Citrus Sinensis ID: 030009

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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----
Protein Sequence
MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEYSVKKQ
Secondary Structure (PSIPRED)
cHHHHHHHcHHcccccccccccHHHHHHHHccccccccHHHHHHHHHHccccEEEEEcccccEEEcccccccccEEEEEEccccccccccccccccccccccEEEcccHHHHHHHHHcccHHccccccccccccHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHcHHHccHHccccccHHHHHHHHccccccccHHHHHHHHHHccccEEEEEccccEEEEEccccccccEEEEEEEcccccccEEEcccccccccccEEEEccccccHcHHcccccccccccccccccHHHHHHHHHHccccHHHHHHHHHHHccccHHHHHHHHHHHHccccccHccc
Coil and Loop (DISEMBL)
MVVQYIVKNRetfepfieddvpfdeycqsmetdgtwagHMELQAASLVTHsnicihrhmsprwyirnfDYHEARMIHLsyhdgehyngvrlkedscigsarpiiikadadisaasiqSKTVTSKLKGAAGIINAGSIKLVMagsgcensEKVEEVLLQVGGDVDAAIEFLIAeqgteeysvkkq
Flexible Loop (DISEMBL)
MVVQYIVknretfepfieddvPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKtvtsklkgaagiINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLiaeqgteeysvkkq
Low Complexity Region (SEG)
MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPiiikadadisaasiQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEYSVKKQ
Disordered region (IsUnstruct)
**VQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE***********
Disordered Region (DISOPRED)
MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDS**G**************************************IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEF***************
Disordered Region (DISEMBL)
MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG*********
Disordered Region (DISPRO)
MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADA**********************INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEYSVKKQ
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	184	2.2.26 [Sep-21-2011]
Q5T2D3	398	OTU domain-containing pro	yes	no	0.668	0.309	0.349	4e-16
Q01804	1113	OTU domain-containing pro	no	no	0.489	0.080	0.32	3e-06
B2RRE7	1107	OTU domain-containing pro	no	no	0.445	0.074	0.325	2e-05

>sp|Q5T2D3|OTUD3_HUMAN OTU domain-containing protein 3 OS=Homo sapiens GN=OTUD3 PE=1 SV=1

 Score = 84.3 bits (207), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 44/126 (34%), Positives = 69/126 (54%), Gaps = 3/126 (2%)

Query: 2   VVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSP 61
            V Y++K RE FEPF+EDD+PF+++  S+   GT+AG+  + A +     N+ IH+  +P
Sbjct: 99  TVDYMIKQREDFEPFVEDDIPFEKHVASLAKPGTFAGNDAIVAFARNHQLNVVIHQLNAP 158

Query: 62  RWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTV 121
            W IR  +    R +H++Y  GEHY+ VR   D+   S  P  ++ D  +      +K  
Sbjct: 159 LWQIRGTEKSSVRELHIAYRYGEHYDSVRRINDN---SEAPAHLQTDFQMLHQDESNKRE 215

Query: 122 TSKLKG 127
             K KG
Sbjct: 216 KIKTKG 221

Homo sapiens (taxid: 9606)

>sp|Q01804|OTUD4_HUMAN OTU domain-containing protein 4 OS=Homo sapiens GN=OTUD4 PE=1 SV=3

 Score = 51.6 bits (122), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/100 (32%), Positives = 54/100 (54%), Gaps = 10/100 (10%)

Query: 3   VQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHR--HMS 60
           + Y+ +NRE FE FIE    F+EY + +E    W G +E+ A SL+   +  I+R  ++S
Sbjct: 69  IHYLRENREKFEAFIEGS--FEEYLKRLENPQEWVGQVEISALSLMYRKDFIIYREPNVS 126

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYN---GVRLKEDSCI 97
           P     N ++ E   + L + +G HY+    ++ KE S +
Sbjct: 127 PSQVTEN-NFPEK--VLLCFSNGNHYDIVYPIKYKESSAM 163

Homo sapiens (taxid: 9606)

>sp|B2RRE7|OTUD4_MOUSE OTU domain-containing protein 4 OS=Mus musculus GN=Otud4 PE=1 SV=1

 Score = 48.9 bits (115), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/89 (32%), Positives = 50/89 (56%), Gaps = 7/89 (7%)

Query: 3   VQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHR--HMS 60
           ++Y+ +NRE FE FIE    F+EY + +E    W G +E+ A SL+   +  I++  ++S
Sbjct: 69  IRYLRENREKFEAFIEGS--FEEYLKRLENPQEWVGQVEISALSLMYRKDFVIYQEPNVS 126

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGV 89
           P     N ++ E   + L + +G HY+ V
Sbjct: 127 PSHVTEN-NFPEK--VLLCFSNGNHYDIV 152

Mus musculus (taxid: 10090)

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	184
296082384	385	unnamed protein product [Vitis vinifera]	0.967	0.462	0.772	7e-78
225438775	467	PREDICTED: OTU domain-containing protein	0.967	0.381	0.772	1e-77
356565555	382	PREDICTED: OTU domain-containing protein	0.983	0.473	0.754	2e-77
224081718	349	predicted protein [Populus trichocarpa]	0.983	0.518	0.741	2e-76
255565284	371	OTU domain-containing protein, putative	0.978	0.485	0.736	7e-76
23306370	375	putative protein [Arabidopsis thaliana]	0.978	0.48	0.703	3e-73
30698282	375	SEC-C motif-containing protein / OTU-lik	0.978	0.48	0.703	5e-73
42573818	374	SEC-C motif-containing protein / OTU-lik	0.978	0.481	0.703	5e-73
10177604	382	unnamed protein product [Arabidopsis tha	0.978	0.471	0.703	7e-73
297797661	374	hypothetical protein ARALYDRAFT_496882 [	0.961	0.473	0.720	2e-72

>gi|296082384|emb|CBI21389.3| unnamed protein product [Vitis vinifera]

 Score =  295 bits (754), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 139/180 (77%), Positives = 156/180 (86%), Gaps = 2/180 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           MVV+YI++NR+ FEPFIEDDVPFD+YCQSME DGTWAGHMELQAASLVT SNICIHRHMS
Sbjct: 72  MVVRYILENRDMFEPFIEDDVPFDDYCQSMEKDGTWAGHMELQAASLVTRSNICIHRHMS 131

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYI+NF+   ARMIHLSYHDGEHYN VRLKED C G ARPIIIKAD D+S AS Q K 
Sbjct: 132 PRWYIQNFNASGARMIHLSYHDGEHYNSVRLKEDPCDGPARPIIIKADTDLSVASHQVKG 191

Query: 121 VTSKLKGAAG--IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178
            +SK K  AG  II+AGSIKLVM GSGCEN+EKVE+VL+++ GDVDAAIE+LIAE+ TEE
Sbjct: 192 ASSKSKSGAGRNIIDAGSIKLVMVGSGCENAEKVEQVLVELSGDVDAAIEYLIAERETEE 251

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225438775|ref|XP_002278347.1| PREDICTED: OTU domain-containing protein 3-like [Vitis vinifera]

 Score =  294 bits (752), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 139/180 (77%), Positives = 156/180 (86%), Gaps = 2/180 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           MVV+YI++NR+ FEPFIEDDVPFD+YCQSME DGTWAGHMELQAASLVT SNICIHRHMS
Sbjct: 72  MVVRYILENRDMFEPFIEDDVPFDDYCQSMEKDGTWAGHMELQAASLVTRSNICIHRHMS 131

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYI+NF+   ARMIHLSYHDGEHYN VRLKED C G ARPIIIKAD D+S AS Q K 
Sbjct: 132 PRWYIQNFNASGARMIHLSYHDGEHYNSVRLKEDPCDGPARPIIIKADTDLSVASHQVKG 191

Query: 121 VTSKLKGAAG--IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178
            +SK K  AG  II+AGSIKLVM GSGCEN+EKVE+VL+++ GDVDAAIE+LIAE+ TEE
Sbjct: 192 ASSKSKSGAGRNIIDAGSIKLVMVGSGCENAEKVEQVLVELSGDVDAAIEYLIAERETEE 251

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565555|ref|XP_003551005.1| PREDICTED: OTU domain-containing protein 3-like [Glycine max]

 Score =  293 bits (750), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 138/183 (75%), Positives = 154/183 (84%), Gaps = 2/183 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           MVV++I+ NRE FEPFIED+VPFDEYCQSME DGTWAGHMELQAASLVT SNICIHR+MS
Sbjct: 72  MVVKHILDNREMFEPFIEDEVPFDEYCQSMENDGTWAGHMELQAASLVTRSNICIHRNMS 131

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYIRNFD    RMIHLSYHDGEHYN VRLK+D C G+ARPI+I+ADAD+S  S Q+K 
Sbjct: 132 PRWYIRNFDNRGVRMIHLSYHDGEHYNSVRLKDDPCDGAARPIVIEADADLSVPSHQTKV 191

Query: 121 VTSKLKGAAG--IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178
           V +K  G AG      GSIKLVMAG+GCEN+EKVE++L QV GDVDAAIEFLIAEQGTEE
Sbjct: 192 VGNKFHGRAGWEAFQPGSIKLVMAGTGCENAEKVEQILEQVNGDVDAAIEFLIAEQGTEE 251

Query: 179 YSV 181
            S 
Sbjct: 252 CSA 254

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224081718|ref|XP_002306480.1| predicted protein [Populus trichocarpa] gi|222855929|gb|EEE93476.1| predicted protein [Populus trichocarpa]

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 135/182 (74%), Positives = 154/182 (84%), Gaps = 1/182 (0%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           MVVQYI+  RE FEPFIEDDVPFDEYCQ ME DGTWAGHMELQAASLVTHSNIC+HR+MS
Sbjct: 71  MVVQYIMNTREMFEPFIEDDVPFDEYCQLMEKDGTWAGHMELQAASLVTHSNICVHRYMS 130

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYIRNFD H ARM+HLSYHD EHYN VR K+D C G A+PIIIK DAD+SA S+Q+K 
Sbjct: 131 PRWYIRNFDQHGARMVHLSYHDEEHYNSVRSKDDPCNGPAQPIIIKVDADLSATSVQAKA 190

Query: 121 VTSKLKG-AAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEY 179
           V+S   G A    +AGS+KLVMAGSGCEN+EKV++VLL+V GDVDAAIEFLIAEQ ++ +
Sbjct: 191 VSSTKAGIAKDSFDAGSLKLVMAGSGCENAEKVKQVLLEVDGDVDAAIEFLIAEQESDSF 250

Query: 180 SV 181
           S 
Sbjct: 251 SA 252

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565284|ref|XP_002523634.1| OTU domain-containing protein, putative [Ricinus communis] gi|223537196|gb|EEF38829.1| OTU domain-containing protein, putative [Ricinus communis]

 Score =  288 bits (737), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 134/182 (73%), Positives = 156/182 (85%), Gaps = 2/182 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           MVVQY++KNR+TFEPFIEDD+PFDEYCQSME DGTWAGHMELQAASLVT SNICIH++MS
Sbjct: 72  MVVQYLMKNRDTFEPFIEDDIPFDEYCQSMEKDGTWAGHMELQAASLVTRSNICIHQYMS 131

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYIRNFD   A M+HLSYHD EHYN VRLKED+CIG ARPIIIKADAD+SA + Q+KT
Sbjct: 132 PRWYIRNFDERGACMVHLSYHDEEHYNSVRLKEDTCIGPARPIIIKADADLSATTCQAKT 191

Query: 121 VTSKLKGAAG--IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178
             SK KG A    I+  SIK+V+AGSGC++++KVE+VLLQV GDVDAAIEFL AE+  ++
Sbjct: 192 AASKSKGGAAKNSIDPSSIKVVIAGSGCQDAQKVEQVLLQVDGDVDAAIEFLRAEREADD 251

Query: 179 YS 180
            S
Sbjct: 252 SS 253

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|23306370|gb|AAN17412.1| putative protein [Arabidopsis thaliana] gi|25084238|gb|AAN72203.1| putative protein [Arabidopsis thaliana]

