Citrus Sinensis ID: 025638

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250
Protein Sequence
MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVRSGSDDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVPGESATSCSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIITNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLILTLLGP
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccHHHHHHHHHHcHHHHHHHHHHHHccccccHHHHcccccccccccccccccccccccccccccHHHHHHccccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEcccccHHHcccccccccHHcccccccccccccccccHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
msagvcgkrvgfeeicgsssptsakrsrcstfgslvrsgsddpvsfllqmfpdvdpeVVKSVLGEHDNKIEDAIDRLRVLSFSNISERiksqgleptiignfsavpgesatscsqmsEEEVRSAHtnfcgenitdgskWVDLFVHEMMSAADLDDARGRAARILEVFERSIITNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLILTLLGP
Flexible Loop (DISEMBL)
msagvcgkrvgfeeicgsssptsakrsrCSTFGSLVRSGSDDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERiksqgleptiIGNFSAVPGESATSCSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIITNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLILTLLGP
Low Complexity Region (SEG)
MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVRSGSDDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVPGESATSCSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSaadlddargraarILEVFERSIITNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHleqeqkekevellklvISQYQDQARNLEVIFLILTLLGP
Disordered region (IsUnstruct)
*******************************************VSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNF***********************TNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIIT***********************************************VELLKLVISQYQDQARNLEVIFLILTLL**
Disordered Region (DISOPRED)
*SAGVCGKRV*********************************VSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSF***************************************************TDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSI*********************LLNDNQILKKAVSIQHE****************LVISQYQDQARNLEVIFLILTLLGP
Disordered Region (DISEMBL)
MSAGVCGKRVGFEEIC*****************SLVRSGSDDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVP*****************AHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIITNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLILTLLGP
Disordered Region (DISPRO)
*********VGFEEIC***********************SDDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSN*************************************************TDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIITNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLILTLLGP
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVRSGSDDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVPGESATSCSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIITNSKASKELExxxxxxxxxxxxxxxxxxxxxVSIQHERHLExxxxxxxxxxxxxxxxxxxxxARNLEVIFLILTLLGP
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	250
255573637	268	conserved hypothetical protein [Ricinus	0.972	0.906	0.603	8e-75
359481792	274	PREDICTED: uncharacterized protein LOC10	0.984	0.897	0.576	3e-67
449448649	249	PREDICTED: uncharacterized protein LOC10	0.884	0.887	0.527	7e-56
147859242	213	hypothetical protein VITISV_023939 [Viti	0.76	0.892	0.544	3e-49
297806185	247	hypothetical protein ARALYDRAFT_349548 [	0.852	0.862	0.436	9e-45
294464579	264	unknown [Picea sitchensis]	0.932	0.882	0.414	4e-36
118483552	286	unknown [Populus trichocarpa]	0.956	0.835	0.401	4e-36
224144158	270	predicted protein [Populus trichocarpa]	0.896	0.829	0.395	3e-35
118488028	285	unknown [Populus trichocarpa]	0.952	0.835	0.386	9e-35
224090347	280	predicted protein [Populus trichocarpa]	0.936	0.835	0.377	6e-34

>gi|255573637|ref|XP_002527741.1| conserved hypothetical protein [Ricinus communis] gi|223532882|gb|EEF34654.1| conserved hypothetical protein [Ricinus communis]

 Score =  286 bits (731), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 152/252 (60%), Positives = 185/252 (73%), Gaps = 9/252 (3%)

Query: 1   MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVRS-----GSDDPVSFLLQMFPDVD 55
           MSAGVCGKRVGFEEI GSSS  +AKRSRCS FGS  RS     GSDD +  LLQMFP +D
Sbjct: 1   MSAGVCGKRVGFEEIFGSSS--AAKRSRCSGFGSPTRSTDFGSGSDDTLFTLLQMFPSLD 58

Query: 56  PEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVPGESATSCSQ 115
           PE+V++    H+NK++DA+  L  +SF +  ER K Q  E   IGN  AVP  S T+C Q
Sbjct: 59  PELVRTAHRNHNNKVDDAVKTLMKISFGDAVERNKLQSFESATIGNCDAVPPMSMTACLQ 118

Query: 116 MSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIITNS 175
           M EEEV    +++  EN  DGSKWVDLFV EMM+AADLDDAR R+A+ILE FERSI   +
Sbjct: 119 MPEEEVEKKASDY--ENAVDGSKWVDLFVQEMMNAADLDDARRRSAQILEAFERSITAQA 176

Query: 176 KASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQA 235
              ++LE  SLKEHLQSLLNDNQILK+AV+IQHER+LEQE+K KEV+ LKL+++QYQ+Q 
Sbjct: 177 NRLEQLELTSLKEHLQSLLNDNQILKRAVAIQHERNLEQEEKTKEVQNLKLLLNQYQEQI 236

Query: 236 RNLEVIFLILTL 247
           R+LE+    L L
Sbjct: 237 RSLELNNYALKL 248

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359481792|ref|XP_002263099.2| PREDICTED: uncharacterized protein LOC100247807 [Vitis vinifera] gi|297740397|emb|CBI30579.3| unnamed protein product [Vitis vinifera]

 Score =  261 bits (666), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 147/255 (57%), Positives = 184/255 (72%), Gaps = 9/255 (3%)

Query: 1   MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVRS-----GSDDPVSFLLQMFPDVD 55
           MSAGVCGKRVGFEEI GSSS +S +   CSTFGS VRS     GSDD VS LLQMFP++D
Sbjct: 1   MSAGVCGKRVGFEEIFGSSSTSSKRSR-CSTFGSPVRSSDFGSGSDDSVSVLLQMFPNLD 59

Query: 56  PEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVPGESATSCSQ 115
            E+V++VL  H+NKIEDAI+ L  LS  +   R +SQGL+  ++GN    P +S     Q
Sbjct: 60  REMVETVLRTHNNKIEDAIESLHALSLGDTIARNESQGLDSAMMGNNDTGPAQSEHEYGQ 119

Query: 116 MSE---EEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSII 172
            +E   E+V+   + F   N  DGSKWVDLFVHEMM+A DL DAR RAARILE FE++++
Sbjct: 120 TTEQKVEDVQDLKSMFEFGNAMDGSKWVDLFVHEMMNATDLSDARARAARILEAFEKNVV 179

Query: 173 TNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQ 232
           ++S   KELEHASLKEHLQ+ L DNQILK+AV+IQH+R+LEQE++ +EV+ LK VI QYQ
Sbjct: 180 SHSMELKELEHASLKEHLQNFLRDNQILKRAVAIQHDRNLEQEERAREVQQLKDVIRQYQ 239

Query: 233 DQARNLEVIFLILTL 247
           +Q R LE+    L L
Sbjct: 240 EQVRALELNNYTLKL 254

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448649|ref|XP_004142078.1| PREDICTED: uncharacterized protein LOC101216078 [Cucumis sativus] gi|449525433|ref|XP_004169722.1| PREDICTED: uncharacterized protein LOC101227012 [Cucumis sativus]

 Score =  223 bits (567), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 136/258 (52%), Positives = 160/258 (62%), Gaps = 37/258 (14%)

Query: 1   MSAGVCGKRVGFEEICGSSSPTS----AKRSRCSTFGSLVRS----GSDDPVSFLLQMFP 52
           MSAGVCGKRVGFEEI GSSS  +    AKRSR STFGS  RS    G DD  S LLQMFP
Sbjct: 1   MSAGVCGKRVGFEEIFGSSSSPTACSSAKRSRWSTFGSPTRSDFGSGPDDSASVLLQMFP 60

Query: 53  DVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVPGESATS 112
            V  EV                      SF + S R  S       IGN S VP E   +
Sbjct: 61  GVGAEVP---------------------SFDDFSARGHS-----ATIGNCSTVPDERTAT 94

Query: 113 CSQMSEEEVRSAH---TNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFER 169
           CSQMS E++  A    +     N   GSKWVD+FV EM  A D+ DAR RAARILE FE 
Sbjct: 95  CSQMSHEKIEEAKDVGSTVAEGNGMHGSKWVDMFVQEMAGAVDVGDARIRAARILEAFEH 154

Query: 170 SIITNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVIS 229
           ++  NS+ S+EL+HASLKEHLQ+L+NDNQILK+AV+IQHER+LEQE+K +EV  LK V+ 
Sbjct: 155 NVTVNSRESEELKHASLKEHLQNLVNDNQILKRAVAIQHERNLEQEEKTREVHQLKHVLC 214

Query: 230 QYQDQARNLEVIFLILTL 247
           QYQ+Q ++LEV    L L
Sbjct: 215 QYQEQIQSLEVRNYTLNL 232

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147859242|emb|CAN79697.1| hypothetical protein VITISV_023939 [Vitis vinifera]

 Score =  201 bits (510), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 105/193 (54%), Positives = 138/193 (71%), Gaps = 3/193 (1%)

Query: 58  VVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVPGESATSCSQMS 117
           +V++VL  H+NKIEDAI+ L  LS  +   R +SQGL+  ++GN    P +S     Q +
Sbjct: 1   MVETVLRTHNNKIEDAIESLHALSLGDTIARNESQGLDSAMMGNNDTAPAQSEHEYGQTT 60

Query: 118 E---EEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIITN 174
           E   E+V+   + F   N  DGSKWVDLFVHEMM+A DL DAR RAARILE FE++++++
Sbjct: 61  EQKVEDVQDLKSMFEFGNAMDGSKWVDLFVHEMMNATDLSDARARAARILEAFEKNVVSH 120

Query: 175 SKASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQ 234
           S   KELEHASLKEHLQ+LL DNQILK+AV+IQH+R+LEQE++ +EV+ LK VI QYQ+Q
Sbjct: 121 SMELKELEHASLKEHLQNLLRDNQILKRAVAIQHDRNLEQEERAREVQQLKDVIRQYQEQ 180

Query: 235 ARNLEVIFLILTL 247
            R LE+    L L
Sbjct: 181 VRALELNNYTLKL 193

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297806185|ref|XP_002870976.1| hypothetical protein ARALYDRAFT_349548 [Arabidopsis lyrata subsp. lyrata] gi|297316813|gb|EFH47235.1| hypothetical protein ARALYDRAFT_349548 [Arabidopsis lyrata subsp. lyrata]

 Score =  186 bits (471), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 107/245 (43%), Positives = 145/245 (59%), Gaps = 32/245 (13%)

Query: 1   MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVRS-----GSDDPVSFLLQMFPDVD 55
           MS  VCGKRVG+++  GSSS  + KRS+ S+FGS +RS     GSDDP + L+ MFP +D
Sbjct: 1   MSTRVCGKRVGYDDFFGSSSSPTNKRSKWSSFGSPIRSSEVGSGSDDPFASLIHMFPSMD 60

Query: 56  PEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTIIGNFSAVPGESATSCSQ 115
           PE V+ VL   +   E+A + L  + F+  S+R        T  G+F    G        
Sbjct: 61  PEFVREVLSNKNYVFEEAKESLSSILFNGDSDR--------TEAGSFDGSVG-------- 104

Query: 116 MSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSIITNS 175
                      ++  E++ DG+KWVD  V EM  A ++DD R R A ILE  E  I  N+
Sbjct: 105 -----------SWKDEDMIDGAKWVDRLVSEMAKAINVDDMRRRVAVILEALEIIIKKNT 153

