Citrus Sinensis ID: 046691

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220--
Protein Sequence
MDYDFRNRANSSYSLYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQGSGHSMGPPVSRTSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAEAEKENQNWSRLGMENIPSKNEPTSSVGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccEccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccccHHHHHHHccccHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mdydfrnranssyslygpppsassggsapshhpmygsslyprigqqgsghsmgppvsrtssynaspspsssssglgirvalkpeyritppptlspqvgdiprsnfhfdfDFERRVLAEAEKENQNwsrlgmenipskneptssvgsgsdpvVSRYIALGLNREAVHIAVAnygdnptkvrEFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA
Flexible Loop (DISEMBL)
MDYDFRNRANSSYSLYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQGSGHSMGPPVSRTSSYNaspspsssssglgIRVALKPEYRItppptlspqvgdipRSNFHFDFDFERRVLAEAEKEnqnwsrlgmenipskneptssvgsgsDPVVSRYIALGLNREAVHIAvanygdnptkVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA
Low Complexity Region (SEG)
MDYDFRNRANssyslygpppsassggsapshhpMYGSSLYPRIGQQGSGHSMGPPVsrtssynaspspsssssGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAEAEKENQNWSRLGMENIPSKNEPTssvgsgsdpvvsRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA
Disordered region (IsUnstruct)
*****************************************************************************************************RSNFHFDFDFERRVL**********************************VVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKAL********
Disordered Region (DISOPRED)
**YD*****************************************************************************************************HFDFDF***************************************VVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS**
Disordered Region (DISEMBL)
********ANSSYSLYG**************HPMYGSSLYPRIG*******************************GIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAEAEKENQNWSRLGMENIP*************DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA
Disordered Region (DISPRO)
************************************************************************SGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAEAEK*************************GSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLL****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDYDFRNRANSSYSLYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQGSGHSMGPPVSRTSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAEAEKENQNWSRLGMENIPSKNEPTSSVGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA
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

No hits with e-value below 0.001 by BLAST

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	222
255545086	222	conserved hypothetical protein [Ricinus	0.995	0.995	0.695	2e-80
225462713	221	PREDICTED: uncharacterized protein LOC10	0.981	0.986	0.644	1e-71
449456359	224	PREDICTED: uncharacterized protein LOC10	0.977	0.968	0.620	2e-65
224116834	223	predicted protein [Populus trichocarpa]	0.963	0.959	0.586	1e-63
297792703	221	hypothetical protein ARALYDRAFT_918411 [	0.959	0.963	0.604	1e-62
224120572	222	predicted protein [Populus trichocarpa]	0.981	0.981	0.613	3e-61
388509236	211	unknown [Lotus japonicus]	0.896	0.943	0.559	8e-60
18423499	221	Ubiquitin-associated/translation elongat	0.959	0.963	0.608	2e-58
14190455	221	AT5g53330/K19E1_13 [Arabidopsis thaliana	0.959	0.963	0.604	4e-58
357463783	203	hypothetical protein MTR_3g090640 [Medic	0.828	0.906	0.584	1e-55

>gi|255545086|ref|XP_002513604.1| conserved hypothetical protein [Ricinus communis] gi|223547512|gb|EEF49007.1| conserved hypothetical protein [Ricinus communis]

 Score =  303 bits (777), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 155/223 (69%), Positives = 180/223 (80%), Gaps = 2/223 (0%)

Query: 1   MDYDFRNRANSSYSLYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQGSGHSMGPPVSRTS 60
           MDYDFRNR   S      P   ++  S PS HPMYG SLYPRIGQQ  GH+  PPV R S
Sbjct: 1   MDYDFRNRTTGSSYDSQTPMYRTTSSSTPSGHPMYGQSLYPRIGQQ-QGHTPVPPVGRHS 59

Query: 61  SYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAEAE 120
           SY+ S +P  SSSGLGIRV++KPEYRITPPP L+PQ+GDIPRSNF F FD ERR+LAEAE
Sbjct: 60  SYHQSSAPPPSSSGLGIRVSVKPEYRITPPPQLAPQMGDIPRSNFQFHFDLERRILAEAE 119

Query: 121 KENQNWSRLGMENIPSK-NEPTSSVGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKV 179
           K+ QNWS+LG+EN+PSK  E TSS+GS +DPVVS+YIA GLNREAV +AVANYGDNPTKV
Sbjct: 120 KDIQNWSKLGLENLPSKTTESTSSLGSAADPVVSKYIASGLNREAVPLAVANYGDNPTKV 179

Query: 180 REFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA 222
           REF NG+++LREMGFS+NNVAE L+MY+NDTDKAL H L SS+
Sbjct: 180 REFVNGFSLLREMGFSANNVAEALLMYDNDTDKALTHFLNSSS 222

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225462713|ref|XP_002267522.1| PREDICTED: uncharacterized protein LOC100260370 [Vitis vinifera] gi|147771502|emb|CAN66995.1| hypothetical protein VITISV_019167 [Vitis vinifera]

 Score =  275 bits (702), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 145/225 (64%), Positives = 174/225 (77%), Gaps = 7/225 (3%)

Query: 1   MDYDFRNRANSSYSLYGP--PPSASSGGSAPSHHPMYGSSLYPRIGQQGSGHSMGPPVSR 58
           M YD+RNRAN  Y    P    + SS  SAP H  +YG+ +YPR+ Q   G    PP  R
Sbjct: 1   MSYDYRNRANQPYDSQIPMYKTTTSSSSSAPGHQ-LYGAPMYPRVSQPSFGAV--PPPGR 57

Query: 59  TSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAE 118
            SSY  + +PSSS  GLGIRV +KPE+RI+PPP LSPQVG+IPRS F FDFD E+++LAE
Sbjct: 58  ASSYQQTSAPSSSP-GLGIRVVIKPEFRISPPPQLSPQVGEIPRSTFQFDFDLEKKILAE 116

Query: 119 AEKENQNWSRLGMENIPSKN-EPTSSVGSGSDPVVSRYIALGLNREAVHIAVANYGDNPT 177
           AEK++QNWSRLG+EN+PSK  E T S+GS +DPVVS+YIA GL+REAV +AVANYGDN T
Sbjct: 117 AEKDSQNWSRLGLENLPSKALESTPSMGSTADPVVSKYIASGLSREAVPLAVANYGDNET 176

Query: 178 KVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA 222
           KVREF NGYT+LREMGFSS+NVAE L+MY+NDTDKALAH L SS+
Sbjct: 177 KVREFTNGYTLLREMGFSSSNVAEALVMYDNDTDKALAHFLNSSS 221

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456359|ref|XP_004145917.1| PREDICTED: uncharacterized protein LOC101219735 [Cucumis sativus] gi|449497294|ref|XP_004160364.1| PREDICTED: uncharacterized protein LOC101225916 [Cucumis sativus]

 Score =  254 bits (650), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 142/229 (62%), Positives = 168/229 (73%), Gaps = 12/229 (5%)

Query: 1   MDYDFRNRA---NSSYSLYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQGSGHSMGPPVS 57
           M YDFRN +   +S   +Y    S +S   +PS HPMY  S+YPRIGQQ    S  PPV+
Sbjct: 1   MAYDFRNNSGHYDSHQPMYT---STASSSPSPSPHPMYSHSMYPRIGQQAP--SSTPPVA 55

Query: 58  R---TSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERR 114
           R       ++     SSSSGLGIRV +KPEYRITPPP LSPQVGDIPRSNF FDF+FE++
Sbjct: 56  RLSSHHYSSSPSPSPSSSSGLGIRVTIKPEYRITPPPQLSPQVGDIPRSNFQFDFEFEKK 115

Query: 115 VLAEAEKENQNWSRLGMENIPSK-NEPTSSVGSGSDPVVSRYIALGLNREAVHIAVANYG 173
           VLAEAEKE  NW+R G+E+ P K  E TSS+GS  DPVVS+Y+A GLNREAV  AVANYG
Sbjct: 116 VLAEAEKEAPNWNRFGLEHPPPKPVESTSSMGSIGDPVVSKYVASGLNREAVSFAVANYG 175

Query: 174 DNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA 222
           DNPTKV+EF  GYT+LREMGFSS  V E L+MY+NDTDKA+AH LG ++
Sbjct: 176 DNPTKVQEFVKGYTLLREMGFSSIKVVEALLMYDNDTDKAVAHFLGGTS 224

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224116834|ref|XP_002331825.1| predicted protein [Populus trichocarpa] gi|222875063|gb|EEF12194.1| predicted protein [Populus trichocarpa]

 Score =  248 bits (634), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 135/230 (58%), Positives = 165/230 (71%), Gaps = 16/230 (6%)

Query: 1   MDYDFRNRANSSYSLYGPPPSASSGGSAPS-----HHPMYGS-SLYPRIGQQGSGHSMGP 54
           MDYDFRNR +S Y      PS     S PS      HPMYG  SLYP + Q   GH++ P
Sbjct: 1   MDYDFRNRTSSPYDT----PSTMHRSSTPSTAPQPSHPMYGPPSLYPTVNQ--PGHTVIP 54

Query: 55  PVSRTSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERR 114
              R  S+    +PSS SSGLGIRV +KPEYRITPPP L+PQ+ +IPRS+F FDF+ ER+
Sbjct: 55  HAPRHHSFTQQ-APSSPSSGLGIRVMIKPEYRITPPPQLTPQIVEIPRSSFQFDFELERQ 113

Query: 115 VLAEAEKENQNWSRL-GMENIPSKNEPT--SSVGSGSDPVVSRYIALGLNREAVHIAVAN 171
           +LAEAEK++ NWSRL G+EN P K  P   SS+  G  PVV +YI++GLNR+AV +AVAN
Sbjct: 114 ILAEAEKDSPNWSRLLGLENSPPKPPPILGSSLIVGKYPVVRKYISMGLNRDAVPLAVAN 173

Query: 172 YGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSS 221
           YGDNP KV+EF NGYT+L+EMGF SN VAE L+MY+N+TD+ALAH L SS
Sbjct: 174 YGDNPPKVQEFVNGYTLLQEMGFPSNKVAEALLMYDNNTDEALAHFLNSS 223

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297792703|ref|XP_002864236.1| hypothetical protein ARALYDRAFT_918411 [Arabidopsis lyrata subsp. lyrata] gi|297310071|gb|EFH40495.1| hypothetical protein ARALYDRAFT_918411 [Arabidopsis lyrata subsp. lyrata]

 Score =  245 bits (625), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 139/230 (60%), Positives = 169/230 (73%), Gaps = 17/230 (7%)

Query: 1   MDYDFRNRANSSYS--LYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQ-GSGHSMGPPVS 57
           MDYD+RN++  SY   +YG     S+  S  S+HPMYG   YP+IGQQ G G    PP  
Sbjct: 1   MDYDYRNKSGPSYPRPMYG---PPSTSPSPASNHPMYG---YPKIGQQTGHGQQFFPPPE 54

Query: 58  RTSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLA 117
           R SS+  + SPSS   GLGI+V LKPEYRITPPP L P+VGDI RS+F FDF  ER+VLA
Sbjct: 55  RNSSFQHNTSPSS---GLGIKVNLKPEYRITPPPQLLPRVGDIHRSSFQFDFGLERKVLA 111

Query: 118 EAEKENQNWSRLGMENIPSKN-EPTSSVGSGS----DPVVSRYIALGLNREAVHIAVANY 172
           EAEK+N +WS+ G +N P+K  EPTSS  +GS    DPVV +Y A GLN EAV+IAVANY
Sbjct: 112 EAEKDNPDWSKFGSDNPPAKFLEPTSSSVNGSFVGVDPVVMKYAASGLNPEAVNIAVANY 171

Query: 173 GDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA 222
           GDNPTKV+EFANG+T +REMGF +N+VA+ L M+ENDT+KALAHLL  S+
Sbjct: 172 GDNPTKVQEFANGFTAIREMGFPTNSVADALFMFENDTEKALAHLLHGSS 221

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224120572|ref|XP_002318363.1| predicted protein [Populus trichocarpa] gi|222859036|gb|EEE96583.1| predicted protein [Populus trichocarpa]

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 138/225 (61%), Positives = 166/225 (73%), Gaps = 7/225 (3%)

Query: 1   MDYDFRNRANSSYSLYGP--PPSASSGGSAPSHHPMYGSSLYPRIGQQGSGHSMGPPVSR 58
           M+YDFRNR +S Y    P    S     + P  HPMYG SLYPR+ Q    H   PPVSR
Sbjct: 1   MEYDFRNRTSSPYDTQSPMYRSSTPLTTAPPPTHPMYGPSLYPRVSQ--PAHPAIPPVSR 58

Query: 59  TSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAE 118
             S+    S SS SSGLGIRV +KPEYRITPPP L+PQ+G+IPRS+  FDF+ ER+++AE
Sbjct: 59  HHSFPQPSS-SSPSSGLGIRVMIKPEYRITPPPQLTPQIGEIPRSSVQFDFELERQIIAE 117

Query: 119 AEKENQNWSRL-GMENIPSKN-EPTSSVGSGSDPVVSRYIALGLNREAVHIAVANYGDNP 176
           AEK + NWSRL G+EN+PSK  E T S G  +DPV  +YIA GL+R+AV +AVANYGDNP
Sbjct: 118 AEKGSVNWSRLLGLENLPSKPLESTPSTGPTADPVERKYIASGLSRDAVPLAVANYGDNP 177

Query: 177 TKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSS 221
           TKV+EF NGYT+LREMGFSS++VAE L+ Y+ND DKALAH LGSS
Sbjct: 178 TKVQEFVNGYTLLREMGFSSSSVAEALLTYDNDADKALAHFLGSS 222

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388509236|gb|AFK42684.1| unknown [Lotus japonicus]

 Score =  235 bits (600), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 131/234 (55%), Positives = 159/234 (67%), Gaps = 35/234 (14%)

Query: 1   MDYDFRNRANSSYSLYGPPPSASSGGSAPSHHPMYGSS--------LYPRIGQQGSGHSM 52
           MDYDFR R               SG   P   PMY +         +YP+IG     H  
Sbjct: 1   MDYDFRTR---------------SGQQQP---PMYRAPPSSSSPSSIYPKIGP----HPP 38

Query: 53  GPPVSRTSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFE 112
           G  V R SSY+ +P+P SSS GLGIRVA+KP+YRITPPP L P V DIPRSNF FDF  E
Sbjct: 39  GAAVGRPSSYHQNPAPPSSS-GLGIRVAIKPDYRITPPPHLLPHVVDIPRSNFQFDFGLE 97

Query: 113 RRVLAEAEKENQNWSRLGMENIPSK----NEPTSSVGSGSDPVVSRYIALGLNREAVHIA 168
           R+VLAE EK+N NWS+ G+EN+P+K       +S   + SDP VS+YIA+GLNREAV IA
Sbjct: 98  RKVLAEGEKDNPNWSKFGLENLPTKVSDHTSSSSPKVTSSDPTVSKYIAMGLNREAVPIA 157

Query: 169 VANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA 222
           + +YGDNPTKV+EF NGYT+LREMGFSS++VAE L+M++NDTDKALAH L  S+
Sbjct: 158 IGHYGDNPTKVQEFVNGYTLLREMGFSSSSVAEALVMHDNDTDKALAHFLSGSS 211

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18423499|ref|NP_568790.1| Ubiquitin-associated/translation elongation factor EF1B protein [Arabidopsis thaliana] gi|21536760|gb|AAM61092.1| proline-rich cell wall protein-like [Arabidopsis thaliana] gi|332008957|gb|AED96340.1| Ubiquitin-associated/translation elongation factor EF1B protein [Arabidopsis thaliana]

 Score =  231 bits (589), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 140/230 (60%), Positives = 168/230 (73%), Gaps = 17/230 (7%)

Query: 1   MDYDFRNRANS-SYS--LYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQ-GSGHSMGPPV 56
           MDYD+RN++   SY   +YG     S+  S  S+HPMYG   YP+IGQQ G G     P 
Sbjct: 1   MDYDYRNKSGGPSYPRPMYG---PPSTSPSPSSNHPMYG---YPKIGQQTGPGPQFFSPP 54

Query: 57  SRTSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVL 116
            R SS+  + SPSS   G+GIRV LKPEYRITPPP L P+VGDI RS+F FDF  ER+VL
Sbjct: 55  ERNSSFQHNTSPSS---GIGIRVNLKPEYRITPPPQLLPRVGDIHRSSFQFDFGLERKVL 111

Query: 117 AEAEKENQNWSRLGMENIPSK-NEPT-SSVGS--GSDPVVSRYIALGLNREAVHIAVANY 172
           AEAEK+N +WS+ G EN P+K +EP+ SSVG   G D VV +Y A GLNREAV+IAVANY
Sbjct: 112 AEAEKDNPDWSKFGSENPPAKFHEPSPSSVGQMQGVDHVVMKYTASGLNREAVNIAVANY 171

Query: 173 GDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA 222
           GDNPTKV+EFANG+T +REMGF +N VA+ L M+ENDTDKALAHLL  S+
Sbjct: 172 GDNPTKVQEFANGFTAIREMGFPTNAVADALFMFENDTDKALAHLLHGSS 221

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|14190455|gb|AAK55708.1|AF380627_1 AT5g53330/K19E1_13 [Arabidopsis thaliana] gi|15809720|gb|AAL06788.1| AT5g53330/K19E1_13 [Arabidopsis thaliana]

 Score =  229 bits (585), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 139/230 (60%), Positives = 168/230 (73%), Gaps = 17/230 (7%)

Query: 1   MDYDFRNRANS-SYS--LYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQ-GSGHSMGPPV 56
           MDYD+RN++   SY   +YG     S+  S  S+HPMYG   YP+IGQQ G G     P 
Sbjct: 1   MDYDYRNKSGGPSYPRPMYG---PPSTSPSPSSNHPMYG---YPKIGQQTGPGPQFFSPP 54

Query: 57  SRTSSYNASPSPSSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVL 116
            R SS+  + SPSS   G+GIRV LKPEYRITPPP L P+VGDI RS+F FDF  ER+VL
Sbjct: 55  ERNSSFQHNTSPSS---GIGIRVNLKPEYRITPPPQLLPRVGDIHRSSFQFDFGLERKVL 111

Query: 117 AEAEKENQNWSRLGMENIPSK-NEPT-SSVGS--GSDPVVSRYIALGLNREAVHIAVANY 172
           AEAEK+N +WS+ G EN P+K +EP+ SSVG   G D VV +Y A GLNREAV+IAVANY
Sbjct: 112 AEAEKDNPDWSKFGSENPPAKFHEPSPSSVGQMQGVDHVVMKYTASGLNREAVNIAVANY 171

Query: 173 GDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSSA 222
           GDNPTKV+EFANG+T +REMGF +N VA+ L M++NDTDKALAHLL  S+
Sbjct: 172 GDNPTKVQEFANGFTAIREMGFPTNAVADALFMFDNDTDKALAHLLHGSS 221

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357463783|ref|XP_003602173.1| hypothetical protein MTR_3g090640 [Medicago truncatula] gi|355491221|gb|AES72424.1| hypothetical protein MTR_3g090640 [Medicago truncatula]

 Score =  222 bits (565), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 114/195 (58%), Positives = 145/195 (74%), Gaps = 11/195 (5%)

Query: 33  PMYGS--SLYPRIGQQGSGHSMGPPVSRTSSYNASPSPSSSSSGLGIRVALKPEYRITPP 90
           PMY +  S+YP+IG     HS  P        N +PSPS    GLGI+VA+KPEY+I PP
Sbjct: 15  PMYRAPPSIYPKIGPHP--HSAAPRPPPFQHQNPNPSPSI---GLGIKVAIKPEYKIAPP 69

Query: 91  PTLSPQVGDIPRSNFHFDFDFERRVLAEAEKENQNWSRLGMENIPSK---NEPTSSVGSG 147
           P L P VGDIPRSNF FDF  ER++LAEAEKEN NW++ G+EN+P+K   + P+S V + 
Sbjct: 70  PHLLPHVGDIPRSNFQFDFGLERKILAEAEKENPNWTKFGVENLPTKASDSSPSSKVTT- 128