 Score =  279 bits (714), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 128/182 (70%), Positives = 152/182 (83%), Gaps = 2/182 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           M+V YIVKNRE FEPFIEDDVPF++YC++M+ DGTWAG+MELQAASLVT SNICIHR+MS
Sbjct: 70  MIVLYIVKNREMFEPFIEDDVPFEDYCKTMDDDGTWAGNMELQAASLVTRSNICIHRNMS 129

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYIRNF+    RMIHLSYHDGEHYN VR KED+C G ARP++I+ADA +SAAS Q+K 
Sbjct: 130 PRWYIRNFEDTRTRMIHLSYHDGEHYNSVRSKEDACGGPARPVVIEADAKVSAASKQAKA 189

Query: 121 VTSKLKGAAGI--INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178
             SK K  A    +NAG+IK+VM+GS C+N+EK E+VLLQV GDVDAAIEFLIA+QG E 
Sbjct: 190 TESKSKNKADKCHVNAGAIKVVMSGSCCDNTEKAEQVLLQVNGDVDAAIEFLIADQGMES 249

Query: 179 YS 180
            +
Sbjct: 250 LT 251

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30698282|ref|NP_201518.2| SEC-C motif-containing protein / OTU-like cysteine protease family protein [Arabidopsis thaliana] gi|332010926|gb|AED98309.1| SEC-C motif-containing protein / OTU-like cysteine protease family protein [Arabidopsis thaliana] gi|407078848|gb|AFS88955.1| OTU-containing deubiquitinating enzyme OTU7 isoform i [Arabidopsis thaliana]

 Score =  278 bits (712), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 128/182 (70%), Positives = 152/182 (83%), Gaps = 2/182 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           M+V YIVKNRE FEPFIEDDVPF++YC++M+ DGTWAG+MELQAASLVT SNICIHR+MS
Sbjct: 70  MIVLYIVKNREMFEPFIEDDVPFEDYCKTMDDDGTWAGNMELQAASLVTRSNICIHRNMS 129

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYIRNF+    RMIHLSYHDGEHYN VR KED+C G ARP++I+ADA +SAAS Q+K 
Sbjct: 130 PRWYIRNFEDTRTRMIHLSYHDGEHYNSVRSKEDACGGPARPVVIEADAKVSAASKQAKA 189

Query: 121 VTSKLKGAAGI--INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178
             SK K  A    +NAG+IK+VM+GS C+N+EK E+VLLQV GDVDAAIEFLIA+QG E 
Sbjct: 190 TESKSKNKADKCHVNAGAIKVVMSGSCCDNTEKAEQVLLQVNGDVDAAIEFLIADQGMES 249

Query: 179 YS 180
            +
Sbjct: 250 LT 251

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42573818|ref|NP_975005.1| SEC-C motif-containing protein / OTU-like cysteine protease family protein [Arabidopsis thaliana] gi|332010927|gb|AED98310.1| SEC-C motif-containing protein / OTU-like cysteine protease family protein [Arabidopsis thaliana]

 Score =  278 bits (712), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 128/182 (70%), Positives = 152/182 (83%), Gaps = 2/182 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           M+V YIVKNRE FEPFIEDDVPF++YC++M+ DGTWAG+MELQAASLVT SNICIHR+MS
Sbjct: 69  MIVLYIVKNREMFEPFIEDDVPFEDYCKTMDDDGTWAGNMELQAASLVTRSNICIHRNMS 128

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYIRNF+    RMIHLSYHDGEHYN VR KED+C G ARP++I+ADA +SAAS Q+K 
Sbjct: 129 PRWYIRNFEDTRTRMIHLSYHDGEHYNSVRSKEDACGGPARPVVIEADAKVSAASKQAKA 188

Query: 121 VTSKLKGAAGI--INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178
             SK K  A    +NAG+IK+VM+GS C+N+EK E+VLLQV GDVDAAIEFLIA+QG E 
Sbjct: 189 TESKSKNKADKCHVNAGAIKVVMSGSCCDNTEKAEQVLLQVNGDVDAAIEFLIADQGMES 248

Query: 179 YS 180
            +
Sbjct: 249 LT 250

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|10177604|dbj|BAB10951.1| unnamed protein product [Arabidopsis thaliana]

 Score =  278 bits (711), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 128/182 (70%), Positives = 152/182 (83%), Gaps = 2/182 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           M+V YIVKNRE FEPFIEDDVPF++YC++M+ DGTWAG+MELQAASLVT SNICIHR+MS
Sbjct: 77  MIVLYIVKNREMFEPFIEDDVPFEDYCKTMDDDGTWAGNMELQAASLVTRSNICIHRNMS 136

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYIRNF+    RMIHLSYHDGEHYN VR KED+C G ARP++I+ADA +SAAS Q+K 
Sbjct: 137 PRWYIRNFEDTRTRMIHLSYHDGEHYNSVRSKEDACGGPARPVVIEADAKVSAASKQAKA 196

Query: 121 VTSKLKGAAGI--INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178
             SK K  A    +NAG+IK+VM+GS C+N+EK E+VLLQV GDVDAAIEFLIA+QG E 
Sbjct: 197 TESKSKNKADKCHVNAGAIKVVMSGSCCDNTEKAEQVLLQVNGDVDAAIEFLIADQGMES 256

Query: 179 YS 180
            +
Sbjct: 257 LT 258

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297797661|ref|XP_002866715.1| hypothetical protein ARALYDRAFT_496882 [Arabidopsis lyrata subsp. lyrata] gi|297312550|gb|EFH42974.1| hypothetical protein ARALYDRAFT_496882 [Arabidopsis lyrata subsp. lyrata]

 Score =  276 bits (706), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 129/179 (72%), Positives = 150/179 (83%), Gaps = 2/179 (1%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           MVVQYIVKNRE FEPFIEDDVPF++YC++M+ DGTWAG+MELQAASLVT SNICIHR+MS
Sbjct: 69  MVVQYIVKNREMFEPFIEDDVPFEDYCKTMDDDGTWAGNMELQAASLVTRSNICIHRNMS 128

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT 120
           PRWYIRNF+    RMIHLSYHDGEHYN VR KED+  G ARP++I+ADA +SAAS Q+K 
Sbjct: 129 PRWYIRNFEDTRTRMIHLSYHDGEHYNSVRSKEDAFGGPARPVVIEADAKVSAASKQAKA 188

Query: 121 VTSKLKGAAGIIN--AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 177
             SK K  A   N  AG+IK+VM+GS C+N+EK E+VL+QV GDVDAAIEFLIAEQG E
Sbjct: 189 TESKSKNKADKCNVDAGAIKVVMSGSCCDNAEKAEQVLVQVNGDVDAAIEFLIAEQGME 247

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	184
TAIR|locus:2155588	375	AT5G67170 [Arabidopsis thalian	0.961	0.472	0.670	2.1e-61
DICTYBASE|DDB_G0267906	438	DDB_G0267906 "OTU domain conta	0.483	0.203	0.510	4.6e-24
ZFIN|ZDB-GENE-040426-2509	357	otud3 "OTU domain containing 3	0.505	0.260	0.344	9.8e-13
GENEDB_PFALCIPARUM|PF10_0308	938	PF10_0308 "OTU-like cysteine p	0.489	0.095	0.362	1.4e-10
UNIPROTKB|Q8IJ91	938	PF10_0308 "OTU-like cysteine p	0.489	0.095	0.362	1.4e-10
UNIPROTKB|Q01804	1113	OTUD4 "OTU domain-containing p	0.489	0.080	0.32	7.2e-07
MGI|MGI:1098801	1107	Otud4 "OTU domain containing 4	0.434	0.072	0.321	2.8e-05
DICTYBASE|DDB_G0279375	340	DDB_G0279375 "OTU domain conta	0.434	0.235	0.385	0.00014
ASPGD|ASPL0000061651	472	AN0173 [Emericella nidulans (t	0.755	0.294	0.259	0.00023
UNIPROTKB|G4NEZ8	304	MGG_11505 "Uncharacterized pro	0.456	0.276	0.319	0.00038

TAIR|locus:2155588 AT5G67170 [Arabidopsis thaliana (taxid:3702)]

 Score = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 120/179 (67%), Positives = 139/179 (77%)

Query:     1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
             M+V YIVKNRE FEPFIEDDVPF++YC++M+ DGTWAG+MELQAASLVT SNICIHR+MS
Sbjct:    70 MIVLYIVKNREMFEPFIEDDVPFEDYCKTMDDDGTWAGNMELQAASLVTRSNICIHRNMS 129

Query:    61 PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPXXXXXXXXXXXXXXQSKT 120
             PRWYIRNF+    RMIHLSYHDGEHYN VR KED+C G ARP              Q+K 
Sbjct:   130 PRWYIRNFEDTRTRMIHLSYHDGEHYNSVRSKEDACGGPARPVVIEADAKVSAASKQAKA 189

Query:   121 VTSKLKGAAGI--INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 177
               SK K  A    +NAG+IK+VM+GS C+N+EK E+VLLQV GDVDAAIEFLIA+QG E
Sbjct:   190 TESKSKNKADKCHVNAGAIKVVMSGSCCDNTEKAEQVLLQVNGDVDAAIEFLIADQGME 248

GO:0005634 "nucleus" evidence=ISM

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008234 "cysteine-type peptidase activity" evidence=ISS

DICTYBASE|DDB_G0267906 DDB_G0267906 "OTU domain containin protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 242 (90.2 bits), Expect = 4.6e-24, Sum P(2) = 4.6e-24
 Identities = 47/92 (51%), Positives = 61/92 (66%)

Query:     2 VVQYIVKNRETFEPFIEDDV--PFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHM 59
             + +YI KN++ F PFI+D+    F+EY Q M  D TW GH+E+QAASL  + NI IH+  
Sbjct:    98 ICKYIEKNKDMFAPFIDDEEFESFEEYIQEMREDATWGGHVEIQAASLAYNVNITIHQMD 157

Query:    60 SPRWYIRN-FDYHEARMIHLSYHDGEHYNGVR 90
              PRW I N F   + + IHLSYH+ EHYN VR
Sbjct:   158 QPRWEIVNHFPPEKNKTIHLSYHNDEHYNSVR 189

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

ZFIN|ZDB-GENE-040426-2509 otud3 "OTU domain containing 3" [Danio rerio (taxid:7955)]

 Score = 174 (66.3 bits), Expect = 9.8e-13, P = 9.8e-13
 Identities = 32/93 (34%), Positives = 54/93 (58%)

Query:     3 VQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPR 62
             V Y+  +R  FEPF+EDDVPF+++  ++   GT+AG+  + A +      + IH+  +P 
Sbjct:    94 VHYMRTHRNDFEPFVEDDVPFEKHLTNLSQQGTFAGNDAIVAFARSQQLKVVIHQLNAPL 153

Query:    63 WYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDS 95
             W I   +    R +H++Y  G+HY+ VR   D+
Sbjct:   154 WEINGTEKPSCRELHIAYRYGDHYDSVRKTGDN 186

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GENEDB_PFALCIPARUM|PF10_0308 PF10_0308 "OTU-like cysteine protease, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 161 (61.7 bits), Expect = 1.4e-10, P = 1.4e-10
 Identities = 33/91 (36%), Positives = 50/91 (54%)

Query:     2 VVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSP 61
             VV++++KN E ++ FIE D  +  Y + +  DGTW G +ELQA   +   NI I++    
Sbjct:    84 VVEHLLKNEELYKNFIEYDESYKSYIERISLDGTWGGQLELQAVGEIYKVNILIYQENGC 143

Query:    62 RWYIRNFDYHEARMIHLSYHDGEHYNGVRLK 92
                I+N    + + + L Y   EHYN VR K
Sbjct:   144 ILEIKNHS-DDNKCLQLHYASSEHYNSVRFK 173

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8IJ91 PF10_0308 "OTU-like cysteine protease, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 161 (61.7 bits), Expect = 1.4e-10, P = 1.4e-10
 Identities = 33/91 (36%), Positives = 50/91 (54%)

Query:     2 VVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSP 61
             VV++++KN E ++ FIE D  +  Y + +  DGTW G +ELQA   +   NI I++    
Sbjct:    84 VVEHLLKNEELYKNFIEYDESYKSYIERISLDGTWGGQLELQAVGEIYKVNILIYQENGC 143

