLQELVNAGCDQEMAGRALKQTGSRSIEAALEYISK   47 (54)
T ss_dssp             SCCHHHHHHHHHHHCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHcCCCHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            45566799999999999999999999988 89999999974

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

Probab=98.12  E-value=1.7e-06  Score=78.99  Aligned_cols=43  Identities=35%  Similarity=0.536  Sum_probs=39.3

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI   80 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi   80 (129)
                      +...++.|..|.+|||+++++++||++.+||++||+||||+++
T Consensus       717 ~~~~~e~i~~l~~mGf~~~~a~~aL~~t~~~~eraidwlfs~~  759 (854)
T 3ihp_A          717 DPPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHI  759 (854)
T ss_dssp             --CCHHHHHHHHTTTCCHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCHHHHHHHHHhhcCcHHHHHHhhhcCc
Confidence            4567899999999999999999999999999999999999983

>2pwq_A Ubiquitin conjugating enzyme; structural genomics consortium, SGC, ligase; 1.90A {Plasmodium yoelii}

Probab=98.06  E-value=5.3e-07  Score=71.15  Aligned_cols=39  Identities=21%  Similarity=0.321  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .+++|++|++|||+++++++||+..+||.++|+|.||+|
T Consensus       177 ~~~~v~~~~~mgf~~~~~~~al~~~~~~~~~~~~~l~~~  215 (216)
T 2pwq_A          177 REVIIKKITEMGFSEDQAKNALIKANWNETLALNTLLEN  215 (216)
T ss_dssp             ---------------------------------------
T ss_pred             hhhHHHHHHHcCCCHHHHHHHHHHcCCchHHHHHHHhcC
Confidence            478999999999999999999999999999999999987

>1wgl_A TOLL-interacting protein; CUE domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, immune system; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=97.76  E-value=3e-05  Score=50.49  Aligned_cols=41  Identities=22%  Similarity=0.274  Sum_probs=38.0

Q ss_pred             CchHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ...|+.|++|.+|  .++++.++.+|++++||+|+|++-|++.
T Consensus         7 ~~~ee~l~~L~emFP~ld~~~I~~vL~a~~gdvd~aI~~LL~m   49 (59)
T 1wgl_A            7 GCSEEDLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQM   49 (59)
T ss_dssp             SSCHHHHHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            4578999999999  7889999999999999999999999976

>1otr_A Protein CUE2; protein-protein complex, cell cycle; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.4

Probab=97.62  E-value=8.8e-05  Score=46.90  Aligned_cols=39  Identities=18%  Similarity=0.227  Sum_probs=36.3

Q ss_pred             hHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          41 YGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        41 ~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .++.|+.|.||  .-++..++.+|++++||.|+|++-|+++
T Consensus         4 ~e~~v~~L~EMFP~~~~~~ik~~L~~~~Gd~d~Ai~~LL~~   44 (49)
T 1otr_A            4 HESKLSILMDMFPAISKSKLQVHLLENNNDLDLTIGLLLKE   44 (49)
T ss_dssp             HHHHHHHHHHHCSSSCHHHHHHHHHHTTTCSHHHHHHHHHH
T ss_pred             hHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            47889999999  7889999999999999999999999977

>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.2

Probab=97.54  E-value=0.00013  Score=48.56  Aligned_cols=39  Identities=15%  Similarity=0.181  Sum_probs=35.1

Q ss_pred             chHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          40 EYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      ...+.|..|.++ |....+|++||..++||++.|++||-.
T Consensus         8 it~~~Vk~LRe~TGag~~dcKkAL~e~~GDi~~Ai~~Lr~   47 (64)
T 2cp9_A            8 SSKELLMKLRRKTGYSFVNCKKALETCGGDLKQAEIWLHK   47 (64)
T ss_dssp             CCCHHHHHHHHHHCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            345779999998 999999999999999999999999963

>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.38  E-value=0.00072  Score=45.06  Aligned_cols=45  Identities=16%  Similarity=0.240  Sum_probs=39.5

Q ss_pred             ccCCCchHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          35 LLMGDEYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        35 ~~~g~~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      -......++.+++|.+|  -++++.++..|++++||+|+|++-|++-
T Consensus        12 ~~~~~~~~~~v~~L~~MFP~lD~~vI~~vL~a~~G~vd~aId~LL~m   58 (67)
T 2dhy_A           12 QVRRLEFNQAMDDFKTMFPNMDYDIIECVLRANSGAVDATIDQLLQM   58 (67)
T ss_dssp             CCCCCCSHHHHHHHHHHCSSSCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             hccCCCHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            34567789999999999  5689999999999999999999999864

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

Probab=97.32  E-value=0.00018  Score=65.74  Aligned_cols=44  Identities=16%  Similarity=0.293  Sum_probs=37.9

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPA   82 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP~   82 (129)
                      ...++.+++|++|||++..+++||.+.+| |.|.|++||++++.+
T Consensus       650 ~~d~~~l~~L~~mGf~~~~~~kal~~t~n~~~e~a~~wl~~hmdd  694 (854)
T 3ihp_A          650 MLDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDD  694 (854)
T ss_dssp             ---CHHHHHHHHHTCCHHHHHHHHHHTTSCCHHHHHHHHHHHTTS
T ss_pred             CcCHHHHHHHHhcCCCHHHHHHHHhhcCCCchHHHhHHHhhccCc
Confidence            35678899999999999999999999977 599999999999654

>1tte_A Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiquitin-dependent degradation, ligase; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.1 d.20.1.1

Probab=97.22  E-value=0.00029  Score=55.40  Aligned_cols=30  Identities=17%  Similarity=0.266  Sum_probs=27.7

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCCCH
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFNNP   69 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~   69 (129)
                      ..+++|++|++|||++++|+.||+..+||.
T Consensus       168 ~~~~~v~~~~~mg~~~~~~~~al~~~~~~~  197 (215)
T 1tte_A          168 IDHDLIDEFESQGFEKDKIVEVLRRLGVKS  197 (215)
T ss_dssp             CSHHHHHHHHHHTCCHHHHHHHHHHSCCSS
T ss_pred             ccHHHHHHHHHcCCCHHHHHHHHHHcCCCc
Confidence            357899999999999999999999999986

>2di0_A Activating signal cointegrator 1 complex subunit 2; ASCC2, CUE domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=97.13  E-value=0.0016  Score=44.07  Aligned_cols=48  Identities=10%  Similarity=0.308  Sum_probs=42.2

Q ss_pred             ccCCCchHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC-CCC
Q psy4260          35 LLMGDEYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG-IPA   82 (129)
Q Consensus        35 ~~~g~~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g-iP~   82 (129)
                      ..++..-++.|+++.++  -+....++++|+..++|+|+.++.||.+ +|.
T Consensus         7 ~~~~~~l~s~I~qV~DLfPdLG~gfi~~~L~~y~~nvE~vin~LLE~~LPp   57 (71)
T 2di0_A            7 GMCGVELDSLISQVKDLLPDLGEGFILACLEYYHYDPEQVINNILEERLAP   57 (71)
T ss_dssp             CCSSHHHHHHHHHHHHHCCSSCHHHHHHHHHHTTTCHHHHHHHHHTTCCCT
T ss_pred             CCcHHHHHHHHHHHHHHcccCCHHHHHHHHHHhCCCHHHHHHHHHccCCCH
Confidence            44677788999999999  6899999999999999999999999987 543

>1v92_A NSFL1 cofactor P47; 3-helix bundle, recombination; NMR {Rattus norvegicus} SCOP: a.5.2.3

Probab=96.94  E-value=0.0017  Score=38.80  Aligned_cols=39  Identities=13%  Similarity=0.070  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          41 YGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        41 ~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .++.|+++++. |-+++.|+.-|+.++||+++||.-.|.+
T Consensus         5 ~~~~i~~F~~iTg~~~~~A~~~L~~~~wdle~Ai~~ff~~   44 (46)
T 1v92_A            5 RQDALREFVAVTGAEEDRARFFLESAGWDLQIALASFYED   44 (46)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHTTSCSHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            56789999987 8999999999999999999999877754