Query: 148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207
           +DP+V++YIA+GL+R+ V IAV NYGDNPTKV+EF  GYT+L EMGFSSN+V E L+MY+
Sbjct: 129 ADPIVNKYIAMGLSRDVVPIAVKNYGDNPTKVQEFVKGYTLLHEMGFSSNSVDEALLMYD 188

Query: 208 NDTDKALAHLLGSSA 222
           NDTDKALA+ L  S+
Sbjct: 189 NDTDKALAYFLNGSS 203

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	222
TAIR|locus:2154237	221	AT5G53330 "AT5G53330" [Arabido	0.963	0.968	0.521	4e-51

TAIR|locus:2154237 AT5G53330 "AT5G53330" [Arabidopsis thaliana (taxid:3702)]

 Score = 531 (192.0 bits), Expect = 4.0e-51, P = 4.0e-51
 Identities = 119/228 (52%), Positives = 141/228 (61%)

Query:     1 MDYDFRNRANXXXXXXXXXXXXXXXXXXXXXXXMYGSSLYPRIGQQ-GSGHSM-GPPVXX 58
             MDYD+RN++                        MYG   YP+IGQQ G G     PP   
Sbjct:     1 MDYDYRNKSGGPSYPRPMYGPPSTSPSPSSNHPMYG---YPKIGQQTGPGPQFFSPP--- 54

Query:    59 XXXXXXXXXXXXXXXGLGIRVALKPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAE 118
                            G+GIRV LKPEYRITPPP L P+VGDI RS+F FDF  ER+VLAE
Sbjct:    55 -ERNSSFQHNTSPSSGIGIRVNLKPEYRITPPPQLLPRVGDIHRSSFQFDFGLERKVLAE 113

Query:   119 AEKENQNWSRLGMENIPSK-NEPTXXXXXXXXXXXX---RYIALGLNREAVHIAVANYGD 174
             AEK+N +WS+ G EN P+K +EP+               +Y A GLNREAV+IAVANYGD
Sbjct:   114 AEKDNPDWSKFGSENPPAKFHEPSPSSVGQMQGVDHVVMKYTASGLNREAVNIAVANYGD 173

Query:   175 NPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLL-GSS 221
             NPTKV+EFANG+T +REMGF +N VA+ L M+ENDTDKALAHLL GSS
Sbjct:   174 NPTKVQEFANGFTAIREMGFPTNAVADALFMFENDTDKALAHLLHGSS 221


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.317   0.135   0.400    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      222       170   0.00086  108 3  11 22  0.43    32
                                                     31  0.47    34


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  573 (61 KB)
  Total size of DFA:  150 KB (2091 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  15.17u 0.08s 15.25t   Elapsed:  00:00:02
  Total cpu time:  15.17u 0.08s 15.25t   Elapsed:  00:00:02
  Start:  Mon May 20 21:03:10 2013   End:  Mon May 20 21:03:12 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00006488001 SubName- Full=Putative uncharacterized protein (Chromosome undetermined scaffold_171, whole genome shotgun sequence); (221 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	222
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	98.55
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	98.52
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	98.47
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	97.6
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	97.58
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	97.49
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	97.48
KOG0944	763	consensus Ubiquitin-specific protease UBP14 [Postt	97.34
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	97.34
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	97.03
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	97.01
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	96.77
smart00546	43	CUE Domain that may be involved in binding ubiquit	96.65
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	95.87
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	95.64
PRK00117	157	recX recombination regulator RecX; Reviewed	94.22
PF09288	55	UBA_3: Fungal ubiquitin-associated domain ; InterP	91.06
PF08938	79	HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This	90.94
PF09288	55	UBA_3: Fungal ubiquitin-associated domain ; InterP	90.03
KOG0418	200	consensus Ubiquitin-protein ligase [Posttranslatio	86.62
COG5207	749	UBP14 Isopeptidase T [Posttranslational modificati	86.08
PRK14136	309	recX recombination regulator RecX; Provisional	84.69
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	84.47
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	83.08
PF02631	121	RecX: RecX family; InterPro: IPR003783 RecX is a p	83.0
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	82.94
PF07223	358	DUF1421: Protein of unknown function (DUF1421); In	82.2
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	82.14
PF06972	60	DUF1296: Protein of unknown function (DUF1296); In	82.13
PF09278	65	MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015	81.73
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	81.55
PRK14135	263	recX recombination regulator RecX; Provisional	81.52
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	80.3
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	80.25

>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=98.55  E-value=6.8e-08  Score=62.26  Aligned_cols=34  Identities=29%  Similarity=0.431  Sum_probs=30.4

Q ss_pred             HHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHH
Q 046691          184 NGYTILREMGFSSNNVAEVLIMYENDTDKALAHL  217 (222)
Q Consensus       184 ~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~L  217 (222)
                      ..+.+|++|||+.+.+.+||..|+||.|+|++.|
T Consensus         4 ~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    4 EKVQQLMEMGFSREQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence            4578999999999999999999999999999976

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=98.52  E-value=1.2e-07  Score=60.41  Aligned_cols=35  Identities=31%  Similarity=0.446  Sum_probs=32.5

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      .+++|.+|||+.+.+..||..|+||.++|++.|++
T Consensus         4 ~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~~   38 (38)
T cd00194           4 KLEQLLEMGFSREEARKALRATNNNVERAVEWLLE   38 (38)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            46899999999999999999999999999999874

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

>smart00165 UBA Ubiquitin associated domain

Probab=98.47  E-value=1.7e-07  Score=59.51  Aligned_cols=34  Identities=29%  Similarity=0.376  Sum_probs=31.8

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL  218 (222)
                      .+++|.+|||+.+.+..||.+|+||.++|++.|+
T Consensus         4 ~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L~   37 (37)
T smart00165        4 KIDQLLEMGFSREEALKALRAANGNVERAAEYLL   37 (37)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence            4689999999999999999999999999999885

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

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

Probab=97.60  E-value=0.00017  Score=67.52  Aligned_cols=42  Identities=29%  Similarity=0.440  Sum_probs=37.0

Q ss_pred             CCCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          144 VGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       144 ~~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      .+...+-.|.++++||+.||.|.+|++.==.||+.++|||..
T Consensus       131 ~G~~~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~  172 (340)
T KOG0011|consen  131 VGSEYEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLN  172 (340)
T ss_pred             ccchhHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhc
Confidence            556678899999999999999999999766799999999754

>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=97.58  E-value=0.00014  Score=46.77  Aligned_cols=35  Identities=17%  Similarity=0.359  Sum_probs=31.9

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFA  183 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl  183 (222)
                      +..|.+|++|||+++.+..||..-+.|.+++.+||
T Consensus         3 ~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    3 EEKVQQLMEMGFSREQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence            46799999999999999999999999999999986

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=97.49  E-value=0.00022  Score=45.22  Aligned_cols=36  Identities=17%  Similarity=0.332  Sum_probs=33.1

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      +..|.+|++|||++++|..||...+.|.+|+.+|+.
T Consensus         2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~   37 (38)
T cd00194           2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWLL   37 (38)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence            357899999999999999999999999999999974

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.

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

Probab=97.48  E-value=0.00011  Score=73.04  Aligned_cols=70  Identities=14%  Similarity=0.269  Sum_probs=62.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHH----------------------------HHHHHhcCCCCchHH
Q 046691          150 PVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANG----------------------------YTILREMGFSSNNVA  200 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~----------------------------~~~L~EMGFp~~~Va  200 (222)
                      -+|++|++|||+.++.++||-+.|. |.+-++.+|-.                            .+-|-||||..+...
T Consensus       560 s~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqHMdDPdlndP~~~~~~vPKkDkeVdE~~~~Slle~Gln~n~~R  639 (749)
T COG5207         560 SLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQHMDDPDLNDPFVPPPNVPKKDKEVDESKARSLLENGLNPNLCR  639 (749)
T ss_pred             HHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhhccCcccCCCCCCCCCCCcccccccHHHHHHHHHcCCCHHHHH
Confidence            3899999999999999999999998 77777777633                            678899999999999


Q ss_pred             HHHHhccCCHHHHHHHHhc
Q 046691          201 EVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       201 eAL~~~dND~DKAL~~LLs  219 (222)
                      +||+..+||.+++.+-+|+
T Consensus       640 kal~~~n~d~~r~V~w~~N  658 (749)
T COG5207         640 KALMDMNTDSKRRVVWCIN  658 (749)
T ss_pred             HHHHHccCCchheEEEEEe
Confidence            9999999999999887765

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

Probab=97.34  E-value=0.00037  Score=70.46  Aligned_cols=72  Identities=21%  Similarity=0.375  Sum_probs=61.5

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhH-HHHHHHH-----------------------------HHHHHhcCCCCch
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTK-VREFANG-----------------------------YTILREMGFSSNN  198 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~K-V~EFl~~-----------------------------~~~L~EMGFp~~~  198 (222)
                      .-+|.+|++|||+.+|..+||-..|.+..+ +.-++..                             ...+-+|||..+-
T Consensus       572 ~s~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl~~HMdDpd~~~p~vvp~~~~~a~~~~~~e~~v~si~smGf~~~q  651 (763)
T KOG0944|consen  572 RSVISQLVEMGFPEEACRRALYYTGNSGAEAASNWLMEHMDDPDIDDPFVVPGNSPKADAREVDEESVASIVSMGFSRNQ  651 (763)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHHHHhccCcccCCceecCCCCCccccCCCChhHheeeeeecCcHHH
Confidence            348999999999999999999999885444 4444433                             7788999999999


Q ss_pred             HHHHHHhccCCHHHHHHHHhcc
Q 046691          199 VAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       199 VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ...||...||+.++|.|-+++.
T Consensus       652 a~~aL~~~n~nveravDWif~h  673 (763)
T KOG0944|consen  652 AIKALKATNNNVERAVDWIFSH  673 (763)
T ss_pred             HHHHHHhcCccHHHHHHHHHhc
Confidence            9999999999999999988764

>smart00165 UBA Ubiquitin associated domain

Probab=97.34  E-value=0.00045  Score=43.69  Aligned_cols=35  Identities=17%  Similarity=0.366  Sum_probs=32.5

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFA  183 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl  183 (222)
                      +..|.++++|||+++.+..||..-+.|.+++.+|+
T Consensus         2 ~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L   36 (37)
T smart00165        2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYL   36 (37)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence            35789999999999999999999999999999987

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

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

Probab=97.03  E-value=0.0032  Score=61.87  Aligned_cols=73  Identities=23%  Similarity=0.323  Sum_probs=62.1

Q ss_pred             CcH-HHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH--------------------HHHHHhcCCCCchHHHHHHhc
Q 046691          148 SDP-VVSRYIALGLNREAVHIAVANYGDNPTKVREFANG--------------------YTILREMGFSSNNVAEVLIMY  206 (222)
Q Consensus       148 ~DP-~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~--------------------~~~L~EMGFp~~~VaeAL~~~  206 (222)
                      -|| -+..|++|||.+++|+.||+.--.|..|..+-++-                    +.+|--|||.....-.||-..
T Consensus       374 vn~rs~~rL~~mGyer~la~eaL~r~~Ndi~~aldllq~esdel~~n~~~~p~~vd~~~la~Lv~mGF~e~~A~~ALe~~  453 (568)
T KOG2561|consen  374 VNPRSLERLVSMGYERELAAEALRRNENDIQKALDLLQDESDELESNKPKRPEQVDGISLAELVSMGFEEGKARSALEAG  453 (568)
T ss_pred             cCHHHHHHHHhcchHhHHHHHHHHhccCcHHHHHHhcCCcchhhhccCCCCCcccchhhHHHHHHhccccchHHHHHHhc
Confidence            355 67789999999999999999765566666655432                    899999999999999999999


Q ss_pred             cCCHHHHHHHHhcc
Q 046691          207 ENDTDKALAHLLGS  220 (222)
Q Consensus       207 dND~DKAL~~LLs~  220 (222)
                      .|..|+|+..|+.+
T Consensus       454 gnn~~~a~~~L~~s  467 (568)
T KOG2561|consen  454 GNNEDTAQRLLSAS  467 (568)
T ss_pred             CCcHHHHHHHHHHh
Confidence            99999999999864

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

Probab=97.01  E-value=0.0017  Score=63.70  Aligned_cols=71  Identities=25%  Similarity=0.351  Sum_probs=60.1

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH--------------------------------------HHHH
Q 046691          148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG--------------------------------------YTIL  189 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~--------------------------------------~~~L  189 (222)
                      -|....-+++|||-..-+.+||..--.+-+.++.|+..                                      ++.|
T Consensus       303 ~d~~lsllv~mGfeesdaRlaLRsc~g~Vd~AvqfI~erre~laq~R~k~~a~Ere~~~r~k~~n~~~~~wvn~rs~~rL  382 (568)
T KOG2561|consen  303 NDETLSLLVGMGFEESDARLALRSCNGDVDSAVQFIIERREKLAQKREKDLAREREILERKKYGNTPMKKWVNPRSLERL  382 (568)
T ss_pred             cchHHHHHHHcCCCchHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCcccccCHHHHHHH
Confidence            46777888999999999999998555566666666543                                      7799


Q ss_pred             HhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691          190 REMGFSSNNVAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       190 ~EMGFp~~~VaeAL~~~dND~DKAL~~LL  218 (222)
                      .+|||....+++||...+||.++||+.|=
T Consensus       383 ~~mGyer~la~eaL~r~~Ndi~~aldllq  411 (568)
T KOG2561|consen  383 VSMGYERELAAEALRRNENDIQKALDLLQ  411 (568)
T ss_pred             HhcchHhHHHHHHHHhccCcHHHHHHhcC
Confidence            99999999999999999999999999874

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=96.77  E-value=0.0014  Score=61.62  Aligned_cols=44  Identities=20%  Similarity=0.394  Sum_probs=38.1

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCc
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSN  197 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~  197 (222)
                      ..+-+|..+++|||+|+.|.+||+.==.|+++++|||.       +|.|.+
T Consensus       155 ~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~-------tGIP~~  198 (378)
T TIGR00601       155 ERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLL-------TGIPED  198 (378)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHH-------hCCCcc
Confidence            34779999999999999999999977779999999986       578854

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

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

Probab=96.65  E-value=0.0032  Score=41.51  Aligned_cols=37  Identities=22%  Similarity=0.390  Sum_probs=31.6

Q ss_pred             HHHHHHHhcCCCC---chHHHHHHhccCCHHHHHHHHhccC
Q 046691          184 NGYTILREMGFSS---NNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       184 ~~~~~L~EMGFp~---~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      ....+|++| ||.   ..|..+|..|+||.|.|++.||..+
T Consensus         4 ~~v~~L~~m-FP~l~~~~I~~~L~~~~g~ve~~i~~LL~~~   43 (43)
T smart00546        4 EALHDLKDM-FPNLDEEVIKAVLEANNGNVEATINNLLEGS   43 (43)
T ss_pred             HHHHHHHHH-CCCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence            457889999 886   5778889999999999999999764

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)

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=95.87  E-value=0.01  Score=55.86  Aligned_cols=40  Identities=28%  Similarity=0.337  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ||....++|.||||+.+.|..||-..-|+.|+|+|.||++
T Consensus       155 ~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~tG  194 (378)
T TIGR00601       155 ERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTG  194 (378)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence            6777788999999999999999999999999999999986

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).

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

Probab=95.64  E-value=0.01  Score=39.08  Aligned_cols=35  Identities=26%  Similarity=0.346  Sum_probs=29.2

Q ss_pred             HHHHHhc--CCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          186 YTILREM--GFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       186 ~~~L~EM--GFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ..+|++|  .++.+.|..+|..|+||.|.|++.||..
T Consensus         5 v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~   41 (42)
T PF02845_consen    5 VQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM   41 (42)
T ss_dssp             HHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            4567777  5667889999999999999999999975

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.

>PRK00117 recX recombination regulator RecX; Reviewed

Probab=94.22  E-value=0.26  Score=39.63  Aligned_cols=70  Identities=19%  Similarity=0.287  Sum_probs=53.2

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHc---C--CChhHHHHHHHH-----------HHHHHhcCCCCchHHHHHHhccCCHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANY---G--DNPTKVREFANG-----------YTILREMGFSSNNVAEVLIMYENDTDK  212 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~y---G--dd~~KV~EFl~~-----------~~~L~EMGFp~~~VaeAL~~~dND~DK  212 (222)
                      -.+..||..+|++.+.+..+|+.+   |  +|..-+..|+..           -..|+.-||+.+.|.+||..++-|.+.
T Consensus        29 ~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g~~~I~~~L~~kGi~~~~I~~~l~~~~~d~~e  108 (157)
T PRK00117         29 AELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRARKGYGPRRIRQELRQKGVDREIIEEALAELDIDWEE  108 (157)
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCchHHHHHHHHHHcCCCHHHHHHHHHHcCccHHH
Confidence            457889999999999999999833   3  365666666544           467899999999999999988755555


Q ss_pred             HHHHHh
Q 046691          213 ALAHLL  218 (222)
Q Consensus       213 AL~~LL  218 (222)
                      ++..++
T Consensus       109 ~a~~~~  114 (157)
T PRK00117        109 LARELA  114 (157)
T ss_pred             HHHHHH
Confidence            544443

>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=91.06  E-value=0.23  Score=36.17  Aligned_cols=25  Identities=20%  Similarity=0.414  Sum_probs=14.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCC
Q 046691          150 PVVSRYIALGLNREAVHIAVANYGD  174 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~~yGd  174 (222)
                      .+|.++++|||++++|-.|++..|-
T Consensus        11 ~lVd~F~~mGF~~dkVvevlrrlgi   35 (55)
T PF09288_consen   11 DLVDQFENMGFERDKVVEVLRRLGI   35 (55)
T ss_dssp             HHHHHHHHHT--HHHHHHHHHHS--
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHhCC
Confidence            4667777777777777777776654

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

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

Probab=90.94  E-value=0.15  Score=37.94  Aligned_cols=27  Identities=33%  Similarity=0.393  Sum_probs=23.3

Q ss_pred             CCchHHHHHHhccCCHHHHHHHHhccC
Q 046691          195 SSNNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       195 p~~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      +...|.+||..|+.|++|||+.||+..
T Consensus        45 ~e~~i~eal~~~~fDvekAl~~Ll~~~   71 (79)
T PF08938_consen   45 PEEQIKEALWHYYFDVEKALDYLLSKF   71 (79)
T ss_dssp             -CCHHHHHHHHTTT-CCHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHcCCHHHHHHHHHHhc
Confidence            889999999999999999999999763

; PDB: 1UFZ_A 3IZQ_1.