Query:    62 RWYIRNFDYHEARMIHLSYHDGEHYNGVRLK 92
                I+N    + + + L Y   EHYN VR K
Sbjct:   144 ILEIKNHS-DDNKCLQLHYASSEHYNSVRFK 173

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q01804 OTUD4 "OTU domain-containing protein 4" [Homo sapiens (taxid:9606)]

 Score = 127 (49.8 bits), Expect = 7.2e-07, P = 7.2e-07
 Identities = 32/100 (32%), Positives = 54/100 (54%)

Query:     3 VQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHR--HMS 60
             + Y+ +NRE FE FIE    F+EY + +E    W G +E+ A SL+   +  I+R  ++S
Sbjct:    69 IHYLRENREKFEAFIEGS--FEEYLKRLENPQEWVGQVEISALSLMYRKDFIIYREPNVS 126

Query:    61 PRWYIRNFDYHEARMIHLSYHDGEHYN---GVRLKEDSCI 97
             P     N ++ E   + L + +G HY+    ++ KE S +
Sbjct:   127 PSQVTEN-NFPEK--VLLCFSNGNHYDIVYPIKYKESSAM 163

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

MGI|MGI:1098801 Otud4 "OTU domain containing 4" [Mus musculus (taxid:10090)]

 Score = 120 (47.3 bits), Expect = 2.8e-05, P = 2.8e-05
 Identities = 28/87 (32%), Positives = 49/87 (56%)

Query:     3 VQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHR--HMS 60
             ++Y+ +NRE FE FIE    F+EY + +E    W G +E+ A SL+   +  I++  ++S
Sbjct:    69 IRYLRENREKFEAFIEGS--FEEYLKRLENPQEWVGQVEISALSLMYRKDFVIYQEPNVS 126

Query:    61 PRWYIRNFDYHEARMIHLSYHDGEHYN 87
             P     N ++ E   + L + +G HY+
Sbjct:   127 PSHVTEN-NFPEK--VLLCFSNGNHYD 150

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

DICTYBASE|DDB_G0279375 DDB_G0279375 "OTU domain containin protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 111 (44.1 bits), Expect = 0.00014, P = 0.00014
 Identities = 37/96 (38%), Positives = 45/96 (46%)

Query:     5 YIVKNRETFEPFI--EDDV-----PFDEYCQSME-TDGTWAGHMELQAASLVTHSNICIH 56
             YI  NR+ F PFI  ED+      P  EYCQ    T G W GH+EL+A S      I I 
Sbjct:   241 YIKNNRDEFLPFIISEDEYSTAEDPIQEYCQEQVLTIGKWGGHIELKALSQSLKKVITIF 300

Query:    57 RHMSPRWYIRNFDYHEARMIHLSYHD-----GEHYN 87
                S    I   ++     I+L+YH      GEHYN
Sbjct:   301 NAYSNDIIIGE-EF--TNPIYLTYHRHAFTLGEHYN 333

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

ASPGD|ASPL0000061651 AN0173 [Emericella nidulans (taxid:162425)]

 Score = 111 (44.1 bits), Expect = 0.00023, P = 0.00023
 Identities = 41/158 (25%), Positives = 65/158 (41%)

Query:    23 FDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNF-DYH-----EARMI 76
             FD        +G W G  E+QA       ++ ++      + I+NF D H     E   I
Sbjct:   163 FDSRVAESRKNGVWGGAEEIQAFCQSFKKDVNVYT----MYGIQNFRDVHAPADEERETI 218

Query:    77 HLSYHDGEHYNGVRLKEDSCIGSARPXXXXXXXXXXXXXXQSKTVTSKLKGAAGIINAGS 136
             H+++HD  HY+ VR     C G   P              Q+ T     +G   + +   
Sbjct:   219 HIAFHDFHHYSSVR----HCEG---PHTGLPRIPKAEQSAQTSTAPPD-EGVVNVASPWK 270

Query:   137 IKLVMAGSGCE-NSEKVEEVLLQVGGDVDAAIEFLIAE 173
             I  + AG G + + E + EVL Q  G++D A   L+ +
Sbjct:   271 ISAIQAGLGDKYDRETIVEVLEQCRGNIDNAFLNLLGD 308

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|G4NEZ8 MGG_11505 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 107 (42.7 bits), Expect = 0.00038, P = 0.00038
 Identities = 31/97 (31%), Positives = 46/97 (47%)

Query:     5 YIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWY 64
             YI  + + F PF+E+  P D+Y + M     W GHMEL A  L +  N+ +      R  
Sbjct:   211 YISDHADDFAPFLEE--PLDDYVRKMRDTAEWGGHMELLA--LASTYNVEVRVIADGRTA 266

Query:    65 I----RNFDYHEARMIHLSYHD-----GEHYNGVRLK 92
             +       +   AR + L+Y+      GEHYN +R K
Sbjct:   267 VVQPKEPKEDEPARQVWLAYYRHGFGLGEHYNSLRKK 303

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0043581 "mycelium development" evidence=IEP

---

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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_V000542 hypothetical protein (349 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	184
pfam02338	123	pfam02338, OTU, OTU-like cysteine protease	7e-14
pfam10275	237	pfam10275, Peptidase_C65, Peptidase C65 Otubain	6e-05

>gnl|CDD|216981 pfam02338, OTU, OTU-like cysteine protease

 Score = 64.5 bits (157), Expect = 7e-14
 Identities = 30/96 (31%), Positives = 50/96 (52%), Gaps = 12/96 (12%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
            VV+Y+ +NRE FE F+E+D   +EY + +  DG W G++E+ A + +    I +++   
Sbjct: 30  AVVEYLRENREDFEKFLEED--ENEYYKWISKDGAWGGNIEIFALAHILRVPIIVYKLQG 87

Query: 61  PR--WYIRNFDYHE----ARMIHLSYH----DGEHY 86
            R   YI+ +  +       +I LSY      G HY
Sbjct: 88  GRITVYIKIYGTYLPLNKKPVIRLSYLGLEYTGNHY 123

This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases. Length = 123

>gnl|CDD|220671 pfam10275, Peptidase_C65, Peptidase C65 Otubain

 Score = 41.9 bits (99), Expect = 6e-05
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 10/94 (10%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYC-QSMETDGTWAGHMELQAASLVTHSNICIHRHM 59
           +   YI +N + ++PFI++ +  +E+C Q +E     + H+++ A  L     I +    
Sbjct: 143 LTSAYIKENADEYQPFIDELLTVEEFCEQEVEPMAKESDHVQIIA--LAEALGIPVRVEY 200

Query: 60  SPRWYIRNFDYHE------ARMIHLSYHDGEHYN 87
             R     +++H       A  I L Y  G HY+
Sbjct: 201 LDRSEGNEYNHHNFPPEPNAPKITLLYRPG-HYD 233

This family of proteins conserved from plants to humans is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryote being a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. Length = 237

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	184
KOG2606	302	consensus OTU (ovarian tumor)-like cysteine protea	99.85
KOG3288	307	consensus OTU-like cysteine protease [Signal trans	99.51
PF02338	121	OTU: OTU-like cysteine protease; InterPro: IPR0033	99.5
KOG3991	256	consensus Uncharacterized conserved protein [Funct	99.36
PF10275	244	Peptidase_C65: Peptidase C65 Otubain; InterPro: IP	99.34
KOG2605	371	consensus OTU (ovarian tumor)-like cysteine protea	98.45
COG5539	306	Predicted cysteine protease (OTU family) [Posttran	98.42
COG5539	306	Predicted cysteine protease (OTU family) [Posttran	98.24
PF02845	42	CUE: CUE domain; InterPro: IPR003892 This domain m	97.55
PF00627	37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	97.42
PF14555	43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	97.29
smart00546	43	CUE Domain that may be involved in binding ubiquit	97.01
cd00194	38	UBA Ubiquitin Associated domain. The UBA domain is	96.97
TIGR00264	116	alpha-NAC-related protein. This hypothetical prote	96.94
PRK06369	115	nac nascent polypeptide-associated complex protein	96.88
smart00165	37	UBA Ubiquitin associated domain. Present in Rad23,	96.42
COG1308	122	EGD2 Transcription factor homologous to NACalpha-B	95.31
PF06972	60	DUF1296: Protein of unknown function (DUF1296); In	95.17
PF03474	39	DMA: DMRTA motif; InterPro: IPR005173 This region	93.94
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	88.8
PF08938	79	HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This	84.08
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	81.56

>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]

Probab=99.85  E-value=5.3e-22  Score=169.30  Aligned_cols=91  Identities=31%  Similarity=0.582  Sum_probs=79.8

Q ss_pred             ChHHHHHhCccccccccCCC--------CCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEee-cccC
Q 030009            1 MVVQYIVKNRETFEPFIEDD--------VPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRN-FDYH   71 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~--------~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~-~~~~   71 (184)
                      ++|+||++|.++|.||+.++        .+|+.||+.|+.++.|||++||.|||.+|++||.||+.++|...++. |.  
T Consensus       195 ~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~~p~~~~geey~--  272 (302)
T KOG2606|consen  195 ETADYMREHVEDFLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQADGPILEYGEEYG--  272 (302)
T ss_pred             HHHHHHHHHHHHhhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecCCCceeechhhC--
Confidence            47999999999999999864        25999999999999999999999999999999999999998776653 32  


Q ss_pred             CCcEEEEEEc-----cCCcccceeccC
Q 030009           72 EARMIHLSYH-----DGEHYNGVRLKE   93 (184)
Q Consensus        72 ~~~~i~L~Y~-----~g~HYdSV~~~~   93 (184)
                      +.++|.|+||     .|+||||+.+..
T Consensus       273 kd~pL~lvY~rH~y~LGeHYNS~~~~~  299 (302)
T KOG2606|consen  273 KDKPLILVYHRHAYGLGEHYNSVTPLK  299 (302)
T ss_pred             CCCCeeeehHHhHHHHHhhhccccccc
Confidence            2579999998     499999998754

>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]

Probab=99.51  E-value=7.4e-15  Score=123.65  Aligned_cols=104  Identities=23%  Similarity=0.372  Sum_probs=84.2

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEeeccc--CCCcEEEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDY--HEARMIHL   78 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~--~~~~~i~L   78 (184)
                      |+++-...|++.|..-|.+ ++-.+||.||+++.+|||.|||..||..|++.|+|++.+.  ..|..|++  .....+.|
T Consensus       144 iiA~~Vasnp~~yn~AiLg-K~n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiqt--~rid~fged~~~~~rv~l  220 (307)
T KOG3288|consen  144 IIAQEVASNPDKYNDAILG-KPNKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQT--VRIDRFGEDKNFDNRVLL  220 (307)
T ss_pred             HHHHHHhcChhhhhHHHhC-CCcHHHHHHHccccccCceEEeeeehhhhceeEEEEecce--eeehhcCCCCCCCceEEE
Confidence            4678889999999877776 7999999999999999999999999999999999999977  44444543  24566778


Q ss_pred             EEccCCcccceeccC-CCCCCCCceeeeccc
Q 030009           79 SYHDGEHYNGVRLKE-DSCIGSARPIIIKAD  108 (184)
Q Consensus        79 ~Y~~g~HYdSV~~~~-~~~~gp~~p~~~~~~  108 (184)
                      .| +|.|||++.... .|..-|..+.+...+
T Consensus       221 ly-dGIHYD~l~m~~~~~~~~~~tifp~~dd  250 (307)
T KOG3288|consen  221 LY-DGIHYDPLAMNEFKPTDVDNTIFPVSDD  250 (307)
T ss_pred             Ee-cccccChhhhccCCccCCcccccccccc
Confidence            77 899999998765 666666665554444

>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae

Probab=99.50  E-value=1.3e-14  Score=108.63  Aligned_cols=77  Identities=39%  Similarity=0.626  Sum_probs=64.8

Q ss_pred             hHHHHH-hCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceE--Eeec----ccCCCc
Q 030009            2 VVQYIV-KNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWY--IRNF----DYHEAR   74 (184)
Q Consensus         2 vv~yi~-~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~--i~~~----~~~~~~   74 (184)
                      +++||+ .|++.|++|+.++        +|+++|+|||++||+|+|.+|+++|.|++...+...  +...    +....+
T Consensus        33 ~~~~l~~~~~~~~~~~~~~~--------~~~~~~~Wg~~~el~a~a~~~~~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~  104 (121)
T PF02338_consen   33 VVDYLRDKNRDKFEEFLEGD--------KMSKPGTWGGEIELQALANVLNRPIIVYSSSDGDNVVFIKFTGKYPPLESPP  104 (121)
T ss_dssp             HHHHHHTHTTTHHHHHHHHH--------HHTSTTSHEEHHHHHHHHHHHTSEEEEECETTTBEEEEEEESCEESTTTTTT
T ss_pred             HHHHHHHhccchhhhhhhhh--------hhccccccCcHHHHHHHHHHhCCeEEEEEcCCCCccceeeecCccccCCCCC
Confidence            789999 9999999999973        999999999999999999999999999988655432  2211    234578


Q ss_pred             EEEEEEcc-----CCcc
Q 030009           75 MIHLSYHD-----GEHY   86 (184)
Q Consensus        75 ~i~L~Y~~-----g~HY   86 (184)
                      +|+|+|+.     +.||
T Consensus       105 ~i~l~~~~~l~~~~~Hy  121 (121)
T PF02338_consen  105 PICLCYHGHLYYTGNHY  121 (121)
T ss_dssp             SEEEEEETEEEEETTEE
T ss_pred             eEEEEEcCCccCCCCCC
Confidence            89999998     9998

In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....