>1q02_A Sequestosome 1; helical bundle, protein binding; NMR {Homo sapiens} SCOP: a.5.2.1 PDB: 2jy7_A 2jy8_A 2k0b_X 2knv_A 2rru_A 3b0f_A

Probab=96.84  E-value=0.00081  Score=43.29  Aligned_cols=39  Identities=13%  Similarity=0.202  Sum_probs=33.6

Q ss_pred             CchHHHHHHHHHcCCChHHH--HHHHHHhCCCHHHHHHHHH
Q psy4260          39 DEYGRMVQNIVDMGYERSAV--TEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv--~~ALras~~n~erAvE~L~   77 (129)
                      +.-.+.|.++++|||+.+-.  .+.|+..+||+.+|+|-|-
T Consensus         8 ~rl~~al~qMl~MGF~negGWLt~LL~~k~gDI~~aLD~lq   48 (52)
T 1q02_A            8 PRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQ   48 (52)
T ss_dssp             HHHHHHHHHHHTTTCCCTTSHHHHHHHHTTTCHHHHHHHHT
T ss_pred             hHHHHHHHHHHHcCCCccccHHHHHHHHccCCHHHHHHHhh
Confidence            34577899999999998877  4899999999999999764

>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=96.68  E-value=0.00029  Score=47.82  Aligned_cols=29  Identities=24%  Similarity=0.275  Sum_probs=25.3

Q ss_pred             CCCCCCCCCCccchhhhh------hhhhhhcCCce
Q psy4260          94 NEPQGNNIKQFSSVKEIE------IPNLMQGDNKV  122 (129)
Q Consensus        94 ~~~~~~n~PqF~~~r~~~------lp~llq~~~~~  122 (129)
                      ...++|++|+|..||++|      |+.|||+.++-
T Consensus         5 ~l~~Lr~~Pqf~qlR~~vqqNP~lL~~lLqqL~~~   39 (72)
T 1pve_A            5 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRE   39 (72)
T ss_dssp             TTGGGTTCTTTTTHHHHHTTCGGGHHHHHHHHHTT
T ss_pred             hHHHHHcChHHHHHHHHHHHCHHHHHHHHHHHHhH
Confidence            356799999999999999      99999987763

>2dal_A Protein KIAA0794; FAS associted factor 1, UBA-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.60  E-value=0.0029  Score=40.89  Aligned_cols=41  Identities=24%  Similarity=0.343  Sum_probs=36.3

Q ss_pred             CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ...+++|++++++ |-+++.|+.-|++++||+++||...|.+
T Consensus        13 ~~~~e~i~qF~~iTg~~~~~A~~~Le~~~WnLe~Av~~ff~~   54 (62)
T 2dal_A           13 SALKGLIQQFTTITGASESVGKHMLEACNNNLEMAVTMFLDG   54 (62)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHTTTSCHHHHHHHHHHS
T ss_pred             ccHHHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            4457789999987 8999999999999999999999977765

>2dam_A ETEA protein; KIAA0887, UBA-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.21  E-value=0.014  Score=38.34  Aligned_cols=42  Identities=17%  Similarity=0.134  Sum_probs=36.7

Q ss_pred             CCchHHHHHHHHHc-C-CChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDM-G-YERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eM-G-F~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ....+++|++++++ | -+.+.|+.-|+.++||++.||.-.|.+
T Consensus        15 s~~~~e~i~qF~~ITg~~d~~~A~~~Le~~~WnLe~Av~~ff~~   58 (67)
T 2dam_A           15 TQEQTEKLLQFQDLTGIESMDQCRHTLEQHNWNIEAAVQDRLNE   58 (67)
T ss_dssp             CHHHHHHHHHHHHHHCCSCHHHHHHHHHHHTSCHHHHHHHHHHS
T ss_pred             ChhHHHHHHHHHHHhCCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            34467789999997 8 789999999999999999999988866

>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=96.12  E-value=0.0003  Score=46.24  Aligned_cols=28  Identities=25%  Similarity=0.296  Sum_probs=24.6

Q ss_pred             CCCCCCCCCccchhhhh------hhhhhhcCCce
Q psy4260          95 EPQGNNIKQFSSVKEIE------IPNLMQGDNKV  122 (129)
Q Consensus        95 ~~~~~n~PqF~~~r~~~------lp~llq~~~~~  122 (129)
                      ..++|++|+|..||++|      |+.|||+.++-
T Consensus         4 l~~Lr~~Pqf~~lR~~vq~NP~~L~~lLqql~~~   37 (61)
T 2f4m_B            4 LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRE   37 (61)
T ss_dssp             GGGGTTCHHHHHHHHHHHHCGGGHHHHHHHHHHH
T ss_pred             HHHHHcChHHHHHHHHHHHCHHHHHHHHHHHHhH
Confidence            46789999999999999      99999987753

>2dzl_A Protein FAM100B; UBA-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.11  E-value=0.019  Score=37.63  Aligned_cols=37  Identities=16%  Similarity=0.204  Sum_probs=34.2

Q ss_pred             HHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          43 RMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        43 e~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      +.|+++++. |=+++.|+.-|++++||.|+||+-.|..
T Consensus        19 ~~i~qF~~iTg~~~~~A~~~Le~~~WdLe~Al~~ff~~   56 (66)
T 2dzl_A           19 VMINQFVLAAGCAADQAKQLLQAAHWQFETALSTFFQE   56 (66)
T ss_dssp             HHHHHHHHHHCCCHHHHHHHHHTTTTCHHHHHHHHHTC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            789999988 8999999999999999999999988865

>4dbg_B Ring finger protein 31; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens}

Probab=95.94  E-value=0.0068  Score=46.71  Aligned_cols=35  Identities=26%  Similarity=0.245  Sum_probs=31.6

Q ss_pred             HHHHHHHHHcC-CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260          42 GRMVQNIVDMG-YERSAVTEALRASFNNPDRAVEYL   76 (129)
Q Consensus        42 ee~I~~L~eMG-F~reqv~~ALras~~n~erAvE~L   76 (129)
                      ..++..|++.| |++++|.+||+.++||+++|+-.|
T Consensus       103 ~~K~~eL~s~G~~~~~~~~~aL~~~~Gdv~~Al~eL  138 (162)
T 4dbg_B          103 RRKVQELQSLGFGPEEGSLQALFQHGGDVSRALTEL  138 (162)
T ss_dssp             HHHHHHHHHTTCCGGGTHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHhcCCchHHHHHHHHHHcCCcHHHHHHHH
Confidence            45889999999 789999999999999999999655

>1xb2_B EF-TS, elongation factor TS, mitochondrial, EF-TSMT; protein-protein complex, translation; HET: MSE; 2.20A {Bos taurus} SCOP: a.5.2.2 d.43.1.1 d.43.1.1

Probab=95.89  E-value=0.0096  Score=49.00  Aligned_cols=37  Identities=16%  Similarity=0.224  Sum_probs=33.9

Q ss_pred             HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      -..|++|-++ |..--+|++||..++||.|.|+|||-.
T Consensus         5 a~~VKeLRe~TGagmmdCKKAL~e~~GD~ekAie~LR~   42 (291)
T 1xb2_B            5 KELLMKLRRKTGYSFINCKKALETCGGDLKQAESWLHK   42 (291)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            3568899998 999999999999999999999999984

>1tr8_A Conserved protein (MTH177); chaperones, nascent polypeptide-associated complex, ribosome domain, ubiquitin, chaperone; 2.27A {Methanothermobacter marburgensis}

Probab=95.82  E-value=0.011  Score=42.09  Aligned_cols=37  Identities=19%  Similarity=0.185  Sum_probs=32.4

Q ss_pred             chHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHH
Q psy4260          40 EYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYL   76 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L   76 (129)
                      ..++.|+.+++- |-+|++|++||+.++||+=.|+-+|
T Consensus        64 i~~edi~lv~~q~~vs~~~A~~aL~~~~gDiv~Ai~~L  101 (102)
T 1tr8_A           64 IPEDDIELVMNQTGASREDATRALQETGGDLAEAIMRL  101 (102)
T ss_dssp             CCHHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHC
T ss_pred             CCHHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHh
Confidence            456778888764 9999999999999999999999776