>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=90.03  E-value=0.33  Score=35.37  Aligned_cols=32  Identities=34%  Similarity=0.485  Sum_probs=20.1

Q ss_pred             HHHHhcCCCCchHHHHHHhccCC---------HHHHHHHHh
Q 046691          187 TILREMGFSSNNVAEVLIMYEND---------TDKALAHLL  218 (222)
Q Consensus       187 ~~L~EMGFp~~~VaeAL~~~dND---------~DKAL~~LL  218 (222)
                      .+|..|||+.++|-+||-.-+-+         .++.|+.||
T Consensus        14 d~F~~mGF~~dkVvevlrrlgik~~n~~dn~t~~~ilEELL   54 (55)
T PF09288_consen   14 DQFENMGFERDKVVEVLRRLGIKSMNGVDNETENKILEELL   54 (55)
T ss_dssp             HHHHHHT--HHHHHHHHHHS--SS--SS--HHHHHHHHHHT
T ss_pred             HHHHHcCCcHHHHHHHHHHhCCCCCCCccchhHHHHHHHHh
Confidence            46778999999999999754322         345666665

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

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

Probab=86.62  E-value=0.73  Score=41.03  Aligned_cols=40  Identities=28%  Similarity=0.160  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+-+....|.+|||..+.+-.+|-..+-+..+|++.||++
T Consensus       161 ~~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~~~~s~  200 (200)
T KOG0418|consen  161 WDKKKVDSLIEMGFSELEAILVLSGSDWNLADATEQLLSG  200 (200)
T ss_pred             hhHHHHHHHHHhcccHHHHHHHhhccccchhhhhHhhccC
Confidence            3444457789999999999999999999999999999874

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

Probab=86.08  E-value=0.79  Score=46.53  Aligned_cols=36  Identities=28%  Similarity=0.410  Sum_probs=30.4

Q ss_pred             HHHHHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHh
Q 046691          183 ANGYTILREMGFSSNNVAEVLIMYEN-DTDKALAHLL  218 (222)
Q Consensus       183 l~~~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LL  218 (222)
                      -.+..||.+||||+...+.||....| |.|-|..-|.
T Consensus       559 qs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLF  595 (749)
T COG5207         559 QSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLF  595 (749)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHH
Confidence            45689999999999999999999988 7777766554

>PRK14136 recX recombination regulator RecX; Provisional

Probab=84.69  E-value=3.8  Score=38.55  Aligned_cols=68  Identities=9%  Similarity=0.102  Sum_probs=51.0

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHH-----HcCCChhHHHHHHHH----------HHHHHhcCCCCchHHHHHHhccCCH-H
Q 046691          148 SDPVVSRYIALGLNREAVHIAVA-----NYGDNPTKVREFANG----------YTILREMGFSSNNVAEVLIMYENDT-D  211 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~-----~yGdd~~KV~EFl~~----------~~~L~EMGFp~~~VaeAL~~~dND~-D  211 (222)
                      .-.+..||..+||+.+.|..+|+     +|-+|..=+..|+..          -..|+.-|...+.|.+||...+.|. +
T Consensus       179 e~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~~kkGp~rIrqELrQKGId~eLIEqALeeieEDE~E  258 (309)
T PRK14136        179 RAELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRASRVGSARIVSELKRHAVGDALVESVGAQLRETEFE  258 (309)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhchhHHHHHHHHHHcCCCHHHHHHHHHhccHhHHH
Confidence            34588899999999999999987     445566666666544          5678899999999999999776444 4


Q ss_pred             HHHH
Q 046691          212 KALA  215 (222)
Q Consensus       212 KAL~  215 (222)
                      .|++
T Consensus       259 ~A~~  262 (309)
T PRK14136        259 RAQA  262 (309)
T ss_pred             HHHH
Confidence            4433

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

Probab=84.47  E-value=1.1  Score=42.65  Aligned_cols=39  Identities=23%  Similarity=0.390  Sum_probs=34.9

Q ss_pred             HHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          182 FANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       182 Fl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +=....++.+||+..+.|--||-..=|+.|+|++.||++
T Consensus       135 ~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~G  173 (340)
T KOG0011|consen  135 YEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLNG  173 (340)
T ss_pred             hHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhcC
Confidence            334567899999999999999999999999999999986

>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=83.08  E-value=2.6  Score=27.88  Aligned_cols=38  Identities=16%  Similarity=0.264  Sum_probs=27.9

Q ss_pred             hHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          177 TKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       177 ~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +||.+|+.    +.  |-..+.....|-+||+|.++||+.++..
T Consensus         2 e~i~~F~~----iT--g~~~~~A~~~L~~~~wdle~Av~~y~~~   39 (43)
T PF14555_consen    2 EKIAQFMS----IT--GADEDVAIQYLEANNWDLEAAVNAYFDD   39 (43)
T ss_dssp             HHHHHHHH----HH---SSHHHHHHHHHHTTT-HHHHHHHHHHS
T ss_pred             HHHHHHHH----HH--CcCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            46666653    33  5677888888999999999999998764

>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []

Probab=83.00  E-value=4.4  Score=31.32  Aligned_cols=50  Identities=16%  Similarity=0.286  Sum_probs=35.0

Q ss_pred             HHHcCCCHHHHHHHHH---HcCC--ChhHHHHHHHH------------HHHHHhcCCCCchHHHHHH
Q 046691          155 YIALGLNREAVHIAVA---NYGD--NPTKVREFANG------------YTILREMGFSSNNVAEVLI  204 (222)
Q Consensus       155 y~amG~~reaV~~Av~---~yGd--d~~KV~EFl~~------------~~~L~EMGFp~~~VaeAL~  204 (222)
                      |..+||+.+.|..+|+   .+|-  |..=+..|+..            -..|+.-|.+.+.|.+||.
T Consensus         1 L~~kg~~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~   67 (121)
T PF02631_consen    1 LKRKGFSEEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALE   67 (121)
T ss_dssp             HHHTT--HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHT
T ss_pred             CcccCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHH
Confidence            4578999998888887   3343  66666667665            4579999999999999998

The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.

>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=82.94  E-value=2.6  Score=32.14  Aligned_cols=55  Identities=20%  Similarity=0.156  Sum_probs=39.1

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691          150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE  207 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d  207 (222)
                      .+++.|-..|+=.-+-   ..+|=.=.++.++.+.....|+++||+.++|++.|...+
T Consensus        15 ~tlRyYe~~GLl~p~~---~~g~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~   69 (107)
T cd04777          15 DTVRHYIDLGLLIPEK---KGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKR   69 (107)
T ss_pred             HHHHHHHHCCCcCCcc---CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcc
Confidence            4889999999832221   112112233555999999999999999999999886643

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>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=82.20  E-value=1.1  Score=42.52  Aligned_cols=25  Identities=24%  Similarity=0.464  Sum_probs=21.2

Q ss_pred             CCCcHHHHHHHHcCCCHHHHHHHHH
Q 046691          146 SGSDPVVSRYIALGLNREAVHIAVA  170 (222)
Q Consensus       146 ~~~DP~V~ky~amG~~reaV~~Av~  170 (222)
                      .+-|.+|+|++.|||.||.|.--|+
T Consensus       319 ~p~ddvidKv~~MGf~rDqV~a~v~  343 (358)
T PF07223_consen  319 HPYDDVIDKVASMGFRRDQVRATVR  343 (358)
T ss_pred             CcHHHHHHHHHHcCCcHHHHHHHHH
Confidence            3469999999999999999965555

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

Probab=82.14  E-value=1.9  Score=42.87  Aligned_cols=44  Identities=25%  Similarity=0.369  Sum_probs=37.2

Q ss_pred             hHHHHHHHHHHHHHhcCCCCc-hHHHHHHhccCCHHHHHHHHhcc
Q 046691          177 TKVREFANGYTILREMGFSSN-NVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       177 ~KV~EFl~~~~~L~EMGFp~~-~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .-=.+|-..|+||.+|||--. .--+||+.-..|..+|++.||..
T Consensus       449 ~pe~r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverll~s  493 (493)
T KOG0010|consen  449 PPEERYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERLLGS  493 (493)
T ss_pred             CchHHHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhcC
Confidence            344689999999999999754 45689999999999999999863

>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=82.13  E-value=3.1  Score=30.95  Aligned_cols=38  Identities=16%  Similarity=0.185  Sum_probs=30.4

Q ss_pred             HHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          182 FANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       182 Fl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      -++.+.....- ++..+|-.+|..|+.|.+.|.+-||+-
T Consensus         8 ~VQ~iKEiv~~-hse~eIya~L~ecnMDpnea~qrLL~q   45 (60)
T PF06972_consen    8 TVQSIKEIVGC-HSEEEIYAMLKECNMDPNEAVQRLLSQ   45 (60)
T ss_pred             HHHHHHHHhcC-CCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence            34444444444 789999999999999999999999973

>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR

Probab=81.73  E-value=2.4  Score=29.13  Aligned_cols=34  Identities=35%  Similarity=0.485  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHH
Q 046691          181 EFANGYTILREMGFSSNNVAEVLIMYENDTDKALA  215 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~  215 (222)
                      +=+.....+++.||+.++|++.|...++ .+...+
T Consensus         2 ~rL~~I~~~r~lGfsL~eI~~~l~l~~~-~~~~~~   35 (65)
T PF09278_consen    2 ERLQFIRRLRELGFSLEEIRELLELYDQ-GDPPCA   35 (65)
T ss_dssp             HHHHHHHHHHHTT--HHHHHHHHHHCCS-HCHHHH
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHhccCC-CCCCHH
Confidence            3456677889999999999999987776 444433

They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....

>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator

Probab=81.55  E-value=2.8  Score=32.94  Aligned_cols=58  Identities=21%  Similarity=0.271  Sum_probs=39.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691          150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN  208 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN  208 (222)
                      .+++.|-..|+=.... +--.+|-.=.....+.+.....|+++||+.+.|++.|-.+++
T Consensus        15 ~tlR~Ye~~GLl~~~~-r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~   72 (126)
T cd04783          15 ETIRYYQRRGLLPEPP-RPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDG   72 (126)
T ss_pred             HHHHHHHHCCCCCCCC-cCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccC
Confidence            3677888888743111 111122224556677788888999999999999999887765

Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK14135 recX recombination regulator RecX; Provisional

Probab=81.52  E-value=6.6  Score=34.07  Aligned_cols=60  Identities=12%  Similarity=0.133  Sum_probs=46.9

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHH---cCC--ChhHHHHHHHH------------HHHHHhcCCCCchHHHHHHhccC
Q 046691          149 DPVVSRYIALGLNREAVHIAVAN---YGD--NPTKVREFANG------------YTILREMGFSSNNVAEVLIMYEN  208 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~---yGd--d~~KV~EFl~~------------~~~L~EMGFp~~~VaeAL~~~dN  208 (222)
                      -.+..||...|++.+.+..+|+.   +|-  |..-+..|+..            -..|+..||+.+.|.+||..++.
T Consensus        75 ~el~~kL~~kg~~~~~Ie~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~~g~~~I~~kL~~kGi~~~~Ie~~l~~l~~  151 (263)
T PRK14135         75 KEVRDYLKKHEISEEIISEVIDKLKEEKYIDDKEYAESYVRTNINTGDKGPRVIKQKLLQKGIEDEIIEEALSEYTE  151 (263)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccccchHHHHHHHHHcCCCHHHHHHHHHhCCh
Confidence            56888999999999999999983   343  55555555543            45688999999999999998754

>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators

Probab=80.30  E-value=3.7  Score=32.25  Aligned_cols=58  Identities=16%  Similarity=0.138  Sum_probs=40.4

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691          150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN  208 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN  208 (222)
                      .+++.|-++|+=....- .--.|-.=..+..+.+.....|+++||+.+.|++.|-.+++
T Consensus        15 ~tLRyYe~~GLl~p~~r-~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~   72 (127)
T cd04784          15 ETIRYYEKEGLLPAPAR-SANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDD   72 (127)
T ss_pred             HHHHHHHHCCCCCCCCc-CCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhc
Confidence            46788888887432111 11123335567788888899999999999999998876543

Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=80.25  E-value=3.7  Score=32.43  Aligned_cols=66  Identities=17%  Similarity=0.192  Sum_probs=42.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC-CHHHHHHH
Q 046691          150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN-DTDKALAH  216 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~  216 (222)
                      .+++.|-.+|+=.... +.--.|-.=..+..+.+.....|+++||+.+.|++.|-..+. +.+..++.
T Consensus        14 ~tlR~Ye~~GLl~~~~-r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~~~~~~~   80 (124)
T TIGR02051        14 ETIRYYERKGLLPEPD-RPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLVDGTHCREMYEL   80 (124)
T ss_pred             HHHHHHHHCCCCCCCc-cCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhcccCCCHHHHHHH
Confidence            3677888888743221 111122223456777788889999999999999998876654 23444443

This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	222
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	4e-13
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	5e-13
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	4e-04

>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 = 62.7 bits (152), Expect = 4e-13
 Identities = 18/76 (23%), Positives = 32/76 (42%)

Query: 142 SSVGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAE 201
           S +       V   + +G + E V  A+   G N  ++ ++   +  L E GF    V E
Sbjct: 2   SHMSPSERQCVETVVNMGYSYECVLRAMKAAGANIEQILDYLFAHGQLCEKGFDPLLVEE 61

Query: 202 VLIMYENDTDKALAHL 217
            L M++   +K +  L
Sbjct: 62  ALEMHQCSEEKMMEFL 77

>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 = 62.3 bits (151), Expect = 5e-13
 Identities = 19/71 (26%), Positives = 34/71 (47%)

Query: 152 VSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTD 211
             +    G +   V  A+  +  +  K+ EF    +  +EMGF   ++ EVL+++ ND D
Sbjct: 46  HGQLCEKGFDPLLVEEALEMHQCSEEKMMEFLQLMSKFKEMGFELKDIKEVLLLHNNDQD 105

Query: 212 KALAHLLGSSA 222
            AL  L+  + 
Sbjct: 106 NALEDLMARAG 116

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 40.1 bits (93), Expect = 4e-04
 Identities = 12/86 (13%), Positives = 26/86 (30%)

Query: 10  NSSYSLYGPPPSASSGGSAPSHHPMYGSSLYPRIGQQGSGHSMGPPVSRTSSYNASPSPS 69
           ++  +     P+     +APS HP  G  +           ++  P++      +  S  
Sbjct: 17  STQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSP 76

Query: 70  SSSSGLGIRVALKPEYRITPPPTLSP 95
                + +       +    P   SP
Sbjct: 77  MGPHSMSVPTTPTLGFSTGSPQLSSP 102

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	222
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	99.71
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	99.19
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	98.67
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	98.52
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	98.52
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	98.49
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	98.49
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	98.38
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	98.35
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	98.33
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	98.32
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	98.24
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	98.2
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	98.18
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	98.16
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	98.14
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	98.12
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	98.1
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	98.09
2dna_A	67	Unnamed protein product; ubiquitin associated doma	98.08
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	98.06
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	98.04
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	97.98
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	97.98
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	97.98
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	97.96
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	97.94
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	97.9
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	97.84
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	97.8
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	97.8
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	97.78
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	97.75
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	97.71
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	97.7
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	97.69
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	97.66
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	97.62
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	97.57
3ihp_A	854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	97.56
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	97.55
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	97.5
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	97.44
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	97.44
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	97.43
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	97.41
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	97.38
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	97.38
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	97.3
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	97.29
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	97.28
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	97.28
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	97.23
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	97.19
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	97.19
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	97.18
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	97.06
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	97.06
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	97.03
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	97.01
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	97.01
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	96.98
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	96.94
2dhy_A	67	CUE domain-containing protein 1; structural genomi	96.8
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	96.7
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	96.69
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	96.53
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	96.32
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	96.29
2cos_A	54	Serine/threonine protein kinase LATS2; UBA domain,	96.09
2pwq_A	216	Ubiquitin conjugating enzyme; structural genomics	95.93
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	95.86
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	95.8
2cos_A	54	Serine/threonine protein kinase LATS2; UBA domain,	95.62
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	95.4
2dna_A	67	Unnamed protein product; ubiquitin associated doma	95.23
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	94.67
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	94.49
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	94.4
1tte_A	215	Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiq	94.39
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	94.27
4dbg_B	162	Ring finger protein 31; ubiquitin fold, ubiquitina	94.25
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	94.21
1q02_A	52	Sequestosome 1; helical bundle, protein binding; N	93.85
3dfg_A	162	Xcrecx, regulatory protein RECX; RECX RECA, homolo	93.46
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	93.13
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	90.82
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	90.79
4fp9_B	335	Mterf domain-containing protein 2; modification en	90.25
1p3q_Q	54	VPS9P, vacuolar protein sorting-associated protein	88.2
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	86.47
3mva_O	343	Transcription termination factor, mitochondrial; a	86.2
4dbg_B	162	Ring finger protein 31; ubiquitin fold, ubiquitina	86.15
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	85.47
1q08_A	99	Zn(II)-responsive regulator of ZNTA; MERR family t	84.75
1tte_A	215	Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiq	84.66
3mva_O	343	Transcription termination factor, mitochondrial; a	84.65
4fp9_B	335	Mterf domain-containing protein 2; modification en	84.49
3c1d_A	159	Protein ORAA, regulatory protein RECX; tandem repe	83.71
2pwq_A	216	Ubiquitin conjugating enzyme; structural genomics	83.38
3d5l_A	221	Regulatory protein RECX; PSI-II, NYSGXRC, DNA repa	83.15
1b0n_B	57	Protein (SINI protein); transcription regulator, a	82.1

>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=99.71  E-value=9.9e-18  Score=132.40  Aligned_cols=75  Identities=27%  Similarity=0.466  Sum_probs=68.8

Q ss_pred             CCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH----------------------------------HHHHHh
Q 046691          146 SGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG----------------------------------YTILRE  191 (222)
Q Consensus       146 ~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~----------------------------------~~~L~E  191 (222)
                      ..+-.+|.+|++|||++++|.+||...|.|.+|++|||..                                  +++|.|
T Consensus         6 ~~e~~~v~~l~~MGFp~~~~~kAl~~~g~~~e~amewL~~h~~L~d~~~d~~~~e~~l~~~~~~~~~~~~~~~~v~~L~e   85 (118)
T 4ae4_A            6 PSERQCVETVVNMGYSYECVLRAMKAAGANIEQILDYLFAHGQLCEKGFDPLLVEEALEMHQCSEEKMMEFLQLMSKFKE   85 (118)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHCSSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHCcCHHHHHHHHHHhchhcccCCChhhhHHHHHhccCCccccccCHHHHHHHHH
Confidence            3455689999999999999999999999999999988754                                  789999


Q ss_pred             cCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          192 MGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       192 MGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      |||+.+.|++||..|+||.|||+|.|++.
T Consensus        86 MGF~~~~a~~AL~~~~nd~erAlewL~~~  114 (118)
T 4ae4_A           86 MGFELKDIKEVLLLHNNDQDNALEDLMAR  114 (118)
T ss_dssp             TTCCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence            99999999999999999999999999975

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

Probab=99.19  E-value=5.7e-11  Score=92.61  Aligned_cols=74  Identities=22%  Similarity=0.292  Sum_probs=66.3

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHH----------------------------------------
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANG----------------------------------------  185 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~----------------------------------------  185 (222)
                      +.+..|.+|++|||+++++.+||..-|. |.+.+.+||..                                        
T Consensus         2 ~d~~~l~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~wL~~~~~d~di~epl~~~~~~s~~~~~~~~l~~~~~~~~~~e~~   81 (126)
T 2lbc_A            2 IDESSVMQLAEMGFPLEACRKAVYFTGNMGAEVAFNWIIVHMEEPDFAEPLTMPGYGGAASAGASVFGASGLDNQPPEEI   81 (126)
T ss_dssp             CCTHHHHHHHTTSSCCHHHHHHHHHHTSCCHHHHHHHHHHGGGCSSSSCTTCCSSCCSSSSSCCCCSTTSSCCCCCCHHH
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHcCCCCHHHHHHHHHHhcccccccccccccccccccccchhhhcccccccCcCHHH
Confidence            3456899999999999999999998877 88888888722                                        


Q ss_pred             HHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          186 YTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +.+|.+|||+.+.+..||..++||.++|++.|++.
T Consensus        82 v~~L~~MGF~~~~a~~AL~~~~~~~e~A~e~L~~~  116 (126)
T 2lbc_A           82 VAIITSMGFQRNQAIQALRATNNNLERALDWIFSH  116 (126)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             HHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            57899999999999999999999999999999975

>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=98.67  E-value=1.5e-08  Score=92.36  Aligned_cols=39  Identities=26%  Similarity=0.468  Sum_probs=35.2

Q ss_pred             CCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHH
Q 046691          145 GSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFA  183 (222)
Q Consensus       145 ~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl  183 (222)
                      +...+..|.+|++|||+|+.|.+||..-+.|+++++|||
T Consensus       165 g~~~~~~i~~l~~MGf~~~~~~~AL~a~~nn~~~A~e~L  203 (368)
T 1oqy_A          165 GSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYL  203 (368)
T ss_dssp             TTTHHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTT
T ss_pred             CcchHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            344577999999999999999999999999999999998

>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=98.52  E-value=6.6e-08  Score=65.47  Aligned_cols=40  Identities=25%  Similarity=0.355  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ++-..+.+|.+|||+.+.+..||-.|+||.|+|++.|+++
T Consensus         7 ~~~~~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~e~L~~g   46 (49)
T 1ify_A            7 EYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTG   46 (49)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHTTTSCSHHHHHHHHHC
T ss_pred             cCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            3555678999999999999999999999999999999875

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

Probab=98.52  E-value=7.8e-08  Score=66.07  Aligned_cols=41  Identities=32%  Similarity=0.477  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHhcCC-CCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          180 REFANGYTILREMGF-SSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       180 ~EFl~~~~~L~EMGF-p~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+|-..+.+|++||| ..+.+..||..++||.++|++.|++.
T Consensus         9 ~~~~~~l~~L~~MGF~~~~~~~~AL~~t~gnve~Ave~L~~~   50 (53)
T 2knz_A            9 VRFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLLGS   50 (53)
T ss_dssp             HHHHHHHHHHHTTTCCCHHHHHHHHHHHTSCHHHHHHHHHHC
T ss_pred             hHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHc
Confidence            467788999999999 99999999999999999999999975