>KOG3991 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.36  E-value=8.9e-13  Score=109.57  Aligned_cols=91  Identities=22%  Similarity=0.350  Sum_probs=79.1

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHh-hhcCCccCCHHHHHHHHhhcCccEEEEEccCCce-EE--eecccCCCcEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQS-METDGTWAGHMELQAASLVTHSNICIHRHMSPRW-YI--RNFDYHEARMI   76 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~-m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~-~i--~~~~~~~~~~i   76 (184)
                      +++.+|+.|+|+|+|||+++++..+||.. +....+-.|||+|.|||+++++.|+|..++.... ..  ..|++...+.|
T Consensus       162 vtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~fpe~s~P~I  241 (256)
T KOG3991|consen  162 VTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDFPEASAPEI  241 (256)
T ss_pred             HHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcCccccCceE
Confidence            36789999999999999999999999996 8999999999999999999999999999976433 22  23667788999


Q ss_pred             EEEEccCCcccceecc
Q 030009           77 HLSYHDGEHYNGVRLK   92 (184)
Q Consensus        77 ~L~Y~~g~HYdSV~~~   92 (184)
                      .|.|..| |||.++++
T Consensus       242 ~LLYrpG-HYdilY~~  256 (256)
T KOG3991|consen  242 YLLYRPG-HYDILYKK  256 (256)
T ss_pred             EEEecCC-ccccccCC
Confidence            9999887 99999873

>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=99.34  E-value=2.4e-12  Score=108.24  Aligned_cols=90  Identities=23%  Similarity=0.403  Sum_probs=69.4

Q ss_pred             ChHHHHHhCccccccccCCC--CCHHHHHHh-hhcCCccCCHHHHHHHHhhcCccEEEEEccCC----ceEEeecc---c
Q 030009            1 MVVQYIVKNRETFEPFIEDD--VPFDEYCQS-METDGTWAGHMELQAASLVTHSNICIHRHMSP----RWYIRNFD---Y   70 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~--~~f~~Y~~~-m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~----~~~i~~~~---~   70 (184)
                      +++.||+.|++.|+||+++.  .++++||++ +...+.-++|+.|.|||++++++|.|+.++..    ......++   .
T Consensus       145 lts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~~~~~~~~~~~~~~~~~  224 (244)
T PF10275_consen  145 LTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRSVEGDEVNRHEFPPDNE  224 (244)
T ss_dssp             HHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSSGCSTTSEEEEES-SST
T ss_pred             HHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCCCCCCccccccCCCccC
Confidence            47899999999999999976  799999975 99999999999999999999999999999854    11222342   3


Q ss_pred             CCCcEEEEEEccCCcccceec
Q 030009           71 HEARMIHLSYHDGEHYNGVRL   91 (184)
Q Consensus        71 ~~~~~i~L~Y~~g~HYdSV~~   91 (184)
                      ...+.|+|.|..| |||.+++
T Consensus       225 ~~~~~i~LLyrpg-HYdIly~  244 (244)
T PF10275_consen  225 SQEPQITLLYRPG-HYDILYP  244 (244)
T ss_dssp             TSS-SEEEEEETB-EEEEEEE
T ss_pred             CCCCEEEEEEcCC-ccccccC
Confidence            4678999999988 9999875

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.

>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]

Probab=98.45  E-value=8.9e-08  Score=85.49  Aligned_cols=90  Identities=21%  Similarity=0.306  Sum_probs=71.9

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHH---hhcCccEEEEEccCCceEEee-cccCCCcEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAAS---LVTHSNICIHRHMSPRWYIRN-FDYHEARMI   76 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala---~~~~v~I~V~~~~~~~~~i~~-~~~~~~~~i   76 (184)
                      ++++++..++++|+.|+..  +|.+|+.+|++++.||.|+|+||+|   .....++.|.+...+.|.-.. -.+.....+
T Consensus       251 ~~~dq~~~e~~~~~~~vt~--~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~  328 (371)
T KOG2605|consen  251 ECVDQLKKERDFYEDYVTE--DFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNITSFKDTCYIQTPPAIEESVKME  328 (371)
T ss_pred             HHHHHHhhccccccccccc--chhhcccccccCCCCcchHHHhhhhhhhhhccccceeecccccceeccCcccccchhhh
Confidence            4789999999999999995  8999999999999999999999999   555777778777776554321 112234457


Q ss_pred             EEEEccCCcccceecc
Q 030009           77 HLSYHDGEHYNGVRLK   92 (184)
Q Consensus        77 ~L~Y~~g~HYdSV~~~   92 (184)
                      ++.|..-.||+.++.-
T Consensus       329 ~~n~~~~~h~~~~~~~  344 (371)
T KOG2605|consen  329 KYNFWVEVHYNTARHS  344 (371)
T ss_pred             hhcccchhhhhhcccc
Confidence            7777788999999884

>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]

Probab=98.42  E-value=1.9e-07  Score=80.29  Aligned_cols=84  Identities=19%  Similarity=0.184  Sum_probs=64.1

Q ss_pred             HHHHhCccccccccCCC-----CCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEeecccCCCcEEEE
Q 030009            4 QYIVKNRETFEPFIEDD-----VPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHL   78 (184)
Q Consensus         4 ~yi~~n~d~F~pFv~~~-----~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~~~~~~i~L   78 (184)
                      .|..++.+.|.+|..|.     .+|++||..|+-+..||+.+|++|||.+|++++.++...+|...-...+.  ....-+
T Consensus       212 ~~~q~~~i~f~g~hfD~~t~~m~~~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~~~~ik~n~c~~--~~~~e~  289 (306)
T COG5539         212 PYVQRISILFTGIHFDEETLAMVLWDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTASPSIKCNICGT--GFVGEK  289 (306)
T ss_pred             hhhhhhhhhhcccccchhhhhcchHHHHHhhhcccccccchHHHHHHHHHhcCceEEeecCCceEEeecccc--ccchhh
Confidence            56778999999999875     37999999999999999999999999999999999988776443322111  111223


Q ss_pred             EE-----ccCCccccee
Q 030009           79 SY-----HDGEHYNGVR   90 (184)
Q Consensus        79 ~Y-----~~g~HYdSV~   90 (184)
                      .|     -.| |||+..
T Consensus       290 ~~~~Ha~a~G-H~n~~~  305 (306)
T COG5539         290 DYYAHALATG-HYNFGE  305 (306)
T ss_pred             HHHHHHHhhc-CccccC
Confidence            33     358 999874

>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]

Probab=98.24  E-value=1.6e-07  Score=80.84  Aligned_cols=87  Identities=15%  Similarity=0.206  Sum_probs=69.7

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccC-CHHHHHHHHhhcCccEEEEEccCCceEEeecc-cCCCcEEEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWA-GHMELQAASLVTHSNICIHRHMSPRWYIRNFD-YHEARMIHL   78 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WG-g~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~-~~~~~~i~L   78 (184)
                      +|+.-+.+|||.|.+.+.+ .+--.||.|+.++..|| |++||.++|..+++.|+++.++.....  .|. ......+.+
T Consensus       143 ~vs~Ev~snPDl~n~~i~~-~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~d--r~~~~~~~q~~~i  219 (306)
T COG5539         143 VVSLEVLSNPDLYNPAILE-IDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSED--RYNSHPYVQRISI  219 (306)
T ss_pred             HHHHHHhhCccccchhhcC-cchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHh--hccCChhhhhhhh
Confidence            3567788999999999997 89999999999999999 999999999999999999999864221  122 122334666


Q ss_pred             EEccCCcccceec
Q 030009           79 SYHDGEHYNGVRL   91 (184)
Q Consensus        79 ~Y~~g~HYdSV~~   91 (184)
                      .| .|.|||....
T Consensus       220 ~f-~g~hfD~~t~  231 (306)
T COG5539         220 LF-TGIHFDEETL  231 (306)
T ss_pred             hh-cccccchhhh
Confidence            66 6889999873

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

Probab=97.55  E-value=0.00027  Score=43.96  Aligned_cols=39  Identities=28%  Similarity=0.296  Sum_probs=32.6

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      .|+.+..-.+-.+.+.|+.+|++++||+|.||+.||+.+
T Consensus         4 ~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~~   42 (42)
T PF02845_consen    4 MVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEMS   42 (42)
T ss_dssp             HHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence            466666666777899999999999999999999999863

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.

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

Probab=97.42  E-value=0.00033  Score=42.38  Aligned_cols=35  Identities=26%  Similarity=0.504  Sum_probs=29.9

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHH
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL  170 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~L  170 (184)
                      ++.|++++.- |. +.+.++++|+.++||++.|+++|
T Consensus         3 ~~~v~~L~~m-Gf-~~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    3 EEKVQQLMEM-GF-SREQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHHH-TS--HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             HHHHHHHHHc-CC-CHHHHHHHHHHcCCCHHHHHHhC
Confidence            4568888886 75 58899999999999999999987

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 ....

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

Probab=97.29  E-value=0.00052  Score=42.94  Aligned_cols=40  Identities=18%  Similarity=0.209  Sum_probs=33.2

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      ..|++.|.-||| +.+..++.|+.+++|++.||..-++...
T Consensus         2 e~i~~F~~iTg~-~~~~A~~~L~~~~wdle~Av~~y~~~~~   41 (43)
T PF14555_consen    2 EKIAQFMSITGA-DEDVAIQYLEANNWDLEAAVNAYFDDGE   41 (43)
T ss_dssp             HHHHHHHHHH-S-SHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred             HHHHHHHHHHCc-CHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            358899999999 7899999999999999999999887654

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

Probab=97.01  E-value=0.0018  Score=40.32  Aligned_cols=38  Identities=21%  Similarity=0.221  Sum_probs=31.9

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      .++.+..-.+--+...|+.+|++++||+|.||..||..
T Consensus         5 ~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~   42 (43)
T smart00546        5 ALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG   42 (43)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence            45556665666789999999999999999999999964

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)

>cd00194 UBA Ubiquitin Associated domain

Probab=96.97  E-value=0.0022  Score=38.51  Aligned_cols=36  Identities=19%  Similarity=0.442  Sum_probs=29.7

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      ..|++++. .|. +.+.++++|+.++||++.|+++|+.
T Consensus         3 ~~v~~L~~-mGf-~~~~~~~AL~~~~~d~~~A~~~L~~   38 (38)
T cd00194           3 EKLEQLLE-MGF-SREEARKALRATNNNVERAVEWLLE   38 (38)
T ss_pred             HHHHHHHH-cCC-CHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            34566665 575 5999999999999999999999973

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.