>1aip_C EF-TS, elongation factor TS; nucleotide exchange, GTP-binding, complex of two elongation factors; 3.00A {Thermus thermophilus} SCOP: a.5.2.2 d.43.1.1

Probab=95.71  E-value=0.014  Score=46.00  Aligned_cols=36  Identities=19%  Similarity=0.252  Sum_probs=33.0

Q ss_pred             HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      -..|..|-++ |..--+|.+||..++||.|.|++||-
T Consensus         4 a~~VKeLRe~TGagmmdCKkAL~e~~GD~ekAie~LR   40 (196)
T 1aip_C            4 MELIKKLREATGAGMMDVKRALEDAGWDEEKAVQLLR   40 (196)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            3568889888 99999999999999999999999996

>3e21_A HFAF1, FAS-associated factor 1; UBA, alternative splicing, apoptosis, nucleus, phosphoprotein; 1.73A {Homo sapiens}

Probab=95.18  E-value=0.032  Score=34.42  Aligned_cols=35  Identities=11%  Similarity=0.123  Sum_probs=32.1

Q ss_pred             chHHHHHHHHHc-CCCh-HHHHHHHHHhCCCHHHHHH
Q psy4260          40 EYGRMVQNIVDM-GYER-SAVTEALRASFNNPDRAVE   74 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~r-eqv~~ALras~~n~erAvE   74 (129)
                      ..+++|.+++++ |-+. ++|+.=|.+++||.+.||.
T Consensus         4 d~de~ia~F~~iTG~~d~~~A~~~Lea~nWDLe~Av~   40 (45)
T 3e21_A            4 DREMILADFQACTGIENIDEAITLLEQNNWDLVAAIN   40 (45)
T ss_dssp             CHHHHHHHHHHHHCCCCHHHHHHHHHHTTTCHHHHHT
T ss_pred             cHHHHHHHHHHHHCCCCHHHHHHHHHHcCCcHHHHHH
Confidence            468899999999 9886 9999999999999999985

>1p3q_Q VPS9P, vacuolar protein sorting-associated protein VPS9; trafficking, post translational modification, mono- ubiquitination; 1.70A {Saccharomyces cerevisiae} SCOP: a.5.2.4 PDB: 1mn3_A

Probab=93.67  E-value=0.027  Score=36.20  Aligned_cols=39  Identities=15%  Similarity=0.232  Sum_probs=30.4

Q ss_pred             chHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          40 EYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        40 ~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      +.++.+++|.+|  .++++-++..|++.+||.+.||+-|+.
T Consensus        11 e~~~~~~~L~~MFP~lD~evI~~Vl~a~~G~~~~~IdaLLq   51 (54)
T 1p3q_Q           11 ERKDTLNTLQNMFPDMDPSLIEDVCIAAASRIGPCVDALLS   51 (54)
T ss_dssp             HHHHHHHHHHHHSTTSCHHHHHHHHHHSCC--CGGGC----
T ss_pred             HHHHHHHHHHHHcccCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            356789999999  799999999999999999999998874

>1ixs_A Holliday junction DNA helicase RUVA; heterodimeric protein complex, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.20A {Thermus thermophilus} SCOP: a.5.1.1

Probab=92.65  E-value=0.31  Score=31.33  Aligned_cols=28  Identities=7%  Similarity=0.224  Sum_probs=24.5

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHh
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRAS   65 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras   65 (129)
                      +...++.++-|+.+||++.++.+|++..
T Consensus        14 ~~~~~ea~~AL~aLGY~~~ea~kav~~v   41 (62)
T 1ixs_A           14 SEAAEEAVMALAALGFKEAQARAVVLDL   41 (62)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            3456789999999999999999999876

>2qho_B E3 ubiquitin-protein ligase EDD1; protein-protein complex, protein binding/ligase complex; 1.85A {Homo sapiens}

Probab=92.00  E-value=0.4  Score=30.65  Aligned_cols=40  Identities=18%  Similarity=0.188  Sum_probs=33.9

Q ss_pred             chHHHHHHHHH--cCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          40 EYGRMVQNIVD--MGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        40 ~~ee~I~~L~e--MGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ..|+.|.+...  -|-+|+-.++-|+.++-|++.||+-|++.
T Consensus         8 vPe~li~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsR   49 (53)
T 2qho_B            8 IPEELISQAQVVLQGKSRSVIIRELQRTNLDVNLAVNNLLSR   49 (53)
T ss_dssp             SCHHHHHHHHHHSTTCCHHHHHHHHHHTTTCHHHHHHHHHC-
T ss_pred             CcHHHHHHHHHHhcCCcHHHHHHHHHHhCccHHHHHHHHhcc
Confidence            45777876544  49999999999999999999999999987

>1oai_A Nuclear RNA export factor; nuclear transport, nuclear transport factor; 1.0A {Homo sapiens} SCOP: a.5.2.3

Probab=90.64  E-value=0.58  Score=29.89  Aligned_cols=36  Identities=17%  Similarity=0.142  Sum_probs=30.8

Q ss_pred             chHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHH
Q psy4260          40 EYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEY   75 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~   75 (129)
                      ..++.|..+... |-..+-+.++|..++||.++|+.-
T Consensus         6 ~q~~mv~~~s~~Tgmn~~~s~~cL~~~~Wd~~~A~~~   42 (59)
T 1oai_A            6 EQQEMLQAFSTQSGMNLEWSQKCLQDNNWDYTRSAQA   42 (59)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            456677777766 999999999999999999999953

>1vdl_A Ubiquitin carboxyl-terminal hydrolase 25; UBA domain, mouse cDNA, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.5.2.1

Probab=90.35  E-value=1.3  Score=30.42  Aligned_cols=40  Identities=20%  Similarity=0.362  Sum_probs=33.0

Q ss_pred             chHHHHHHHHHc-CCChHHHH-HHHHHhCCCHHHHHHHHHcC
Q psy4260          40 EYGRMVQNIVDM-GYERSAVT-EALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~reqv~-~ALras~~n~erAvE~L~~g   79 (129)
                      ..+-.+++|.|. |...-++. .||++++||+..||.+|...
T Consensus        23 ~~q~lLnQLrEITGiqD~~~L~~ALkas~Gdl~~AV~~LT~~   64 (80)
T 1vdl_A           23 HQQTFLNQLREITGINDAQILQQALKDSNGNLELAVAFLTAK   64 (80)
T ss_dssp             CHHHHHHHHHHHSCCCCHHHHHHHHHHHTSCHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHhccCCHHHHHHHHhcc
Confidence            345578999998 88776665 49999999999999999865

>1ufz_A Hypothetical protein BAB28515; HBS1-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, translatio; NMR {Mus musculus} SCOP: a.5.9.1

Probab=88.55  E-value=0.69  Score=32.01  Aligned_cols=27  Identities=15%  Similarity=0.156  Sum_probs=25.4

Q ss_pred             CChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          53 YERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        53 F~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .++.+.+.|.-+++.|+++|++++|+.
T Consensus        49 V~e~~Lv~ailk~dfD~ekALd~vL~~   75 (83)
T 1ufz_A           49 VPDDILTEAILKHKFDVQKALSVVLEQ   75 (83)
T ss_dssp             SCHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhcCCHHHHHHHHHhc
Confidence            899999999999999999999999965

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=84.48  E-value=1.5  Score=27.08  Aligned_cols=24  Identities=25%  Similarity=0.333  Sum_probs=22.1

Q ss_pred             CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260          53 YERSAVTEALRASFNNPDRAVEYL   76 (129)
Q Consensus        53 F~reqv~~ALras~~n~erAvE~L   76 (129)
                      |+++-+++||+.++||..+|++.|
T Consensus        19 ~E~~~i~~aL~~~~gn~~~aA~~L   42 (63)
T 3e7l_A           19 FEKIFIEEKLREYDYDLKRTAEEI   42 (63)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHH
Confidence            688999999999999999999866

>2jp7_A MRNA export factor MEX67; solution MEX67, UBA, translation; NMR {Saccharomyces cerevisiae} PDB: 2khh_A

Probab=83.15  E-value=1.5  Score=27.87  Aligned_cols=35  Identities=9%  Similarity=-0.114  Sum_probs=29.7