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

Probab=98.49  E-value=7.2e-08  Score=66.12  Aligned_cols=40  Identities=33%  Similarity=0.499  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHhcCC-CCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGF-SSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGF-p~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +|-..+.+|.+||| ..+.+..||..++||.++|++.|++.
T Consensus        11 ~~~~~l~~L~~MGF~~~~~~~~AL~~t~gn~e~A~e~L~~~   51 (52)
T 2jy5_A           11 RFQQQLEQLSAMGFLNREANLQALIATGGDINAAIERLLGS   51 (52)
T ss_dssp             TTHHHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            45667899999999 88999999999999999999999975

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

Probab=98.49  E-value=8.6e-08  Score=62.53  Aligned_cols=36  Identities=28%  Similarity=0.323  Sum_probs=33.4

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+.+|.+|||+.+.+..||-.|+||.|+|++.|+++
T Consensus         7 ~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~L~~~   42 (43)
T 2g3q_A            7 AVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDS   42 (43)
T ss_dssp             HHHHHHTTTSCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhCcCHHHHHHHHHcC
Confidence            468999999999999999999999999999999875

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

Probab=98.38  E-value=2.2e-07  Score=58.78  Aligned_cols=37  Identities=30%  Similarity=0.343  Sum_probs=33.2

Q ss_pred             HHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691          182 FANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       182 Fl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL  218 (222)
                      +-....+|.+|||+.+.+..||-.|+||.++|++.|+
T Consensus         4 ~~~~i~~L~~mGf~~~~a~~AL~~~~~n~e~A~~~L~   40 (40)
T 1z96_A            4 LNSKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL   40 (40)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHC
Confidence            3446789999999999999999999999999999885

>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=98.35  E-value=1.6e-07  Score=69.10  Aligned_cols=34  Identities=26%  Similarity=0.366  Sum_probs=20.2

Q ss_pred             HHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          187 TILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       187 ~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ++|.+|||+.+.|..||-+|+||.|+|++.|++.
T Consensus        34 ~~L~eMGF~r~~a~~AL~~~~~nve~Ave~Ll~~   67 (73)
T 1vg5_A           34 QKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQ   67 (73)
T ss_dssp             HHHHTTTCCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             HHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHC
Confidence            4555555555555555566666666666666653

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

Probab=98.33  E-value=4.2e-07  Score=61.18  Aligned_cols=41  Identities=22%  Similarity=0.297  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHhcCCC-CchHHHHHHhccCCHHHHHHHHhcc
Q 046691          180 REFANGYTILREMGFS-SNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       180 ~EFl~~~~~L~EMGFp-~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ..|-..+.+|++|||. .+.+..||..++||.++|++.|+++
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            3566778999999996 5568999999999999999999874

>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=98.32  E-value=3.2e-07  Score=65.39  Aligned_cols=36  Identities=33%  Similarity=0.437  Sum_probs=30.2

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+.+|.+|||+.+.+..||..|+||.|+|++.|++.
T Consensus        12 ~I~~L~~MGF~~~~a~~AL~~~~~nve~A~e~L~~~   47 (63)
T 1wji_A           12 ALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTS   47 (63)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHC
Confidence            356888888888888888888888899998888864

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

Probab=98.24  E-value=7.4e-07  Score=62.93  Aligned_cols=42  Identities=21%  Similarity=0.294  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHhcCCC-CchHHHHHHhccCCHHHHHHHHhccC
Q 046691          180 REFANGYTILREMGFS-SNNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       180 ~EFl~~~~~L~EMGFp-~~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      ..|-..+.+|++|||. .+.+..||..++||.++|++.|+++.
T Consensus        15 ~~~~~qi~~L~~MGF~d~~~~~~AL~~~~gnve~Ave~L~~~~   57 (58)
T 1wr1_B           15 ERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNGD   57 (58)
T ss_dssp             HHTHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence            5677789999999996 66789999999999999999999864

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

Probab=98.20  E-value=7.3e-07  Score=62.75  Aligned_cols=36  Identities=11%  Similarity=0.326  Sum_probs=18.7

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHH
Q 046691          148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFA  183 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl  183 (222)
                      .+..|.+|++|||+++++..||...+.|.+++.|||
T Consensus         9 ~~~~v~~L~~MGF~~~~a~~AL~~t~~nve~A~e~L   44 (63)
T 2dak_A            9 PEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWI   44 (63)
T ss_dssp             CHHHHHHHHHHTCCHHHHHHHHHHTTSCSHHHHHHH
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            344555555555555555555554444555555554

>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=98.18  E-value=1.1e-06  Score=62.59  Aligned_cols=35  Identities=20%  Similarity=0.301  Sum_probs=24.8

Q ss_pred             HHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhcc
Q 046691          186 YTILREMGFSSNNVAEVLIMYEN-DTDKALAHLLGS  220 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs~  220 (222)
                      +.+|.+|||+.+.+..||..|+| |.|+|++.|++.
T Consensus        23 i~~L~~MGF~~~~a~~AL~~t~~~nve~A~ewL~~~   58 (64)
T 2cpw_A           23 LDVLLSMGFPRARAQKALASTGGRSVQTACDWLFSH   58 (64)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTTTSCHHHHHHHHHSC
T ss_pred             HHHHHHcCCCHHHHHHHHHHcCCCCHHHHHHHHHhC
Confidence            45667777777777777777776 777777777754

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

Probab=98.16  E-value=7.8e-07  Score=61.74  Aligned_cols=40  Identities=33%  Similarity=0.400  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHhcCCCCc-hHHHHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGFSSN-NVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~-~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +|-..+.+|++|||... .+..||..+++|.++|++.|++.
T Consensus         8 ~~~~~l~~L~~MGF~d~~~n~~AL~~~~Gdv~~Ave~L~~~   48 (54)
T 2dah_A            8 HFQVQLEQLRSMGFLNREANLQALIATGGDVDAAVEKLRQS   48 (54)
T ss_dssp             SSHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            45567899999999775 47999999999999999999964

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

Probab=98.14  E-value=1.1e-06  Score=64.98  Aligned_cols=39  Identities=23%  Similarity=0.493  Sum_probs=33.0

Q ss_pred             HHHHHHHHHhcCCC-CchHHHHHHhccCCHHHHHHHHhcc
Q 046691          182 FANGYTILREMGFS-SNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       182 Fl~~~~~L~EMGFp-~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      |-..+.+|++|||. .+.+..||..++||.++|++.|++.
T Consensus        29 ye~qi~qL~eMGF~dr~~~~~AL~~t~Gnve~Ave~L~~~   68 (74)
T 1vej_A           29 YQQELEELKALGFANRDANLQALVATDGDIHAAIEMLLGA   68 (74)
T ss_dssp             SHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            44467899999994 6788999999999999999999875

>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=98.12  E-value=1.7e-06  Score=63.05  Aligned_cols=35  Identities=20%  Similarity=0.302  Sum_probs=29.4

Q ss_pred             HHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          186 YTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +++|.+|||+.+.+..||..|+||.++|++.|++.
T Consensus        33 v~~L~~MGF~~~~a~~AL~~t~~nve~Ave~L~~~   67 (73)
T 1wiv_A           33 VDTLLSFGFAEDVARKALKASGGDIEKATDWVFNN   67 (73)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHHS
T ss_pred             HHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            46788888888888888888888888888888875

>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=98.10  E-value=1.5e-06  Score=61.99  Aligned_cols=34  Identities=26%  Similarity=0.326  Sum_probs=21.1

Q ss_pred             HHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhc
Q 046691          186 YTILREMGFSSNNVAEVLIMYEN-DTDKALAHLLG  219 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs  219 (222)
                      +.+|.+|||+.+.+.+||..++| |.+.|++.|+.
T Consensus        13 v~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~wL~~   47 (64)
T 2crn_A           13 LEPLLAMGFPVHTALKALAATGRKTAEEALAWLHD   47 (64)
T ss_dssp             HHHHHHTSCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHh
Confidence            34566666666666666666655 66666666654

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

Probab=98.09  E-value=1.9e-06  Score=57.22  Aligned_cols=35  Identities=26%  Similarity=0.376  Sum_probs=25.6

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+.+|.+|||+.+.+..||..+ ||.|.|++.|++.
T Consensus        12 ~v~~L~~MGF~~~~a~~AL~~~-~n~e~A~~~L~~h   46 (47)
T 2ekk_A           12 QLQQLMDMGFTREHAMEALLNT-STMEQATEYLLTH   46 (47)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHS-CSHHHHHHHHHTC
T ss_pred             HHHHHHHcCCCHHHHHHHHHHc-CCHHHHHHHHHcC
Confidence            3567777777777777777777 4788888777754

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

Probab=98.08  E-value=3.1e-06  Score=61.82  Aligned_cols=41  Identities=29%  Similarity=0.413  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHhcCCCCc-hHHHHHHhccCCHHHHHHHHhcc
Q 046691          180 REFANGYTILREMGFSSN-NVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       180 ~EFl~~~~~L~EMGFp~~-~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ..|-..+.+|++|||... .+..||..++||.++|++.|++.
T Consensus        17 ~~y~~ql~qL~~MGF~d~~an~~AL~at~Gnve~Ave~L~~~   58 (67)
T 2dna_A           17 VRFSKEMECLQAMGFVNYNANLQALIATDGDTNAAIYKLKSS   58 (67)
T ss_dssp             HHTHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            467788999999999655 45899999999999999999975

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

Probab=98.06  E-value=2.1e-06  Score=62.75  Aligned_cols=33  Identities=21%  Similarity=0.372  Sum_probs=16.4

Q ss_pred             HHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhc
Q 046691          187 TILREMGFSSNNVAEVLIMYEN-DTDKALAHLLG  219 (222)
Q Consensus       187 ~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs  219 (222)
                      .+|.+|||+.+.+..||..|+| |.|+|++.|+.
T Consensus        14 ~~L~~MGF~~~~a~~AL~~t~n~~ve~A~ewL~~   47 (74)
T 2dag_A           14 IQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMS   47 (74)
T ss_dssp             HHHHHHSCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHh
Confidence            3444555555555555555543 45555555543

>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=98.04  E-value=2.6e-06  Score=60.47  Aligned_cols=33  Identities=24%  Similarity=0.416  Sum_probs=15.8

Q ss_pred             HHHHhcCCCCchHHHHHHhc-cCCHHHHHHHHhc
Q 046691          187 TILREMGFSSNNVAEVLIMY-ENDTDKALAHLLG  219 (222)
Q Consensus       187 ~~L~EMGFp~~~VaeAL~~~-dND~DKAL~~LLs  219 (222)
                      .+|.+|||+.+.+..||..| +||.|+|++.|+.
T Consensus        14 ~~L~~MGF~~~~a~~AL~~t~~~nve~A~ewLl~   47 (64)
T 1whc_A           14 ESLIEMGFPRGRAEKALALTGNQGIEAAMDWLME   47 (64)
T ss_dssp             HHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHhcCCCHHHHHHHHHh
Confidence            34444444444444444444 3445555554443

>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=97.98  E-value=4.4e-06  Score=58.98  Aligned_cols=40  Identities=23%  Similarity=0.162  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHhcCC-CCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGF-SSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGF-p~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .|...+.+|.|||| -.+.-..||.+|++|.++|++.||..
T Consensus         8 ~~a~~L~~L~eMGF~D~~~N~~aL~~~~gnv~~aI~~Ll~~   48 (54)
T 2cp8_A            8 QTAALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELLQL   48 (54)
T ss_dssp             THHHHHHHHHHHTCCCHHHHHHHHTTTTTCHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            47788999999999 77888999999999999999999964

>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=97.98  E-value=5.4e-06  Score=68.82  Aligned_cols=72  Identities=26%  Similarity=0.303  Sum_probs=54.3

Q ss_pred             CCcHHHHHHHHcCCCHHH----HHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          147 GSDPVVSRYIALGLNREA----VHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       147 ~~DP~V~ky~amG~~rea----V~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      |.+..++++...  ++++    |..-++.|...+.+..+|-....+|.+|||..+.|-+||..|++|.++|++.|++.
T Consensus       126 p~n~~aa~~~~~--~~~~f~~~a~~~~~~~a~~~~~~~~~eekV~~l~~MGf~~~~a~~AL~~~~wd~~~A~e~L~~~  201 (201)
T 3k9o_A          126 PQDAVVANQYKQ--NPEMFKQTARLWAHVYAGAPVSSPEYTKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLSN  201 (201)
T ss_dssp             CSCHHHHHHHHH--CHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHTTTCCHHHHHHHHHHTTTCHHHHHHHHHHC
T ss_pred             cccHHHHHHHHH--CHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence            455556555533  2333    33334456666666678888899999999999999999999999999999999873

>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=97.98  E-value=2.2e-06  Score=57.76  Aligned_cols=37  Identities=22%  Similarity=0.362  Sum_probs=33.8

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhccC
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      ...+|.+|||+.+.|.+||..|++|.+.|...|++..
T Consensus         7 aI~rL~~mGF~~~~a~~Al~a~~~n~e~A~~~Lf~~~   43 (47)
T 1dv0_A            7 AIERLKALGFPESLVIQAYFACEKNENLAANFLLSQN   43 (47)
T ss_dssp             HHTTTTTTTCCHHHHHHHHTTTTSCHHHHHHHTTSCC
T ss_pred             HHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhCc
Confidence            4678999999999999999999999999999998753

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

Probab=97.96  E-value=4.7e-06  Score=62.32  Aligned_cols=34  Identities=26%  Similarity=0.426  Sum_probs=21.7

Q ss_pred             HHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          186 YTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      +.+|.+|||+.+.+..||..|+||.+.|++.|++
T Consensus        33 i~~L~~MGF~~~~a~~AL~~t~~nve~A~ewL~~   66 (83)
T 2dai_A           33 LRQLTEMGFPENRATKALQLNHMSVPQAMEWLIE   66 (83)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            4556666666666666666666666666666664

>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=97.94  E-value=5.4e-06  Score=62.56  Aligned_cols=41  Identities=15%  Similarity=0.242  Sum_probs=30.7

Q ss_pred             CCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          145 GSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       145 ~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      ..+.+..|.+|++|||++++|..||...+.|.+++.|||..
T Consensus        26 ~~~~ee~I~~Lv~MGF~~~~A~~AL~~t~gdve~A~e~L~s   66 (83)
T 1veg_A           26 ASPSQESINQLVYMGFDTVVAEAALRVFGGNVQLAAQTLAH   66 (83)
T ss_dssp             CCCCHHHHHHHHHHSCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            34456678888888888888888888777777777777643

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

Probab=97.90  E-value=7.8e-06  Score=61.42  Aligned_cols=36  Identities=28%  Similarity=0.364  Sum_probs=30.4

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+.+|.+|||+.+.+.+||..+++|.|.|++.|+..
T Consensus        24 ~I~qL~~MGF~~~~a~~AL~~~n~n~e~A~ewL~~h   59 (85)
T 2dkl_A           24 LIKQLTDMGFPREPAEEALKSNNMNLDQAMSALLEK   59 (85)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHTT
T ss_pred             HHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHC
Confidence            367888888888888888888888999999888864

>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=97.84  E-value=1.1e-05  Score=63.36  Aligned_cols=40  Identities=20%  Similarity=0.297  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHhcCCCC-chHHHHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGFSS-NNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~-~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .|-..+.+|+||||.. +.+..||..+++|.++||+.|+++
T Consensus        65 ~~~~qL~qL~eMGF~d~~~ni~AL~~t~Gdve~AVe~L~~~  105 (108)
T 2cwb_A           65 QWQPQLQQLRDMGIQDDELSLRALQATGGDIQAALELIFAG  105 (108)
T ss_dssp             TTHHHHHHHHTTTCCCHHHHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             chHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence            4566789999999965 699999999999999999999975

>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=97.80  E-value=1.2e-05  Score=63.25  Aligned_cols=36  Identities=17%  Similarity=0.237  Sum_probs=33.7

Q ss_pred             HHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          184 NGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       184 ~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      ..+.+|.+|||+.+.|..||..+.||.|+|++.|+.
T Consensus        10 ~~v~~l~~MGFp~~~~~kAl~~~g~~~e~amewL~~   45 (118)
T 4ae4_A           10 QCVETVVNMGYSYECVLRAMKAAGANIEQILDYLFA   45 (118)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHCSCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            457899999999999999999999999999999986

>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=97.80  E-value=7.3e-05  Score=54.96  Aligned_cols=41  Identities=24%  Similarity=0.363  Sum_probs=36.9

Q ss_pred             CCCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          144 VGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       144 ~~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      .....|..|.+|++|||+++.|..||...+.|.+++.|||.
T Consensus        25 ~~~~~ee~I~~L~eMGF~r~~a~~AL~~~~~nve~Ave~Ll   65 (73)
T 1vg5_A           25 RVAASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILM   65 (73)
T ss_dssp             CSCCCHHHHHHHHTTTCCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCcccHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            34445789999999999999999999999999999999985

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

Probab=97.78  E-value=1.9e-05  Score=51.28  Aligned_cols=38  Identities=16%  Similarity=0.190  Sum_probs=34.5

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      |.+..|.+|++|||+++.|..||...+.|.+++.|||.
T Consensus         3 p~e~~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~L~   40 (43)
T 2g3q_A            3 PKSLAVEELSGMGFTEEEAHNALEKCNWDLEAATNFLL   40 (43)
T ss_dssp             HHHHHHHHHHTTTSCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHhCcCHHHHHHHHH
Confidence            34568999999999999999999999999999999984

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

Probab=97.75  E-value=1.9e-05  Score=61.27  Aligned_cols=36  Identities=19%  Similarity=0.300  Sum_probs=33.1

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYEN-DTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs~  220 (222)
                      .+++|.+|||+...+++||..|+| |.++|++.|+..
T Consensus         6 ~l~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~wL~~~   42 (126)
T 2lbc_A            6 SVMQLAEMGFPLEACRKAVYFTGNMGAEVAFNWIIVH   42 (126)
T ss_dssp             HHHHHHTTSSCCHHHHHHHHHHTSCCHHHHHHHHHHG
T ss_pred             HHHHHHHcCCCHHHHHHHHHHcCCCCHHHHHHHHHHh
Confidence            468999999999999999999988 999999999864

>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=97.71  E-value=4.3e-05  Score=51.55  Aligned_cols=37  Identities=22%  Similarity=0.402  Sum_probs=34.3

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      +..|.+|++|||+++.|..||...+.|.+++.|||..
T Consensus         9 ~~~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~e~L~~   45 (49)
T 1ify_A            9 ETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLT   45 (49)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHTTTSCSHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            5689999999999999999999999999999999854

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

Probab=97.70  E-value=6.4e-05  Score=52.75  Aligned_cols=36  Identities=22%  Similarity=0.364  Sum_probs=33.5

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+.+|.+|||+.+.+..||..|+||.|+|++.|+..
T Consensus        12 ~v~~L~~MGF~~~~a~~AL~~t~~nve~A~e~L~~~   47 (63)
T 2dak_A           12 CVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSH   47 (63)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHTTSCSHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            467999999999999999999999999999999864

>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=97.69  E-value=5.1e-05  Score=59.60  Aligned_cols=41  Identities=20%  Similarity=0.319  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhc-CCCCchHHHHHHhccCCHHHHHHHHhccC
Q 046691          181 EFANGYTILREM-GFSSNNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       181 EFl~~~~~L~EM-GFp~~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      +|-....+|.|| ||..+.+..||..||||.++||+.|+.+.
T Consensus        38 d~eekVk~L~EmtG~seeeAr~AL~~~ngDl~~AI~~Lleg~   79 (104)
T 1wj7_A           38 DFEEKVKQLIDITGKNQDECVIALHDCNGDVNRAINVLLEGN   79 (104)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHTCS
T ss_pred             cHHHHHHHHHHhhCCCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence            565667899999 99999999999999999999999999763

>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=97.66  E-value=2.7e-05  Score=58.12  Aligned_cols=40  Identities=10%  Similarity=0.237  Sum_probs=32.2