>TIGR00264 alpha-NAC-related protein

Probab=96.94  E-value=0.0014  Score=49.68  Aligned_cols=39  Identities=33%  Similarity=0.445  Sum_probs=34.8

Q ss_pred             CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009          132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI  171 (184)
Q Consensus       132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll  171 (184)
                      ++++.|+.||..|||+ .+..+++|++|+||+-.||.+|-
T Consensus        77 i~~eDI~lV~eq~gvs-~e~A~~AL~~~~gDl~~AI~~L~  115 (116)
T TIGR00264        77 ITEDDIELVMKQCNVS-KEEARRALEECGGDLAEAIMKLE  115 (116)
T ss_pred             CCHHHHHHHHHHhCcC-HHHHHHHHHHcCCCHHHHHHHhh
Confidence            4566799999999995 89999999999999999999873

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

>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed

Probab=96.88  E-value=0.0018  Score=49.10  Aligned_cols=41  Identities=29%  Similarity=0.375  Sum_probs=35.9

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      .++++.|+.||..|||+ .+..+++|++|+||+-.||.+|-.
T Consensus        74 ~i~~edI~lv~~q~gvs-~~~A~~AL~~~~gDl~~AI~~L~~  114 (115)
T PRK06369         74 EIPEEDIELVAEQTGVS-EEEARKALEEANGDLAEAILKLSS  114 (115)
T ss_pred             CCCHHHHHHHHHHHCcC-HHHHHHHHHHcCCcHHHHHHHHhc
Confidence            35566799999999996 899999999999999999998853

>smart00165 UBA Ubiquitin associated domain

Probab=96.42  E-value=0.0081  Score=35.83  Aligned_cols=34  Identities=26%  Similarity=0.457  Sum_probs=28.0

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI  171 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll  171 (184)
                      .+++++. .| .+.+.++++|..++||++.|+++|+
T Consensus         4 ~v~~L~~-mG-f~~~~a~~aL~~~~~d~~~A~~~L~   37 (37)
T smart00165        4 KIDQLLE-MG-FSREEALKALRAANGNVERAAEYLL   37 (37)
T ss_pred             HHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence            4555555 46 5688999999999999999999985

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

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

Probab=95.31  E-value=0.036  Score=42.41  Aligned_cols=40  Identities=38%  Similarity=0.474  Sum_probs=35.6

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI  171 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll  171 (184)
                      .+.++-|+.||..||.+ .+.++.+|++++||+-.||..|.
T Consensus        82 ~i~eeDIkLV~eQa~Vs-reeA~kAL~e~~GDlaeAIm~L~  121 (122)
T COG1308          82 DISEEDIKLVMEQAGVS-REEAIKALEEAGGDLAEAIMKLT  121 (122)
T ss_pred             CCCHHHHHHHHHHhCCC-HHHHHHHHHHcCCcHHHHHHHhc
Confidence            46677899999999985 99999999999999999998874

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

Probab=95.17  E-value=0.05  Score=36.61  Aligned_cols=39  Identities=18%  Similarity=0.400  Sum_probs=33.4

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      .||.+=..+||+.-+-|..+|.+|+.|.+.|+..||..+
T Consensus         8 ~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~qD   46 (60)
T PF06972_consen    8 TVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQD   46 (60)
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Confidence            356666678998888999999999999999999999854

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

Probab=93.94  E-value=0.12  Score=31.90  Aligned_cols=28  Identities=29%  Similarity=0.345  Sum_probs=23.5

Q ss_pred             CCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009          144 SGCENSEKVEEVLLQVGGDVDAAIEFLI  171 (184)
Q Consensus       144 tG~~d~~~i~~~L~~~~gdid~Ai~~Ll  171 (184)
                      ..-.....+..+|+.|+||+-.|||.+|
T Consensus        12 FP~~kr~~Le~iL~~C~GDvv~AIE~~l   39 (39)
T PF03474_consen   12 FPHQKRSVLELILQRCNGDVVQAIEQFL   39 (39)
T ss_pred             CCCCChHHHHHHHHHcCCcHHHHHHHhC
Confidence            3445678888899999999999999875

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

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=88.80  E-value=0.7  Score=41.78  Aligned_cols=38  Identities=29%  Similarity=0.403  Sum_probs=33.4

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      +.+|+.+|.= | ++.+.|+.+|++.=+|-|.||||||.-
T Consensus       157 e~~I~~i~eM-G-f~R~qV~~ALRAafNNPdRAVEYL~tG  194 (378)
T TIGR00601       157 ETTIEEIMEM-G-YEREEVERALRAAFNNPDRAVEYLLTG  194 (378)
T ss_pred             HHHHHHHHHh-C-CCHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence            4578888883 4 799999999999999999999999964

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

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

Probab=84.08  E-value=0.68  Score=32.50  Aligned_cols=41  Identities=20%  Similarity=0.314  Sum_probs=29.8

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE  177 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~  177 (184)
                      .|+.+|..+-- .-..|+++|-.+.+|++.||.+||......
T Consensus        34 ~vr~~Lg~~~~-~e~~i~eal~~~~fDvekAl~~Ll~~~~~~   74 (79)
T PF08938_consen   34 QVREVLGDYVP-PEEQIKEALWHYYFDVEKALDYLLSKFKKK   74 (79)
T ss_dssp             CHHHHCCCCC---CCHHHHHHHHTTT-CCHHHHHHHHCCHSS
T ss_pred             HHHHHHcccCC-CHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence            36677764221 567788999999999999999999876544

; PDB: 1UFZ_A 3IZQ_1.

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

Probab=81.56  E-value=2.3  Score=26.02  Aligned_cols=22  Identities=27%  Similarity=0.525  Sum_probs=18.3

Q ss_pred             hHHHHHHHHHhCCCHHHHHHHH
Q 030009          149 SEKVEEVLLQVGGDVDAAIEFL  170 (184)
Q Consensus       149 ~~~i~~~L~~~~gdid~Ai~~L  170 (184)
                      .+.|+++|+.++||+..|-..|
T Consensus         7 ~~~i~~aL~~~~gn~~~aA~~L   28 (42)
T PF02954_consen    7 KQLIRQALERCGGNVSKAARLL   28 (42)
T ss_dssp             HHHHHHHHHHTTT-HHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHH
Confidence            5789999999999999887765

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

---

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	184
3pfy_A	185	OTU domain-containing protein 5; structural genomi	4e-24
3phx_A	185	RNA-directed RNA polymerase L; OTU domain, DE-ubiq	3e-22
3phu_A	219	RNA-directed RNA polymerase L; OTU domain, DE-ubiq	4e-21
3by4_A	212	OTU1, ubiquitin thioesterase OTU1; ubiquitin hydro	3e-19
2zfy_A	234	Ubiquitin thioesterase OTUB1; otubain, structural	4e-13
1tff_A	234	Ubiquitin thiolesterase protein OTUB2; hydrolase;	4e-10
4dhi_B	284	Ubiquitin thioesterase otubain-like; ubiquitin E2	4e-08

>3pfy_A OTU domain-containing protein 5; structural genomics, structural genomics consortium, SGC, PE C65 otubain, hydrolase; HET: MSE PG4; 1.70A {Homo sapiens} PDB: 3tmp_A* 3tmo_A* Length = 185

 Score = 92.5 bits (229), Expect = 4e-24
 Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 3/96 (3%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
             + Y++KN + F  ++ +D  F  Y      +     H+E+QA + + +  + ++++ +
Sbjct: 92  HCMDYLMKNADYFSNYVTED--FTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYST 149

Query: 61  PRW-YIRNFDYHEARMIHLSYHDGEHYNGVRLKEDS 95
                      +E   I +SYH   HYN V     +
Sbjct: 150 EPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNPNKA 185

>3phx_A RNA-directed RNA polymerase L; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Crimean-congo hemorrhagic fever virus} PDB: 3phw_A 3pt2_A 3pse_A 3prp_A 3prm_A Length = 185

 Score = 87.8 bits (217), Expect = 3e-22
 Identities = 10/101 (9%), Positives = 31/101 (30%), Gaps = 7/101 (6%)

Query: 1   MVVQYIVKNRETFEPFIED----DVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIH 56
            + +        +     +     +  ++Y + M +D  W   +E    +      I I 
Sbjct: 62  YIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIW 121

Query: 57  RHMSPRWYIRNFDYHE---ARMIHLSYHDGEHYNGVRLKED 94
              +         + +      ++L +    H++ +R+   
Sbjct: 122 TVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQ 162

>3phu_A RNA-directed RNA polymerase L; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase; 2.20A {Crimean-congo hemorrhagic fever VIRUSIBAR10200} Length = 219

 Score = 85.6 bits (211), Expect = 4e-21
 Identities = 13/123 (10%), Positives = 37/123 (30%), Gaps = 4/123 (3%)

Query: 2   VVQYIVKNRETFEPF-IEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           + +   +     EP      +  ++Y + M +D  W   +E    +      I I    +
Sbjct: 66  LTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAA 125

Query: 61  PRWYIRNFDYHE---ARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQ 117
                    + +      ++L +    H++ +R+       +   + +            
Sbjct: 126 SDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSLMDRVIAVDQLTS 185

Query: 118 SKT 120
           S +
Sbjct: 186 SSS 188

>3by4_A OTU1, ubiquitin thioesterase OTU1; ubiquitin hydrolase, deubiquitinase, cell cycle, hydrolase; 1.55A {Saccharomyces cerevisiae} PDB: 3c0r_A Length = 212

 Score = 80.4 bits (198), Expect = 3e-19
 Identities = 20/103 (19%), Positives = 40/103 (38%), Gaps = 3/103 (2%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60
           MV + ++ N   F   I D  P  +Y Q +    +W G +E+   S      I +    +
Sbjct: 52  MVSKEVLNNPVKFNDAILDK-PNKDYAQWILKMESWGGAIEIGIISDALAVAIYVVDIDA 110

Query: 61  PRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGSARPI 103
            +    N D  +  ++     +G HY+ + + E   + +    
Sbjct: 111 VKIEKFNEDKFDNYILI--LFNGIHYDSLTMNEFKTVFNKNQP 151

>2zfy_A Ubiquitin thioesterase OTUB1; otubain, structural genomics, structural genomics consortium, SGC, alternative splicing, hydrolase, immune response; 1.69A {Homo sapiens} PDB: 4ddg_B 4ddi_A Length = 234

 Score = 64.3 bits (156), Expect = 4e-13
 Identities = 21/93 (22%), Positives = 35/93 (37%), Gaps = 9/93 (9%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYC-QSMETDGTWAGHMELQAASLVTHSNICIH--- 56
           +   Y+ +  + FE FIE      E+C Q +E     + H+ + A  L    ++ I    
Sbjct: 141 LTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPMCKESDHIHIIA--LAQALSVSIQVEY 198

Query: 57  --RHMSPRWYIRNFDYHEARMIHLSYHDGEHYN 87
             R          F       ++L Y  G HY+
Sbjct: 199 MDRGEGGTTNPHIFPEGSEPKVYLLYRPG-HYD 230

>1tff_A Ubiquitin thiolesterase protein OTUB2; hydrolase; 2.10A {Homo sapiens} SCOP: d.3.1.11 Length = 234

 Score = 56.2 bits (135), Expect = 4e-10
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 8/92 (8%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYC-QSMETDGTWAGHMELQAASLVTHSNICIH--- 56
           +   +I    + F  FI++++   ++C   +E   T   H+++ A  L    +I +    
Sbjct: 138 LTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITA--LSQALSIALQVEY 195

Query: 57  -RHMSPRWYIRNFDYHEARMIHLSYHDGEHYN 87
              M        F       ++L Y    HYN
Sbjct: 196 VDEMDTALNHHVFPEAATPSVYLLYKTS-HYN 226

>4dhi_B Ubiquitin thioesterase otubain-like; ubiquitin E2 enzyme fold, ubiquitination, hydrolase-ligase C; 1.80A {Caenorhabditis elegans} PDB: 4dhj_A 4dhz_A Length = 284

 Score = 50.5 bits (120), Expect = 4e-08
 Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 13/97 (13%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYC-QSMETDGTWAGHMELQAASLVTHSNICIH--- 56
           +   ++ +N E + PFI++ +   +YC Q +E     A H+ + +  L+  +   +    
Sbjct: 176 ITSAFLKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINS--LIKAAGTRVRIEY 233

Query: 57  ------RHMSPRWYIRNFDYHEARMIHLSYHDGEHYN 87
                  +    + I + D   A  I L Y  G HY+
Sbjct: 234 MDRTAAPNGGWHYDIPSDDQQIAPEITLLYRPG-HYD 269