Query: 176 KASKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQA 235
            AS +LE+ASLKE LQSL+NDNQILK+ ++ QH+R  E E+K K+V+ LK V+ QYQDQ 
Sbjct: 154 NASNKLEYASLKESLQSLINDNQILKRVIANQHQRSSENEEKAKQVQHLKGVVGQYQDQV 213

Query: 236 RNLEV 240
             LE+
Sbjct: 214 HKLEL 218

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294464579|gb|ADE77799.1| unknown [Picea sitchensis]

 Score =  157 bits (397), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 107/258 (41%), Positives = 155/258 (60%), Gaps = 25/258 (9%)

Query: 1   MSAGVCGKRVG-FEEICGSSSPTSAKRSRCSTFGSLVRSGSDDPVSFLLQMFPDVDPEVV 59
           MSA VCGKR+  FE++ GS  P  AKR R ++  SL  S   D +S L+ +FP +DP++V
Sbjct: 1   MSAAVCGKRLPPFEDVHGSP-PIVAKRLRYTS--SLSPS---DNLSRLIALFPAMDPQLV 54

Query: 60  KSVLGEHDNKIEDAIDRLRVLSFSNISERI--KSQGL-----EPTIIGNFSAVPGESATS 112
           +SV    D  ++ AI  L  L  +   + I     GL     +P        VPG + ++
Sbjct: 55  ESVFESCDENMDHAIKSLSNLCLNPFEKNIFTADDGLVHSDAQPV------QVPGSTQST 108

Query: 113 CSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARGRAARILEVFERSII 172
            +  S  E   A  +       DG +WV+  V EM +A+DLDDAR RA+RILE FE++++
Sbjct: 109 DADSSNLEF--AQLDGKSGCPADGVEWVEFLVIEMKNASDLDDARSRASRILEAFEKTVM 166

Query: 173 TNSKASKEL---EHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVIS 229
           + S A  E+   E+ SLKE +Q+LL++N ILK+AV+IQHER LEQE+K KEV+ L+ +++
Sbjct: 167 SRSGAMAEVLYKENTSLKEQVQNLLHENNILKRAVAIQHERQLEQEEKSKEVQQLRQLVT 226

Query: 230 QYQDQARNLEVIFLILTL 247
           QYQ+Q R LE+    L L
Sbjct: 227 QYQEQVRTLELNNYALKL 244

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118483552|gb|ABK93674.1| unknown [Populus trichocarpa]

 Score =  157 bits (397), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 110/274 (40%), Positives = 156/274 (56%), Gaps = 35/274 (12%)

Query: 1   MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVR-------SGSDDPVSF------- 46
           MSA VCGKR  FEE+  +S P S KR RCS+  S VR       + + +P SF       
Sbjct: 1   MSAIVCGKRSFFEELTVTSPPVS-KRIRCSS-SSPVRFSPPRSNTLASNPPSFNFGSSSS 58

Query: 47  --------LLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTI 98
                   L  +FPD+D ++++ VL E  + ++ AI  L  L   + +E   +   +  +
Sbjct: 59  SSSTLIEQLAAIFPDMDKQLIEKVLEECGDDLDSAIRSLNDLRLGS-AENFSAAADKSDV 117

Query: 99  IGNFSAVPGES-ATSCSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDAR 157
           I   S VP +  AT+ ++    E  SA  +       DG++WV+LFV EMMSA+++DDAR
Sbjct: 118 IDE-SNVPAQGVATTGAEAPPTEDLSASAHLS----LDGAEWVELFVREMMSASNIDDAR 172

Query: 158 GRAARILEVFERSIITNSKASK----ELEHASLKEHLQSLLNDNQILKKAVSIQHERHLE 213
            RA+R LEV E+SI   + A        EH  LKE +Q+L+ +N ILK+AVSIQHER  E
Sbjct: 173 ARASRALEVLEKSICARAGAEAVKNFHQEHMILKEQVQALIQENTILKRAVSIQHERQKE 232

Query: 214 QEQKEKEVELLKLVISQYQDQARNLEVIFLILTL 247
            E++ +E++ LK ++SQYQDQ R LEV    LTL
Sbjct: 233 YEERNQEMQQLKQLVSQYQDQLRTLEVNNYALTL 266

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144158|ref|XP_002325204.1| predicted protein [Populus trichocarpa] gi|222866638|gb|EEF03769.1| predicted protein [Populus trichocarpa]

 Score =  154 bits (390), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 152/273 (55%), Gaps = 49/273 (17%)

Query: 1   MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVR-------SGSDDPVSF------- 46
           MSA VCGKR  FEE+  +S P S KR RCS+  S VR       + + +P SF       
Sbjct: 1   MSAIVCGKRSFFEELTVTSPPVS-KRIRCSS-SSPVRFSPPRSNTLASNPPSFNFGSSSS 58

Query: 47  --------LLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTI 98
                   L  +FPD+D ++++ VL E  + ++ AI  L  L   + +E   +   +  +
Sbjct: 59  SSSTLIEQLAAIFPDMDKQLIEKVLEECGDDLDSAIRSLNDLRLGS-AENFSAAADKSDV 117

Query: 99  IGNFSAVPGESATSCSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARG 158
           I   S VP ++             SAH +       DG++WV+LFV EMMSA+++DDAR 
Sbjct: 118 IDE-SNVPAQA-------------SAHLSL------DGAEWVELFVREMMSASNIDDARA 157

Query: 159 RAARILEVFERSIITNSKASK----ELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQ 214
           RA+R LEV E+SI   + A        EH  LKE +Q+L+ +N ILK+AVSIQHER  E 
Sbjct: 158 RASRALEVLEKSICARAGAEAVKNFHQEHMILKEQVQALIQENTILKRAVSIQHERQKEY 217

Query: 215 EQKEKEVELLKLVISQYQDQARNLEVIFLILTL 247
           E++ +E++ LK ++SQYQDQ R LEV    LTL
Sbjct: 218 EERNQEMQQLKQLVSQYQDQLRTLEVNNYALTL 250

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118488028|gb|ABK95835.1| unknown [Populus trichocarpa]

 Score =  152 bits (385), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 106/274 (38%), Positives = 154/274 (56%), Gaps = 36/274 (13%)

Query: 1   MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVR-------SGSDDPVSF------- 46
           MSA VCGKR  FEE+  +S P S KR RCS+  S VR       + + +P SF       
Sbjct: 1   MSAIVCGKRSFFEELTVTSPPVS-KRIRCSS-SSPVRFSPPRSNTIASNPASFNFSSSSS 58

Query: 47  --------LLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTI 98
                   L  +FPD+D ++++  L E  + ++ AI  L  L  +++ E   +  ++  +
Sbjct: 59  SSSAFVEQLAAIFPDMDKQLLEKALEECGDDLDLAIRSLNELRLASV-ENFSAAAVKSDV 117

Query: 99  IGNFSAVP-GESATSCSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDAR 157
           +   +  P G + T     +E+   SA  +       DG +WV+LFV EMMSA+++DDAR
Sbjct: 118 MDKANVPPQGLAPTDAEAPTEDPSASALLSM------DGMEWVELFVREMMSASNIDDAR 171

Query: 158 GRAARILEVFERSIITNSKA----SKELEHASLKEHLQSLLNDNQILKKAVSIQHERHLE 213
            RA+R LE  E+SI T + A    S   E+  LKE +Q+L+ +N ILK+AVSIQHER  E
Sbjct: 172 ARASRALEALEKSICTRAGAEAAKSFHQENMMLKEQMQALIQENTILKRAVSIQHERQKE 231

Query: 214 QEQKEKEVELLKLVISQYQDQARNLEVIFLILTL 247
            E+  +E++ LK ++SQYQDQ R LEV    LTL
Sbjct: 232 FEESSQELQQLKQLVSQYQDQLRTLEVNNYALTL 265

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224090347|ref|XP_002308974.1| predicted protein [Populus trichocarpa] gi|222854950|gb|EEE92497.1| predicted protein [Populus trichocarpa]

 Score =  150 bits (378), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 103/273 (37%), Positives = 152/273 (55%), Gaps = 39/273 (14%)

Query: 1   MSAGVCGKRVGFEEICGSSSPTSAKRSRCSTFGSLVR-------SGSDDPVSF------- 46
           MSA VCGKR  FEE+  +S P S KR RCS+  S VR       + + +P SF       
Sbjct: 1   MSAIVCGKRSFFEELTVTSPPVS-KRIRCSS-SSPVRFSPPRSNTIASNPASFNFSSSSS 58

Query: 47  --------LLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNISERIKSQGLEPTI 98
                   L  +FPD+D ++++  L E  + ++ AI  L  L  +++ E   +  ++  +
Sbjct: 59  SSSAFVEQLAAIFPDMDKQLLEKALEECGDDLDLAIRSLNELRLASV-ENFSAAAVKSDV 117

Query: 99  IGNFSAVPGESATSCSQMSEEEVRSAHTNFCGENITDGSKWVDLFVHEMMSAADLDDARG 158
           +   +  P ++       S   + S           DG +WV+LFV EMMSA+++DDAR 
Sbjct: 118 MDKANVPPQDAEAPTEDPSASALLS----------MDGMEWVELFVREMMSASNIDDARA 167

Query: 159 RAARILEVFERSIITNS--KASKEL--EHASLKEHLQSLLNDNQILKKAVSIQHERHLEQ 214
           RA+R LE  E+SI T +  +A+K    E+  LKE +Q+L+ +N ILK+AVSIQHER  E 
Sbjct: 168 RASRALEALEKSICTRAGAEAAKSFHQENMMLKEQMQALIQENTILKRAVSIQHERQKEF 227

Query: 215 EQKEKEVELLKLVISQYQDQARNLEVIFLILTL 247
           E+  +E++ LK ++SQYQDQ R LEV    LTL
Sbjct: 228 EESSQELQQLKQLVSQYQDQLRTLEVNNYALTL 260

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	250
TAIR|locus:2181738	179	AT5G02510 "AT5G02510" [Arabido	0.44	0.614	0.409	4.1e-17

TAIR|locus:2181738 AT5G02510 "AT5G02510" [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 4.1e-17, P = 4.1e-17
 Identities = 45/110 (40%), Positives = 60/110 (54%)

Query:   131 ENITDGSKWVDLFVHEMMSXXXXXXXXXXXXXILEVFERSIITNSKASKELEHASLKEHL 190
             E++ DG+KWVD  V EM               ILE  E  I  N+ ASK+LE+AS+KE L
Sbjct:    42 EDMIDGAKWVDRLVSEMTKAINIDDMRRRVAVILEALESIIKKNTNASKKLEYASMKESL 101

Query:   191 QSLLNDNQILKKAVSIQHERHXXXXXXXXXXXXXXXXISQYQDQARNLEV 240
             QSL+NDNQILK+ ++ QH+R                 + QYQ+Q   LE+
Sbjct:   102 QSLINDNQILKRVIANQHQRSSENEEKAKQVLHLRGVVGQYQEQVHKLEL 151


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        0.315   0.131   0.366    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      250       221   0.00095  112 3  11 22  0.41    33
                                                     32  0.40    36


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:  599 (64 KB)
  Total size of DFA:  166 KB (2098 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:  19.87u 0.21s 20.08t   Elapsed:  00:00:00
  Total cpu time:  19.87u 0.21s 20.08t   Elapsed:  00:00:00
  Start:  Fri May 10 19:23:41 2013   End:  Fri May 10 19:23:41 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: GSVIVG00021296001 SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (274 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

ID	Length	Definition	E-value
Query	250
pfam02845	42	pfam02845, CUE, CUE domain	1e-06
smart00546	43	smart00546, CUE, Domain that may be involved in bi	1e-04