Q ss_pred             CCCCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q 046691          145 GSGSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFAN  184 (222)
Q Consensus       145 ~~~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~  184 (222)
                      ..+.+..|.+|++|||++++|.+||..-++ |.+.++|||.
T Consensus        26 ~~~~e~~v~~L~~MGF~~~~a~~AL~~t~n~n~e~A~ewL~   66 (84)
T 1vek_A           26 PVANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLL   66 (84)
T ss_dssp             CCCCHHHHHHHHHHTCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            345677889999999999999999887764 8888888874

>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=97.62  E-value=8.7e-05  Score=52.73  Aligned_cols=39  Identities=15%  Similarity=0.233  Sum_probs=35.5

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      +.+..|.+|++|||++++|..||...+.|.+++.|||..
T Consensus         8 ~~~~~I~~L~~MGF~~~~a~~AL~~~~~nve~A~e~L~~   46 (63)
T 1wji_A            8 VDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLT   46 (63)
T ss_dssp             SCHHHHHHHHTTTCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            467799999999999999999999999999999999853

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

Probab=97.57  E-value=3.2e-05  Score=56.36  Aligned_cols=36  Identities=17%  Similarity=0.234  Sum_probs=32.4

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +...|..|||..+.+..||-+++||.|+|+|-|.+.
T Consensus        22 ~V~~LvsMGFs~~qA~kALKat~~NvErAaDWLFSH   57 (63)
T 1wgn_A           22 CVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAH   57 (63)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            367888999999999999999999999999998864

>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=97.56  E-value=0.00018  Score=71.13  Aligned_cols=74  Identities=19%  Similarity=0.332  Sum_probs=62.3

Q ss_pred             CCCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHH---------------------------------HHHHHHHh
Q 046691          146 SGSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFA---------------------------------NGYTILRE  191 (222)
Q Consensus       146 ~~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl---------------------------------~~~~~L~E  191 (222)
                      .+...++..|++|||++.+...|+..-|. +.+-+.+++                                 ..+..|.+
T Consensus       650 ~~d~~~l~~L~~mGf~~~~~~kal~~t~n~~~e~a~~wl~~hmdd~di~~p~~~~~~~~~~s~~~~~~~~~~e~i~~l~~  729 (854)
T 3ihp_A          650 MLDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDPDFANPLILPGSSGPGSTSAAADPPPEDCVTTIVS  729 (854)
T ss_dssp             ---CHHHHHHHHHTCCHHHHHHHHHHTTSCCHHHHHHHHHHHTTSCGGGSCCCCC--------------CCHHHHHHHHT
T ss_pred             CcCHHHHHHHHhcCCCHHHHHHHHhhcCCCchHHHhHHHhhccCcccccccccccccccccccccccCCCCHHHHHHHHH
Confidence            45667999999999999999999998877 566666655                                 23678999


Q ss_pred             cCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          192 MGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       192 MGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      |||..+....||...+||.++|++.+.+
T Consensus       730 mGf~~~~a~~aL~~t~~~~eraidwlfs  757 (854)
T 3ihp_A          730 MGFSRDQALKALRATNNSLERAVDWIFS  757 (854)
T ss_dssp             TTCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHhhcCcHHHHHHhhhc
Confidence            9999999999999999999999999875

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

Probab=97.55  E-value=0.00011  Score=48.71  Aligned_cols=38  Identities=16%  Similarity=0.244  Sum_probs=34.0

Q ss_pred             CCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          146 SGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       146 ~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      .+.+..|.+|++|||+++++..||..-| |.+.+.|||.
T Consensus         7 ~~~~~~v~~L~~MGF~~~~a~~AL~~~~-n~e~A~~~L~   44 (47)
T 2ekk_A            7 GVNQQQLQQLMDMGFTREHAMEALLNTS-TMEQATEYLL   44 (47)
T ss_dssp             SSCHHHHHHHHHHHCCHHHHHHHHHHSC-SHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHcC-CHHHHHHHHH
Confidence            3467799999999999999999999887 8999999974

>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=97.50  E-value=0.00014  Score=51.78  Aligned_cols=40  Identities=15%  Similarity=0.259  Sum_probs=35.1

Q ss_pred             CCCCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q 046691          145 GSGSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFAN  184 (222)
Q Consensus       145 ~~~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~  184 (222)
                      +.+....|.+|++|||++++|.+||..-|. |.+.++|||.
T Consensus         6 ~~~~e~~v~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~wL~   46 (64)
T 2crn_A            6 SGSSPSLLEPLLAMGFPVHTALKALAATGRKTAEEALAWLH   46 (64)
T ss_dssp             CCCSCSSHHHHHHTSCCHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            345566899999999999999999998877 9999999984

>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=97.44  E-value=0.00022  Score=53.74  Aligned_cols=35  Identities=20%  Similarity=0.233  Sum_probs=33.1

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      .+.+|.+|||..+.|..||-+++||.++|++.|++
T Consensus        32 ~I~~Lv~MGF~~~~A~~AL~~t~gdve~A~e~L~s   66 (83)
T 1veg_A           32 SINQLVYMGFDTVVAEAALRVFGGNVQLAAQTLAH   66 (83)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            35789999999999999999999999999999997

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

Probab=97.44  E-value=0.0003  Score=48.00  Aligned_cols=37  Identities=24%  Similarity=0.199  Sum_probs=34.1

Q ss_pred             CcHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHH
Q 046691          148 SDPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       148 ~DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      -+..|.+|++||| +++++..||...+.|.+++.|||.
T Consensus        12 ~~~~l~~L~~MGF~~~~~~~~AL~~t~gn~e~A~e~L~   49 (52)
T 2jy5_A           12 FQQQLEQLSAMGFLNREANLQALIATGGDINAAIERLL   49 (52)
T ss_dssp             THHHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            3568999999999 999999999999999999999984

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

Probab=97.43  E-value=0.00012  Score=63.78  Aligned_cols=72  Identities=25%  Similarity=0.280  Sum_probs=54.6

Q ss_pred             CCcHHHHHHHHcCCCHHH----HHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          147 GSDPVVSRYIALGLNREA----VHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       147 ~~DP~V~ky~amG~~rea----V~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      |.+..++++...  +++.    |..-++.|...+.+..+|-....+|.||||..+.|-.||-.|+.|.++|++.|+++
T Consensus       178 Pln~eaa~l~~~--d~~~f~~~ar~~t~~yA~~~~~~~~~~~~v~~l~~mgf~~~~~~~al~~~nWd~~~A~e~L~~~  253 (253)
T 3e46_A          178 PQDAVVANQYKQ--NPEMFKQTARLWAHVYAGAPVSSPEYTKKIENLCAAGFDRNAVIVALSSKSWDVETATELLLSN  253 (253)
T ss_dssp             CSCHHHHHHHHH--CHHHHHHHHHHHHHHHHCCSCCCHHHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHHHC
T ss_pred             hhhHHHHHHHHH--CHHHHHHHHHHHHHHhcccccCcchHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence            455555555433  2333    33344466666666778888899999999999999999999999999999999973

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

Probab=97.41  E-value=0.00024  Score=44.66  Aligned_cols=35  Identities=9%  Similarity=0.228  Sum_probs=32.6

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFA  183 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl  183 (222)
                      +..|.+|++|||+++.+..||..-+.|.+++.+|+
T Consensus         5 ~~~i~~L~~mGf~~~~a~~AL~~~~~n~e~A~~~L   39 (40)
T 1z96_A            5 NSKIAQLVSMGFDPLEAAQALDAANGDLDVAASFL   39 (40)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            55899999999999999999999999999999987

>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=97.38  E-value=0.00049  Score=48.80  Aligned_cols=38  Identities=13%  Similarity=0.253  Sum_probs=34.6

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFAN  184 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~  184 (222)
                      +.+..|.+|++|||++++|..||..-+. |.+.++|||.
T Consensus        18 ~~e~~i~~L~~MGF~~~~a~~AL~~t~~~nve~A~ewL~   56 (64)
T 2cpw_A           18 KHGSALDVLLSMGFPRARAQKALASTGGRSVQTACDWLF   56 (64)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHTTTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            5567899999999999999999999887 9999999984

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

Probab=97.38  E-value=0.00022  Score=48.77  Aligned_cols=37  Identities=24%  Similarity=0.263  Sum_probs=33.5

Q ss_pred             cHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          149 DPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       149 DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      +..|.+|++||| +++++..||...+.|.+++.|||..
T Consensus        12 ~~~l~~L~~MGF~~~~~~~~AL~~t~gnve~Ave~L~~   49 (53)
T 2knz_A           12 QQQLEQLNSMGFINREANLQALIATGGDINAAIERLLG   49 (53)
T ss_dssp             HHHHHHHHTTTCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            346899999999 9999999999999999999999853

>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=97.30  E-value=0.00041  Score=49.14  Aligned_cols=39  Identities=15%  Similarity=0.189  Sum_probs=34.5

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcC-CChhHHHHHHHH
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYG-DNPTKVREFANG  185 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yG-dd~~KV~EFl~~  185 (222)
                      +.+..|.+|++|||++++|.+||..-| .|.+.++|||..
T Consensus         8 ~~~~~v~~L~~MGF~~~~a~~AL~~t~~~nve~A~ewLl~   47 (64)
T 1whc_A            8 AELTALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLME   47 (64)
T ss_dssp             CCCCHHHHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHhcCCCHHHHHHHHHh
Confidence            456689999999999999999999996 699999999853

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

Probab=97.29  E-value=0.00041  Score=50.51  Aligned_cols=39  Identities=15%  Similarity=0.270  Sum_probs=35.1

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHH
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANG  185 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~  185 (222)
                      +.+..|.+|++|||++++|.+||..-+. |.+.++|||..
T Consensus         8 ~~e~~v~~L~~MGF~~~~a~~AL~~t~n~~ve~A~ewL~~   47 (74)
T 2dag_A            8 LDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMS   47 (74)
T ss_dssp             SCHHHHHHHHHHSCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHh
Confidence            5677999999999999999999998886 89999999853

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

Probab=97.28  E-value=0.00011  Score=66.96  Aligned_cols=39  Identities=23%  Similarity=0.333  Sum_probs=35.1

Q ss_pred             HHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          182 FANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       182 Fl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      |-....+|.+|||+.+.|..||-.++||.|+|++.|+++
T Consensus       168 ~~~~i~~l~~MGf~~~~~~~AL~a~~nn~~~A~e~L~~g  206 (368)
T 1oqy_A          168 YETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTG  206 (368)
T ss_dssp             HHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTTTTS
T ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            344458999999999999999999999999999999875

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

Probab=97.28  E-value=0.0002  Score=50.44  Aligned_cols=34  Identities=21%  Similarity=0.224  Sum_probs=23.7

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL  218 (222)
                      ...+|.+|||+.+.|-.||...+||.|-|...|+
T Consensus        14 ~Ia~Lm~mGFsr~~ai~AL~~a~nnve~AaniLl   47 (52)
T 2ooa_A           14 KIAKLMGEGYAFEEVKRALEIAQNNVEVARSILR   47 (52)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            3456777777777777777777777777776665

>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=97.23  E-value=0.00052  Score=49.89  Aligned_cols=39  Identities=13%  Similarity=0.264  Sum_probs=35.6

Q ss_pred             CCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          146 SGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       146 ~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      .+.+..|.+|++|||++++|..||..-+.|.++++|||.
T Consensus        27 ~~~~~~v~~L~~MGF~~~~a~~AL~~t~~nve~Ave~L~   65 (73)
T 1wiv_A           27 DIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVF   65 (73)
T ss_dssp             SSCHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            356779999999999999999999999999999999985

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

Probab=97.19  E-value=0.00025  Score=50.14  Aligned_cols=34  Identities=21%  Similarity=0.302  Sum_probs=26.5

Q ss_pred             HHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          186 YTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      ..+|.+|||+.+.|-.||..++||.|-|...|+.
T Consensus        13 I~~L~~lGF~r~~ai~AL~~a~nnve~Aa~iL~e   46 (53)
T 2d9s_A           13 IERLMSQGYSYQDIQKALVIAHNNIEMAKNILRE   46 (53)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            5677788888888888888888888888777764

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

Probab=97.19  E-value=0.00049  Score=46.11  Aligned_cols=36  Identities=8%  Similarity=0.075  Sum_probs=33.0

Q ss_pred             cHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHH
Q 046691          149 DPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       149 DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      +..|.+|++||| +++++..||...+.|.++++|||.
T Consensus         8 ~~~i~~L~~MGF~d~~~~~~AL~~~~gnv~~Ave~L~   44 (46)
T 2bwb_A            8 EHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLL   44 (46)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHH
Confidence            567899999999 689999999999999999999985

>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=97.18  E-value=0.00066  Score=50.59  Aligned_cols=36  Identities=25%  Similarity=0.278  Sum_probs=32.0

Q ss_pred             HHHHHHhcCCCCchHHHHHHhcc-CCHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYE-NDTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~d-ND~DKAL~~LLs~  220 (222)
                      .+.+|.+|||+.+.+..||..+. +|.++|++.|++.
T Consensus        32 ~v~~L~~MGF~~~~a~~AL~~t~n~n~e~A~ewL~~h   68 (84)
T 1vek_A           32 IVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSH   68 (84)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            35689999999999999999885 6999999999974

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

Probab=97.06  E-value=0.00049  Score=47.50  Aligned_cols=35  Identities=20%  Similarity=0.295  Sum_probs=32.0

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      ....|.+|||..+.|..||..++||.+.|.+.|+.
T Consensus         7 ~I~~L~s~Gf~~~~~~rAL~ia~Nnie~A~nIL~e   41 (46)
T 2oo9_A            7 EIENLMSQGYSYQDIQKALVIAQNNIEMAKNILRE   41 (46)
T ss_dssp             HHHHHHHTTBCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhhccHHHHHHHHHH
Confidence            46789999999999999999999999999998874

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

Probab=97.06  E-value=0.00034  Score=49.95  Aligned_cols=35  Identities=20%  Similarity=0.295  Sum_probs=31.0

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      ...+|.+|||..+.|-.||...+||.+-|...|+.
T Consensus        10 ~Ia~L~smGfsr~da~~AL~ia~Ndv~~AtNiLlE   44 (56)
T 2juj_A           10 EIENLMSQGYSYQDIQKALVIAQNNIEMAKNILRE   44 (56)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHTTTCSHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhcccHHHHHHHHHH
Confidence            45789999999999999999999999999988874

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

Probab=97.03  E-value=0.0013  Score=48.59  Aligned_cols=37  Identities=24%  Similarity=0.256  Sum_probs=34.0

Q ss_pred             cHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          149 DPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       149 DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      +..|.+|++||| ++++|..||...+.|.++++|||..
T Consensus        30 e~qi~qL~eMGF~dr~~~~~AL~~t~Gnve~Ave~L~~   67 (74)
T 1vej_A           30 QQELEELKALGFANRDANLQALVATDGDIHAAIEMLLG   67 (74)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            568999999999 7999999999999999999999863

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

Probab=97.01  E-value=0.00086  Score=50.02  Aligned_cols=38  Identities=8%  Similarity=0.083  Sum_probs=34.5

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      +.+..|.+|++|||++++|..||..-+.|.+.++|||.
T Consensus        28 ~~e~~i~~L~~MGF~~~~a~~AL~~t~~nve~A~ewL~   65 (83)
T 2dai_A           28 VDEAALRQLTEMGFPENRATKALQLNHMSVPQAMEWLI   65 (83)
T ss_dssp             CCHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            45668999999999999999999988889999999984

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

Probab=97.01  E-value=0.00074  Score=50.65  Aligned_cols=37  Identities=14%  Similarity=0.156  Sum_probs=33.3

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      +..|.+|++|||++++|..||..-+.|.+.+.|||..
T Consensus        22 ~~~I~qL~~MGF~~~~a~~AL~~~n~n~e~A~ewL~~   58 (85)
T 2dkl_A           22 SRLIKQLTDMGFPREPAEEALKSNNMNLDQAMSALLE   58 (85)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            6689999999999999999998878899999999753

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

Probab=96.98  E-value=0.001  Score=46.81  Aligned_cols=37  Identities=8%  Similarity=0.077  Sum_probs=33.6

Q ss_pred             cHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          149 DPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       149 DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      +..+.+|.+||| +++++..||...+.|.+++.|||..
T Consensus        18 ~~qi~~L~~MGF~d~~~~~~AL~~~~gnve~Ave~L~~   55 (58)
T 1wr1_B           18 EHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN   55 (58)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            568899999999 6999999999999999999999853

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

Probab=96.80  E-value=0.00067  Score=49.23  Aligned_cols=39  Identities=23%  Similarity=0.350  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHhcCCCC---chHHHHHHhccCCHHHHHHHHhc
Q 046691          180 REFANGYTILREMGFSS---NNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       180 ~EFl~~~~~L~EMGFp~---~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      .||-..+.+|++| ||.   ..|..+|..|+||.|+||+.||.
T Consensus        16 ~~~~~~v~~L~~M-FP~lD~~vI~~vL~a~~G~vd~aId~LL~   57 (67)
T 2dhy_A           16 LEFNQAMDDFKTM-FPNMDYDIIECVLRANSGAVDATIDQLLQ   57 (67)
T ss_dssp             CCSHHHHHHHHHH-CSSSCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-CCCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            3556678889999 985   56899999999999999999996

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

Probab=96.70  E-value=0.0015  Score=46.04  Aligned_cols=36  Identities=22%  Similarity=0.384  Sum_probs=31.1

Q ss_pred             HHHHHHHhcCCCC---chHHHHHHhccCCHHHHHHHHhcc
Q 046691          184 NGYTILREMGFSS---NNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       184 ~~~~~L~EMGFp~---~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ..+.+|++| ||.   ..|..+|..|+||.|+||+.||.-
T Consensus        11 e~l~~L~em-FP~ld~~~I~~vL~a~~gdvd~aI~~LL~m   49 (59)
T 1wgl_A           11 EDLKAIQDM-FPNMDQEVIRSVLEAQRGNKDAAINSLLQM   49 (59)
T ss_dssp             HHHHHHHHH-CSSSCHHHHHHHHTTTTTCHHHHHHHHHHS
T ss_pred             HHHHHHHHH-CCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            456789999 875   669999999999999999999974

>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=96.69  E-value=0.0024  Score=44.07  Aligned_cols=38  Identities=21%  Similarity=0.189  Sum_probs=33.9

Q ss_pred             CcHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          148 SDPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       148 ~DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      -+..+.+|.+||| +++++..||...+.|-+++.|||..
T Consensus         9 ~~~~l~~L~~MGF~d~~~n~~AL~~~~Gdv~~Ave~L~~   47 (54)
T 2dah_A            9 FQVQLEQLRSMGFLNREANLQALIATGGDVDAAVEKLRQ   47 (54)
T ss_dssp             SHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            3678999999999 6678899999999999999999864

>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=96.53  E-value=0.00072  Score=45.40  Aligned_cols=36  Identities=22%  Similarity=0.202  Sum_probs=33.2

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      +..|.+|++|||++..|..|+..-|.|.+.+.+||-
T Consensus         5 ~eaI~rL~~mGF~~~~a~~Al~a~~~n~e~A~~~Lf   40 (47)
T 1dv0_A            5 KEAIERLKALGFPESLVIQAYFACEKNENLAANFLL   40 (47)
T ss_dssp             HHHHTTTTTTTCCHHHHHHHHTTTTSCHHHHHHHTT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            458999999999999999999999999999999873

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

Probab=96.32  E-value=0.0063  Score=42.83  Aligned_cols=42  Identities=26%  Similarity=0.367  Sum_probs=33.5

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCC
Q 046691          148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFS  195 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp  195 (222)
                      -+..|++|++|||+|+.|..||..-..|-+-+..+      |+|..||
T Consensus        11 ~~~~Ia~Lm~mGFsr~~ai~AL~~a~nnve~Aani------Llef~~~   52 (52)
T 2ooa_A           11 VDAKIAKLMGEGYAFEEVKRALEIAQNNVEVARSI------LREFAFP   52 (52)
T ss_dssp             CHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHH------HHHHCCC
T ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHH------HHHhcCC
Confidence            34789999999999999999999888887766544      4555554

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

Probab=96.29  E-value=0.0082  Score=42.39  Aligned_cols=36  Identities=11%  Similarity=0.205  Sum_probs=30.1