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	184
3pfy_A	185	OTU domain-containing protein 5; structural genomi	99.93
3by4_A	212	OTU1, ubiquitin thioesterase OTU1; ubiquitin hydro	99.91
3phu_A	219	RNA-directed RNA polymerase L; OTU domain, DE-ubiq	99.9
3phx_A	185	RNA-directed RNA polymerase L; OTU domain, DE-ubiq	99.9
1tff_A	234	Ubiquitin thiolesterase protein OTUB2; hydrolase;	99.87
2zfy_A	234	Ubiquitin thioesterase OTUB1; otubain, structural	99.86
4dhi_B	284	Ubiquitin thioesterase otubain-like; ubiquitin E2	99.79
4ddg_A	399	Ubiquitin-conjugating enzyme E2 D2, ubiquitin THI	99.7
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	97.62
2dhy_A	67	CUE domain-containing protein 1; structural genomi	97.56
1wj7_A	104	Hypothetical protein (RSGI RUH-015); UBA domain, u	97.41
2cp9_A	64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	97.27
2bwb_A	46	Ubiquitin-like protein DSK2; UBA, signaling protei	97.24
1otr_A	49	Protein CUE2; protein-protein complex, cell cycle;	97.18
1wji_A	63	Tudor domain containing protein 3; UBA domain, str	97.07
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	96.99
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	96.98
1wr1_B	58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	96.94
2dah_A	54	Ubiquilin-3; UBA domain, structural genomics, NPPS	96.94
2g3q_A	43	Protein YBL047C; endocytosis, solution structure,	96.86
2dna_A	67	Unnamed protein product; ubiquitin associated doma	96.84
1p3q_Q	54	VPS9P, vacuolar protein sorting-associated protein	96.77
1vej_A	74	Riken cDNA 4931431F19; UBA domain, three helix bun	96.77
2jy5_A	52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	96.76
1ify_A	49	HHR23A, UV excision repair protein RAD23 homolog A	96.75
2cp8_A	54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	96.67
1vg5_A	73	RSGI RUH-014, rhomboid family protein; UBA domain,	96.63
2dak_A	63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	96.62
3e21_A	45	HFAF1, FAS-associated factor 1; UBA, alternative s	96.54
1tr8_A	102	Conserved protein (MTH177); chaperones, nascent po	96.48
2dam_A	67	ETEA protein; KIAA0887, UBA-like domain, structura	96.43
1wiv_A	73	UBP14, ubiquitin-specific protease 14; ubiquitin a	96.12
2cwb_A	108	Chimera of immunoglobulin G binding protein G and	96.1
1veg_A	83	NEDD8 ultimate buster-1; ubiquitin associated doma	95.82
1whc_A	64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	95.78
1v92_A	46	NSFL1 cofactor P47; 3-helix bundle, recombination;	95.59
2dal_A	62	Protein KIAA0794; FAS associted factor 1, UBA-like	95.49
2dag_A	74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	95.43
1dv0_A	47	DNA repair protein HHR23A; helical bundle, DNA bin	95.4
2ekk_A	47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	95.27
2dai_A	83	Ubadc1, ubiquitin associated domain containing 1;	95.19
1vdl_A	80	Ubiquitin carboxyl-terminal hydrolase 25; UBA doma	95.16
1wgn_A	63	UBAP1, ubiquitin associated protein; ubiquitin ass	94.99
2cpw_A	64	CBL-interacting protein STS-1 variant; ubiquitin a	94.91
2crn_A	64	Ubash3A protein; compact three-helix bundle, struc	94.59
2lva_A	129	Ubiquitin carboxyl-terminal hydrolase 28; UIM, ubi	93.32
2ooa_A	52	E3 ubiquitin-protein ligase CBL-B; alpha-helical d	94.03
2dkl_A	85	Trinucleotide repeat containing 6C protein; TNRC6C	94.01
2d9s_A	53	CBL E3 ubiquitin protein ligase; UBA domain, dimer	93.42
2dzl_A	66	Protein FAM100B; UBA-like domain, structural genom	92.77
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	92.73
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	92.51
1vek_A	84	UBP14, ubiquitin-specific protease 14, putative; U	91.41
2oo9_A	46	E3 ubiquitin-protein ligase CBL; alpha-helical dom	91.04
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	90.59
3dkb_A	390	Tumor necrosis factor, alpha-induced protein 3; OT	90.31
3k9o_A	201	Ubiquitin-conjugating enzyme E2 K; E2-25K, complex	90.12
3zrh_A	454	Ubiquitin thioesterase zranb1; hydrolase, deubiqui	90.12
2juj_A	56	E3 ubiquitin-protein ligase CBL; alpha helix, UBA	90.04
2qsf_X	171	RAD23, UV excision repair protein RAD23; alpha-bet	89.61
2lbc_A	126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	86.3
1ufz_A	83	Hypothetical protein BAB28515; HBS1-like domain, s	85.28
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	84.86
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	82.95
3e46_A	253	Ubiquitin-conjugating enzyme E2-25 kDa; huntington	82.16

>3pfy_A OTU domain-containing protein 5; structural genomics, structural genomics consortium, SGC, PE C65 otubain, hydrolase; HET: MSE PG4; 1.70A {Homo sapiens} PDB: 3tmp_A* 3tmo_A*

Probab=99.93  E-value=1.7e-26  Score=186.68  Aligned_cols=91  Identities=21%  Similarity=0.371  Sum_probs=63.6

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEe-ecccCCCcEEEEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIR-NFDYHEARMIHLS   79 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~-~~~~~~~~~i~L~   79 (184)
                      +||+||++|+++|+|||++  +|++||++|+++++|||++||+|||++|+++|+|++.+++.+.+. +......++|+|+
T Consensus        92 ~vv~yi~~n~d~f~~Fv~~--~~e~Y~~~m~~~~~WGg~iEL~AlS~~~~v~I~V~~~~~~~i~i~~g~~~~~~~~I~L~  169 (185)
T 3pfy_A           92 HCMDYLMKNADYFSNYVTE--DFTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTEPINTFHGIHQNEDEPIRVS  169 (185)
T ss_dssp             HHHHHHHHTHHHHTTCC-------------------CCHHHHHHHHHHHTSCEEEESSCSSCSEEECTTSCCTTSCEEEE
T ss_pred             HHHHHHHHHHHHHHHHHhc--cHHHHHHHhhCCCccchHHHHHHHHHhhCCcEEEEECCCCCeEEecCccCCCCCEEEEE
Confidence            4899999999999999985  899999999999999999999999999999999999987655443 3333457899999


Q ss_pred             EccCCcccceeccC
Q 030009           80 YHDGEHYNGVRLKE   93 (184)
Q Consensus        80 Y~~g~HYdSV~~~~   93 (184)
                      |+.++|||||+...
T Consensus       170 Y~~~~HYnSv~~p~  183 (185)
T 3pfy_A          170 YHRNIHYNSVVNPN  183 (185)
T ss_dssp             EETTTEEEEEECC-
T ss_pred             ECCCCCcccccCCC
Confidence            99999999998754

>3by4_A OTU1, ubiquitin thioesterase OTU1; ubiquitin hydrolase, deubiquitinase, cell cycle, hydrolase; 1.55A {Saccharomyces cerevisiae} PDB: 3c0r_A

Probab=99.91  E-value=4.1e-25  Score=181.86  Aligned_cols=87  Identities=22%  Similarity=0.335  Sum_probs=75.3

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEeecccC-CCcEEEEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYH-EARMIHLS   79 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~~-~~~~i~L~   79 (184)
                      +||+||++|+++|.+|+.+ ++|++||++|+++++|||++||+|||++|+++|+|++.++..+.+  |++. ..++|+|+
T Consensus        52 ~vv~yi~~n~d~f~e~~~~-~~~e~Y~~~m~~~~~WGg~iEL~Als~~~~~~I~V~~~~~~~~~~--~~~~~~~~~I~L~  128 (212)
T 3by4_A           52 MVSKEVLNNPVKFNDAILD-KPNKDYAQWILKMESWGGAIEIGIISDALAVAIYVVDIDAVKIEK--FNEDKFDNYILIL  128 (212)
T ss_dssp             HHHHHHHHCTTTTCHHHHT-SCHHHHHHHTTSTTSCCCHHHHHHHHHHHTCEEEEEETTTTEEEE--ESTTTCSEEEEEE
T ss_pred             HHHHHHHHCHHHHhhhhcC-CCHHHHHHHhcCCCEEccHHHHHHHHHHHCCCEEEEECCCCCeEE--eCCCCCCCeEEEE
Confidence            4899999999999866665 799999999999999999999999999999999999987543333  3322 47899999


Q ss_pred             EccCCcccceec
Q 030009           80 YHDGEHYNGVRL   91 (184)
Q Consensus        80 Y~~g~HYdSV~~   91 (184)
                      |+ |+|||||+.
T Consensus       129 Y~-g~HYdsl~~  139 (212)
T 3by4_A          129 FN-GIHYDSLTM  139 (212)
T ss_dssp             EC-SSCEEEEEE
T ss_pred             Ec-CCcceEEec
Confidence            98 899999999

>3phu_A RNA-directed RNA polymerase L; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase; 2.20A {Crimean-congo hemorrhagic fever VIRUSIBAR10200}

Probab=99.90  E-value=2.1e-24  Score=178.42  Aligned_cols=102  Identities=13%  Similarity=0.181  Sum_probs=87.0

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCC--ceEEeecccC-CCcEEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSP--RWYIRNFDYH-EARMIH   77 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~--~~~i~~~~~~-~~~~i~   77 (184)
                      +||+||++|++.   |+.+ ++|++||++|+++|+|||++||+|||++|+++|+|++.+.+  .+.+..|+.+ ..++|+
T Consensus        70 ~va~yi~~n~d~---~~~~-~~feeY~~~m~~~g~WGG~iEL~AlS~~~~v~I~V~~~d~~g~~~~i~~fge~~~~~~I~  145 (219)
T 3phu_A           70 AARKYYQEEPEA---RLVG-LSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVN  145 (219)
T ss_dssp             HHHHHGGGCHHH---HHHC-CCHHHHHHHHHSTTCCCCHHHHHHHHHHTTCCEEEEEESSSSBEEEEEEESSCCTTTSEE
T ss_pred             HHHHHHHhChhh---hhcC-CCHHHHHHHhcCCCccCCHHHHHHHHHHhCCCEEEEEecCCCCceeEEEecCCCCCCeEE
Confidence            379999999999   3333 69999999999999999999999999999999999998876  4445455433 368999


Q ss_pred             EEEccCCcccceeccCCCCCCCCceeeec
Q 030009           78 LSYHDGEHYNGVRLKEDSCIGSARPIIIK  106 (184)
Q Consensus        78 L~Y~~g~HYdSV~~~~~~~~gp~~p~~~~  106 (184)
                      |+|++|+|||||+++.+.+.+|+.|..|-
T Consensus       146 L~Y~g~~HYdSL~~~~d~~~~~~~~~~l~  174 (219)
T 3phu_A          146 LLHSGQTHFDALRILPQFETDTREALSLM  174 (219)
T ss_dssp             EEEETTTEEEEEEECTTTCCSCCCCCCHH
T ss_pred             EEECCCcCchhheECCCCCCCCCcchhHH
Confidence            99998899999999999999998876643

>3phx_A RNA-directed RNA polymerase L; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Crimean-congo hemorrhagic fever virus} PDB: 3phw_A 3pt2_A 3pse_A 3prp_A 3prm_A

Probab=99.90  E-value=4.5e-24  Score=172.44  Aligned_cols=102  Identities=13%  Similarity=0.187  Sum_probs=77.5