Q ss_pred             chHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHH
Q psy4260          40 EYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVE   74 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE   74 (129)
                      ..++.|.+|... |-..+-+.++|..++||.++|+.
T Consensus         5 ~q~~mv~~~s~~T~Mn~e~S~~cL~~n~Wd~~~A~~   40 (57)
T 2jp7_A            5 VQLELLNKLHLETKLNAEYTFMLAEQSNWNYEVAIK   40 (57)
T ss_dssp             HHHHHHHHHHHHHCSCHHHHHHHHHHTTTCSHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHH
Confidence            345667777666 99999999999999999999995

>3avx_A Elongation factor TS, elongation factor TU, linke replicase; RNA polymerase, translation, transferase-RNA complex; HET: GH3; 2.41A {Escherichia coli O157} PDB: 3agq_A 3agp_A* 3avu_A 3avv_A 3avt_A* 3avw_A* 3avy_A* 3mmp_A* 3mmp_G* 1efu_B

Probab=81.69  E-value=0.23  Score=48.12  Aligned_cols=35  Identities=17%  Similarity=0.238  Sum_probs=31.6

Q ss_pred             HHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          44 MVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        44 ~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      .|++|-++ |..--+|++||..++||.|.|+|||-.
T Consensus         8 ~VKeLRe~TGagmmdCKKAL~e~~GD~ekAie~LRk   43 (1289)
T 3avx_A            8 LVKELRERTGAGMMDCKKALTEANGDIELAIENMRK   43 (1289)
T ss_dssp             CTHHHHTTTCCCTTTTTTTTTTTTTCHHHHHHHHHT
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            47888888 888889999999999999999999974

>2ekf_A Ancient ubiquitous protein 1; CUE, ubiquitin ligase complex, ubiquitin-conjugating enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.29  E-value=5.7  Score=25.83  Aligned_cols=41  Identities=12%  Similarity=0.189  Sum_probs=36.6

Q ss_pred             CCchHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .+..+..++++.+|  -++++.++.-|+.++ +++..+|-++.|
T Consensus        10 ~~ql~~mv~~V~~mfP~vp~~~I~~DL~~Tg-sVe~TienILeG   52 (61)
T 2ekf_A           10 DVQLATLAQRVKEVLPHVPLGVIQRDLAKTG-CVDLTITNLLEG   52 (61)
T ss_dssp             CCCHHHHHHHHHHHCSSSCHHHHHHHHHTSC-CHHHHHHHHHSC
T ss_pred             cHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC-CHHHHHHHHHcC
Confidence            45678889999999  699999999999886 999999999988

>2ejs_A Autocrine motility factor receptor, isoform 2; CUE, ubiquitin ligase complex, ubiquitin-conjugating enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.83  E-value=7  Score=25.10  Aligned_cols=41  Identities=15%  Similarity=0.261  Sum_probs=36.7

Q ss_pred             CCchHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .+..+..|+++.+|  -++++.++.-|+.++ ++|..+|-++.|
T Consensus        10 ~~q~~~mv~~V~~mfP~vp~~~I~~DL~~Tg-sVe~TienILeG   52 (58)
T 2ejs_A           10 NSQLNAMAHQIQEMFPQVPYHLVLQDLQLTR-SVEITTDNILEG   52 (58)
T ss_dssp             CCHHHHHHHHHHHHCCSSCHHHHHHHHHHHC-SHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC-CHHHHHHHHHhc
Confidence            45678889999999  699999999999998 999999999987

---

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	129
d1oqya1	41	a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Hum	5e-15
d1wjia_	63	a.5.2.1 (A:) Tudor domain containing protein 3, TD	4e-10
d1wgna_	63	a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1	6e-10
d1wiva_	73	a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress	6e-10
d1vg5a_	73	a.5.2.1 (A:) Rhomboid family protein At3g58460 {Th	7e-08
d1whca_	64	a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus	3e-05
d2crna1	51	a.5.2.1 (A:8-58) Suppressor of T-cell receptor sig	3e-04
d2cpwa1	51	a.5.2.1 (A:8-58) Cbl-interacting protein p70, STS1	0.001
d1veka_	84	a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress	0.003

>d1oqya1 a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]} Length = 41

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.9 bits (151), Expect = 5e-15
 Identities = 26/41 (63%), Positives = 30/41 (73%)

Query: 38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
          G EY  M+  I+ MGYER  V  ALRAS+NNP RAVEYL+T
Sbjct: 1  GSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLT 41

>d1wjia_ a.5.2.1 (A:) Tudor domain containing protein 3, TDRD3 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Tudor domain containing protein 3, TDRD3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.2 bits (120), Expect = 4e-10
 Identities = 12/52 (23%), Positives = 26/52 (50%)

Query: 43 RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEEAPVAAN 94
          + +++I +MG+ + A  +AL  + NN + A+  L+T      V       ++
Sbjct: 11 KALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQKPVMGPPSGPSS 62

>d1wgna_ a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 1, UBAP1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (118), Expect = 6e-10
 Identities = 11/57 (19%), Positives = 25/57 (43%)

Query: 27 TPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAA 83
          + G      ++     + V+ +V+MGY    V  A++    N ++ ++YL      +
Sbjct: 5  SSGAYSELQMLSPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHSGPS 61

>d1wiva_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 49.8 bits (119), Expect = 6e-10
 Identities = 9/54 (16%), Positives = 23/54 (42%)

Query: 30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAA 83
          +A  +    D     V  ++  G+      +AL+AS  + ++A +++      +
Sbjct: 18 DAPISHQTSDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNSGPS 71

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Rhomboid family protein At3g58460
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 44.5 bits (105), Expect = 7e-08
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 4/70 (5%)

Query: 10 STPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNP 69
          S+ S+   QA     A  P +              +Q +V MG++R+ V  AL A+ ++ 
Sbjct: 2  SSGSSGSRQAPIANAAVLPQSQGRV----AASEEQIQKLVAMGFDRTQVEVALAAADDDL 57

Query: 70 DRAVEYLITG 79
            AVE L++ 
Sbjct: 58 TVAVEILMSQ 67

>d1whca_ a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 64

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA/UBX 33.3 kDa protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.1 bits (86), Expect = 3e-05
 Identities = 10/52 (19%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 44 MVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPAAVVGEEAPVAAN 94
           ++++++MG+ R    +AL  + N   + A+++L+       V E     ++
Sbjct: 12 ALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDDPDVDEPLSGPSS 63

>d2crna1 a.5.2.1 (A:8-58) Suppressor of T-cell receptor signaling 2 (STS-2) {Human (Homo sapiens) [TaxId: 9606]} Length = 51

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Suppressor of T-cell receptor signaling 2 (STS-2)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (79), Expect = 3e-04
 Identities = 7/36 (19%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 44 MVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLIT 78
          +++ ++ MG+      +AL A+     + A+ +L  
Sbjct: 5  LLEPLLAMGFPVHTALKALAATGRKTAEEALAWLHD 40

>d2cpwa1 a.5.2.1 (A:8-58) Cbl-interacting protein p70, STS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 51

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Cbl-interacting protein p70, STS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (75), Expect = 0.001
 Identities = 7/35 (20%), Positives = 19/35 (54%), Gaps = 1/35 (2%)

Query: 45 VQNIVDMGYERSAVTEALRASFN-NPDRAVEYLIT 78
          +  ++ MG+ R+   +AL ++   +   A ++L +
Sbjct: 16 LDVLLSMGFPRARAQKALASTGGRSVQTACDWLFS 50

>d1veka_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 84

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 32.5 bits (74), Expect = 0.003
 Identities = 8/36 (22%), Positives = 19/36 (52%), Gaps = 1/36 (2%)

Query: 44 MVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLIT 78
          +V  +V MG+ +    +A   + N   + A+ +L++
Sbjct: 32 IVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLS 67