>gnl|CDD|202430 pfam02845, CUE, CUE domain

 Score = 44.0 bits (105), Expect = 1e-06
 Identities = 15/34 (44%), Positives = 23/34 (67%)

Query: 44 VSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRL 77
          +  L +MFPD+D EV+++VL   +  +E AID L
Sbjct: 5  LETLKEMFPDLDEEVIRAVLQASNGNVEAAIDAL 38

CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Length = 42

>gnl|CDD|214715 smart00546, CUE, Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs)

 Score = 38.2 bits (90), Expect = 1e-04
 Identities = 12/32 (37%), Positives = 21/32 (65%)

Query: 47 LLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLR 78
          L +MFP++D EV+++VL  +   +E  I+ L 
Sbjct: 9  LKEMFPNLDEEVIEAVLEANTGNVEATINNLL 40

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). Length = 43

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	250
PF14817	632	HAUS5: HAUS augmin-like complex subunit 5	98.91
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	98.33
smart00546	43	CUE Domain that may be involved in binding ubiquit	98.28
PF03474	39	DMA: DMRTA motif; InterPro: IPR005173 This region	97.37
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	97.0
PRK15422	79	septal ring assembly protein ZapB; Provisional	96.43
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	95.7
PF09744	158	Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; Inte	94.26
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	93.94
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	93.48
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	92.64
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	92.57
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	92.37
PRK09413	121	IS2 repressor TnpA; Reviewed	88.9
PRK10884	206	SH3 domain-containing protein; Provisional	87.23
PF15058	200	Speriolin_N: Speriolin N terminus	86.71
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	84.26
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	84.1
PF10226	195	DUF2216: Uncharacterized conserved proteins (DUF22	83.41
PRK13182	175	racA polar chromosome segregation protein; Reviewe	82.77
PHA02047	101	phage lambda Rz1-like protein	81.14
PF05010	207	TACC: Transforming acidic coiled-coil-containing p	80.68
PF10205	102	KLRAQ: Predicted coiled-coil domain-containing pro	80.43
TIGR03495	135	phage_LysB phage lysis regulatory protein, LysB fa	80.23
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	80.22

>PF14817 HAUS5: HAUS augmin-like complex subunit 5

Probab=98.91  E-value=9.1e-09  Score=103.93  Aligned_cols=116  Identities=25%  Similarity=0.212  Sum_probs=101.6

Q ss_pred             CChhhhHHHHHHHHhcCC-CchHHHHHHHHHHHHHHHHHHhhhhh-h--hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Q 025638          134 TDGSKWVDLFVHEMMSAA-DLDDARGRAARILEVFERSIITNSKA-S--KELEHASLKEHLQSLLNDNQILKKAVSIQHE  209 (250)
Q Consensus       134 ~~g~eWVEl~V~EM~sAs-d~dDARaRAsRvLEafEksi~~rs~a-a--~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~  209 (250)
                      -.|-.+|.-||.|.+..- ...+...|..+.++..|+.+...+.. +  +..|..++|..++.|..+...|+++++.+++
T Consensus       307 qe~~a~v~q~~~e~~~l~~eaq~l~~~L~~~~~e~~~~~~~~s~~~al~~ele~~~l~A~l~~L~se~q~L~~~~~~r~e  386 (632)
T PF14817_consen  307 QEQWAHVQQFLAEEDALNKEAQALSQRLQRLLEEIERRLSGSSEREALALELEVAGLKASLNALRSECQRLKEAAAERQE  386 (632)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456666777666665544 47888889999999999997766544 3  7789999999999999999999999999999


Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccC
Q 025638          210 RHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLILTLLG  249 (250)
Q Consensus       210 R~~e~e~~~~E~~~lkq~v~qYqeqir~LE~~NYaLs~hl  249 (250)
                      ...++..+.|+++++++++.+||+|||+|..+||++..||
T Consensus       387 ~~~~Lq~K~q~I~~frqlv~e~QeqIr~LiK~Nsaakt~L  426 (632)
T PF14817_consen  387 ALRSLQAKWQRILDFRQLVSEKQEQIRALIKGNSAAKTQL  426 (632)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            9999999999999999999999999999999999999886

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

Probab=98.33  E-value=7.4e-07  Score=60.09  Aligned_cols=38  Identities=42%  Similarity=0.655  Sum_probs=34.6

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhh
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVL   80 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L   80 (250)
                      .|..|+.+||++++..|+.+|+++++|+|.||..|.++
T Consensus         4 ~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~   41 (42)
T PF02845_consen    4 MVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM   41 (42)
T ss_dssp             HHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            47899999999999999999999999999999999764

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.

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

Probab=98.28  E-value=1.1e-06  Score=59.32  Aligned_cols=38  Identities=34%  Similarity=0.606  Sum_probs=35.3

Q ss_pred             CcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           42 DPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        42 ~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      ..++.|+.+||++++..++.+|+++++|+|.||..|.+
T Consensus         4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~   41 (43)
T smart00546        4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLE   41 (43)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence            35889999999999999999999999999999999864

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)

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

Probab=97.37  E-value=0.00028  Score=48.42  Aligned_cols=35  Identities=23%  Similarity=0.559  Sum_probs=32.8

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHH
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRL   77 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL   77 (250)
                      +++-|..+||+..+.+||.+|+.||.|+-.||+-+
T Consensus         4 pidiL~rvFP~~kr~~Le~iL~~C~GDvv~AIE~~   38 (39)
T PF03474_consen    4 PIDILTRVFPHQKRSVLELILQRCNGDVVQAIEQF   38 (39)
T ss_pred             HHHHHHHHCCCCChHHHHHHHHHcCCcHHHHHHHh
Confidence            38999999999999999999999999999999864

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

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.00  E-value=0.0096  Score=46.06  Aligned_cols=67  Identities=31%  Similarity=0.400  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHhhhhh-h-hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025638          162 RILEVFERSIITNSKA-S-KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNL  238 (250)
Q Consensus       162 RvLEafEksi~~rs~a-a-~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir~L  238 (250)
                      -|||-+|.-|.+..-. + +|.|...|||.-..|..|-.      ..||.|    |...+|-+|||+--..+||.||+|
T Consensus         4 Ev~ekLE~KiqqAvdTI~LLQmEieELKEknn~l~~e~q------~~q~~r----eaL~~eneqlk~e~~~WQerlrsL   72 (79)
T COG3074           4 EVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQ------NAQHQR----EALERENEQLKEEQNGWQERLRAL   72 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhHHHHH------HHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3566666666665555 3 99999999998877776643      346777    889999999999999999999997

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=96.43  E-value=0.043  Score=42.94  Aligned_cols=67  Identities=28%  Similarity=0.361  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHhhhhh-h-hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025638          162 RILEVFERSIITNSKA-S-KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNL  238 (250)
Q Consensus       162 RvLEafEksi~~rs~a-a-~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir~L  238 (250)
                      -+|+-+|.=|-+..-. + ++.|...||++-..|..++.-+      .+.|    ++..+|.++||+--..+|+.||+|
T Consensus         4 EvleqLE~KIqqAvdtI~LLqmEieELKekn~~L~~e~~~~------~~~r----~~L~~en~qLk~E~~~WqerLr~L   72 (79)
T PRK15422          4 EVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNA------QHQR----EELERENNHLKEQQNGWQERLQAL   72 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HhhH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4666677667665555 3 9999999999999888887754      3555    778899999999999999999987

>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=95.70  E-value=0.019  Score=37.56  Aligned_cols=34  Identities=26%  Similarity=0.442  Sum_probs=29.8

Q ss_pred             CcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHH
Q 025638           42 DPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRL   77 (250)
Q Consensus        42 ~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL   77 (250)
                      ..|..|..+  +.++....+||..||||++.||.-|
T Consensus         4 ~~v~~L~~m--Gf~~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    4 EKVQQLMEM--GFSREQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHH--TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             HHHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence            357889999  9999999999999999999999865

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 ....

>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans

Probab=94.26  E-value=0.97  Score=39.12  Aligned_cols=81  Identities=30%  Similarity=0.332  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHhhHHHHHHHHHHHHH-hhhhHH-HHHHHHHHHHHHHHHHHHHHHHH
Q 025638          161 ARILEVFERSIITNSKASKELEHASLKEHLQSLLNDNQILKKAVSIQHE-RHLEQE-QKEKEVELLKLVISQYQDQARNL  238 (250)
Q Consensus       161 sRvLEafEksi~~rs~aa~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~-R~~e~e-~~~~E~~~lkq~v~qYqeqir~L  238 (250)
                      =+|||.+|..+..+-..  .-|...|++..+.|..+..- ++...-|-+ +..+++ .-.+|.+.|...|.+.|++.|.|
T Consensus        32 V~vLE~Le~~~~~n~~~--~~e~~~L~~d~e~L~~q~~~-ek~~r~~~e~~l~~~Ed~~~~e~k~L~~~v~~Le~e~r~L  108 (158)
T PF09744_consen   32 VRVLELLESLASRNQEH--EVELELLREDNEQLETQYER-EKELRKQAEEELLELEDQWRQERKDLQSQVEQLEEENRQL  108 (158)
T ss_pred             HHHHHHHHHHHHhhhhh--hhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            37899999888876644  33455666666666655543 333333333 333333 46778888888999999999999


Q ss_pred             H--hhhhh
Q 025638          239 E--VIFLI  244 (250)
Q Consensus       239 E--~~NYa  244 (250)
                      +  ..||+
T Consensus       109 ~~~~~~~~  116 (158)
T PF09744_consen  109 ELKLKNLS  116 (158)
T ss_pred             HHHhhhhh
Confidence            9  44554

Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.

>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation

Probab=93.94  E-value=0.81  Score=34.88  Aligned_cols=60  Identities=32%  Similarity=0.431  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHhhhhh-h-hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025638          162 RILEVFERSIITNSKA-S-KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNL  238 (250)
Q Consensus       162 RvLEafEksi~~rs~a-a-~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir~L  238 (250)
                      .+|+-+|.=|.+..-. + ++.|+..||++...|..+|.-|+                 +|.++||+--.++++.|+.|
T Consensus         4 E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~-----------------~en~~L~~e~~~~~~rl~~L   65 (72)
T PF06005_consen    4 ELLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELK-----------------EENEQLKQERNAWQERLRSL   65 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH-----------------HHHHHHHHHHHHHHHHHHHH
Confidence            3566777777665555 3 88888888888777775555444                 44555555555566666554

It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=93.48  E-value=0.56  Score=41.58  Aligned_cols=61  Identities=33%  Similarity=0.384  Sum_probs=43.8

Q ss_pred             hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHH-----------HHHHHHHHHHHHHHHHHHHH
Q 025638          179 KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEK-----------EVELLKLVISQYQDQARNLE  239 (250)
Q Consensus       179 ~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e~~~~-----------E~~~lkq~v~qYqeqir~LE  239 (250)
                      ++-+...|...++.+..||.+||+.=.-|-.....|++-+.           |+..|+..+-.||++.+++|
T Consensus        17 L~n~l~elq~~l~~l~~ENk~Lk~lq~Rq~kAL~k~e~~e~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r~~~   88 (194)
T PF15619_consen   17 LQNELAELQRKLQELRKENKTLKQLQKRQEKALQKYEDTEAELPQLLQRHNEEVRVLRERLRKSQEQERELE   88 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            78899999999999999999999976666656666665444           44455555555555555554