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      +--|++|++|||+|+.|..||..-..|-+-+..+|.
T Consensus        10 e~~I~~L~~lGF~r~~ai~AL~~a~nnve~Aa~iL~   45 (53)
T 2d9s_A           10 SSEIERLMSQGYSYQDIQKALVIAHNNIEMAKNILR   45 (53)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhcCCHHHHHHHHH
Confidence            345999999999999999999998888776665543

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

Probab=96.09  E-value=0.0029  Score=44.85  Aligned_cols=41  Identities=17%  Similarity=0.273  Sum_probs=29.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHHHHHHHhcCCCC
Q 046691          150 PVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANGYTILREMGFSS  196 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~  196 (222)
                      .-+..|++|||++++|++||..=|. +-+-+.||      |..|+|+.
T Consensus        11 qmlq~L~eMGFd~erae~Alk~Tg~~Gle~Amew------L~k~~~~~   52 (54)
T 2cos_A           11 QMLQELVNAGCDQEMAGRALKQTGSRSIEAALEY------ISKMSGPS   52 (54)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHHTSCCHHHHHHH------HHHHSCSC
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhCcccHHHHHHH------HHHhcCCC
Confidence            4577888888888888888887666 55555554      45677765

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

Probab=95.93  E-value=0.003  Score=53.65  Aligned_cols=72  Identities=22%  Similarity=0.268  Sum_probs=12.2

Q ss_pred             CCcHHHHHHHHcCCCHHH----HHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhccC
Q 046691          147 GSDPVVSRYIALGLNREA----VHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       147 ~~DP~V~ky~amG~~rea----V~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      |.++.++++...  ++++    |..-++.|...+.. .++-....+|.+|||..+.+-.||..++-|+++|++.||+++
T Consensus       141 Pln~eaa~~~~~--d~~~f~~~ar~~t~~ya~~~~~-~~~~~~v~~~~~mgf~~~~~~~al~~~~~~~~~~~~~l~~~~  216 (216)
T 2pwq_A          141 PQDAEVAKMYKE--NHALFVKTASVWTKTFATGPKE-EPREVIIKKITEMGFSEDQAKNALIKANWNETLALNTLLENS  216 (216)
T ss_dssp             CSCHHHHHHHHH--CHHHHHHHHHHHHHHHSCCC---------------------------------------------
T ss_pred             cccHHHHHHHHH--CHHHHHHHHHHHHHHhcCCCcc-cchhhHHHHHHHcCCCHHHHHHHHHHcCCchHHHHHHHhcCC
Confidence            455555555432  3332    23333445543221 145566788999999999999999999999999999999763

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

Probab=95.86  E-value=0.0077  Score=43.87  Aligned_cols=37  Identities=19%  Similarity=0.318  Sum_probs=34.0

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      +...|..+++|||+++.|..||+.-|.|-+++.||+-
T Consensus        19 e~e~V~~LvsMGFs~~qA~kALKat~~NvErAaDWLF   55 (63)
T 1wgn_A           19 ERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLF   55 (63)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHCSCHHHHHHHHH
T ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4557999999999999999999999999999999973

>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=95.80  E-value=0.0099  Score=49.18  Aligned_cols=36  Identities=19%  Similarity=0.275  Sum_probs=34.3

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      |..|.+|++|||+++.|..||...+.|.+++.|+|.
T Consensus       164 eekV~~l~~MGf~~~~a~~AL~~~~wd~~~A~e~L~  199 (201)
T 3k9o_A          164 TKKIENLCAMGFDRNAVIVALSSKSWDVETATELLL  199 (201)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHh
Confidence            779999999999999999999999999999999985

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

Probab=95.62  E-value=0.019  Score=40.68  Aligned_cols=34  Identities=15%  Similarity=0.109  Sum_probs=31.3

Q ss_pred             HHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhc
Q 046691          186 YTILREMGFSSNNVAEVLIMYEN-DTDKALAHLLG  219 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs  219 (222)
                      +.+|.||||+++.|..||-+-+| ..+.||+.|+-
T Consensus        13 lq~L~eMGFd~erae~Alk~Tg~~Gle~AmewL~k   47 (54)
T 2cos_A           13 LQELVNAGCDQEMAGRALKQTGSRSIEAALEYISK   47 (54)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            68999999999999999999888 79999999874

>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=95.40  E-value=0.018  Score=45.12  Aligned_cols=38  Identities=16%  Similarity=0.208  Sum_probs=34.4

Q ss_pred             CcHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          148 SDPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       148 ~DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      -+..+.+|.+||| +++++.+||..-+.|.++++|+|..
T Consensus        66 ~~~qL~qL~eMGF~d~~~ni~AL~~t~Gdve~AVe~L~~  104 (108)
T 2cwb_A           66 WQPQLQQLRDMGIQDDELSLRALQATGGDIQAALELIFA  104 (108)
T ss_dssp             THHHHHHHHTTTCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            3779999999999 6789999999999999999999864

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

Probab=95.23  E-value=0.029  Score=40.81  Aligned_cols=36  Identities=14%  Similarity=0.038  Sum_probs=32.3

Q ss_pred             HHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          150 PVVSRYIALGL-NREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       150 P~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      ..+.+|.+||| +++++..||..-+.|.++++|||..
T Consensus        21 ~ql~qL~~MGF~d~~an~~AL~at~Gnve~Ave~L~~   57 (67)
T 2dna_A           21 KEMECLQAMGFVNYNANLQALIATDGDTNAAIYKLKS   57 (67)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            37899999998 7888899999999999999999864

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

Probab=94.67  E-value=0.038  Score=39.44  Aligned_cols=34  Identities=9%  Similarity=0.186  Sum_probs=28.4

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREF  182 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EF  182 (222)
                      |..|++|++|||+|+.|.+||..=..|-+-+..+
T Consensus         8 e~~Ia~L~smGfsr~da~~AL~ia~Ndv~~AtNi   41 (56)
T 2juj_A            8 SSEIENLMSQGYSYQDIQKALVIAQNNIEMAKNI   41 (56)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHTTTCSHHHHHH
T ss_pred             hHHHHHHHHcCCCHHHHHHHHHHhcccHHHHHHH
Confidence            5589999999999999999999877777665544

>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=94.49  E-value=0.053  Score=38.11  Aligned_cols=38  Identities=11%  Similarity=0.076  Sum_probs=33.9

Q ss_pred             cHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHHHH
Q 046691          149 DPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFANGY  186 (222)
Q Consensus       149 DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~~~  186 (222)
                      .+...+|.+||| ++++-.+||...+.|-++|+|-|..+
T Consensus        10 a~~L~~L~eMGF~D~~~N~~aL~~~~gnv~~aI~~Ll~~   48 (54)
T 2cp8_A           10 AALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELLQL   48 (54)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHTTTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            348889999999 99999999999999999999987654

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

Probab=94.40  E-value=0.029  Score=38.50  Aligned_cols=36  Identities=28%  Similarity=0.424  Sum_probs=30.2

Q ss_pred             HHHHHHhcCCCC---chHHHHHHhccCCHHHHHHHHhccC
Q 046691          185 GYTILREMGFSS---NNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       185 ~~~~L~EMGFp~---~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      ...+|.|| ||.   ..|+-+|.+|++|.|+|++.||...
T Consensus         7 ~v~~L~EM-FP~~~~~~ik~~L~~~~Gd~d~Ai~~LL~~~   45 (49)
T 1otr_A            7 KLSILMDM-FPAISKSKLQVHLLENNNDLDLTIGLLLKEN   45 (49)
T ss_dssp             HHHHHHHH-CSSSCHHHHHHHHHHTTTCSHHHHHHHHHHT
T ss_pred             HHHHHHHH-CCCCCHHHHHHHHHHcCCCHHHHHHHHHhcc
Confidence            45678888 664   6788999999999999999999763

>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=94.39  E-value=0.028  Score=47.69  Aligned_cols=31  Identities=23%  Similarity=0.433  Sum_probs=23.8

Q ss_pred             HHHhcCCCCchHHHHHHhccCCH---------HHHHHHHh
Q 046691          188 ILREMGFSSNNVAEVLIMYENDT---------DKALAHLL  218 (222)
Q Consensus       188 ~L~EMGFp~~~VaeAL~~~dND~---------DKAL~~LL  218 (222)
                      +|.+|||..+.|-+||-.|+.|.         +|.|+.||
T Consensus       175 ~~~~mg~~~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~  214 (215)
T 1tte_A          175 EFESQGFEKDKIVEVLRRLGVKSLDPNDNNTANRIIEELL  214 (215)
T ss_dssp             HHHHHTCCHHHHHHHHHHSCCSSCCSSCCHHHHHHHHHHT
T ss_pred             HHHHcCCCHHHHHHHHHHcCCCcccchhhhhHHHHHHHHh
Confidence            34678888888888888887775         67777776

>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=94.27  E-value=0.051  Score=47.28  Aligned_cols=37  Identities=19%  Similarity=0.235  Sum_probs=34.5

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      |..|.+|++|||++++|..||...+-|.+++.|+|..
T Consensus       216 ~~~v~~l~~mgf~~~~~~~al~~~nWd~~~A~e~L~~  252 (253)
T 3e46_A          216 TKKIENLCAAGFDRNAVIVALSSKSWDVETATELLLS  252 (253)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            6799999999999999999999999999999999853

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

Probab=94.25  E-value=0.16  Score=42.70  Aligned_cols=58  Identities=17%  Similarity=0.143  Sum_probs=51.3

Q ss_pred             CCHHHHHHHHHHcCCChhHHHHHHHH-----HHHHHhcC-CCCchHHHHHHhccCCHHHHHHHH
Q 046691          160 LNREAVHIAVANYGDNPTKVREFANG-----YTILREMG-FSSNNVAEVLIMYENDTDKALAHL  217 (222)
Q Consensus       160 ~~reaV~~Av~~yGdd~~KV~EFl~~-----~~~L~EMG-Fp~~~VaeAL~~~dND~DKAL~~L  217 (222)
                      ++...+..|+..-|.|..+++.-|..     |.+|...| |..+.+-+||-.|.+|++.||-.|
T Consensus        75 ~s~~EAr~Aw~~~~Gd~~~Av~~ci~~R~~K~~eL~s~G~~~~~~~~~aL~~~~Gdv~~Al~eL  138 (162)
T 4dbg_B           75 FSCQEARRAWLDRHGNLDEAVEECVRTRRRKVQELQSLGFGPEEGSLQALFQHGGDVSRALTEL  138 (162)
T ss_dssp             CCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHHHTTCCGGGTHHHHHHHTTTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHccCChHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHcCCcHHHHHHHH
Confidence            67788999999999999998888754     99999999 567889999999999999999776

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

Probab=94.21  E-value=0.037  Score=39.91  Aligned_cols=31  Identities=29%  Similarity=0.274  Sum_probs=25.2

Q ss_pred             HHHh-cCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691          188 ILRE-MGFSSNNVAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       188 ~L~E-MGFp~~~VaeAL~~~dND~DKAL~~LL  218 (222)
                      +||| -|-.-.+.++||..||+|.++|++.|=
T Consensus        15 ~LRe~TGag~~dcKkAL~e~~GDi~~Ai~~Lr   46 (64)
T 2cp9_A           15 KLRRKTGYSFVNCKKALETCGGDLKQAEIWLH   46 (64)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            3444 367778999999999999999999873

>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=93.85  E-value=0.075  Score=37.40  Aligned_cols=35  Identities=23%  Similarity=0.362  Sum_probs=30.1

Q ss_pred             HHHHHHHhcCCCCch--HHHHHHhccCCHHHHHHHHh
Q 046691          184 NGYTILREMGFSSNN--VAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       184 ~~~~~L~EMGFp~~~--VaeAL~~~dND~DKAL~~LL  218 (222)
                      .++.++..|||.-+.  ...+|...+.|..|||+.+=
T Consensus        12 ~al~qMl~MGF~negGWLt~LL~~k~gDI~~aLD~lq   48 (52)
T 1q02_A           12 ESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQ   48 (52)
T ss_dssp             HHHHHHHTTTCCCTTSHHHHHHHHTTTCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCccccHHHHHHHHccCCHHHHHHHhh
Confidence            467899999999765  47999999999999999863

>3dfg_A Xcrecx, regulatory protein RECX; RECX RECA, homologous recombination, tandem repeats, three-helix bundle, cytoplasm; 1.50A {Xanthomonas campestris PV}

Probab=93.46  E-value=0.28  Score=39.17  Aligned_cols=70  Identities=21%  Similarity=0.294  Sum_probs=53.8

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHHc---C--CChhHHHHHHHH-----------HHHHHhcCCCCchHHHHHHhccCCHH
Q 046691          148 SDPVVSRYIALGLNREAVHIAVANY---G--DNPTKVREFANG-----------YTILREMGFSSNNVAEVLIMYENDTD  211 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~y---G--dd~~KV~EFl~~-----------~~~L~EMGFp~~~VaeAL~~~dND~D  211 (222)
                      .-.+..||..+|++.+.|..+|+.+   |  ||..-+..|+..           -..|+.-|+..+.|.+||..++.|..
T Consensus        34 ~~EL~~KL~~kg~~~e~Ie~vl~~l~~~g~ldD~rfA~~~v~~~~~~~~G~~~I~~eL~~KGI~~~~I~~al~~~~~de~  113 (162)
T 3dfg_A           34 KKELNRKLQARGIEPEAAQAAVERLAGEGWQDDVRFAASVVRNRASSGYGPLHIRAELGTHGLDSDAVSAAMATFEGDWT  113 (162)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCCHHHHHHHHHHHHHTTTCCHHHHHHHHHHTTCCHHHHHHHHTTCCSCHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccccHHHHHHHHHHcCCCHHHHHHHHHhCcHhHH
Confidence            4568899999999999999999843   4  355556666554           55789999999999999999887765


Q ss_pred             HHHHHH
Q 046691          212 KALAHL  217 (222)
Q Consensus       212 KAL~~L  217 (222)
                      .++..|
T Consensus       114 e~a~~l  119 (162)
T 3dfg_A          114 ENALDL  119 (162)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            544444

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

Probab=93.13  E-value=0.18  Score=34.69  Aligned_cols=32  Identities=9%  Similarity=0.178  Sum_probs=26.9

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVR  180 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~  180 (222)
                      +-.+++|++|||+++.|.+||..=..|-+-+.
T Consensus         5 e~~I~~L~s~Gf~~~~~~rAL~ia~Nnie~A~   36 (46)
T 2oo9_A            5 SSEIENLMSQGYSYQDIQKALVIAQNNIEMAK   36 (46)
T ss_dssp             HHHHHHHHHTTBCHHHHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhhccHHHHH
Confidence            55789999999999999999998777765544

>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=90.79  E-value=0.31  Score=38.20  Aligned_cols=36  Identities=17%  Similarity=0.281  Sum_probs=33.4

Q ss_pred             cHHHHHHHHc-CCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          149 DPVVSRYIAL-GLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       149 DP~V~ky~am-G~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      |.-|.+|++| ||+++.|..||...+.|..++.+||.
T Consensus        40 eekVk~L~EmtG~seeeAr~AL~~~ngDl~~AI~~Ll   76 (104)
T 1wj7_A           40 EEKVKQLIDITGKNQDECVIALHDCNGDVNRAINVLL   76 (104)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHhhCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            5678999999 99999999999999999999999875

>4fp9_B Mterf domain-containing protein 2; modification enzyme, transferase; HET: SAM; 2.90A {Homo sapiens}

Probab=90.25  E-value=0.55  Score=42.07  Aligned_cols=21  Identities=19%  Similarity=0.412  Sum_probs=11.1

Q ss_pred             HHHHHhcCCCCchHHHHHHhc
Q 046691          186 YTILREMGFSSNNVAEVLIMY  206 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~  206 (222)
                      +.-|+++||..+.|..+|..|
T Consensus       117 l~fL~~lGl~~~~i~~ll~~~  137 (335)
T 4fp9_B          117 SSYLQKLGLGEGKLKRVLYCC  137 (335)
T ss_dssp             HHHHHHTTCTTTTHHHHHHHC
T ss_pred             HHHHHHcCCCHHHHHHHHHhC
Confidence            344455555555555555544

>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=88.20  E-value=0.18  Score=35.42  Aligned_cols=43  Identities=19%  Similarity=0.223  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHhc--CCCCchHHHHHHhccCCHHHHHHHHhccC
Q 046691          179 VREFANGYTILREM--GFSSNNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       179 V~EFl~~~~~L~EM--GFp~~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      -.|+-..+.+|++|  .+..+.|..+|..++++.|+|++.||.=|
T Consensus         9 ~~e~~~~~~~L~~MFP~lD~evI~~Vl~a~~G~~~~~IdaLLqms   53 (54)
T 1p3q_Q            9 ENERKDTLNTLQNMFPDMDPSLIEDVCIAAASRIGPCVDALLSLS   53 (54)
T ss_dssp             HHHHHHHHHHHHHHSTTSCHHHHHHHHHHSCC--CGGGC------
T ss_pred             HHHHHHHHHHHHHHcccCCHHHHHHHHHHcCCCHHHHHHHHHhhc
Confidence            46888999999999  34468899999999999999999999754

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A

Probab=86.47  E-value=1.1  Score=37.22  Aligned_cols=21  Identities=14%  Similarity=0.099  Sum_probs=9.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHHH
Q 046691          150 PVVSRYIALGLNREAVHIAVA  170 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~  170 (222)
                      |.++-|.+.|++.+.+...+.
T Consensus        78 p~v~~L~~~Gls~~~i~~~l~   98 (270)
T 3m66_A           78 TRVAYLHSKNFSKADVAQMVR   98 (270)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHH
Confidence            334444444444444444443

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A*

Probab=86.20  E-value=1.5  Score=38.14  Aligned_cols=58  Identities=19%  Similarity=0.244  Sum_probs=42.1

Q ss_pred             cHHHHHHH-HcCCCHHHHHHHHHHcC-----CChhHHHHH-HHHHHHHHhcCCCCchHHHHHHhc
Q 046691          149 DPVVSRYI-ALGLNREAVHIAVANYG-----DNPTKVREF-ANGYTILREMGFSSNNVAEVLIMY  206 (222)
Q Consensus       149 DP~V~ky~-amG~~reaV~~Av~~yG-----dd~~KV~EF-l~~~~~L~EMGFp~~~VaeAL~~~  206 (222)
                      ++.|..|. .+|++.+.+..+|..++     .+.+.+++= ....+.|+++||+.++|..++..|
T Consensus       200 ~~~v~fL~~~~G~~~~~~~~~i~~~~~~~l~~s~~~l~~~~~~l~e~~~~lG~s~~ev~~~v~~~  264 (343)
T 3mva_O          200 KANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEVQKFVLSY  264 (343)
T ss_dssp             HHHHHHHHHHSCCCHHHHHHHHHTTTGGGGGCCTTHHHHHHHHHHHHHHTTTCCHHHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHhcCChHHhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            56677777 59999999888887654     455555542 223345678999999999998765

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

Probab=86.15  E-value=0.88  Score=38.16  Aligned_cols=60  Identities=13%  Similarity=0.251  Sum_probs=41.6

Q ss_pred             cCCCHHHHHHHHHHcCCChhHHHHHHHH-----HHHHH----hc-----CCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          158 LGLNREAVHIAVANYGDNPTKVREFANG-----YTILR----EM-----GFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       158 mG~~reaV~~Av~~yGdd~~KV~EFl~~-----~~~L~----EM-----GFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      .||..|.|..|+ .|+.+.. =.++|+.     +.+..    ..     .|+..++++||+.+.+|.++|...|+-
T Consensus        27 ~GfspEEV~aAl-~~~g~~~-P~~WLk~ewp~ll~~V~~la~~~~~~~g~~s~~EAr~Aw~~~~Gd~~~Av~~ci~  100 (162)
T 4dbg_B           27 AGACPEEIFSAL-QYSGTEV-PLQWLRSELPYVLEMVAELAGQQDPGLGAFSCQEARRAWLDRHGNLDEAVEECVR  100 (162)
T ss_dssp             SCCCHHHHHHHH-HHHTCCC-CHHHHHHHSCSHHHHHHHHHHHHCGGGCCCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHH-HhcCCCC-cHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHHHccCChHHHHHHHHH
Confidence            499999999999 5643221 2333332     11111    12     367799999999999999999999873