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	129
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	99.71
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	99.66
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	99.64
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	99.61
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	99.58
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	99.53
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	99.47
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	99.42
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	99.38
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	99.34
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.06
d2bwba1	44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.03
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	98.87
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	98.78
d3e46a1	42	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal	98.69
d1oqya2	44	DNA repair protein Hhr23a {Human (Homo sapiens) [T	98.52
d1vega_	83	NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculu	98.34
d1z96a1	38	UBA-domain protein mud1 {Schizosaccharomyces pombe	98.28
d1wj7a1	91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	97.84
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	97.57
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	97.49
d1ttea1	55	Ubiquitin-protein ligase ubc1 {Baker's yeast (Sacc	97.43
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	97.4
d2cosa1	41	Serine/threonine protein kinase LATS2 {Mouse (Mus	97.24
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	97.13
d1v92a_	46	NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {	96.92
d2f4mb1	58	XPC-binding domain of Rad23 homolog B (Hhr23b) {Hu	96.86
d2dkla1	72	Trinucleotide repeat containing 6c protein, TNRC6C	96.56
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	96.17
d2cp8a1	41	Migration-inducing protein 19 NBR1 {Human (Homo sa	94.85
d2k0bx1	52	Sequestosome 1 (Sqstm1) {Human (Homo sapiens) [Tax	93.6
d2di0a1	63	Activating signal cointegrator 1 complex subunit 2	92.89
d1vdla_	80	Ubiquitin carboxyl-terminal hydrolase 25 {Mouse (M	92.82
d1oaia_	59	FG-binding, C-terminal domain of TAP {Human (Homo	90.45
d1cuka1	48	DNA helicase RuvA subunit, C-terminal domain {Esch	89.83
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	88.66
d1ufza_	83	HBS1-like protein {Mouse (Mus musculus) [TaxId: 10	84.86
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	81.5

>d1oqya1 a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.3e-18  Score=105.86  Aligned_cols=41  Identities=63%  Similarity=1.041  Sum_probs=39.3

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      |+..|++|++|++|||+|++|++||++++||+|+|+||||+
T Consensus         1 G~~~e~~i~~L~~MGF~~~~a~~AL~~~~~N~e~A~~~LlS   41 (41)
T d1oqya1           1 GSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLT   41 (41)
T ss_dssp             TTTHHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTTTT
T ss_pred             ChhHHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            57889999999999999999999999999999999999985

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Rhomboid family protein At3g58460
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.66  E-value=1.8e-16  Score=106.23  Aligned_cols=43  Identities=30%  Similarity=0.393  Sum_probs=40.2

Q ss_pred             CCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          37 MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ....+|+.|++|++|||+|++|++||++++||+|+|+||||++
T Consensus        25 ~~~~~ee~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~Ll~~   67 (73)
T d1vg5a_          25 RVAASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQ   67 (73)
T ss_dssp             CSCCCHHHHHHHHTTTCCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             CcCcCHHHHHHHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            3456799999999999999999999999999999999999988

>d1wjia_ a.5.2.1 (A:) Tudor domain containing protein 3, TDRD3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Tudor domain containing protein 3, TDRD3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2e-16  Score=103.03  Aligned_cols=47  Identities=23%  Similarity=0.328  Sum_probs=42.4

Q ss_pred             CCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCC
Q psy4260          37 MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAA   83 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~   83 (129)
                      ....+++.|++|++|||+|++|++||++++||+++|++|||+|.++.
T Consensus         5 ~~~~d~~~v~~L~~MGF~~~~a~~AL~~~~~~~e~A~~wL~~~~~~~   51 (63)
T d1wjia_           5 SSGVDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQK   51 (63)
T ss_dssp             CCSSCHHHHHHHHTTTCCHHHHHHHHHHTTSCHHHHHHHHHHHSSCC
T ss_pred             CCccCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHCCCCC
Confidence            34567999999999999999999999999999999999999995443

>d1wgna_ a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 1, UBAP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.7e-16  Score=103.94  Aligned_cols=42  Identities=24%  Similarity=0.444  Sum_probs=39.6

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .+.+++.|++|++|||+|++|++||++++||+|+|+||||+|
T Consensus        16 ~~~de~~v~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~Lls~   57 (63)
T d1wgna_          16 SPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAH   57 (63)
T ss_dssp             CHHHHHHHHHHHHHHCCHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            456789999999999999999999999999999999999987

>d1wiva_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.58  E-value=1.2e-15  Score=102.16  Aligned_cols=42  Identities=19%  Similarity=0.391  Sum_probs=39.8

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ...+++.|++|++|||+|++|++||++++||+++|++|||++
T Consensus        26 ~~~d~~~i~~L~~MGF~~~~a~~AL~~~~~n~e~Av~~Lls~   67 (73)
T d1wiva_          26 SDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNN   67 (73)
T ss_dssp             CSSCHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            446789999999999999999999999999999999999999

>d1whca_ a.5.2.1 (A:) UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA/UBX 33.3 kDa protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=3.7e-15  Score=97.48  Aligned_cols=45  Identities=18%  Similarity=0.323  Sum_probs=40.0

Q ss_pred             CCchHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCCC
Q psy4260          38 GDEYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPA   82 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP~   82 (129)
                      ...+++.|++|++|||++++|++||++++| ++|+|++|||+|+.+
T Consensus         6 s~~d~~~l~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~d   51 (64)
T d1whca_           6 SGAELTALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDD   51 (64)
T ss_dssp             CCCCCCHHHHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHHHHTTC
T ss_pred             CccCHHHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHHCCCC
Confidence            345678999999999999999999999988 899999999999543

>d2cpwa1 a.5.2.1 (A:8-58) Cbl-interacting protein p70, STS1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Cbl-interacting protein p70, STS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=1.9e-14  Score=90.84  Aligned_cols=40  Identities=20%  Similarity=0.418  Sum_probs=36.9

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITG   79 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~g   79 (129)
                      ..++.|++|++|||++++|++||++++| |+|+|+||||+|
T Consensus        11 ~~~~~l~~L~~MGF~~~~a~~AL~~t~n~~ve~A~~WLl~H   51 (51)
T d2cpwa1          11 KHGSALDVLLSMGFPRARAQKALASTGGRSVQTACDWLFSH   51 (51)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHTTTSCHHHHHHHHHSC
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHHCCCCHHHHHHHHHcC
Confidence            4566799999999999999999999988 999999999986

>d2crna1 a.5.2.1 (A:8-58) Suppressor of T-cell receptor signaling 2 (STS-2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Suppressor of T-cell receptor signaling 2 (STS-2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=4.1e-14  Score=89.00  Aligned_cols=39  Identities=18%  Similarity=0.327  Sum_probs=35.6

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCC
Q psy4260          42 GRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGI   80 (129)
Q Consensus        42 ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~gi   80 (129)
                      ++.|++|++|||++++|++||+.++| |+++|++|||+|.
T Consensus         3 p~~v~~L~~MGF~~~~a~~Al~~t~n~~ve~A~~Wl~~h~   42 (51)
T d2crna1           3 PSLLEPLLAMGFPVHTALKALAATGRKTAEEALAWLHDHC   42 (51)
T ss_dssp             CSSHHHHHHTSCCHHHHHHHHHHHTSCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHCCCCHHHHHHHHHHcC
Confidence            34589999999999999999999966 9999999999994

>d2g3qa1 a.5.2.1 (A:1339-1381) Endocytic protein Ede1, YBL047C {Saccharomyces cerevisiae [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Endocytic protein Ede1, YBL047C
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=99.38  E-value=2.9e-13  Score=83.04  Aligned_cols=40  Identities=18%  Similarity=0.313  Sum_probs=37.5

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      +.+..|++|++|||++++|++||++++||.+.|++||+.+
T Consensus         3 pk~~ai~eL~~MGF~e~~A~~AL~k~~wnleaAtN~LLd~   42 (43)
T d2g3qa1           3 PKSLAVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDS   42 (43)
T ss_dssp             HHHHHHHHHHTTTSCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             cHHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            4567899999999999999999999999999999999976

>d1veka_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin isopeptidase T
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.34  E-value=9.5e-13  Score=89.89  Aligned_cols=44  Identities=18%  Similarity=0.339  Sum_probs=39.6

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCCC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPA   82 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP~   82 (129)
                      ..+++.|++|++|||++++|++||+.++| |+|+|++|||+|..+
T Consensus        27 ~~d~~~v~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~d   71 (84)
T d1veka_          27 VANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDD   71 (84)
T ss_dssp             CCCHHHHHHHHHHTCCHHHHHHHHHHTTTCCHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHHHcCCC
Confidence            35789999999999999999999999865 999999999999543