>smart00165 UBA Ubiquitin associated domain

Probab=92.64  E-value=0.24  Score=31.82  Aligned_cols=33  Identities=24%  Similarity=0.331  Sum_probs=29.0

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHH
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRL   77 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL   77 (250)
                      .|.+|..+  +++++....+|..||+|++.|+.-|
T Consensus         4 ~v~~L~~m--Gf~~~~a~~aL~~~~~d~~~A~~~L   36 (37)
T smart00165        4 KIDQLLEM--GFSREEALKALRAANGNVERAAEYL   36 (37)
T ss_pred             HHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence            46778887  8889999999999999999999765

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

>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6

Probab=92.57  E-value=1.9  Score=33.76  Aligned_cols=87  Identities=22%  Similarity=0.243  Sum_probs=69.1

Q ss_pred             HHHHHHHHHhhh-hhh-------hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 025638          164 LEVFERSIITNS-KAS-------KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQA  235 (250)
Q Consensus       164 LEafEksi~~rs-~aa-------~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqi  235 (250)
                      .+.|.+++..|. ...       +.++...++.+++.|..+-..+-+.|+.--.-..+.++...|+..+|.-+..+.+++
T Consensus        11 ~e~v~~~l~~R~~~~~~vd~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~   90 (108)
T PF02403_consen   11 PEEVRENLKKRGGDEEDVDEIIELDQERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQL   90 (108)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHH
Confidence            467777787774 221       677888888888888888888888777655444688899999999999999999999


Q ss_pred             HHHHhhhhhccccCC
Q 025638          236 RNLEVIFLILTLLGP  250 (250)
Q Consensus       236 r~LE~~NYaLs~hl~  250 (250)
                      +.+|..=+.+-+.+|
T Consensus        91 ~~~e~~l~~~l~~iP  105 (108)
T PF02403_consen   91 KELEEELNELLLSIP  105 (108)
T ss_dssp             HHHHHHHHHHHCTS-
T ss_pred             HHHHHHHHHHHHcCC
Confidence            999998888877776

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....

>cd00194 UBA Ubiquitin Associated domain

Probab=92.37  E-value=0.28  Score=31.56  Aligned_cols=34  Identities=26%  Similarity=0.409  Sum_probs=29.1

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHh
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLR   78 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~   78 (250)
                      .|.+|..+  +.+.+.+..||..|++|++.||.-|.
T Consensus         4 ~v~~L~~m--Gf~~~~~~~AL~~~~~d~~~A~~~L~   37 (38)
T cd00194           4 KLEQLLEM--GFSREEARKALRATNNNVERAVEWLL   37 (38)
T ss_pred             HHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence            46777776  67799999999999999999998764

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.

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=88.90  E-value=0.68  Score=37.31  Aligned_cols=32  Identities=22%  Similarity=0.245  Sum_probs=28.3

Q ss_pred             hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Q 025638          179 KELEHASLKEHLQSLLNDNQILKKAVSIQHER  210 (250)
Q Consensus       179 ~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R  210 (250)
                      .++|+..|+.++..|..||.|||+|..|=..|
T Consensus        76 ~~~ei~~L~~el~~L~~E~diLKKa~~~~~~~  107 (121)
T PRK09413         76 AMKQIKELQRLLGKKTMENELLKEAVEYGRAK  107 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhchh
Confidence            67889999999999999999999999885443

>PRK10884 SH3 domain-containing protein; Provisional

Probab=87.23  E-value=5.2  Score=35.87  Aligned_cols=66  Identities=14%  Similarity=0.086  Sum_probs=42.8

Q ss_pred             hhHHHHHHHHHHHHHHhhHHHHHHHHHHHH---HhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Q 025638          179 KELEHASLKEHLQSLLNDNQILKKAVSIQH---ERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLILT  246 (250)
Q Consensus       179 ~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh---~R~~e~e~~~~E~~~lkq~v~qYqeqir~LE~~NYaLs  246 (250)
                      +++|...||.++..+-.+..  .+.--+|.   ++.+...+...|.++|++.+.+-|.+++.||..|=.+.
T Consensus        98 le~el~~l~~~l~~~~~~~~--~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~  166 (206)
T PRK10884         98 LENQVKTLTDKLNNIDNTWN--QRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDDKQ  166 (206)
T ss_pred             HHHHHHHHHHHHHHHHhHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66677777777777665543  11111122   24444555777888888888888888888888876543

>PF15058 Speriolin_N: Speriolin N terminus

Probab=86.71  E-value=0.63  Score=41.97  Aligned_cols=22  Identities=36%  Similarity=0.496  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHH
Q 025638          181 LEHASLKEHLQSLLNDNQILKKA  203 (250)
Q Consensus       181 kEn~~LKe~l~~l~~eN~iLKrA  203 (250)
                      .||+.||+++ +||+||+-||||
T Consensus        19 ~ENeeLKKlV-rLirEN~eLksa   40 (200)
T PF15058_consen   19 RENEELKKLV-RLIRENHELKSA   40 (200)
T ss_pred             hhhHHHHHHH-HHHHHHHHHHHH
Confidence            4777777776 577777777777

>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=84.26  E-value=23  Score=33.49  Aligned_cols=91  Identities=20%  Similarity=0.115  Sum_probs=48.9

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhhhhh--hhhHHHHHHHHHHHHHHhhHHHHH----HHHHHHHHhhhhHHHHHHHHHHHH
Q 025638          152 DLDDARGRAARILEVFERSIITNSKA--SKELEHASLKEHLQSLLNDNQILK----KAVSIQHERHLEQEQKEKEVELLK  225 (250)
Q Consensus       152 d~dDARaRAsRvLEafEksi~~rs~a--a~~kEn~~LKe~l~~l~~eN~iLK----rAv~iQh~R~~e~e~~~~E~~~lk  225 (250)
                      +.+........-|+.+|+-...-...  .+++|...|.+++..+..+-.-|+    +-....+.-+.++-+...|++.++
T Consensus        40 ~~~~~~~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~  119 (314)
T PF04111_consen   40 DSEEDIEELEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLK  119 (314)
T ss_dssp             --HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333344444444444333333  155555555555555555544443    233334444555567778888888


Q ss_pred             HHHHHHHHHHHHHHhhh
Q 025638          226 LVISQYQDQARNLEVIF  242 (250)
Q Consensus       226 q~v~qYqeqir~LE~~N  242 (250)
                      ..+...++|+..|+-.|
T Consensus       120 ~q~~~~~~~L~~L~ktN  136 (314)
T PF04111_consen  120 NQYEYASNQLDRLRKTN  136 (314)
T ss_dssp             HHHHHHHHHHHCHHT--
T ss_pred             HHHHHHHHHHHHHHhcC
Confidence            88888899998888655

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=84.10  E-value=9.9  Score=38.42  Aligned_cols=59  Identities=29%  Similarity=0.242  Sum_probs=27.3

Q ss_pred             hhHHHHHHHHHHHHHHhhHHHH----HHHH-HHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025638          179 KELEHASLKEHLQSLLNDNQIL----KKAV-SIQHERHLEQEQKEKEVELLKLVISQYQDQARN  237 (250)
Q Consensus       179 ~~kEn~~LKe~l~~l~~eN~iL----KrAv-~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir~  237 (250)
                      +.+||+.||++.++|.+...-+    -.|| ..+-+-.++.+....|+++++.++.+.|.|+..
T Consensus        78 l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l~~  141 (472)
T TIGR03752        78 LISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQRRLAG  141 (472)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4555555555555554422211    1122 222222334444555556666666666655543

Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.

>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain

Probab=83.41  E-value=5.7  Score=35.87  Aligned_cols=62  Identities=27%  Similarity=0.322  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHH-HhhhhHHHHHHHHH--------HHHHHHHHHHHHHHHHHhhhhh
Q 025638          182 EHASLKEHLQSLLNDNQILKKAVSIQH-ERHLEQEQKEKEVE--------LLKLVISQYQDQARNLEVIFLI  244 (250)
Q Consensus       182 En~~LKe~l~~l~~eN~iLKrAv~iQh-~R~~e~e~~~~E~~--------~lkq~v~qYqeqir~LE~~NYa  244 (250)
                      |+.+||+-.++|..||.=|+-.-.+.- .|||--. ..+|-|        -+++-|++||.+++.||..--.
T Consensus        56 EIR~LKe~NqkLqedNqELRdLCCFLDddRqKgrk-larEWQrFGryta~vmr~eV~~Y~~KL~eLE~kq~~  126 (195)
T PF10226_consen   56 EIRGLKEVNQKLQEDNQELRDLCCFLDDDRQKGRK-LAREWQRFGRYTASVMRQEVAQYQQKLKELEDKQEE  126 (195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcccchhHHHhHH-HhHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            889999999999999999988777664 3555433 445544        3578899999999999876433

Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=82.77  E-value=18  Score=31.75  Aligned_cols=95  Identities=14%  Similarity=0.195  Sum_probs=55.1

Q ss_pred             hhhhHHHHHHHHhcCCCchHHHHHHHHHH---HHH---HHHHHhhhhhhhhHHHHHHHHHHHHHHhhHHHHHHHH----H
Q 025638          136 GSKWVDLFVHEMMSAADLDDARGRAARIL---EVF---ERSIITNSKASKELEHASLKEHLQSLLNDNQILKKAV----S  205 (250)
Q Consensus       136 g~eWVEl~V~EM~sAsd~dDARaRAsRvL---Eaf---Eksi~~rs~aa~~kEn~~LKe~l~~l~~eN~iLKrAv----~  205 (250)
                      --+|++++.+...+.-.+.|-+.+..==|   +..   +..+..|-. .+......+.++++.|-+.-..+-.-|    .
T Consensus        42 dl~~L~~I~~l~~~Gm~i~~i~~~~~~~l~~~~l~~~G~~t~~~R~~-lLe~~~~~l~~ri~eLe~~l~~kad~vvsYql  120 (175)
T PRK13182         42 DLQLLEYVKSQIEEGQNMQDTQKPSSNDVEETQVNTIVQNISSVDFE-QLEAQLNTITRRLDELERQLQQKADDVVSYQL  120 (175)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhhhhhhHHHHHHcCCccHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHH
Confidence            44899999999999999999988663111   000   001111100 033333333344444433333332222    3


Q ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 025638          206 IQHERHLEQEQKEKEVELLKLVISQYQD  233 (250)
Q Consensus       206 iQh~R~~e~e~~~~E~~~lkq~v~qYqe  233 (250)
                      .||.|  |.|++...++.|.+.+++-.+
T Consensus       121 l~hr~--e~ee~~~~l~~le~~~~~~e~  146 (175)
T PRK13182        121 LQHRR--EMEEMLERLQKLEARLKKLEP  146 (175)
T ss_pred             HHhHH--HHHHHHHHHHHHHHHHHHHHh
Confidence            57876  899999999999999999443

>PHA02047 phage lambda Rz1-like protein

Probab=81.14  E-value=5  Score=32.82  Aligned_cols=38  Identities=21%  Similarity=0.323  Sum_probs=27.4

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025638          201 KKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNLEVI  241 (250)
Q Consensus       201 KrAv~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir~LE~~  241 (250)
                      .|+..|=|++-+   ....++.+++.-+.+||+||..||.+
T Consensus        26 ~r~~g~~h~~a~---~la~qLE~a~~r~~~~Q~~V~~l~~k   63 (101)
T PHA02047         26 YRALGIAHEEAK---RQTARLEALEVRYATLQRHVQAVEAR   63 (101)
T ss_pred             HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456667777653   44557888888888888888888764

>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules

Probab=80.68  E-value=30  Score=31.29  Aligned_cols=88  Identities=25%  Similarity=0.309  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHHhhhhh-h-----hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHH----HHHHHHHHHHHHH
Q 025638          161 ARILEVFERSIITNSKA-S-----KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQK----EKEVELLKLVISQ  230 (250)
Q Consensus       161 sRvLEafEksi~~rs~a-a-----~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e~~----~~E~~~lkq~v~q  230 (250)
                      ..|.+.|||.|...... .     .+.+...+......+..+-.-+-++|.=-|.|..-+.+.    ..-=.-||.-+..
T Consensus        43 ~~i~~e~Ek~i~~~i~e~~~~~~~~~~~i~~~~~erdq~~~dL~s~E~sfsdl~~ryek~K~vi~~~k~NEE~Lkk~~~e  122 (207)
T PF05010_consen   43 RKIMEEYEKTIAQMIEEKQKQKELSEAEIQKLLKERDQAYADLNSLEKSFSDLHKRYEKQKEVIEGYKKNEETLKKCIEE  122 (207)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHhHHHHHHHHHhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            46889999988886665 2     233444444555556666667888999888886544332    2223457889999


Q ss_pred             HHHHHHHHHhhhhhcccc
Q 025638          231 YQDQARNLEVIFLILTLL  248 (250)
Q Consensus       231 Yqeqir~LE~~NYaLs~h  248 (250)
                      |.+.|+..|-..=+|.-|
T Consensus       123 y~~~l~~~eqry~aLK~h  140 (207)
T PF05010_consen  123 YEERLKKEEQRYQALKAH  140 (207)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999887788766

The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].