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A

Probab=85.47  E-value=1  Score=37.50  Aligned_cols=22  Identities=9%  Similarity=0.256  Sum_probs=10.4

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHH
Q 046691          150 PVVSRYIALGLNREAVHIAVAN  171 (222)
Q Consensus       150 P~V~ky~amG~~reaV~~Av~~  171 (222)
                      ++++.|..+|++...+......
T Consensus         7 ~~l~~L~~lGv~~~~i~k~p~~   28 (270)
T 3m66_A            7 ETLQKLVLLGVDLSKIEKHPEA   28 (270)
T ss_dssp             HHHHHHHHTTCCHHHHTTSHHH
T ss_pred             HHHHHHHHcCCCHHHHhhccch
Confidence            3444455555555544444443

>1q08_A Zn(II)-responsive regulator of ZNTA; MERR family transcriptional regulator; 1.90A {Escherichia coli} SCOP: a.6.1.3 PDB: 1q09_A 1q0a_A

Probab=84.75  E-value=0.94  Score=32.34  Aligned_cols=29  Identities=21%  Similarity=0.189  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691          179 VREFANGYTILREMGFSSNNVAEVLIMYE  207 (222)
Q Consensus       179 V~EFl~~~~~L~EMGFp~~~VaeAL~~~d  207 (222)
                      ..+.+.....|+++||+.+.|++.|-..+
T Consensus         2 dl~rL~~I~~lr~lGfsL~eIk~~l~~~~   30 (99)
T 1q08_A            2 DLQRLKFIRHARQLGFSLESIRELLSIRI   30 (99)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHh
Confidence            35678888999999999999999997664

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

Probab=84.66  E-value=1.9  Score=36.43  Aligned_cols=31  Identities=6%  Similarity=0.287  Sum_probs=26.8

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHHcCCChhH
Q 046691          148 SDPVVSRYIALGLNREAVHIAVANYGDNPTK  178 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~K  178 (222)
                      .+..|.++++|||++++|-.|+...|-|...
T Consensus       169 ~~~~v~~~~~mg~~~~~~~~al~~~~~~~~~  199 (215)
T 1tte_A          169 DHDLIDEFESQGFEKDKIVEVLRRLGVKSLD  199 (215)
T ss_dssp             SHHHHHHHHHHTCCHHHHHHHHHHSCCSSCC
T ss_pred             cHHHHHHHHHcCCCHHHHHHHHHHcCCCccc
Confidence            4669999999999999999999988876544

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A*

Probab=84.65  E-value=0.73  Score=40.12  Aligned_cols=53  Identities=15%  Similarity=0.372  Sum_probs=30.6

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHH-cCC---ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691          148 SDPVVSRYIALGLNREAVHIAVAN-YGD---NPTKVREFANGYTILREMGFSSNNVAEVLIMY  206 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~-yGd---d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~  206 (222)
                      .|.+|..|..+|++.+.+..+-.. +-.   +++.|.+|      |+++||+...|+.++..|
T Consensus        19 ~~~~v~~L~s~Gl~~~~~~~~~p~l~~~s~~~~~~vl~f------L~~~G~s~~~i~~iv~~~   75 (343)
T 3mva_O           19 NEDLLKNLLTMGVDIDMARKRQPGVFHRMITNEQDLKMF------LLSKGASKEVIASIISRY   75 (343)
T ss_dssp             -CCHHHHHHHHTCCHHHHHHHCGGGGGCSCCCHHHHHHH------HHHTTCCHHHHHHHHHHC
T ss_pred             cHHHHHHHHHcCCCHHHHHHhCchhhccCcccHHHHHHH------HHHcCCCHHHHHHHHHhC
Confidence            466788888888887765443211 122   34444433      347777777777766554

>4fp9_B Mterf domain-containing protein 2; modification enzyme, transferase; HET: SAM; 2.90A {Homo sapiens}

Probab=84.49  E-value=2.6  Score=37.68  Aligned_cols=55  Identities=13%  Similarity=0.187  Sum_probs=38.5

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANGYTILREMGFSSNNVAEVLIMY  206 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~  206 (222)
                      +.++++|.+|||+.+.|..+|..+-. -...+.   ...+.|..+||+.+.|..+|..|
T Consensus        47 e~~l~~L~d~Gfs~~~i~~il~~~P~il~~~l~---~~i~~L~~LGls~e~V~kiL~k~  102 (335)
T 4fp9_B           47 ERVMSSLLDMGFSNAHINELLSVRRGASLQQLL---DIISEFILLGLNPEPVCVVLKKS  102 (335)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHCSSCCHHHHH---HHHHHHHHTTCCHHHHHHHHHHC
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHhCcccchhHHH---HHHHHHHHcCCCHHHHHHHHHhC
Confidence            45788888888888888888875544 443333   33556666788888888887665

>3c1d_A Protein ORAA, regulatory protein RECX; tandem repeats, helix-turn-helix, cytoplasm, DNA damage, DNA repair, SOS response, DNA binding protein; 1.80A {Escherichia coli}

Probab=83.71  E-value=3.9  Score=32.21  Aligned_cols=67  Identities=18%  Similarity=0.182  Sum_probs=47.5

Q ss_pred             CcHHHHHHHHc-----C-----CCHHHHHHHHH-----HcCCChhHHHHHHHH-----------HHHHHhcCCCCchHHH
Q 046691          148 SDPVVSRYIAL-----G-----LNREAVHIAVA-----NYGDNPTKVREFANG-----------YTILREMGFSSNNVAE  201 (222)
Q Consensus       148 ~DP~V~ky~am-----G-----~~reaV~~Av~-----~yGdd~~KV~EFl~~-----------~~~L~EMGFp~~~Vae  201 (222)
                      .-.+..||..+     |     ++.+.|..+|+     +|=||..=+..|+..           -..|+.-|+..+.|.+
T Consensus        22 ~~EL~~kL~~k~~~~~g~e~~~~~~~~i~~vl~~l~~~g~ldD~rfA~~~v~~~~~~g~G~~~I~~eL~~KGI~~~~i~~  101 (159)
T 3c1d_A           22 EQELRRKLAAPIMGKNGPEEIDATAEDYERVIAWCHEHGYLDDSRFVARFIASRSRKGYGPARIRQELNQKGISREATEK  101 (159)
T ss_dssp             HHHHHHHHHCC-----------CCHHHHHHHHHHHHHTTSCCHHHHHHHHHHHHHHTTCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHhhcccCccccCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHHhCCccHHHHHHHHHHcCCCHHHHHH
Confidence            34566777774     7     88888888887     334466666666654           4578888999999999


Q ss_pred             HHHhccCCHHHHH
Q 046691          202 VLIMYENDTDKAL  214 (222)
Q Consensus       202 AL~~~dND~DKAL  214 (222)
                      ||..++.|...++
T Consensus       102 al~~~~~d~~~~a  114 (159)
T 3c1d_A          102 AMREADIDWAALA  114 (159)
T ss_dssp             HHHHHCCCHHHHH
T ss_pred             HHHHcCHhHHHHH
Confidence            9998887755433

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

Probab=83.38  E-value=0.23  Score=42.15  Aligned_cols=36  Identities=11%  Similarity=0.141  Sum_probs=0.0

Q ss_pred             cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      |..|.++++|||+++.|-+|+...|-|.+++.|.|.
T Consensus       178 ~~~v~~~~~mgf~~~~~~~al~~~~~~~~~~~~~l~  213 (216)
T 2pwq_A          178 EVIIKKITEMGFSEDQAKNALIKANWNETLALNTLL  213 (216)
T ss_dssp             ------------------------------------
T ss_pred             hhHHHHHHHcCCCHHHHHHHHHHcCCchHHHHHHHh
Confidence            789999999999999999999999999999988754

>3d5l_A Regulatory protein RECX; PSI-II, NYSGXRC, DNA repair, 10123K, structural genomi protein structure initiative; 2.35A {Lactobacillus reuteri}

Probab=83.15  E-value=2.4  Score=35.35  Aligned_cols=61  Identities=13%  Similarity=0.244  Sum_probs=48.4

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHH-----HcCCChhHHHHHHHH------------HHHHHhcCCCCchHHHHHHhccC
Q 046691          148 SDPVVSRYIALGLNREAVHIAVA-----NYGDNPTKVREFANG------------YTILREMGFSSNNVAEVLIMYEN  208 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~-----~yGdd~~KV~EFl~~------------~~~L~EMGFp~~~VaeAL~~~dN  208 (222)
                      .-.+..||..+|++.+.|..+|+     +|=||..=+..|+..            -..|+.-|++.+.|.+||..++.
T Consensus        78 ~~EL~~KL~~kg~~~e~i~~vl~~L~~~g~ldD~rfA~~~v~~~~~~~~~G~~~I~~eL~~KGI~~~~I~~al~~~~~  155 (221)
T 3d5l_A           78 ESDIVKKLKEIDTPEEFVEPILKKLRGQQLIDDHAYAASYVRTMINTDLKGPGIIRQHLRQKGIGESDIDDALTQFTP  155 (221)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHTTCCHHHHHHHGGGCCH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhccccHHHHHHHHHHcCCCHHHHHHHHHhCCH
Confidence            56788999999999999999887     344466666666654            45788899999999999998754

>1b0n_B Protein (SINI protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1

Probab=82.10  E-value=1  Score=31.72  Aligned_cols=43  Identities=14%  Similarity=0.190  Sum_probs=28.1

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCH---HHHHHHHh
Q 046691          176 PTKVREFANGYTILREMGFSSNNVAEVLIMYENDT---DKALAHLL  218 (222)
Q Consensus       176 ~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~---DKAL~~LL  218 (222)
                      .+...|++..+.+.+++||+.++|.+-|..++-+.   +.+..|-+
T Consensus         9 ~~~d~ewl~LI~~Ak~lGlsleEIrefL~l~~~~~~~~~~~rs~~~   54 (57)
T 1b0n_B            9 FELDQEWVELMVEAKEANISPEEIRKYLLLNKKSAHPGPAARSHTV   54 (57)
T ss_dssp             CCCCHHHHHHHHHHHHTTCCHHHHHHHHHHC---------------
T ss_pred             hHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhccCCCcchHHHhcCC
Confidence            34568999999999999999999999999887665   35555543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	222
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	98.61
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	98.38
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	98.37
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	98.29
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	98.18
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	98.1
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	98.01
d2bwba1	44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.0
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	97.97
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	97.89
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	97.87
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	97.86
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	97.8
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	97.76
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	97.73
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	97.49
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	97.47
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	97.46
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	97.44
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	97.42
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	97.3
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	96.69
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	96.65
d1oqya2	44	DNA repair protein Hhr23a {Human (Homo sapiens) [T	96.03
d3e46a1	42	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal	95.91
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	95.76
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	95.51
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	94.38
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	94.34
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	93.81
d2dkla1	72	Trinucleotide repeat containing 6c protein, TNRC6C	93.52
d1z96a1	38	UBA-domain protein mud1 {Schizosaccharomyces pombe	93.5
d3e46a1	42	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal	92.58
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	92.57
d1wj7a1	91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	92.21
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	91.02
d1ttea1	55	Ubiquitin-protein ligase ubc1 {Baker's yeast (Sacc	90.15
d2cp8a1	41	Migration-inducing protein 19 NBR1 {Human (Homo sa	90.13
d1vega_	83	NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculu	87.81
d1ttea1	55	Ubiquitin-protein ligase ubc1 {Baker's yeast (Sacc	87.56
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	85.17
d1vega_	83	NEDD8 ultimate buster-1 (Nub1) {Mouse (Mus musculu	83.87
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	82.85

>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=98.61  E-value=8.8e-09  Score=67.06  Aligned_cols=39  Identities=26%  Similarity=0.360  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          181 EFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      ||=....+|.+|||+.+.+..||..++||.|+|++.||+
T Consensus         3 ~~e~~i~~L~~MGF~~~~a~~AL~~~~~N~e~A~~~LlS   41 (41)
T d1oqya1           3 EYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLT   41 (41)
T ss_dssp             THHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTTTT
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            344567899999999999999999999999999999985

>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=98.38  E-value=1e-07  Score=68.11  Aligned_cols=35  Identities=26%  Similarity=0.349  Sum_probs=26.4

Q ss_pred             HHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          186 YTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +.+|.+|||..+.+..||..|+||.|+|++.||+.
T Consensus        33 i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~Ll~~   67 (73)
T d1vg5a_          33 IQKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQ   67 (73)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             HHHHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            44577777777777777778888888888888875

>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=98.37  E-value=6.3e-08  Score=67.68  Aligned_cols=37  Identities=16%  Similarity=0.234  Sum_probs=33.7

Q ss_pred             HHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          184 NGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       184 ~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ..+.+|.+|||+.+.+.+||..|+||.|+|++.||+.
T Consensus        21 ~~v~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~Lls~   57 (63)
T d1wgna_          21 QCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAH   57 (63)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            4578999999999999999999999999999999975

>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=98.29  E-value=1.9e-07  Score=64.67  Aligned_cols=36  Identities=33%  Similarity=0.437  Sum_probs=28.4

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+++|.+|||+.+.+..||.+|+||.++|++.||..
T Consensus        12 ~v~~L~~MGF~~~~a~~AL~~~~~~~e~A~~wL~~~   47 (63)
T d1wjia_          12 ALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTS   47 (63)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHHC
Confidence            356778888888888888888888888888888764

>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=98.18  E-value=5e-07  Score=64.43  Aligned_cols=35  Identities=20%  Similarity=0.302  Sum_probs=28.2

Q ss_pred             HHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          186 YTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +.+|.+|||+.+.+.+||..|+||.++|++.||+.
T Consensus        33 i~~L~~MGF~~~~a~~AL~~~~~n~e~Av~~Lls~   67 (73)
T d1wiva_          33 VDTLLSFGFAEDVARKALKASGGDIEKATDWVFNN   67 (73)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHHS
T ss_pred             HHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            56777888888888888888888888888888865

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

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

Probab=98.10  E-value=9.5e-07  Score=59.62  Aligned_cols=34  Identities=21%  Similarity=0.311  Sum_probs=25.4

Q ss_pred             HHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhc
Q 046691          186 YTILREMGFSSNNVAEVLIMYEN-DTDKALAHLLG  219 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs  219 (222)
                      +.+|.||||+.+.+..||...+| |.|.|++.||+
T Consensus        16 l~~L~~MGF~~~~a~~AL~~t~n~~ve~A~~WLl~   50 (51)
T d2cpwa1          16 LDVLLSMGFPRARAQKALASTGGRSVQTACDWLFS   50 (51)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTTTSCHHHHHHHHHS
T ss_pred             HHHHHHcCCCHHHHHHHHHHHCCCCHHHHHHHHHc
Confidence            56777777777777777777776 77777777764

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

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

Probab=98.01  E-value=1.5e-06  Score=60.58  Aligned_cols=34  Identities=26%  Similarity=0.418  Sum_probs=18.9

Q ss_pred             HHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhc
Q 046691          186 YTILREMGFSSNNVAEVLIMYEN-DTDKALAHLLG  219 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs  219 (222)
                      +.+|.+|||+.+.+..||..++| |.|+|++.||+
T Consensus        13 l~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~Wl~~   47 (64)
T d1whca_          13 LESLIEMGFPRGRAEKALALTGNQGIEAAMDWLME   47 (64)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            44555555555555555555544 55555555554

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

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

Probab=98.00  E-value=3.3e-06  Score=55.82  Aligned_cols=40  Identities=23%  Similarity=0.299  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHhcCCCCchHH-HHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGFSSNNVA-EVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~~Va-eAL~~~dND~DKAL~~LLs~  220 (222)
                      -|-..+.+|+||||.-...- .||..+++|.+.||+.||++
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            47788999999999766654 99999999999999999975

>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=97.97  E-value=2.7e-06  Score=56.40  Aligned_cols=37  Identities=27%  Similarity=0.324  Sum_probs=34.1

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhccC
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~s  221 (222)
                      ..++|-+|||..+.+.+||.+||-|.+.|+..||.++
T Consensus         7 ai~eL~~MGF~e~~A~~AL~k~~wnleaAtN~LLd~a   43 (43)
T d2g3qa1           7 AVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDSA   43 (43)
T ss_dssp             HHHHHHTTTSCHHHHHHHHHHHTSCHHHHHHHHHTCC
T ss_pred             HHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHHHhcC
Confidence            4678999999999999999999999999999999763

>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=97.89  E-value=3.8e-06  Score=54.72  Aligned_cols=38  Identities=32%  Similarity=0.428  Sum_probs=33.5

Q ss_pred             HHHHHHHHHhcCCCCchH-HHHHHhccCCHHHHHHHHhc
Q 046691          182 FANGYTILREMGFSSNNV-AEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       182 Fl~~~~~L~EMGFp~~~V-aeAL~~~dND~DKAL~~LLs  219 (222)
                      |-..+.+|++|||.-... ..||...++|.++||+.|+.
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            567899999999987654 59999999999999999985

>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=97.87  E-value=6.9e-06  Score=55.63  Aligned_cols=41  Identities=32%  Similarity=0.483  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHhcCCCCchH-HHHHHhccCCHHHHHHHHhccC
Q 046691          181 EFANGYTILREMGFSSNNV-AEVLIMYENDTDKALAHLLGSS  221 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~~V-aeAL~~~dND~DKAL~~LLs~s  221 (222)
                      -|-..+.+|+||||.-... -.||..+++|.+.||+.||+++
T Consensus         7 ry~~QL~qL~~MGF~d~~~Ni~AL~~t~GdV~~Aie~Ll~~~   48 (50)
T d2dnaa1           7 RFSKEMECLQAMGFVNYNANLQALIATDGDTNAAIYKLKSSQ   48 (50)
T ss_dssp             HTHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHHhcC
Confidence            4778899999999976555 4999999999999999999874

>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=97.86  E-value=5.6e-06  Score=58.03  Aligned_cols=40  Identities=23%  Similarity=0.517  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHhcCCCCchH-HHHHHhccCCHHHHHHHHhcc
Q 046691          181 EFANGYTILREMGFSSNNV-AEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       181 EFl~~~~~L~EMGFp~~~V-aeAL~~~dND~DKAL~~LLs~  220 (222)
                      -|-..+.+|+||||.-..+ -.||..+++|.+.||+.||.+
T Consensus        21 ry~~QL~qL~eMGF~d~~~Nl~AL~~t~Gdv~~Aie~Ll~~   61 (61)
T d1veja1          21 RYQQELEELKALGFANRDANLQALVATDGDIHAAIEMLLGA   61 (61)
T ss_dssp             TSHHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence            3667899999999986666 799999999999999999964

>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=97.80  E-value=5.9e-06  Score=55.30  Aligned_cols=35  Identities=26%  Similarity=0.315  Sum_probs=29.8

Q ss_pred             HHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhcc
Q 046691          186 YTILREMGFSSNNVAEVLIMYEN-DTDKALAHLLGS  220 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs~  220 (222)
                      +++|.+|||+.+.+.+||....| +.+.|++-|+..
T Consensus         6 v~~L~~MGF~~~~a~~Al~~t~n~~ve~A~~Wl~~h   41 (51)
T d2crna1           6 LEPLLAMGFPVHTALKALAATGRKTAEEALAWLHDH   41 (51)
T ss_dssp             HHHHHHTSCCHHHHHHHHHHHTSCCHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHCCCCHHHHHHHHHHc
Confidence            67888999999999999988755 899999988864

>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=97.76  E-value=6.5e-06  Score=53.14  Aligned_cols=37  Identities=22%  Similarity=0.395  Sum_probs=34.4

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      -|..|.+|++|||+|+.|..||...+.|.+++.|||.
T Consensus         4 ~e~~i~~L~~MGF~~~~a~~AL~~~~~N~e~A~~~Ll   40 (41)
T d1oqya1           4 YETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLL   40 (41)
T ss_dssp             HHHHHHHHHTTTCCSHHHHHHHHHSCSSTTHHHHTTT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence            4678999999999999999999999999999999974

>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=97.73  E-value=2.3e-05  Score=53.92  Aligned_cols=41  Identities=15%  Similarity=0.228  Sum_probs=36.7