>d1veja1 a.5.2.1 (A:8-68) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.06  E-value=2.2e-10  Score=74.49  Aligned_cols=45  Identities=24%  Similarity=0.420  Sum_probs=39.1

Q ss_pred             cccCCCchHHHHHHHHHcCCC-hHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          34 TLLMGDEYGRMVQNIVDMGYE-RSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        34 ~~~~g~~~ee~I~~L~eMGF~-reqv~~ALras~~n~erAvE~L~~   78 (129)
                      +......++..+++|.+|||. ++..++||++++||+++|||+|+.
T Consensus        15 ~~~~e~ry~~QL~qL~eMGF~d~~~Nl~AL~~t~Gdv~~Aie~Ll~   60 (61)
T d1veja1          15 SLFTEGRYQQELEELKALGFANRDANLQALVATDGDIHAAIEMLLG   60 (61)
T ss_dssp             GGGTTTTSHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            444567789999999999995 666699999999999999999985

>d2bwba1 a.5.2.1 (A:328-371) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.03  E-value=2.2e-10  Score=70.24  Aligned_cols=40  Identities=28%  Similarity=0.462  Sum_probs=36.1

Q ss_pred             chHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          40 EYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        40 ~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .+...+++|.+||| +++..++||++++||+++|||+|++|
T Consensus         4 ry~~QL~qL~~MGF~d~~~Ni~AL~~t~GdV~~Aie~Ll~g   44 (44)
T d2bwba1           4 RYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG   44 (44)
T ss_dssp             HTHHHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHhCc
Confidence            35677999999998 68888899999999999999999986

>d2dnaa1 a.5.2.1 (A:12-61) Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquilin-like protein Ubqlnl
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.87  E-value=1.6e-09  Score=67.98  Aligned_cols=40  Identities=20%  Similarity=0.317  Sum_probs=36.3

Q ss_pred             chHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          40 EYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        40 ~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .+...+++|.+||| +++..++||++++||+++|||+|+++
T Consensus         7 ry~~QL~qL~~MGF~d~~~Ni~AL~~t~GdV~~Aie~Ll~~   47 (50)
T d2dnaa1           7 RFSKEMECLQAMGFVNYNANLQALIATDGDTNAAIYKLKSS   47 (50)
T ss_dssp             HTHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            46778999999998 68888999999999999999999976

>d2daha1 a.5.2.1 (A:8-48) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.78  E-value=4.9e-09  Score=63.19  Aligned_cols=38  Identities=32%  Similarity=0.368  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHcCCC-hHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          41 YGRMVQNIVDMGYE-RSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        41 ~ee~I~~L~eMGF~-reqv~~ALras~~n~erAvE~L~~   78 (129)
                      ++..+++|.+|||. ++..++||++++||+++|||+|+.
T Consensus         2 y~~QL~~L~~MGF~d~~~Ni~AL~~t~Gdv~~Aie~Ll~   40 (41)
T d2daha1           2 FQVQLEQLRSMGFLNREANLQALIATGGDVDAAVEKLRQ   40 (41)
T ss_dssp             SHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            56789999999986 777789999999999999999974

>d3e46a1 a.5.2.1 (A:157-198) Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.69  E-value=1.4e-08  Score=60.88  Aligned_cols=41  Identities=29%  Similarity=0.491  Sum_probs=38.0

Q ss_pred             CCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          37 MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      +.+++-.+|++|+.|||++..|+.||..-.||+|.|.|.|+
T Consensus         2 sspeyt~kidklca~gf~knavi~alsskswdvetatelll   42 (42)
T d3e46a1           2 SSPEYTKKIENLCAAGFDRNAVIVALSSKSWDVETATELLL   42 (42)
T ss_dssp             CCHHHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHccccccceeeeeccCccchhhHHHhhC
Confidence            45678899999999999999999999999999999999875

>d1oqya2 a.5.2.1 (A:317-360) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.52  E-value=1.2e-08  Score=62.51  Aligned_cols=41  Identities=20%  Similarity=0.330  Sum_probs=37.8

Q ss_pred             CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ++..+.|++|++|||+|+.|+.|--+|+-|.+.|++|||++
T Consensus         2 ~ee~~aIeRL~~LGF~r~~viqay~ACdKNEelAaN~L~~~   42 (44)
T d1oqya2           2 PQEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQ   42 (44)
T ss_dssp             TTTHHHHHHHHHHTCCSHHHHHHTSSSSSCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHhCcCHHHHHHHHHHc
Confidence            35677899999999999999999999999999999999964

>d1vega_ a.5.2.1 (A:) NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: NEDD8 ultimate buster-1 (Nub1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.34  E-value=8.2e-07  Score=60.17  Aligned_cols=49  Identities=22%  Similarity=0.327  Sum_probs=41.2

Q ss_pred             CCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc-C--CCCCcC
Q psy4260          37 MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT-G--IPAAVV   85 (129)
Q Consensus        37 ~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~-g--iP~~~~   85 (129)
                      ..+.+.++|++|+-|||+++.|..|||...||+..|.--|.- |  +|.+.+
T Consensus        25 q~~~sQesidqLvYMGF~~~~Ae~ALRvfrGnVQlAaQtLahngG~LP~dLq   76 (83)
T d1vega_          25 QASPSQESINQLVYMGFDTVVAEAALRVFGGNVQLAAQTLAHHGGSLPPDLQ   76 (83)
T ss_dssp             SCCCCHHHHHHHHHHSCCHHHHHHHHHHTTTCHHHHHHHHHHHTSSCCTTSS
T ss_pred             cCCCCHHHHHHHHHhcccHHHHHHHHHHhcccHHHHHHHHHHcCCcCCcccc
Confidence            355678999999999999999999999999999999987753 3  665543

>d1z96a1 a.5.2.1 (A:295-332) UBA-domain protein mud1 {Schizosaccharomyces pombe [TaxId: 4896]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: UBA-domain protein mud1
species: Schizosaccharomyces pombe [TaxId: 4896]

Probab=98.28  E-value=6e-07  Score=52.42  Aligned_cols=36  Identities=25%  Similarity=0.476  Sum_probs=33.5

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      ..+|.+|++|||+.-.+..||.+++||.|.|..||+
T Consensus         3 nskiaqlvsmgfdpleaaqaldaangdldvaasfll   38 (38)
T d1z96a1           3 NSKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL   38 (38)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             chHHHHHHHcCCCHHHHHHHHhhhcCcHHHHHHhhC
Confidence            357999999999999999999999999999999884

>d1wj7a1 a.5.2.1 (A:8-98) Ubiquitin-associated protein 2-like Ubap2l {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 2-like Ubap2l
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.84  E-value=1.7e-05  Score=54.56  Aligned_cols=44  Identities=23%  Similarity=0.486  Sum_probs=40.1

Q ss_pred             CCchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260          38 GDEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITGIP   81 (129)
Q Consensus        38 g~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~giP   81 (129)
                      ....+++|++|++| |=++++|.-||--|++|+++||++||.|-+
T Consensus        29 D~~i~~kVkql~e~T~rsede~~~ALhDcn~D~~~AIn~lLEg~~   73 (91)
T d1wj7a1          29 DADFEEKVKQLIDITGKNQDECVIALHDCNGDVNRAINVLLEGNP   73 (91)
T ss_dssp             CHHHHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHTCSS
T ss_pred             cHHHHHHHHHHHHHhCCCHHHHHHHHhcCCccHHHHHHHHHhcCC
Confidence            44568899999999 899999999999999999999999998843

>d1aipc1 a.5.2.2 (C:2-53) Elongation factor Ts (EF-Ts), N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=97.57  E-value=5.8e-05  Score=46.94  Aligned_cols=35  Identities=20%  Similarity=0.292  Sum_probs=32.0

Q ss_pred             HHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          43 RMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        43 e~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      +.|.+|-+. |+.--+|.+||..++||+|.|++||-
T Consensus         4 elvK~LR~~Tga~~~dcKkAL~e~~gD~ekA~e~Lr   39 (52)
T d1aipc1           4 ELIKKLREATGAGMMDVKRALEDAGWDEEKAVQLLR   39 (52)
T ss_dssp             HHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            567888777 99999999999999999999999995