>PF10205 KLRAQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019343 This entry represents a N-terminal 100 residues long domain, which contains a conserved KLRAQ motif

Probab=80.43  E-value=14  Score=30.32  Aligned_cols=52  Identities=17%  Similarity=0.244  Sum_probs=28.3

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 025638          189 HLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFL  243 (250)
Q Consensus       189 ~l~~l~~eN~iLKrAv~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir~LE~~NY  243 (250)
                      +-..|-.+|.|||+||.-=-.+   ......+|..-.+.+-..++.+-.|..+|-
T Consensus         6 eYsKLraQ~~vLKKaVieEQ~k---~~~L~e~Lk~ke~~LRk~eqE~dSL~FrN~   57 (102)
T PF10205_consen    6 EYSKLRAQNQVLKKAVIEEQAK---NAELKEQLKEKEQALRKLEQENDSLTFRNQ   57 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456677899999999732222   223333444444445555555555555543

This domain is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain a C-terminal TTKRSYEDQ motif domain (IPR019348 from INTERPRO). The function of these proteins is not known.

>TIGR03495 phage_LysB phage lysis regulatory protein, LysB family

Probab=80.23  E-value=20  Score=30.57  Aligned_cols=67  Identities=16%  Similarity=0.109  Sum_probs=50.1

Q ss_pred             hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Q 025638          179 KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQE-QKEKEVELLKLVISQYQDQARNLEVIFLILT  246 (250)
Q Consensus       179 ~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e-~~~~E~~~lkq~v~qYqeqir~LE~~NYaLs  246 (250)
                      +..-+..++.+-..+..-|+-|.++ .++-++...++ ...+++.+...++.+.+.+|+.|-..|-.|+
T Consensus        28 ~~~a~~~~~~~~~~l~~~~~qL~~l-~~~a~~~~~~Q~~Lr~~~~~~~~~l~~re~~i~rL~~ENe~lR   95 (135)
T TIGR03495        28 LERANRVLKAQQAELASKANQLIVL-LALAKRNEEAQAQLRQQLAQARALLAQREQRIERLKRENEDLR   95 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHH
Confidence            5556666677777777777777665 55665544444 4778899999999999999999998887664

Members of this protein family are phage lysis regulatory protein, including the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. For members of this family, genes are found in phage or in prophage regions of bacterial genomes, typically near a phage lysozyme or phage holin.

>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=80.22  E-value=2.8  Score=28.25  Aligned_cols=36  Identities=14%  Similarity=0.229  Sum_probs=27.5

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +|.++..+- +.++.+-...|+.|+.||+.||..+.+
T Consensus         3 ~i~~F~~iT-g~~~~~A~~~L~~~~wdle~Av~~y~~   38 (43)
T PF14555_consen    3 KIAQFMSIT-GADEDVAIQYLEANNWDLEAAVNAYFD   38 (43)
T ss_dssp             HHHHHHHHH--SSHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred             HHHHHHHHH-CcCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            345555555 568999999999999999999988765

---

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	250
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
2dhy_A	67	CUE domain-containing protein 1; structural genomi	6e-05

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 50.6 bits (120), Expect = 2e-07
 Identities = 39/227 (17%), Positives = 70/227 (30%), Gaps = 50/227 (22%)

Query: 46  FLLQMFP-------DV-DPEVVKSVLGEHDN--KI------EDAIDRLRVLSFSNISERI 89
              + +        +V + +   +     +   KI      +   D L   + ++IS   
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAF----NLSCKILLTTRFKQVTDFLSAATTTHISLDH 293

Query: 90  KSQGLEPT-IIGNFSAVPGESATSCSQMSEEEVRSA--HTNFCGENITDG-SKWVDLFVH 145
            S  L P  +                 +  E + +     +   E+I DG + W D + H
Sbjct: 294 HSMTLTPDEVKSLLLKYLD---CRPQDLPREVLTTNPRRLSIIAESIRDGLATW-DNWKH 349

Query: 146 EM---------MSAADLDDARGRAA-RILEVFERSI-IT--------NSKASKELEHASL 186
                       S   L+ A  R     L VF  S  I               ++     
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVN 409

Query: 187 KEHLQSLLNDNQILKKAVSIQHERHLE-QEQKEKEVELLKLVISQYQ 232
           K H  SL+      +  +SI    +LE + + E E  L + ++  Y 
Sbjct: 410 KLHKYSLVEKQP-KESTISI-PSIYLELKVKLENEYALHRSIVDHYN 454

>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 67

 Score = 39.3 bits (91), Expect = 6e-05
 Identities = 9/44 (20%), Positives = 24/44 (54%)

Query: 41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSN 84
          +  +     MFP++D ++++ VL  +   ++  ID+L  ++  +
Sbjct: 19 NQAMDDFKTMFPNMDYDIIECVLRANSGAVDATIDQLLQMNLES 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	250
2dhy_A	67	CUE domain-containing protein 1; structural genomi	99.05
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	99.0
1p3q_Q	54	VPS9P, vacuolar protein sorting-associated protein	98.03
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	97.74
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	96.78
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	96.4
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	94.43
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	94.21
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	93.64
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	92.82
2dae_A	75	KIAA0733 protein; mitogen-activated protein kinase	92.79
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	92.78
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	92.65
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	92.63
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	92.48
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	92.26
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	91.75
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	91.37
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	91.31
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	91.02
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	90.68
2ejs_A	58	Autocrine motility factor receptor, isoform 2; CUE	89.32
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	88.97
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	88.95
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	88.15
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	87.27
2ekf_A	61	Ancient ubiquitous protein 1; CUE, ubiquitin ligas	86.81
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	85.66
4g3o_A	58	E3 ubiquitin-protein ligase AMFR; all-helical stru	84.79
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	83.93
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	82.6
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	82.55
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	81.37
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	81.33
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	81.32
2dna_A	67	Unnamed protein product; ubiquitin associated doma	80.03

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

Probab=99.05  E-value=1.1e-10  Score=86.37  Aligned_cols=45  Identities=20%  Similarity=0.463  Sum_probs=41.8

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhhccccc
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNI   85 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L~L~sa   85 (250)
                      +..+++|+.+||+||+++|+.+|++||+|+|+||++|.++...+.
T Consensus        19 ~~~v~~L~~MFP~lD~~vI~~vL~a~~G~vd~aId~LL~ms~~~~   63 (67)
T 2dhy_A           19 NQAMDDFKTMFPNMDYDIIECVLRANSGAVDATIDQLLQMNLESG   63 (67)
T ss_dssp             HHHHHHHHHHCSSSCHHHHHHHHHHHTSCHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhcCCCCC
Confidence            667899999999999999999999999999999999999987653

>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=99.00  E-value=2.8e-10  Score=82.18  Aligned_cols=45  Identities=27%  Similarity=0.468  Sum_probs=41.5

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhhccccc
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSFSNI   85 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L~L~sa   85 (250)
                      +.-+.+|+.+||+||+++|+.+|++|++|+|.||+.|.++...+.
T Consensus        10 ee~l~~L~emFP~ld~~~I~~vL~a~~gdvd~aI~~LL~m~~~~~   54 (59)
T 1wgl_A           10 EEDLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQMGEEPS   54 (59)
T ss_dssp             HHHHHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHSSCCCC
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcCcCCCC
Confidence            445899999999999999999999999999999999999887665

>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=98.03  E-value=9.4e-07  Score=63.14  Aligned_cols=39  Identities=33%  Similarity=0.578  Sum_probs=30.2

Q ss_pred             CcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhh
Q 025638           42 DPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVL   80 (250)
Q Consensus        42 ~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L   80 (250)
                      ..+..|+.+||+||+++|+.||++++.++|+||.+|.++
T Consensus        14 ~~~~~L~~MFP~lD~evI~~Vl~a~~G~~~~~IdaLLqm   52 (54)
T 1p3q_Q           14 DTLNTLQNMFPDMDPSLIEDVCIAAASRIGPCVDALLSL   52 (54)
T ss_dssp             HHHHHHHHHSTTSCHHHHHHHHHHSCC--CGGGC-----
T ss_pred             HHHHHHHHHcccCCHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence            347889999999999999999999999999999999775

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

Probab=97.74  E-value=2.3e-05  Score=54.80  Aligned_cols=37  Identities=27%  Similarity=0.409  Sum_probs=35.0

Q ss_pred             HHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhh
Q 025638           44 VSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVL   80 (250)
Q Consensus        44 l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L   80 (250)
                      +..|..+||..+...++.+|+.|++|+|.||..|.+.
T Consensus         8 v~~L~EMFP~~~~~~ik~~L~~~~Gd~d~Ai~~LL~~   44 (49)
T 1otr_A            8 LSILMDMFPAISKSKLQVHLLENNNDLDLTIGLLLKE   44 (49)
T ss_dssp             HHHHHHHCSSSCHHHHHHHHHHTTTCSHHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            6789999999999999999999999999999999874

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

Probab=96.78  E-value=0.0012  Score=49.50  Aligned_cols=39  Identities=18%  Similarity=0.267  Sum_probs=37.3

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      .+.+.+++.|||++....+++.|+.+|+|.+.+|-.|.+
T Consensus        14 ~s~I~qV~DLfPdLG~gfi~~~L~~y~~nvE~vin~LLE   52 (71)
T 2di0_A           14 DSLISQVKDLLPDLGEGFILACLEYYHYDPEQVINNILE   52 (71)
T ss_dssp             HHHHHHHHHHCCSSCHHHHHHHHHHTTTCHHHHHHHHHT
T ss_pred             HHHHHHHHHHcccCCHHHHHHHHHHhCCCHHHHHHHHHc
Confidence            667999999999999999999999999999999999988