Q ss_pred             CCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          145 GSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       145 ~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      ..+.+..|.+|++|||+++++.+||..-+.|.+++++||..
T Consensus         6 ~~~d~~~v~~L~~MGF~~~~a~~AL~~~~~~~e~A~~wL~~   46 (63)
T d1wjia_           6 SGVDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLT   46 (63)
T ss_dssp             CSSCHHHHHHHHTTTCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            34567799999999999999999999989999999999854

>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=97.49  E-value=3.2e-05  Score=56.16  Aligned_cols=38  Identities=11%  Similarity=0.272  Sum_probs=29.7

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFAN  184 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~  184 (222)
                      +.+.+|.+|++|||++.++.+||..-+. |.+.+.+||.
T Consensus        28 ~d~~~v~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~Wl~   66 (84)
T d1veka_          28 ANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLL   66 (84)
T ss_dssp             CCHHHHHHHHHHTCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4556888888888888888888887765 7888888764

>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=97.47  E-value=0.00017  Score=50.98  Aligned_cols=41  Identities=24%  Similarity=0.363  Sum_probs=36.9

Q ss_pred             CCCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          144 VGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       144 ~~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      ...+.+..|.+|++|||+++++..||..-+.|.+.+.|||.
T Consensus        25 ~~~~~ee~i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~Ll   65 (73)
T d1vg5a_          25 RVAASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILM   65 (73)
T ss_dssp             CSCCCHHHHHHHHTTTCCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             CcCcCHHHHHHHHHhCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            34456889999999999999999999999999999999984

>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=97.46  E-value=9e-05  Score=51.25  Aligned_cols=41  Identities=15%  Similarity=0.197  Sum_probs=35.5

Q ss_pred             CCCCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHH
Q 046691          145 GSGSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANG  185 (222)
Q Consensus       145 ~~~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~  185 (222)
                      ..+...+|.+|++|||+++++.+||..-|. +.+.++|||..
T Consensus         6 s~~d~~~l~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~Wl~~   47 (64)
T d1whca_           6 SGAELTALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLME   47 (64)
T ss_dssp             CCCCCCHHHHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            344567999999999999999999998877 89999999854

>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=97.44  E-value=4.9e-05  Score=52.64  Aligned_cols=38  Identities=18%  Similarity=0.314  Sum_probs=34.9

Q ss_pred             CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      .+..|.+|++|||+++.|.+||+..|.|.+.++|||..
T Consensus        19 de~~v~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~Lls   56 (63)
T d1wgna_          19 ERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFA   56 (63)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHCSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            45689999999999999999999999999999999854

>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=97.42  E-value=0.00024  Score=50.15  Aligned_cols=41  Identities=12%  Similarity=0.258  Sum_probs=36.5

Q ss_pred             CCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          145 GSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       145 ~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      ..+....|.+|++|||++++|.+||..-|.|.+.++|||..
T Consensus        26 ~~~d~~~i~~L~~MGF~~~~a~~AL~~~~~n~e~Av~~Lls   66 (73)
T d1wiva_          26 SDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFN   66 (73)
T ss_dssp             CSSCHHHHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence            34556689999999999999999999999999999999853

>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=97.30  E-value=0.00021  Score=47.77  Aligned_cols=41  Identities=12%  Similarity=0.185  Sum_probs=36.1

Q ss_pred             CCCCCcHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q 046691          144 VGSGSDPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFAN  184 (222)
Q Consensus       144 ~~~~~DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~  184 (222)
                      ...+.+..|..|++|||+++++..||..-|. |-+.++|||.
T Consensus         8 ~~~~~~~~l~~L~~MGF~~~~a~~AL~~t~n~~ve~A~~WLl   49 (51)
T d2cpwa1           8 GTIKHGSALDVLLSMGFPRARAQKALASTGGRSVQTACDWLF   49 (51)
T ss_dssp             CSSSCCCHHHHHHHHTCCHHHHHHHHHHTTTSCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHcCCCHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            4456778999999999999999999998787 8999999974

>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=96.69  E-value=0.0016  Score=46.86  Aligned_cols=36  Identities=28%  Similarity=0.315  Sum_probs=32.0

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHhcc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYEN-DTDKALAHLLGS  220 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LLs~  220 (222)
                      .+++|.+|||+.+.+.+||....| |.+.|++.|++.
T Consensus        32 ~v~~L~~MGF~~~~a~~AL~~t~n~~~e~A~~Wl~~h   68 (84)
T d1veka_          32 IVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSH   68 (84)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHHHc
Confidence            467899999999999999988655 999999999864

>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=96.65  E-value=0.00094  Score=44.25  Aligned_cols=34  Identities=15%  Similarity=0.274  Sum_probs=30.7

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q 046691          151 VVSRYIALGLNREAVHIAVANYGD-NPTKVREFAN  184 (222)
Q Consensus       151 ~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~  184 (222)
                      +|.+|++|||+++++.+||..-|. +-+.++||+.
T Consensus         5 ~v~~L~~MGF~~~~a~~Al~~t~n~~ve~A~~Wl~   39 (51)
T d2crna1           5 LLEPLLAMGFPVHTALKALAATGRKTAEEALAWLH   39 (51)
T ss_dssp             SHHHHHHTSCCHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            689999999999999999998776 8899999875

>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=96.03  E-value=0.0014  Score=43.29  Aligned_cols=37  Identities=22%  Similarity=0.362  Sum_probs=33.6

Q ss_pred             HHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          184 NGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       184 ~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      ....+|.+|||+.+.|-+|-+.||-|.+-|...|+..
T Consensus         6 ~aIeRL~~LGF~r~~viqay~ACdKNEelAaN~L~~~   42 (44)
T d1oqya2           6 EAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQ   42 (44)
T ss_dssp             HHHHHHHHHTCCSHHHHHHTSSSSSCSSHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhCcCHHHHHHHHHHc
Confidence            3567999999999999999999999999999999864

>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=95.91  E-value=0.0052  Score=39.75  Aligned_cols=39  Identities=28%  Similarity=0.291  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691          180 REFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       180 ~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL  218 (222)
                      .||......|-.|||..+.|-.||-.-.=|.|-|.+.||
T Consensus         4 peyt~kidklca~gf~knavi~alsskswdvetatelll   42 (42)
T d3e46a1           4 PEYTKKIENLCAAGFDRNAVIVALSSKSWDVETATELLL   42 (42)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHccccccceeeeeccCccchhhHHHhhC
Confidence            478888899999999999999999999999999999886

>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=95.76  E-value=0.0044  Score=40.63  Aligned_cols=39  Identities=15%  Similarity=0.198  Sum_probs=34.5

Q ss_pred             CCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691          146 SGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       146 ~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      +|.+-.|.+|+.|||+++.+..||+...-|.+-+..||.
T Consensus         2 tpk~~ai~eL~~MGF~e~~A~~AL~k~~wnleaAtN~LL   40 (43)
T d2g3qa1           2 TPKSLAVEELSGMGFTEEEAHNALEKCNWDLEAATNFLL   40 (43)
T ss_dssp             CHHHHHHHHHHTTTSCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             CcHHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            356779999999999999999999999999998888764

>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=95.51  E-value=0.006  Score=41.58  Aligned_cols=32  Identities=28%  Similarity=0.264  Sum_probs=26.6

Q ss_pred             HHHHhc-CCCCchHHHHHHhccCCHHHHHHHHh
Q 046691          187 TILREM-GFSSNNVAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       187 ~~L~EM-GFp~~~VaeAL~~~dND~DKAL~~LL  218 (222)
                      .+|||. |.+--+.++||..|+||.|||++.|-
T Consensus         9 k~LRe~Tga~~~dcKkAL~e~~gD~ekA~e~Lr   41 (56)
T d1xb2b1           9 MKLRRKTGYSFINCKKALETCGGDLKQAESWLH   41 (56)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            344443 78888999999999999999999884

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

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

Probab=94.38  E-value=0.025  Score=37.84  Aligned_cols=30  Identities=33%  Similarity=0.276  Sum_probs=25.8

Q ss_pred             HHHh-cCCCCchHHHHHHhccCCHHHHHHHH
Q 046691          188 ILRE-MGFSSNNVAEVLIMYENDTDKALAHL  217 (222)
Q Consensus       188 ~L~E-MGFp~~~VaeAL~~~dND~DKAL~~L  217 (222)
                      +||+ -|++--..++||..++||.|+|++.|
T Consensus         8 ~LR~~Tga~~~dcKkAL~e~~gD~ekA~e~L   38 (52)
T d1aipc1           8 KLREATGAGMMDVKRALEDAGWDEEKAVQLL   38 (52)
T ss_dssp             HHHHHHCCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            3443 38888999999999999999999987

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

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

Probab=94.34  E-value=0.026  Score=38.06  Aligned_cols=30  Identities=23%  Similarity=0.296  Sum_probs=25.4

Q ss_pred             HHHhc-CCCCchHHHHHHhccCCHHHHHHHH
Q 046691          188 ILREM-GFSSNNVAEVLIMYENDTDKALAHL  217 (222)
Q Consensus       188 ~L~EM-GFp~~~VaeAL~~~dND~DKAL~~L  217 (222)
                      +||++ |.+--+.++||..++||.|||++.|
T Consensus        10 ~LR~~Tgag~~dCKkAL~e~~gD~ekA~e~L   40 (54)
T d1efub3          10 ELRERTGAGMMDCKKALTEANGDIELAIENM   40 (54)
T ss_dssp             HHHHHHCCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            34443 7778899999999999999999987

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

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

Probab=93.81  E-value=0.026  Score=38.05  Aligned_cols=41  Identities=17%  Similarity=0.265  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHhc--CCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          179 VREFANGYTILREM--GFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       179 V~EFl~~~~~L~EM--GFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      -.||-..+.+|++|  .+..+-|+.+|..++++.|+|++.||.
T Consensus         9 ~~e~~e~~~~Lk~MFP~~D~~VI~~VL~a~~G~vd~aidaLL~   51 (54)
T d1mn3a_           9 ENERKDTLNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLS   51 (54)
T ss_dssp             HHHHHHHHHHHHHHCTTSCHHHHHHHHSCSSCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            46888899999999  455688999999999999999999996

>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=93.52  E-value=0.028  Score=40.08  Aligned_cols=35  Identities=29%  Similarity=0.374  Sum_probs=31.2

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      ...||..|||+.+...++|..++.|.|.|+-.|+-
T Consensus        17 ~~KQfsnMGf~re~~e~~l~sN~m~L~~a~~~l~d   51 (72)
T d2dkla1          17 LIKQLTDMGFPREPAEEALKSNNMNLDQAMSALLE   51 (72)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             HHHHHhhcCCcCCChHHhhhccCcchhhcccchhh
Confidence            35688999999999999999999999999988764

>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=93.50  E-value=0.039  Score=34.72  Aligned_cols=34  Identities=32%  Similarity=0.347  Sum_probs=30.4

Q ss_pred             HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691          185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLL  218 (222)
Q Consensus       185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL  218 (222)
                      ...||-.|||.+-+.+.||-..|+|.|-|-..||
T Consensus         5 kiaqlvsmgfdpleaaqaldaangdldvaasfll   38 (38)
T d1z96a1           5 KIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL   38 (38)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             HHHHHHHcCCCHHHHHHHHhhhcCcHHHHHHhhC
Confidence            4678999999999999999999999999987765

>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=92.58  E-value=0.1  Score=33.45  Aligned_cols=33  Identities=21%  Similarity=0.296  Sum_probs=25.9

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHH
Q 046691          151 VVSRYIALGLNREAVHIAVANYGDNPTKVREFA  183 (222)
Q Consensus       151 ~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl  183 (222)
                      -+.||++|||.+.||-.|+-.---|-+.+-|.+
T Consensus         9 kidklca~gf~knavi~alsskswdvetatell   41 (42)
T d3e46a1           9 KIENLCAAGFDRNAVIVALSSKSWDVETATELL   41 (42)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHccccccceeeeeccCccchhhHHHhh
Confidence            578999999999999999986555666555543

>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=92.57  E-value=0.042  Score=37.56  Aligned_cols=35  Identities=20%  Similarity=0.332  Sum_probs=29.5

Q ss_pred             HHHHHhc--CCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          186 YTILREM--GFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       186 ~~~L~EM--GFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      +..|++|  .+..+.|.-+|..|+++.|+|++.||.-
T Consensus        13 i~~LkeMFP~~D~~vI~~VL~a~~G~vd~aid~LL~M   49 (59)
T d1wgla_          13 LKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQM   49 (59)
T ss_dssp             HHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHS
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            5677888  3446789999999999999999999964

>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=92.21  E-value=0.14  Score=37.70  Aligned_cols=44  Identities=20%  Similarity=0.280  Sum_probs=35.3

Q ss_pred             CChhHHHHHHHHHHHHHhc-CCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691          174 DNPTKVREFANGYTILREM-GFSSNNVAEVLIMYENDTDKALAHLLGS  220 (222)
Q Consensus       174 dd~~KV~EFl~~~~~L~EM-GFp~~~VaeAL~~~dND~DKAL~~LLs~  220 (222)
                      .+...+.|.++.   |.|| |=.++.|--||.-||||.++|+.+||-+
T Consensus        27 ~~D~~i~~kVkq---l~e~T~rsede~~~ALhDcn~D~~~AIn~lLEg   71 (91)
T d1wj7a1          27 HNDADFEEKVKQ---LIDITGKNQDECVIALHDCNGDVNRAINVLLEG   71 (91)
T ss_dssp             SCCHHHHHHHHH---HHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             CCcHHHHHHHHH---HHHHhCCCHHHHHHHHhcCCccHHHHHHHHHhc
Confidence            455556666655   4554 7789999999999999999999999975

>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=91.02  E-value=0.33  Score=33.13  Aligned_cols=37  Identities=24%  Similarity=0.256  Sum_probs=31.6

Q ss_pred             cHHHHHHHHcCC-CHHHHHHHHHHcCCChhHHHHHHHH
Q 046691          149 DPVVSRYIALGL-NREAVHIAVANYGDNPTKVREFANG  185 (222)
Q Consensus       149 DP~V~ky~amG~-~reaV~~Av~~yGdd~~KV~EFl~~  185 (222)
                      -..+..|.+||| ++++--.||..=|.|-+.+.|||.+
T Consensus        23 ~~QL~qL~eMGF~d~~~Nl~AL~~t~Gdv~~Aie~Ll~   60 (61)
T d1veja1          23 QQELEELKALGFANRDANLQALVATDGDIHAAIEMLLG   60 (61)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            458899999999 5666689999999999999999853

>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=90.15  E-value=0.16  Score=34.37  Aligned_cols=28  Identities=7%  Similarity=0.259  Sum_probs=18.3

Q ss_pred             CCcHHHHHHHHcCCCHHHHHHHHHHcCC
Q 046691          147 GSDPVVSRYIALGLNREAVHIAVANYGD  174 (222)
Q Consensus       147 ~~DP~V~ky~amG~~reaV~~Av~~yGd  174 (222)
                      -++..|.++.+|||+|+-|-.+++..|-
T Consensus         8 id~~~V~~f~~mGF~rdKvI~VLrrlgi   35 (55)
T d1ttea1           8 IDHDLIDEFESQGFEKDKIVEVLRRLGV   35 (55)
T ss_dssp             CSHHHHHHHHHHTCCHHHHHHHHHHSCC
T ss_pred             CCHHHHHHHHHcCCCchhHHHHHHHhCc
Confidence            3455777777777777766666665554

>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=90.13  E-value=0.21  Score=32.05  Aligned_cols=36  Identities=22%  Similarity=0.260  Sum_probs=30.1

Q ss_pred             HHHHHHHhcCCCCchHH-HHHHhccCCHHHHHHHHhc
Q 046691          184 NGYTILREMGFSSNNVA-EVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       184 ~~~~~L~EMGFp~~~Va-eAL~~~dND~DKAL~~LLs  219 (222)
                      ..|..|-||||--..+- ..|-+|+|+..+++..||.
T Consensus         4 ~lM~~L~EMGF~DR~lNq~LL~KH~~nl~~vV~eLlq   40 (41)
T d2cp8a1           4 ALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELLQ   40 (41)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHTTTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHhCcchhHHHHHHHHHccCcHHHHHHHHHc
Confidence            46889999999877765 5667899999999999874

>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=87.81  E-value=0.71  Score=33.29  Aligned_cols=37  Identities=16%  Similarity=0.285  Sum_probs=30.3

Q ss_pred             CCCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHH
Q 046691          144 VGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVR  180 (222)
Q Consensus       144 ~~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~  180 (222)
                      -..+.-.-|.+|+-|||.++++.-||+.+++|-.-+.
T Consensus        25 q~~~sQesidqLvYMGF~~~~Ae~ALRvfrGnVQlAa   61 (83)
T d1vega_          25 QASPSQESINQLVYMGFDTVVAEAALRVFGGNVQLAA   61 (83)
T ss_dssp             SCCCCHHHHHHHHHHSCCHHHHHHHHHHTTTCHHHHH
T ss_pred             cCCCCHHHHHHHHHhcccHHHHHHHHHHhcccHHHHH
Confidence            3445556899999999999999999999999865443

>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=87.56  E-value=0.23  Score=33.66  Aligned_cols=32  Identities=28%  Similarity=0.516  Sum_probs=23.1

Q ss_pred             HHHHhcCCCCchHHHHHHhcc------CC---HHHHHHHHh
Q 046691          187 TILREMGFSSNNVAEVLIMYE------ND---TDKALAHLL  218 (222)
Q Consensus       187 ~~L~EMGFp~~~VaeAL~~~d------ND---~DKAL~~LL  218 (222)
                      .+|..|||+.++|-++|-.-+      ||   .+|.|+.||
T Consensus        14 ~~f~~mGF~rdKvI~VLrrlgik~~~~~~~~~~n~ilEELL   54 (55)
T d1ttea1          14 DEFESQGFEKDKIVEVLRRLGVKSLDPNDNNTANRIIEELL   54 (55)
T ss_dssp             HHHHHHTCCHHHHHHHHHHSCCSSCCSSCCHHHHHHHHHHT
T ss_pred             HHHHHcCCCchhHHHHHHHhCcCCCCcccchHHHHHHHHHh
Confidence            466789999999999996421      22   457888876

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=85.17  E-value=0.63  Score=32.48  Aligned_cols=40  Identities=23%  Similarity=0.249  Sum_probs=30.4

Q ss_pred             hHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHH
Q 046691          177 TKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAH  216 (222)
Q Consensus       177 ~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~  216 (222)
                      .+..+-+.....|+++||+.+.|++.|-..+-|...+++.
T Consensus        43 ~~~~~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~l~~   82 (109)
T d1r8da_          43 DADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAALQS   82 (109)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHHCTTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHhccCccHHHHHHH
Confidence            3556667778889999999999999887666666666654

>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=83.87  E-value=0.44  Score=34.44  Aligned_cols=34  Identities=21%  Similarity=0.236  Sum_probs=31.2

Q ss_pred             HHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691          186 YTILREMGFSSNNVAEVLIMYENDTDKALAHLLG  219 (222)
Q Consensus       186 ~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs  219 (222)
                      ++||-=|||..+.++.||-+..+|+.-|.+.|..
T Consensus        33 idqLvYMGF~~~~Ae~ALRvfrGnVQlAaQtLah   66 (83)
T d1vega_          33 INQLVYMGFDTVVAEAALRVFGGNVQLAAQTLAH   66 (83)
T ss_dssp             HHHHHHHSCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHhcccHHHHHHHHHHhcccHHHHHHHHHH
Confidence            5788889999999999999999999999998864

>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=82.85  E-value=1.2  Score=28.01  Aligned_cols=34  Identities=21%  Similarity=0.190  Sum_probs=28.7

Q ss_pred             HHHHHHHcCCC-HHHHHHHHHHcCCChhHHHHHHH
Q 046691          151 VVSRYIALGLN-REAVHIAVANYGDNPTKVREFAN  184 (222)
Q Consensus       151 ~V~ky~amG~~-reaV~~Av~~yGdd~~KV~EFl~  184 (222)
                      ....|-+|||. +++-..||..-|.|-+++.|+|.
T Consensus         5 QL~~L~~MGF~d~~~Ni~AL~~t~Gdv~~Aie~Ll   39 (41)
T d2daha1           5 QLEQLRSMGFLNREANLQALIATGGDVDAAVEKLR   39 (41)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            46789999995 56666899999999999999985