>d1xb2b1 a.5.2.2 (B:56-111) Elongation factor Ts (EF-Ts), N-terminal domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=97.49  E-value=8.3e-05  Score=46.89  Aligned_cols=37  Identities=16%  Similarity=0.206  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          41 YGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        41 ~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      .-+.|.+|-+. |+.--+|.+||..++||+|.|++||-
T Consensus         4 s~~lvk~LRe~Tga~~~dcKkAL~e~~gD~ekA~e~Lr   41 (56)
T d1xb2b1           4 SKELLMKLRRKTGYSFINCKKALETCGGDLKQAESWLH   41 (56)
T ss_dssp             HHHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            34678888888 99999999999999999999999996

>d1ttea1 a.5.2.1 (A:161-215) Ubiquitin-protein ligase ubc1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-protein ligase ubc1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.43  E-value=0.0001  Score=46.41  Aligned_cols=38  Identities=21%  Similarity=0.357  Sum_probs=30.4

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCCC---------HHHHHHHHH
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFNN---------PDRAVEYLI   77 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~n---------~erAvE~L~   77 (129)
                      .+++.|.++.+|||+|++++.+||+-+-.         .++.+|-|+
T Consensus         8 id~~~V~~f~~mGF~rdKvI~VLrrlgik~~~~~~~~~~n~ilEELL   54 (55)
T d1ttea1           8 IDHDLIDEFESQGFEKDKIVEVLRRLGVKSLDPNDNNTANRIIEELL   54 (55)
T ss_dssp             CSHHHHHHHHHHTCCHHHHHHHHHHSCCSSCCSSCCHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHcCCCchhHHHHHHHhCcCCCCcccchHHHHHHHHHh
Confidence            35788999999999999999999986542         456666654

>d1efub3 a.5.2.2 (B:1-54) Elongation factor Ts (EF-Ts), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TS-N domain
domain: Elongation factor Ts (EF-Ts), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.40  E-value=0.00013  Score=45.63  Aligned_cols=37  Identities=16%  Similarity=0.210  Sum_probs=33.6

Q ss_pred             hHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          41 YGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        41 ~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~   77 (129)
                      .-+.|.+|-++ |..--+|.+||..++||.|.|++||-
T Consensus         4 s~~~iK~LR~~Tgag~~dCKkAL~e~~gD~ekA~e~Lr   41 (54)
T d1efub3           4 TASLVKELRERTGAGMMDCKKALTEANGDIELAIENMR   41 (54)
T ss_dssp             CHHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            34678888888 99999999999999999999999995

>d2cosa1 a.5.2.1 (A:8-48) Serine/threonine protein kinase LATS2 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Serine/threonine protein kinase LATS2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.24  E-value=0.00021  Score=42.19  Aligned_cols=35  Identities=26%  Similarity=0.489  Sum_probs=30.4

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHH
Q psy4260          43 RMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLI   77 (129)
Q Consensus        43 e~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~   77 (129)
                      ...+.|+.-||+++-|++|||..++ ++|.|+||+-
T Consensus         4 QMlqdl~~aG~D~~m~iral~qt~~rsieaaie~is   39 (41)
T d2cosa1           4 QMLQELVNAGCDQEMAGRALKQTGSRSIEAALEYIS   39 (41)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhCcccHHHHHHHHh
Confidence            3467778889999999999999987 8999999974

>d1wgla_ a.5.2.4 (A:) Toll-interacting protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Toll-interacting protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.13  E-value=0.00034  Score=44.33  Aligned_cols=40  Identities=23%  Similarity=0.280  Sum_probs=36.5

Q ss_pred             chHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          40 EYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        40 ~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ..|+.|+.|.+|  .++++-++..|++++||+|+|++-|+.-
T Consensus         8 ~~Ee~i~~LkeMFP~~D~~vI~~VL~a~~G~vd~aid~LL~M   49 (59)
T d1wgla_           8 CSEEDLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQM   49 (59)
T ss_dssp             SCHHHHHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHS
T ss_pred             CcHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            356779999999  8999999999999999999999999875

>d1v92a_ a.5.2.3 (A:) NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TAP-C domain-like
domain: NSFL1 (p97 ATPase) cofactor p47, UBA-like domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.92  E-value=0.00092  Score=39.88  Aligned_cols=40  Identities=15%  Similarity=0.120  Sum_probs=35.8

Q ss_pred             CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      +..++.|+++++. |=+++.|+.=|.+++||++.||..-|.
T Consensus         3 ~~~~~lI~qF~~iTg~~~~~A~~~Le~~~w~Le~Ai~~yfe   43 (46)
T d1v92a_           3 EERQDALREFVAVTGAEEDRARFFLESAGWDLQIALASFYE   43 (46)
T ss_dssp             THHHHHHHHHHHHTCCCHHHHHHHHHHTTSCSHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHHh
Confidence            4567899999998 999999999999999999999986663

>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=96.86  E-value=2.5e-05  Score=49.67  Aligned_cols=26  Identities=27%  Similarity=0.378  Sum_probs=23.7

Q ss_pred             CCCCCCCCccchhhhh------hhhhhhcCCc
Q psy4260          96 PQGNNIKQFSSVKEIE------IPNLMQGDNK  121 (129)
Q Consensus        96 ~~~~n~PqF~~~r~~~------lp~llq~~~~  121 (129)
                      .++||+|+|+.||++|      ||.|||+.|+
T Consensus         3 ~~Lr~~PqFq~lR~~vq~nP~~L~~lLqql~~   34 (58)
T d2f4mb1           3 EFLRNQPQFQQMRQIIQQNPSLLPALLQQIGR   34 (58)
T ss_dssp             GGGTTCHHHHHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             HHHhcChHHHHHHHHHHHCHHHHHHHHHHHHh
Confidence            4689999999999999      9999998875

>d2dkla1 a.5.2.1 (A:8-79) Trinucleotide repeat containing 6c protein, TNRC6C {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Trinucleotide repeat containing 6c protein, TNRC6C
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.56  E-value=0.0017  Score=42.59  Aligned_cols=37  Identities=32%  Similarity=0.592  Sum_probs=33.4

Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          43 RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        43 e~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      ..|.||.+|||.|+.+..+|+..+.|.+.|+.-|+.-
T Consensus        16 p~~KQfsnMGf~re~~e~~l~sN~m~L~~a~~~l~dK   52 (72)
T d2dkla1          16 RLIKQLTDMGFPREPAEEALKSNNMNLDQAMSALLEK   52 (72)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHTT
T ss_pred             HHHHHHhhcCCcCCChHHhhhccCcchhhcccchhhh
Confidence            3579999999999999999999999999999878743

>d1mn3a_ a.5.2.4 (A:) Vacuolar protein sorting-associated protein vps9 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Vacuolar protein sorting-associated protein vps9
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.17  E-value=0.0024  Score=39.65  Aligned_cols=39  Identities=15%  Similarity=0.237  Sum_probs=35.5

Q ss_pred             chHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260          40 EYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLIT   78 (129)
Q Consensus        40 ~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~   78 (129)
                      +.++.++.|.+|  .++++-++..|++++||+|.|++-|+.
T Consensus        11 e~~e~~~~Lk~MFP~~D~~VI~~VL~a~~G~vd~aidaLL~   51 (54)
T d1mn3a_          11 ERKDTLNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLS   51 (54)
T ss_dssp             HHHHHHHHHHHHCTTSCHHHHHHHHSCSSCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            457789999999  899999999999999999999999874

>d2cp8a1 a.5.2.1 (A:8-48) Migration-inducing protein 19 NBR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Migration-inducing protein 19 NBR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.85  E-value=0.022  Score=33.52  Aligned_cols=35  Identities=20%  Similarity=0.293  Sum_probs=29.1