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=96.40  E-value=0.041  Score=42.09  Aligned_cols=67  Identities=25%  Similarity=0.328  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHHhhhhh-h-hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025638          162 RILEVFERSIITNSKA-S-KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQARNL  238 (250)
Q Consensus       162 RvLEafEksi~~rs~a-a-~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir~L  238 (250)
                      -+|+-+|.=|-+..-. + ++.|...||++...|..+|.-++.      .|    +.+.+|.++||+-...+|++|+.|
T Consensus         6 ElleqLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~------~~----~~L~~en~qLk~E~~~wq~Rl~~L   74 (81)
T 2jee_A            6 EVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQH------QR----EELERENNHLKEQQNGWQERLQAL   74 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HH----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh------hh----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4677777777765555 3 899999999999999999886653      23    778899999999999999999987

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

Probab=94.43  E-value=0.056  Score=34.33  Aligned_cols=34  Identities=21%  Similarity=0.310  Sum_probs=30.6

Q ss_pred             CcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHH
Q 025638           42 DPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRL   77 (250)
Q Consensus        42 ~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL   77 (250)
                      ..|.+|..+  +.+++...+||..|++|++.||..|
T Consensus         6 ~~i~~L~~m--Gf~~~~a~~AL~~~~~n~e~A~~~L   39 (40)
T 1z96_A            6 SKIAQLVSM--GFDPLEAAQALDAANGDLDVAASFL   39 (40)
T ss_dssp             HHHHHHHHT--TCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            357889998  8999999999999999999999876

>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=94.21  E-value=0.055  Score=40.23  Aligned_cols=37  Identities=22%  Similarity=0.355  Sum_probs=33.4

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..|  +++.+.+.+||..|++|++.|+..|..
T Consensus        30 ee~I~~L~eM--GF~r~~a~~AL~~~~~nve~Ave~Ll~   66 (73)
T 1vg5_A           30 EEQIQKLVAM--GFDRTQVEVALAAADDDLTVAVEILMS   66 (73)
T ss_dssp             HHHHHHHHTT--TCCHHHHHHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            4568899998  789999999999999999999999876

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=93.64  E-value=1.1  Score=38.77  Aligned_cols=63  Identities=17%  Similarity=0.129  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHH-HHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 025638          182 EHASLKEHLQSLLNDNQILKKAVSIQ-HERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLI  244 (250)
Q Consensus       182 En~~LKe~l~~l~~eN~iLKrAv~iQ-h~R~~e~e~~~~E~~~lkq~v~qYqeqir~LE~~NYa  244 (250)
                      =+..|+.++..|..|..-+|.=+..+ .+-.+.....+.|+.+|+....+|+.+||.||+.|=-
T Consensus        57 ~~~~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~ireLEq~NDd  120 (189)
T 2v71_A           57 RNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDD  120 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            35556666666666666666544333 2334456678889999999999999999999999843

>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=92.82  E-value=0.36  Score=34.60  Aligned_cols=51  Identities=20%  Similarity=0.246  Sum_probs=40.3

Q ss_pred             CCcccccCCCCCCCCCCCCcHHHHHhcCCCCCHHHHHHHHhhchh-hHHHHHHHHhh
Q 025638           24 AKRSRCSTFGSLVRSGSDDPVSFLLQMFPDVDPEVVKSVLGEHDN-KIEDAIDRLRV   79 (250)
Q Consensus        24 sKR~Rcsss~sp~r~~~~~~l~~L~~lFP~md~q~le~aLe~cgn-dlDaAIksL~~   79 (250)
                      +||.+-.....   ...+..|.+|..|  +++++...+||..||| |++.|+.-|.+
T Consensus         6 ~~r~~t~~ya~---~~~e~~i~~L~~M--GF~~~~a~~AL~~t~~~nve~A~ewL~~   57 (64)
T 2cpw_A            6 SGRNRQQRPGT---IKHGSALDVLLSM--GFPRARAQKALASTGGRSVQTACDWLFS   57 (64)
T ss_dssp             CSCCSCCSSCS---SSCCCHHHHHHHH--TCCHHHHHHHHHHTTTSCHHHHHHHHHS
T ss_pred             ccchhhhcccc---cCCHHHHHHHHHc--CCCHHHHHHHHHHcCCCCHHHHHHHHHh
Confidence            67765433322   2336779999998  7889999999999998 99999999976

>2dae_A KIAA0733 protein; mitogen-activated protein kinase kinase kinase 7 interacting protein 2, MAP3K7IP2, CUE domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=92.79  E-value=0.083  Score=39.84  Aligned_cols=37  Identities=24%  Similarity=0.320  Sum_probs=35.0

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +++.|+..||.+...||...+-+.++++|+.|..|.+
T Consensus        13 vfheLkQrFPEvPd~VVsqc~~qN~~Nl~aC~~~L~q   49 (75)
T 2dae_A           13 VLHDLRQKFPEVPEVVVSRCMLQNNNNLDACCAVLSQ   49 (75)
T ss_dssp             HHHHHHHHSSSSCHHHHHHHHTTTTSCSHHHHHHHHH
T ss_pred             HHHHHHHhcccCcHHHHHHHHHHhccCHHHHHHHHHH
Confidence            4899999999999999999999999999999999976

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

Probab=92.78  E-value=0.15  Score=35.18  Aligned_cols=37  Identities=24%  Similarity=0.230  Sum_probs=32.5

Q ss_pred             CCcHHHHHhcCCCC-CHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDV-DPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~m-d~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +.-|.+|..|  +. |.+...+||..||+|++.||..|..
T Consensus        13 ~~~l~~L~~M--GF~~~~~~~~AL~~t~gn~e~A~e~L~~   50 (52)
T 2jy5_A           13 QQQLEQLSAM--GFLNREANLQALIATGGDINAAIERLLG   50 (52)
T ss_dssp             HHHHHHHHHT--TCCCHHHHHHHHHHHTTCHHHHHHHHTT
T ss_pred             HHHHHHHHHc--CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            3458999998  78 9999999999999999999998854

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

Probab=92.65  E-value=0.14  Score=35.34  Aligned_cols=36  Identities=25%  Similarity=0.223  Sum_probs=32.0

Q ss_pred             CcHHHHHhcCCCC-CHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           42 DPVSFLLQMFPDV-DPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        42 ~~l~~L~~lFP~m-d~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      .-|.+|..|  +. |.+...+||..||+|++.||..|..
T Consensus        13 ~~l~~L~~M--GF~~~~~~~~AL~~t~gnve~Ave~L~~   49 (53)
T 2knz_A           13 QQLEQLNSM--GFINREANLQALIATGGDINAAIERLLG   49 (53)
T ss_dssp             HHHHHHHTT--TCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            347889888  67 9999999999999999999999876

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

Probab=92.63  E-value=0.092  Score=37.28  Aligned_cols=37  Identities=22%  Similarity=0.338  Sum_probs=33.2

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..|  +++.....+||..|+||++.|+.-|.+
T Consensus        10 ~~~v~~L~~M--GF~~~~a~~AL~~t~~nve~A~e~L~~   46 (63)
T 2dak_A           10 EDCVTTIVSM--GFSRDQALKALRATNNSLERAVDWIFS   46 (63)
T ss_dssp             HHHHHHHHHH--TCCHHHHHHHHHHTTSCSHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4668999998  677899999999999999999999987

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

Probab=92.48  E-value=0.14  Score=38.26  Aligned_cols=36  Identities=19%  Similarity=0.181  Sum_probs=31.7

Q ss_pred             CcHHHHHhcCCCC-CHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           42 DPVSFLLQMFPDV-DPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        42 ~~l~~L~~lFP~m-d~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      .-|.+|..|  ++ |.+...+||..+++|++.||..|..
T Consensus        31 ~qi~qL~eM--GF~dr~~~~~AL~~t~Gnve~Ave~L~~   67 (74)
T 1vej_A           31 QELEELKAL--GFANRDANLQALVATDGDIHAAIEMLLG   67 (74)
T ss_dssp             HHHHHHHHH--TCCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHc--CCCcHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            357888888  54 7899999999999999999999986

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

Probab=92.26  E-value=0.18  Score=32.92  Aligned_cols=36  Identities=22%  Similarity=0.116  Sum_probs=30.7

Q ss_pred             CcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           42 DPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        42 ~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      ..|.+|..+  +.++....+||..|++|++.|+.-|-+
T Consensus         6 ~~i~~L~~M--GF~~~~a~~AL~~~~~n~e~A~~~L~~   41 (43)
T 2g3q_A            6 LAVEELSGM--GFTEEEAHNALEKCNWDLEAATNFLLD   41 (43)
T ss_dssp             HHHHHHHTT--TSCHHHHHHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHHHHHHc--CCCHHHHHHHHHHhCcCHHHHHHHHHc
Confidence            347788887  678899999999999999999988754

>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=91.75  E-value=0.19  Score=35.02  Aligned_cols=37  Identities=19%  Similarity=0.232  Sum_probs=31.8

Q ss_pred             CcHHHHHhcCCCC-CHHHHHHHHhhchhhHHHHHHHHhhh
Q 025638           42 DPVSFLLQMFPDV-DPEVVKSVLGEHDNKIEDAIDRLRVL   80 (250)
Q Consensus        42 ~~l~~L~~lFP~m-d~q~le~aLe~cgndlDaAIksL~~L   80 (250)
                      .-|.+|..|  ++ |.+...+||..+++|++.||..|...
T Consensus        11 ~~l~~L~~M--GF~d~~~n~~AL~~~~Gdv~~Ave~L~~~   48 (54)
T 2dah_A           11 VQLEQLRSM--GFLNREANLQALIATGGDVDAAVEKLRQS   48 (54)
T ss_dssp             HHHHHHHHH--TCCCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCCcHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            358999998  56 67788999999999999999999873

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=91.37  E-value=1.6  Score=34.91  Aligned_cols=62  Identities=18%  Similarity=0.121  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHH-HhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 025638          183 HASLKEHLQSLLNDNQILKKAVSIQH-ERHLEQEQKEKEVELLKLVISQYQDQARNLEVIFLI  244 (250)
Q Consensus       183 n~~LKe~l~~l~~eN~iLKrAv~iQh-~R~~e~e~~~~E~~~lkq~v~qYqeqir~LE~~NYa  244 (250)
                      +..|+.....|..|.--+|.=+.-++ +-.+..-..+.|+.+|+..-..|+.+||.||+.|=-
T Consensus         5 ~rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDD   67 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDD   67 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchH
Confidence            45577777777777777776555443 334456668889999999999999999999999843

>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=91.31  E-value=0.24  Score=35.54  Aligned_cols=37  Identities=19%  Similarity=0.371  Sum_probs=33.1

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..|  +++.....+||..|++|++.|+.-|..
T Consensus        10 ~~~I~~L~~M--GF~~~~a~~AL~~~~~nve~A~e~L~~   46 (63)
T 1wji_A           10 EKALKHITEM--GFSKEASRQALMDNGNNLEAALNVLLT   46 (63)
T ss_dssp             HHHHHHHHTT--TCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            4568889888  789999999999999999999999876

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

Probab=91.02  E-value=0.3  Score=32.96  Aligned_cols=35  Identities=20%  Similarity=0.212  Sum_probs=29.8

Q ss_pred             cHHHHHhcCCCC-CHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           43 PVSFLLQMFPDV-DPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        43 ~l~~L~~lFP~m-d~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      -|.+|..|  +. |.+...+||..+++|++.||..|..
T Consensus        10 ~i~~L~~M--GF~d~~~~~~AL~~~~gnv~~Ave~L~~   45 (46)
T 2bwb_A           10 QLRQLNDM--GFFDFDRNVAALRRSGGSVQGALDSLLN   45 (46)
T ss_dssp             HHHHHHHT--TCCCHHHHHHHHHHHTTCHHHHHHHHHC
T ss_pred             HHHHHHHc--CCCcHHHHHHHHHHhCCCHHHHHHHHHc
Confidence            47888887  54 7888999999999999999998853