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCc--eEEeecccC-CCcEEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPR--WYIRNFDYH-EARMIH   77 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~--~~i~~~~~~-~~~~i~   77 (184)
                      +||+||++|+++   |+.+ ++|++||++|+++|+|||++||+|||++|+++|+|++.+.+.  +.+..|+++ ..++|+
T Consensus        70 ~~~~yi~~~~~~---~~~~-~~~~~Y~~~m~~~~~WGg~iEL~Als~~~~v~I~V~~~d~~~~~~~i~~f~~~~~~~~I~  145 (185)
T 3phx_A           70 AARKYYQEEPEA---RLVG-LSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVN  145 (185)
T ss_dssp             HHHHHGGGCTTH---HHHC-CCHHHHHHHHTSTTCCCBHHHHHHHHHHHCCCEEEEEC--CCBCCEEEEESSCCTTTSEE
T ss_pred             HHHHHHHhChHh---hhcC-CCHHHHHHHhhCCCccCcHHHHHHHHHHHCCcEEEEEecCCCCceEEEEcCCCCCCCEEE
Confidence            378999999999   3333 699999999999999999999999999999999999987655  444455433 378999


Q ss_pred             EEEccCCcccceeccCCCCCCCCceeeec
Q 030009           78 LSYHDGEHYNGVRLKEDSCIGSARPIIIK  106 (184)
Q Consensus        78 L~Y~~g~HYdSV~~~~~~~~gp~~p~~~~  106 (184)
                      |+|++|+|||||+++.+.+.++..|+.|.
T Consensus       146 L~Y~g~~HYdsl~~~~~~~~~~~~~~~~~  174 (185)
T 3phx_A          146 LLHSGQTHFDALRILPQFETDTREALSLM  174 (185)
T ss_dssp             EEEETTTEEEEEEECGGGC----------
T ss_pred             EEECCCcCchhceECCCCCCCCcccccHH
Confidence            99998899999999998888777765543

>1tff_A Ubiquitin thiolesterase protein OTUB2; hydrolase; 2.10A {Homo sapiens} SCOP: d.3.1.11

Probab=99.87  E-value=1.9e-22  Score=168.24  Aligned_cols=92  Identities=17%  Similarity=0.316  Sum_probs=78.4

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHH-hhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEE--eecccCCCcEEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQ-SMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYI--RNFDYHEARMIH   77 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~-~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i--~~~~~~~~~~i~   77 (184)
                      +++.||++|+++|+||++++.+|++||+ .|+..++||||+||+|||++++++|+|++++++...+  ..|++...+.|+
T Consensus       138 lta~~i~~~~d~f~pFi~~~~~~~~yC~~~ve~~~~~~~~iei~ALa~aL~v~I~V~~~d~~~~~~~~~~~~~~~~~~I~  217 (234)
T 1tff_A          138 LTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVY  217 (234)
T ss_dssp             HHHHHHHHTHHHHGGGSCTTSCHHHHHHHHTSSTTCCCCHHHHHHHHHHHTCCEEEEECC-------CCCCCCCSSCSEE
T ss_pred             HHHHHHHHCHHHHhhhhcCCCCHHHHHHHHhhhhhcccccHHHHHHHHHhCCCEEEEEcCCCCCccccccCCCCCCCeEE
Confidence            4789999999999999998779999999 7999999999999999999999999999998765333  346666678899


Q ss_pred             EEEccCCcccceeccC
Q 030009           78 LSYHDGEHYNGVRLKE   93 (184)
Q Consensus        78 L~Y~~g~HYdSV~~~~   93 (184)
                      |+|+.| |||+|++..
T Consensus       218 LlY~pg-HYdily~~~  232 (234)
T 1tff_A          218 LLYKTS-HYNILYAAD  232 (234)
T ss_dssp             EEEETT-EEEEEEECC
T ss_pred             EEECCC-CceecccCC
Confidence            999976 999999864

>2zfy_A Ubiquitin thioesterase OTUB1; otubain, structural genomics, structural genomics consortium, SGC, alternative splicing, hydrolase, immune response; 1.69A {Homo sapiens} PDB: 4ddg_B 4ddi_A

Probab=99.86  E-value=4.2e-22  Score=165.99  Aligned_cols=90  Identities=21%  Similarity=0.295  Sum_probs=78.9

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHH-hhhcCCccCCHHHHHHHHhhcCccEEEEEccCCc---eEEeecccCCCcEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQ-SMETDGTWAGHMELQAASLVTHSNICIHRHMSPR---WYIRNFDYHEARMI   76 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~-~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~---~~i~~~~~~~~~~i   76 (184)
                      +++.||++|+++|+|||+++.+|++||. .++.+++||||+||+|||++|+++|+|++++++.   +....|++...++|
T Consensus       141 lta~yi~~~~d~f~pFi~~~~~~e~yc~~~ve~~~~~~~~i~i~ALa~al~v~I~V~~~d~~~~~~v~~~~f~~~~~p~I  220 (234)
T 2zfy_A          141 LTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPMCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKV  220 (234)
T ss_dssp             HHHHHHHHTHHHHGGGCCSSCCHHHHHHHHTSSTTCCCCHHHHHHHHHHHTCCEEEEECC-CCSSCCEEEEESTTCCCSE
T ss_pred             HHHHHHHHCHHHHhcccCCCCCHHHHHHHHhhhHhhcCCHHHHHHHHHHhCCCEEEEEcCCCCCCcccceeCCCCCCCeE
Confidence            4789999999999999998789999998 5999999999999999999999999999998754   44455666667889


Q ss_pred             EEEEccCCcccceec
Q 030009           77 HLSYHDGEHYNGVRL   91 (184)
Q Consensus        77 ~L~Y~~g~HYdSV~~   91 (184)
                      +|+|+.| |||++++
T Consensus       221 ~LlY~pg-HYdiLy~  234 (234)
T 2zfy_A          221 YLLYRPG-HYDILYK  234 (234)
T ss_dssp             EEEEETT-EEEEEEC
T ss_pred             EEEECCC-CcccCCC
Confidence            9999987 9999985

>4dhi_B Ubiquitin thioesterase otubain-like; ubiquitin E2 enzyme fold, ubiquitination, hydrolase-ligase C; 1.80A {Caenorhabditis elegans} PDB: 4dhj_A 4dhz_A

Probab=99.79  E-value=1.3e-19  Score=154.59  Aligned_cols=92  Identities=21%  Similarity=0.368  Sum_probs=77.2

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHH-hhhcCCccCCHHHHHHHHhhcCccEEEEEccCC-ceEE--ee-cccCC---
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQ-SMETDGTWAGHMELQAASLVTHSNICIHRHMSP-RWYI--RN-FDYHE---   72 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~-~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~-~~~i--~~-~~~~~---   72 (184)
                      +++.||+.|+++|+|||+++.++++||+ +|+..++||||+||+|||++|+++|+|+++++. ...+  .. |+++.   
T Consensus       176 lts~yi~~~~d~f~pFi~~~~~v~~yC~~eVe~~~~e~d~leI~ALa~aL~v~I~V~ylDrs~g~~v~~h~~fp~~~~~~  255 (284)
T 4dhi_B          176 ITSAFLKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMDRTAAPNGGWHYDIPSDDQQI  255 (284)
T ss_dssp             HHHHHHHHTHHHHGGGSCTTCCHHHHHHHHTSSTTCCCCHHHHHHHHHHTTCCEEEEESSGGGCTTSSSEEEESCCCSCC
T ss_pred             HHHHHHHHCHHHHHhhcCCCCCHHHHHHHhceehhhcccHHHHHHHHHHhCCcEEEEEecCCCCCCCcccccCCCCCCCC
Confidence            5789999999999999998789999999 799999999999999999999999999998752 1111  11 44332   


Q ss_pred             CcEEEEEEccCCcccceeccC
Q 030009           73 ARMIHLSYHDGEHYNGVRLKE   93 (184)
Q Consensus        73 ~~~i~L~Y~~g~HYdSV~~~~   93 (184)
                      .+.|+|.|+.| |||.|++..
T Consensus       256 ~p~I~LLYrpg-HYDILY~~~  275 (284)
T 4dhi_B          256 APEITLLYRPG-HYDVIYKKD  275 (284)
T ss_dssp             CCSEEEEEETT-EEEEEEECC
T ss_pred             CCEEEEeecCC-CccccccCC
Confidence            37899999876 999999973

>4ddg_A Ubiquitin-conjugating enzyme E2 D2, ubiquitin THI OTUB1; inhibition, hydrolase-ligase complex; 3.30A {Homo sapiens} PDB: 4ddi_A

Probab=99.70  E-value=1.3e-17  Score=148.18  Aligned_cols=90  Identities=21%  Similarity=0.293  Sum_probs=78.3

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHH-hhhcCCccCCHHHHHHHHhhcCccEEEEEccCC---ceEEeecccCCCcEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQ-SMETDGTWAGHMELQAASLVTHSNICIHRHMSP---RWYIRNFDYHEARMI   76 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~-~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~---~~~i~~~~~~~~~~i   76 (184)
                      |++.||+.|+++|+||++++.++++||+ .|+..++||||++|+|||++|+++|.|+.+++.   .+....+++...+.|
T Consensus       306 lts~~i~~~~d~f~pFi~~~~~v~~yc~~~ve~~~~e~d~l~I~ALa~al~v~I~V~yld~~~~~~v~~~~~~~~~~~~I  385 (399)
T 4ddg_A          306 LTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPMCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKV  385 (399)
T ss_dssp             HHHHHHHHTHHHHGGGSSSSCCHHHHHHHHTSSTTCCBCHHHHHHHHHHHTCCCEEEECSCCSSSCCCEEETTTTCCCCC
T ss_pred             HHHHHHHHCHHHHhcccCCCCCHHHHHHHhceeHHhhCcHHHHHHHHHHcCCcEEEEEcCCCCCCccceeeCCCCCCCEE
Confidence            4789999999999999998779999999 899999999999999999999999999988762   222233565667899


Q ss_pred             EEEEccCCcccceec
Q 030009           77 HLSYHDGEHYNGVRL   91 (184)
Q Consensus        77 ~L~Y~~g~HYdSV~~   91 (184)
                      +|+|+.| |||.+++
T Consensus       386 ~LLYrPg-HYDiLY~  399 (399)
T 4ddg_A          386 YLLYRPG-HYDILYK  399 (399)
T ss_dssp             EEEEETB-EEEEEEC
T ss_pred             EEEEcCC-ccccCCC
Confidence            9999887 9999985

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

Probab=97.62  E-value=0.00012  Score=48.28  Aligned_cols=46  Identities=22%  Similarity=0.185  Sum_probs=38.5

Q ss_pred             CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009          132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE  177 (184)
Q Consensus       132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~  177 (184)
                      ..+..++.+..-..--|.+.|+.+|++|+||+|+||..||.+....
T Consensus         8 ~~ee~l~~L~emFP~ld~~~I~~vL~a~~gdvd~aI~~LL~m~~~~   53 (59)
T 1wgl_A            8 CSEEDLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQMGEEP   53 (59)
T ss_dssp             SCHHHHHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHSSCCC
T ss_pred             CCHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcCcCCC
Confidence            3355677777777778999999999999999999999999987654

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

Probab=97.56  E-value=0.00013  Score=49.30  Aligned_cols=46  Identities=20%  Similarity=0.095  Sum_probs=38.9

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCCcc
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEY  179 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~~~  179 (184)
                      ..+++.+..-.+--|.+.|+.+|++|+||+|+||+.||.+......
T Consensus        19 ~~~v~~L~~MFP~lD~~vI~~vL~a~~G~vd~aId~LL~ms~~~~~   64 (67)
T 2dhy_A           19 NQAMDDFKTMFPNMDYDIIECVLRANSGAVDATIDQLLQMNLESGP   64 (67)
T ss_dssp             HHHHHHHHHHCSSSCHHHHHHHHHHHTSCHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCC
Confidence            3456777777787899999999999999999999999998866554

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

Probab=97.41  E-value=0.00018  Score=52.57  Aligned_cols=41  Identities=22%  Similarity=0.339  Sum_probs=36.7

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      .+.|+.||.-|||+ .+.++.+|.+|+||++.||.+||....
T Consensus        40 eekVk~L~EmtG~s-eeeAr~AL~~~ngDl~~AI~~Lleg~~   80 (104)
T 1wj7_A           40 EEKVKQLIDITGKN-QDECVIALHDCNGDVNRAINVLLEGNP   80 (104)
T ss_dssp             HHHHHHHHHHTCCC-HHHHHHHHHHHTSCHHHHHHHHHTCSS
T ss_pred             HHHHHHHHHhhCCC-HHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            45689999999985 899999999999999999999997653