Q ss_pred             HHHHHHHHcCCC-hHHHHHHHHHhCCCHHHHHHHHH
Q psy4260          43 RMVQNIVDMGYE-RSAVTEALRASFNNPDRAVEYLI   77 (129)
Q Consensus        43 e~I~~L~eMGF~-reqv~~ALras~~n~erAvE~L~   77 (129)
                      .....|+||||- |..=.+-|++-++|...+|.-|+
T Consensus         4 ~lM~~L~EMGF~DR~lNq~LL~KH~~nl~~vV~eLl   39 (41)
T d2cp8a1           4 ALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELL   39 (41)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHTTTTTCHHHHHHHHH
T ss_pred             HHHHHHHHhCcchhHHHHHHHHHccCcHHHHHHHHH
Confidence            457899999997 55556789999999999998775

>d2k0bx1 a.5.2.1 (X:1-52) Sequestosome 1 (Sqstm1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Sequestosome 1 (Sqstm1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.60  E-value=0.029  Score=34.49  Aligned_cols=39  Identities=13%  Similarity=0.262  Sum_probs=33.1

Q ss_pred             CCchHHHHHHHHHcCCChHH--HHHHHHHhCCCHHHHHHHH
Q psy4260          38 GDEYGRMVQNIVDMGYERSA--VTEALRASFNNPDRAVEYL   76 (129)
Q Consensus        38 g~~~ee~I~~L~eMGF~req--v~~ALras~~n~erAvE~L   76 (129)
                      .+...+.|.+++.|||+-|-  -.+-|.+.++|+.+|+|-|
T Consensus         7 dp~l~~al~qM~aMGFsneGGWLt~LL~skn~dI~~aLD~i   47 (52)
T d2k0bx1           7 DPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTI   47 (52)
T ss_dssp             STTHHHHHHHHHHHTCCCSSSCHHHHHHHTTSCHHHHHHHT
T ss_pred             ChHHHHHHHHHHHcCCCCcchHHHHHHHHcCCCHHHHHHHH
Confidence            34567899999999999875  4678999999999999865

>d2di0a1 a.5.2.4 (A:8-70) Activating signal cointegrator 1 complex subunit 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Activating signal cointegrator 1 complex subunit 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.89  E-value=0.17  Score=31.92  Aligned_cols=46  Identities=11%  Similarity=0.343  Sum_probs=38.1

Q ss_pred             CCchHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC-CCCC
Q psy4260          38 GDEYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG-IPAA   83 (129)
Q Consensus        38 g~~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g-iP~~   83 (129)
                      |-+-+..|.++.++  -+...=++++|...++|+|+.+..|+.+ +|.+
T Consensus         3 ~vel~s~I~qV~Dl~PdLG~GFi~~~L~~Y~~n~E~vI~~lLe~~Lpp~   51 (63)
T d2di0a1           3 GVELDSLISQVKDLLPDLGEGFILACLEYYHYDPEQVINNILEERLAPT   51 (63)
T ss_dssp             SHHHHHHHHHHHHHCCSSCHHHHHHHHHHTTTCHHHHHHHHHTTCCCTT
T ss_pred             hhHHHHHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHccCCCHH
Confidence            45667889998888  4677789999999999999999999987 4543

>d1vdla_ a.5.2.1 (A:) Ubiquitin carboxyl-terminal hydrolase 25 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin carboxyl-terminal hydrolase 25
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.82  E-value=0.25  Score=32.33  Aligned_cols=43  Identities=19%  Similarity=0.328  Sum_probs=35.6

Q ss_pred             CCCchHHHHHHHHHc-CCChHHHH-HHHHHhCCCHHHHHHHHHcC
Q psy4260          37 MGDEYGRMVQNIVDM-GYERSAVT-EALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        37 ~g~~~ee~I~~L~eM-GF~reqv~-~ALras~~n~erAvE~L~~g   79 (129)
                      ++....-.+++|.|. |...-++. .||++++||+..||.+|-..
T Consensus        20 s~~hqQ~lLNQLrEITGIqD~q~L~~ALkas~Gdl~~AV~~LT~~   64 (80)
T d1vdla_          20 AQKHQQTFLNQLREITGINDAQILQQALKDSNGNLELAVAFLTAK   64 (80)
T ss_dssp             TTSCHHHHHHHHHHHSCCCCHHHHHHHHHHHTSCHHHHHHHHHTT
T ss_pred             hhhHHHHHHHHHHHHhCCCcHHHHHHHHHhcCCCHHHHHHHHhcC
Confidence            355566778999998 88777765 49999999999999999866

>d1oaia_ a.5.2.3 (A:) FG-binding, C-terminal domain of TAP {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TAP-C domain-like
domain: FG-binding, C-terminal domain of TAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.45  E-value=0.27  Score=30.14  Aligned_cols=35  Identities=17%  Similarity=0.167  Sum_probs=30.0

Q ss_pred             chHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHH
Q psy4260          40 EYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVE   74 (129)
Q Consensus        40 ~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE   74 (129)
                      +.++.|..+... |-..+=++++|..++||.++|+.
T Consensus         6 ~Qq~mv~~~s~~T~mn~e~s~~cLe~~~Wd~~~A~~   41 (59)
T d1oaia_           6 EQQEMLQAFSTQSGMNLEWSQKCLQDNNWDYTRSAQ   41 (59)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHH
Confidence            456677776665 99999999999999999999995

>d1cuka1 a.5.1.1 (A:156-203) DNA helicase RuvA subunit, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: DNA helicase RuvA subunit, C-terminal domain
family: DNA helicase RuvA subunit, C-terminal domain
domain: DNA helicase RuvA subunit, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.83  E-value=0.16  Score=30.02  Aligned_cols=28  Identities=14%  Similarity=0.261  Sum_probs=24.8

Q ss_pred             chHHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260          40 EYGRMVQNIVDMGYERSAVTEALRASFN   67 (129)
Q Consensus        40 ~~ee~I~~L~eMGF~reqv~~ALras~~   67 (129)
                      ..++.|+-|+..||.+.+|.+|+++..+
T Consensus         4 ~~~eAi~AL~~LGY~~~ea~~av~~i~~   31 (48)
T d1cuka1           4 AEQEAVARLVALGYKPQEASRMVSKIAR   31 (48)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHSCC
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHHHhcC
Confidence            4578999999999999999999988754

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=88.66  E-value=0.12  Score=31.19  Aligned_cols=24  Identities=8%  Similarity=0.025  Sum_probs=22.1

Q ss_pred             CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260          53 YERSAVTEALRASFNNPDRAVEYL   76 (129)
Q Consensus        53 F~reqv~~ALras~~n~erAvE~L   76 (129)
                      ++++.+.+||+.++||..+|++.|
T Consensus        20 ~Er~~I~~aL~~~~gn~~~aA~~L   43 (60)
T d1umqa_          20 VRWEHIQRIYEMCDRNVSETARRL   43 (60)
T ss_dssp             HHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHH
Confidence            578999999999999999999877

>d1ufza_ a.5.9.1 (A:) HBS1-like protein {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: HBS1-like domain
family: HBS1-like domain
domain: HBS1-like protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.86  E-value=0.68  Score=30.43  Aligned_cols=27  Identities=15%  Similarity=0.156  Sum_probs=25.4

Q ss_pred             CChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260          53 YERSAVTEALRASFNNPDRAVEYLITG   79 (129)
Q Consensus        53 F~reqv~~ALras~~n~erAvE~L~~g   79 (129)
                      .++++.++|.-+++.|+++|++++|+.
T Consensus        49 vpe~~lv~avlk~dydvekALd~vL~~   75 (83)
T d1ufza_          49 VPDDILTEAILKHKFDVQKALSVVLEQ   75 (83)
T ss_dssp             SCHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHccCCHHHHHHHHHhc
Confidence            889999999999999999999999965

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=81.50  E-value=0.42  Score=30.84  Aligned_cols=24  Identities=17%  Similarity=0.210  Sum_probs=22.8

Q ss_pred             CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260          53 YERSAVTEALRASFNNPDRAVEYL   76 (129)
Q Consensus        53 F~reqv~~ALras~~n~erAvE~L   76 (129)
                      |+|.-++.||+.++||..+|+++|
T Consensus        49 ~E~~~i~~aL~~~~gn~~~aA~~L   72 (89)
T d1etxa_          49 VEQPLLDMVMQYTRGNATRAALMM   72 (89)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHH
Confidence            889999999999999999999987