>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=90.68  E-value=0.25  Score=33.57  Aligned_cols=37  Identities=19%  Similarity=0.231  Sum_probs=32.3

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..|  +.++....+||..|+||++.|+.-|.+
T Consensus         9 ~~~i~~L~~M--GF~~~~a~~AL~~~~~n~e~A~e~L~~   45 (49)
T 1ify_A            9 ETMLTEIMSM--GYERERVVAALRASYNNPHRAVEYLLT   45 (49)
T ss_dssp             HHHHHHHHHT--TCCHHHHHHHHHTTTSCSHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            3457888888  789999999999999999999998865

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

Probab=89.32  E-value=0.31  Score=35.02  Aligned_cols=41  Identities=20%  Similarity=0.186  Sum_probs=36.7

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhhcc
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSF   82 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L~L   82 (250)
                      ++.+++++.+||+++...+..=|+..| +++..|..+.+=+|
T Consensus        14 ~~mv~~V~~mfP~vp~~~I~~DL~~Tg-sVe~TienILeGrl   54 (58)
T 2ejs_A           14 NAMAHQIQEMFPQVPYHLVLQDLQLTR-SVEITTDNILEGRI   54 (58)
T ss_dssp             HHHHHHHHHHCCSSCHHHHHHHHHHHC-SHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHhC-CHHHHHHHHHhcCC
Confidence            567899999999999999999999999 99999998876444

>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=88.97  E-value=0.42  Score=37.98  Aligned_cols=36  Identities=17%  Similarity=0.240  Sum_probs=31.8

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      -|..|..+ .+++++-...||..|++||..||..|.+
T Consensus        42 kVk~L~Em-tG~seeeAr~AL~~~ngDl~~AI~~Lle   77 (104)
T 1wj7_A           42 KVKQLIDI-TGKNQDECVIALHDCNGDVNRAINVLLE   77 (104)
T ss_dssp             HHHHHHHH-TCCCHHHHHHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHHHHHh-hCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            46677777 6899999999999999999999999986

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

Probab=88.95  E-value=0.46  Score=33.67  Aligned_cols=36  Identities=19%  Similarity=0.210  Sum_probs=31.1

Q ss_pred             CcHHHHHhcCCCC-CHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           42 DPVSFLLQMFPDV-DPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        42 ~~l~~L~~lFP~m-d~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      .-|.+|..|  ++ |.+...+||..+++|++.||+.|..
T Consensus        19 ~qi~~L~~M--GF~d~~~~~~AL~~~~gnve~Ave~L~~   55 (58)
T 1wr1_B           19 HQLRQLNDM--GFFDFDRNVAALRRSGGSVQGALDSLLN   55 (58)
T ss_dssp             HHHHHHHHH--TCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCCcHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            357889988  44 7889999999999999999999865

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

Probab=88.15  E-value=0.25  Score=36.08  Aligned_cols=40  Identities=13%  Similarity=-0.012  Sum_probs=31.5

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhhc
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLS   81 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L~   81 (250)
                      ...|..||.. -+....--.+||++|++||+.||.-|..-.
T Consensus        10 ~~~Vk~LRe~-TGag~~dcKkAL~e~~GDi~~Ai~~Lr~kg   49 (64)
T 2cp9_A           10 KELLMKLRRK-TGYSFVNCKKALETCGGDLKQAEIWLHKEA   49 (64)
T ss_dssp             CHHHHHHHHH-HCCCHHHHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-hCCCHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence            4568888876 345555678999999999999999998643

>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=87.27  E-value=1.2  Score=31.69  Aligned_cols=37  Identities=22%  Similarity=0.204  Sum_probs=33.2

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhch-hhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHD-NKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cg-ndlDaAIksL~~   79 (250)
                      +..|.+|..|  +++....++||..|| +|++.|+.-|.+
T Consensus        10 ~~~v~~L~~M--GF~~~~a~~AL~~t~~~nve~A~ewLl~   47 (64)
T 1whc_A           10 LTALESLIEM--GFPRGRAEKALALTGNQGIEAAMDWLME   47 (64)
T ss_dssp             CCHHHHHHTT--TCCHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHhcCCCHHHHHHHHHh
Confidence            5678999998  778899999999994 899999999987

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

Probab=86.81  E-value=0.8  Score=33.20  Aligned_cols=41  Identities=15%  Similarity=0.149  Sum_probs=37.1

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhhcc
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSF   82 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L~L   82 (250)
                      ++.+++++.+||++....+..=|+..| +++..|..+.+=++
T Consensus        14 ~~mv~~V~~mfP~vp~~~I~~DL~~Tg-sVe~TienILeGr~   54 (61)
T 2ekf_A           14 ATLAQRVKEVLPHVPLGVIQRDLAKTG-CVDLTITNLLEGAV   54 (61)
T ss_dssp             HHHHHHHHHHCSSSCHHHHHHHHHTSC-CHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHhC-CHHHHHHHHHcCCC
Confidence            556899999999999999999999999 99999999887555

>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=85.66  E-value=1.7  Score=31.16  Aligned_cols=38  Identities=18%  Similarity=0.155  Sum_probs=34.2

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchh-hHHHHHHHHhhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDN-KIEDAIDRLRVL   80 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgn-dlDaAIksL~~L   80 (250)
                      +..|.+|..|  +++.....+||..||| |++.|+.-|.+.
T Consensus        10 e~~v~~L~~M--GF~~~~a~~AL~~t~n~~~e~A~~wL~~h   48 (64)
T 2crn_A           10 PSLLEPLLAM--GFPVHTALKALAATGRKTAEEALAWLHDH   48 (64)
T ss_dssp             CSSHHHHHHT--SCCHHHHHHHHHHHTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHhCCCCHHHHHHHHHhC
Confidence            5678999997  7889999999999999 999999999873

>4g3o_A E3 ubiquitin-protein ligase AMFR; all-helical structure, BAG6; 1.60A {Homo sapiens}

Probab=84.79  E-value=0.71  Score=33.24  Aligned_cols=38  Identities=21%  Similarity=0.237  Sum_probs=33.1

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      ++.+++++.+||+++...+..-|+.. ++++..|..+.+
T Consensus        18 ~~Mve~V~~mFPqv~~~~I~~DL~rT-gSVe~TienILe   55 (58)
T 4g3o_A           18 NAMAHQIQEMFPQVPYHLVLQDLQLT-RSVEITTDNILE   55 (58)
T ss_dssp             HHHHHHHHHHCTTSCHHHHHHHHHHH-CCHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHh-CCHHHHHHHHHc
Confidence            45689999999999999999999988 589999988754

>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=83.93  E-value=1.2  Score=33.81  Aligned_cols=37  Identities=19%  Similarity=0.268  Sum_probs=34.4

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..|  ++++...++||..|++|++-|+.-|..
T Consensus        30 ee~I~~Lv~M--GF~~~~A~~AL~~t~gdve~A~e~L~s   66 (83)
T 1veg_A           30 QESINQLVYM--GFDTVVAEAALRVFGGNVQLAAQTLAH   66 (83)
T ss_dssp             HHHHHHHHHH--SCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            5678999999  899999999999999999999999987

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

Probab=82.60  E-value=1.2  Score=29.47  Aligned_cols=36  Identities=19%  Similarity=0.235  Sum_probs=30.4

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..+  +.++....+||..|| |++.|+.-|.+
T Consensus        10 ~~~v~~L~~M--GF~~~~a~~AL~~~~-n~e~A~~~L~~   45 (47)
T 2ekk_A           10 QQQLQQLMDM--GFTREHAMEALLNTS-TMEQATEYLLT   45 (47)
T ss_dssp             HHHHHHHHHH--HCCHHHHHHHHHHSC-SHHHHHHHHHT
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHcC-CHHHHHHHHHc
Confidence            4568889888  667799999999997 89999998864

>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=82.55  E-value=0.7  Score=31.19  Aligned_cols=35  Identities=11%  Similarity=0.011  Sum_probs=29.8

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      .|.+|..|  ++++..+.+||.+||+|.+.|..-|-.
T Consensus         7 aI~rL~~m--GF~~~~a~~Al~a~~~n~e~A~~~Lf~   41 (47)
T 1dv0_A            7 AIERLKAL--GFPESLVIQAYFACEKNENLAANFLLS   41 (47)
T ss_dssp             HHTTTTTT--TCCHHHHHHHHTTTTSCHHHHHHHTTS
T ss_pred             HHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            36667777  788999999999999999999988754

>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=81.37  E-value=1.8  Score=31.69  Aligned_cols=37  Identities=24%  Similarity=0.316  Sum_probs=33.2

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..+  +++.+...+||..||||++.|+.-|.+
T Consensus        30 ~~~v~~L~~M--GF~~~~a~~AL~~t~~nve~Ave~L~~   66 (73)
T 1wiv_A           30 QSSVDTLLSF--GFAEDVARKALKASGGDIEKATDWVFN   66 (73)
T ss_dssp             HHHHHHHHHH--TCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            5568999998  678999999999999999999999876

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=81.33  E-value=12  Score=30.33  Aligned_cols=95  Identities=17%  Similarity=0.187  Sum_probs=65.7

Q ss_pred             CChhhhHHHHHHHHhcC---CCchHHHHHHHHHHHHHHHHHHhhhhhh-----hhHHHHHHHHHHHHHHhhHHHHHHHHH
Q 025638          134 TDGSKWVDLFVHEMMSA---ADLDDARGRAARILEVFERSIITNSKAS-----KELEHASLKEHLQSLLNDNQILKKAVS  205 (250)
Q Consensus       134 ~~g~eWVEl~V~EM~sA---sd~dDARaRAsRvLEafEksi~~rs~aa-----~~kEn~~LKe~l~~l~~eN~iLKrAv~  205 (250)
                      ..-+..|+-=++||...   ..+++-|           .+|.+.-.-+     .++++..|+++++.+.+|..-||-=+.
T Consensus        31 ~~vA~~vd~km~ei~~~~~~~~l~~~r-----------~aVLaALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~   99 (138)
T 3hnw_A           31 QRVASYINNKITEFNKEESYRRMSAEL-----------RTDMMYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELI   99 (138)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHTSCHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccCCCCCCHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566777777888754   3333333           3444443331     677888888889888888888886332


Q ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025638          206 IQHERHLEQEQKEKEVELLKLVISQYQDQARNLEVIF  242 (250)
Q Consensus       206 iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir~LE~~N  242 (250)
                      --   +-.+++..+|+..|+.-+...|+|+..||-.+
T Consensus       100 ~~---~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~  133 (138)
T 3hnw_A          100 AA---QIKAESSAKEIKELKSEINKYQKNIVKLETEL  133 (138)
T ss_dssp             HH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            22   22467788899999999999999999998654

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

Probab=81.32  E-value=1.7  Score=31.94  Aligned_cols=38  Identities=13%  Similarity=0.156  Sum_probs=33.6

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchh-hHHHHHHHHhhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDN-KIEDAIDRLRVL   80 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgn-dlDaAIksL~~L   80 (250)
                      +..|.+|..|  +++....++||..||| |++.|+.-|.+.
T Consensus        10 e~~v~~L~~M--GF~~~~a~~AL~~t~n~~ve~A~ewL~~~   48 (74)
T 2dag_A           10 ESVIIQLVEM--GFPMDACRKAVYYTGNSGAEAAMNWVMSH   48 (74)
T ss_dssp             HHHHHHHHHH--SCCHHHHHHHHHHHTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHhCCCCHHHHHHHHHhC
Confidence            5668999998  7789999999999997 899999999873

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

Probab=80.03  E-value=1.4  Score=32.33  Aligned_cols=35  Identities=26%  Similarity=0.290  Sum_probs=30.5

Q ss_pred             cHHHHHhc-CCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           43 PVSFLLQM-FPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        43 ~l~~L~~l-FP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      -|.+|+.| |  .|.+...+||.+|++|++.||..|..
T Consensus        22 ql~qL~~MGF--~d~~an~~AL~at~Gnve~Ave~L~~   57 (67)
T 2dna_A           22 EMECLQAMGF--VNYNANLQALIATDGDTNAAIYKLKS   57 (67)
T ss_dssp             HHHHHHHHTC--CCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHcCC--CcHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            47778876 4  57888899999999999999999988

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	250
d1wgla_	59	a.5.2.4 (A:) Toll-interacting protein {Human (Homo	4e-07
d1mn3a_	54	a.5.2.4 (A:) Vacuolar protein sorting-associated p	2e-05

>d1wgla_ a.5.2.4 (A:) Toll-interacting protein {Human (Homo sapiens) [TaxId: 9606]} Length = 59

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]

 Score = 43.6 bits (103), Expect = 4e-07
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 33 GSLVRSG-SDDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSF 82
          GS   SG S++ +  +  MFP++D EV++SVL       + AI+ L  +  
Sbjct: 1  GSSGSSGCSEEDLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQMGE 51

>d1mn3a_ a.5.2.4 (A:) Vacuolar protein sorting-associated protein vps9 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 54

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]

 Score = 38.9 bits (91), Expect = 2e-05
 Identities = 14/38 (36%), Positives = 23/38 (60%)

Query: 44 VSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLS 81
          ++ L  MFPD+DP +++ V     ++IE  +D L  LS
Sbjct: 16 LNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLSLS 53

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	250
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	98.36
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	98.32
d2di0a1	63	Activating signal cointegrator 1 complex subunit 2	95.64
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	90.09
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	89.58
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	88.55
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	88.18
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	87.85
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	87.41
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	84.15
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	82.96
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	80.79

>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=98.36  E-value=1.3e-07  Score=65.84  Aligned_cols=38  Identities=34%  Similarity=0.610  Sum_probs=35.5

Q ss_pred             cHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhh
Q 025638           43 PVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVL   80 (250)
Q Consensus        43 ~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L   80 (250)
                      .+..|+.+||+||..||+.||++|+.++|.||..|..+
T Consensus        15 ~~~~Lk~MFP~~D~~VI~~VL~a~~G~vd~aidaLL~M   52 (54)
T d1mn3a_          15 TLNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLSL   52 (54)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHSCSSCSHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            36889999999999999999999999999999999765

>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=98.32  E-value=2e-07  Score=65.95  Aligned_cols=42  Identities=29%  Similarity=0.521  Sum_probs=38.5

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhhhcc
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRVLSF   82 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~L~L   82 (250)
                      +..+..|..+||+||+.+|+.||++|+.++|.||..|.++.-
T Consensus        10 Ee~i~~LkeMFP~~D~~vI~~VL~a~~G~vd~aid~LL~Msd   51 (59)
T d1wgla_          10 EEDLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQMGE   51 (59)
T ss_dssp             HHHHHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhcCC
Confidence            455899999999999999999999999999999999988654

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

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

Probab=95.64  E-value=0.004  Score=43.93  Aligned_cols=39  Identities=18%  Similarity=0.267  Sum_probs=36.8

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      ++++.+.+.+|||+.+.+|.+.|+..|+|.+.+|-.|.+
T Consensus         7 ~s~I~qV~Dl~PdLG~GFi~~~L~~Y~~n~E~vI~~lLe   45 (63)
T d2di0a1           7 DSLISQVKDLLPDLGEGFILACLEYYHYDPEQVINNILE   45 (63)
T ss_dssp             HHHHHHHHHHCCSSCHHHHHHHHHHTTTCHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHhCCCHHHHHHHHHc
Confidence            357899999999999999999999999999999999988

>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=90.09  E-value=0.079  Score=36.21  Aligned_cols=23  Identities=17%  Similarity=0.130  Sum_probs=20.4

Q ss_pred             HHHHHHhhchhhHHHHHHHHhhh
Q 025638           58 VVKSVLGEHDNKIEDAIDRLRVL   80 (250)
Q Consensus        58 ~le~aLe~cgndlDaAIksL~~L   80 (250)
                      -..+||++||+|||.||.-|..-
T Consensus        21 dcKkAL~e~~gD~ekA~e~Lrkk   43 (56)
T d1xb2b1          21 NCKKALETCGGDLKQAESWLHKQ   43 (56)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHH
Confidence            36799999999999999999874

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=89.58  E-value=1.3  Score=32.01  Aligned_cols=85  Identities=25%  Similarity=0.219  Sum_probs=62.3

Q ss_pred             HHHHHHHHHhhhhh-h------hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025638          164 LEVFERSIITNSKA-S------KELEHASLKEHLQSLLNDNQILKKAVSIQHERHLEQEQKEKEVELLKLVISQYQDQAR  236 (250)
Q Consensus       164 LEafEksi~~rs~a-a------~~kEn~~LKe~l~~l~~eN~iLKrAv~iQh~R~~e~e~~~~E~~~lkq~v~qYqeqir  236 (250)
                      .+.|.+++..|-.. .      +.++...+..+++.|..+...+=+-|.. . ...+.++.-.++..||.-+..+.++++
T Consensus        11 ~e~v~~~l~~R~~~~~ld~i~~ld~~rr~l~~~~e~l~~~rN~~sk~i~k-~-~~~~~~~l~~~~k~lk~~i~~le~~~~   88 (110)
T d1seta1          11 PEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPK-A-PPEEKEALIARGKALGEEAKRLEEALR   88 (110)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGG-C-CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-h-hccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            35666777666444 1      6667777777788777777666555542 1 123456677889999999999999999


Q ss_pred             HHHhhhhhccccCC
Q 025638          237 NLEVIFLILTLLGP  250 (250)
Q Consensus       237 ~LE~~NYaLs~hl~  250 (250)
                      .+|-.=|.+-+++|
T Consensus        89 ~~~~~l~~~ll~iP  102 (110)
T d1seta1          89 EKEARLEALLLQVP  102 (110)
T ss_dssp             HHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHcCC
Confidence            99999888888877

>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=88.55  E-value=0.25  Score=33.59  Aligned_cols=37  Identities=19%  Similarity=0.371  Sum_probs=34.0

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..|  +.+....++||..|+||++.|+.-|.+
T Consensus        10 ~~~v~~L~~M--GF~~~~a~~AL~~~~~~~e~A~~wL~~   46 (63)
T d1wjia_          10 EKALKHITEM--GFSKEASRQALMDNGNNLEAALNVLLT   46 (63)
T ss_dssp             HHHHHHHHTT--TCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            5668889888  899999999999999999999999988

>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=88.18  E-value=0.13  Score=34.53  Aligned_cols=25  Identities=28%  Similarity=0.189  Sum_probs=21.2

Q ss_pred             HHHHHHhhchhhHHHHHHHHhhhcc
Q 025638           58 VVKSVLGEHDNKIEDAIDRLRVLSF   82 (250)
Q Consensus        58 ~le~aLe~cgndlDaAIksL~~L~L   82 (250)
                      -..+||++||+|||.||+-|...-+
T Consensus        19 dcKkAL~e~~gD~ekA~e~Lr~~G~   43 (52)
T d1aipc1          19 DVKRALEDAGWDEEKAVQLLRERGA   43 (52)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHhH
Confidence            3679999999999999999987433

>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=87.85  E-value=0.14  Score=34.62  Aligned_cols=28  Identities=29%  Similarity=0.267  Sum_probs=22.8

Q ss_pred             HHHHHHhhchhhHHHHHHHHhhhccccc
Q 025638           58 VVKSVLGEHDNKIEDAIDRLRVLSFSNI   85 (250)
Q Consensus        58 ~le~aLe~cgndlDaAIksL~~L~L~sa   85 (250)
                      -..+||++||+|+|.||.-|..--+..+
T Consensus        21 dCKkAL~e~~gD~ekA~e~Lr~kG~~~A   48 (54)
T d1efub3          21 DCKKALTEANGDIELAIENMRKSGAIKA   48 (54)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHhHHHH
Confidence            3679999999999999999987544433

>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=87.41  E-value=0.21  Score=35.06  Aligned_cols=37  Identities=22%  Similarity=0.355  Sum_probs=32.7

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..|  +++.+...+||+.|+||++.||.-|..
T Consensus        30 ee~i~~L~~M--GF~~~~a~~AL~~~~~n~e~A~~~Ll~   66 (73)
T d1vg5a_          30 EEQIQKLVAM--GFDRTQVEVALAAADDDLTVAVEILMS   66 (73)
T ss_dssp             HHHHHHHHTT--TCCHHHHHHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHh--CCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            5568888887  578999999999999999999999876

>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=84.15  E-value=0.42  Score=30.46  Aligned_cols=34  Identities=24%  Similarity=0.387  Sum_probs=26.6

Q ss_pred             HHHHHhc-CCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           44 VSFLLQM-FPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        44 l~~L~~l-FP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +++|+.| |  .|.+.--.||..+|.|++.||+.|..
T Consensus         6 L~~L~~MGF--~d~~~Ni~AL~~t~Gdv~~Aie~Ll~   40 (41)
T d2daha1           6 LEQLRSMGF--LNREANLQALIATGGDVDAAVEKLRQ   40 (41)
T ss_dssp             HHHHHHHTC--CCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            3445554 3  46778889999999999999999864

>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=82.96  E-value=0.32  Score=33.33  Aligned_cols=37  Identities=22%  Similarity=0.257  Sum_probs=31.9

Q ss_pred             CCcHHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           41 DDPVSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        41 ~~~l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +..|.+|..|  +.+++...+||..||||++.||.-|..
T Consensus        20 e~~v~~L~~M--GF~~~~a~~AL~~~~~n~e~A~~~Lls   56 (63)
T d1wgna_          20 RQCVETVVNM--GYSYECVLRAMKKKGENIEQILDYLFA   56 (63)
T ss_dssp             HHHHHHHHHH--HCCHHHHHHHHHHHCSCHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4557888887  557899999999999999999999876

>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=80.79  E-value=0.68  Score=30.69  Aligned_cols=35  Identities=23%  Similarity=0.171  Sum_probs=28.4

Q ss_pred             HHHHHhcCCCCCHHHHHHHHhhchhhHHHHHHHHhh
Q 025638           44 VSFLLQMFPDVDPEVVKSVLGEHDNKIEDAIDRLRV   79 (250)
Q Consensus        44 l~~L~~lFP~md~q~le~aLe~cgndlDaAIksL~~   79 (250)
                      +.+|+.| =-.|.+.--+||.+||-|+++||+.|.+
T Consensus        12 L~qL~~M-GF~d~~~Ni~AL~~t~GdV~~Aie~Ll~   46 (50)
T d2dnaa1          12 MECLQAM-GFVNYNANLQALIATDGDTNAAIYKLKS   46 (50)
T ss_dssp             HHHHHHH-TCCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHc-CCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            5666665 2247888889999999999999999875