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

Probab=97.27  E-value=0.00042  Score=46.44  Aligned_cols=43  Identities=19%  Similarity=0.173  Sum_probs=37.3

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      .+....|+++...||.. ..-.+++|++++||++.||++|-...
T Consensus         7 ~it~~~Vk~LRe~TGag-~~dcKkAL~e~~GDi~~Ai~~Lr~kg   49 (64)
T 2cp9_A            7 GSSKELLMKLRRKTGYS-FVNCKKALETCGGDLKQAEIWLHKEA   49 (64)
T ss_dssp             CCCCHHHHHHHHHHCCC-HHHHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHhCCC-HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence            34456799999999975 99999999999999999999997654

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

Probab=97.24  E-value=0.00062  Score=42.52  Aligned_cols=37  Identities=19%  Similarity=0.323  Sum_probs=31.5

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      ..|++++. -|.+|.+.++++|+.++||++.||++|+.
T Consensus         9 ~~i~~L~~-MGF~d~~~~~~AL~~~~gnv~~Ave~L~~   45 (46)
T 2bwb_A            9 HQLRQLND-MGFFDFDRNVAALRRSGGSVQGALDSLLN   45 (46)
T ss_dssp             HHHHHHHH-TTCCCHHHHHHHHHHHTTCHHHHHHHHHC
T ss_pred             HHHHHHHH-cCCCcHHHHHHHHHHhCCCHHHHHHHHHc
Confidence            35666665 48889999999999999999999999984

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

Probab=97.18  E-value=0.00086  Score=42.57  Aligned_cols=40  Identities=23%  Similarity=0.338  Sum_probs=33.0

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      .++.++.-.+-.+...|+.+|+.++||+|.||..||.+..
T Consensus         7 ~v~~L~EMFP~~~~~~ik~~L~~~~Gd~d~Ai~~LL~~~~   46 (49)
T 1otr_A            7 KLSILMDMFPAISKSKLQVHLLENNNDLDLTIGLLLKEND   46 (49)
T ss_dssp             HHHHHHHHCSSSCHHHHHHHHHHTTTCSHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhccc
Confidence            4555555555568999999999999999999999999843

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

Probab=97.07  E-value=0.002  Score=42.81  Aligned_cols=45  Identities=18%  Similarity=0.374  Sum_probs=37.3

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE  177 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~  177 (184)
                      +.++.+|++++. -| .+.+.++++|+.++||++.|+++|+.-....
T Consensus         7 ~~~~~~I~~L~~-MG-F~~~~a~~AL~~~~~nve~A~e~L~~~~~~~   51 (63)
T 1wji_A            7 GVDEKALKHITE-MG-FSKEASRQALMDNGNNLEAALNVLLTSNKQK   51 (63)
T ss_dssp             SSCHHHHHHHHT-TT-CCHHHHHHHHHHTTSCHHHHHHHHHHHSSCC
T ss_pred             CCCHHHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHHHCCCCc
Confidence            456778888876 46 5799999999999999999999999876544

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

Probab=96.99  E-value=0.00094  Score=39.75  Aligned_cols=36  Identities=25%  Similarity=0.424  Sum_probs=30.6

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI  171 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll  171 (184)
                      ++.|++++.- |. +.+.++++|..++||++.|+++|+
T Consensus         5 ~~~i~~L~~m-Gf-~~~~a~~AL~~~~~n~e~A~~~L~   40 (40)
T 1z96_A            5 NSKIAQLVSM-GF-DPLEAAQALDAANGDLDVAASFLL   40 (40)
T ss_dssp             HHHHHHHHHT-TC-CHHHHHHHHHHTTTCHHHHHHHHC
T ss_pred             HHHHHHHHHc-CC-CHHHHHHHHHHcCCCHHHHHHHHC
Confidence            4467888875 75 689999999999999999999984

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

Probab=96.98  E-value=0.0016  Score=41.69  Aligned_cols=37  Identities=32%  Similarity=0.497  Sum_probs=31.6

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      .|++++. -|..|.+.++++|..++||++.||++|+.-
T Consensus        14 ~l~~L~~-MGF~~~~~~~~AL~~t~gnve~Ave~L~~~   50 (53)
T 2knz_A           14 QLEQLNS-MGFINREANLQALIATGGDINAAIERLLGS   50 (53)
T ss_dssp             HHHHHHT-TTCCCHHHHHHHHHHHTSCHHHHHHHHHHC
T ss_pred             HHHHHHH-cCCCCHHHHHHHHHHhCCCHHHHHHHHHHc
Confidence            4566655 587799999999999999999999999974

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

Probab=96.94  E-value=0.00095  Score=43.76  Aligned_cols=36  Identities=19%  Similarity=0.345  Sum_probs=31.3

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      .|++++. -|.+|.+.++++|+.++||++.||++|+.
T Consensus        20 qi~~L~~-MGF~d~~~~~~AL~~~~gnve~Ave~L~~   55 (58)
T 1wr1_B           20 QLRQLND-MGFFDFDRNVAALRRSGGSVQGALDSLLN   55 (58)
T ss_dssp             HHHHHHH-HTCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHH-cCCCcHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            4666655 48889999999999999999999999986

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

Probab=96.94  E-value=0.0013  Score=42.42  Aligned_cols=40  Identities=33%  Similarity=0.402  Sum_probs=33.3

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      ...+++++. -|.+|.+.++++|..++||++.||++|+.-.
T Consensus        10 ~~~l~~L~~-MGF~d~~~n~~AL~~~~Gdv~~Ave~L~~~~   49 (54)
T 2dah_A           10 QVQLEQLRS-MGFLNREANLQALIATGGDVDAAVEKLRQSS   49 (54)
T ss_dssp             HHHHHHHHH-HTCCCHHHHHHHHHHHTSCHHHHHHHHHHHS
T ss_pred             HHHHHHHHH-cCCCcHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence            345666655 4888999999999999999999999999754

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

Probab=96.86  E-value=0.0017  Score=39.49  Aligned_cols=37  Identities=22%  Similarity=0.320  Sum_probs=31.1

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      +.+|++++. -| .+.+.++++|..++||++.|+++|+.
T Consensus         5 e~~i~~L~~-MG-F~~~~a~~AL~~~~~n~e~A~~~L~~   41 (43)
T 2g3q_A            5 SLAVEELSG-MG-FTEEEAHNALEKCNWDLEAATNFLLD   41 (43)
T ss_dssp             HHHHHHHHT-TT-SCHHHHHHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHHHHhCcCHHHHHHHHHc
Confidence            346777776 46 57899999999999999999999985

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

Probab=96.84  E-value=0.0013  Score=44.48  Aligned_cols=40  Identities=30%  Similarity=0.340  Sum_probs=32.7

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT  176 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~  176 (184)
                      .++++.. -|..|.+.+.++|++++||++.||++|+.-...
T Consensus        22 ql~qL~~-MGF~d~~an~~AL~at~Gnve~Ave~L~~~~~~   61 (67)
T 2dna_A           22 EMECLQA-MGFVNYNANLQALIATDGDTNAAIYKLKSSQGF   61 (67)
T ss_dssp             HHHHHHH-HTCCCHHHHHHHHHHTTSCHHHHHHHHHHCCSS
T ss_pred             HHHHHHH-cCCCcHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            3444443 588899999999999999999999999986554

>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=96.77  E-value=0.00046  Score=44.72  Aligned_cols=39  Identities=8%  Similarity=0.167  Sum_probs=26.2

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      +++.+..-.+--|.+.|+.+|+.++|++|+||++||++.
T Consensus        15 ~~~~L~~MFP~lD~evI~~Vl~a~~G~~~~~IdaLLqms   53 (54)
T 1p3q_Q           15 TLNTLQNMFPDMDPSLIEDVCIAAASRIGPCVDALLSLS   53 (54)
T ss_dssp             HHHHHHHHSTTSCHHHHHHHHHHSCC--CGGGC------
T ss_pred             HHHHHHHHcccCCHHHHHHHHHHcCCCHHHHHHHHHhhc
Confidence            455555556667999999999999999999999999975

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

Probab=96.77  E-value=0.0019  Score=44.42  Aligned_cols=39  Identities=28%  Similarity=0.439  Sum_probs=33.1

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      ...|++++. -|..|.+.++++|+.++||++.||++|+.-
T Consensus        30 e~qi~qL~e-MGF~dr~~~~~AL~~t~Gnve~Ave~L~~~   68 (74)
T 1vej_A           30 QQELEELKA-LGFANRDANLQALVATDGDIHAAIEMLLGA   68 (74)
T ss_dssp             HHHHHHHHH-HTCCCHHHHHHHHHHTTSCHHHHHHHHHTC
T ss_pred             HHHHHHHHH-cCCCcHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            345666666 488899999999999999999999999964

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

Probab=96.76  E-value=0.0021  Score=41.00  Aligned_cols=38  Identities=34%  Similarity=0.490  Sum_probs=32.2

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      ...|++++. -|.+|.+.++++|..++||++.||++|+.
T Consensus        13 ~~~l~~L~~-MGF~~~~~~~~AL~~t~gn~e~A~e~L~~   50 (52)
T 2jy5_A           13 QQQLEQLSA-MGFLNREANLQALIATGGDINAAIERLLG   50 (52)
T ss_dssp             HHHHHHHHH-TTCCCHHHHHHHHHHHTTCHHHHHHHHTT
T ss_pred             HHHHHHHHH-cCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            345666665 58779999999999999999999999974

>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=96.75  E-value=0.0015  Score=41.17  Aligned_cols=37  Identities=22%  Similarity=0.346  Sum_probs=31.7

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      +..|++++. -|. +.+.++.+|+.++||++.|+++|+.
T Consensus         9 ~~~i~~L~~-MGF-~~~~a~~AL~~~~~n~e~A~e~L~~   45 (49)
T 1ify_A            9 ETMLTEIMS-MGY-ERERVVAALRASYNNPHRAVEYLLT   45 (49)
T ss_dssp             HHHHHHHHH-TTC-CHHHHHHHHHTTTSCSHHHHHHHHH
T ss_pred             HHHHHHHHH-cCC-CHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            456777766 464 8999999999999999999999997

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

Probab=96.67  E-value=0.002  Score=41.73  Aligned_cols=37  Identities=11%  Similarity=0.082  Sum_probs=32.6

Q ss_pred             HhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009          141 MAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE  177 (184)
Q Consensus       141 ~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~  177 (184)
                      +..-|.+|.++-.++|..++||++.||+.||+...+.
T Consensus        16 L~eMGF~D~~~N~~aL~~~~gnv~~aI~~Ll~~~~~~   52 (54)
T 2cp8_A           16 LFEMGFCDRQLNLRLLKKHNYNILQVVTELLQLSGPS   52 (54)
T ss_dssp             HHHHTCCCHHHHHHHHTTTTTCHHHHHHHHHHHSSSC
T ss_pred             HHHcCCCcHHHHHHHHHHcCCCHHHHHHHHHhccCCC
Confidence            3345888999999999999999999999999987664

>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=96.63  E-value=0.0038  Score=42.75  Aligned_cols=42  Identities=24%  Similarity=0.374  Sum_probs=35.0

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      +..++.|++++. -| .+.+.++++|+.++||++.|+++|+.-.
T Consensus        27 ~~~ee~I~~L~e-MG-F~r~~a~~AL~~~~~nve~Ave~Ll~~~   68 (73)
T 1vg5_A           27 AASEEQIQKLVA-MG-FDRTQVEVALAAADDDLTVAVEILMSQS   68 (73)
T ss_dssp             CCCHHHHHHHHT-TT-CCHHHHHHHHHHHTSCHHHHHHHHHTCS
T ss_pred             cccHHHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHHHCC
Confidence            334667888877 46 5899999999999999999999999743

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

Probab=96.62  E-value=0.0036  Score=41.32  Aligned_cols=45  Identities=7%  Similarity=0.226  Sum_probs=37.4

Q ss_pred             CcCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009          130 GIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT  176 (184)
Q Consensus       130 ~~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~  176 (184)
                      ..+++..|++++. -|. +.+.++++|+.++||++.|+++|+.-...
T Consensus         6 ~~~~~~~v~~L~~-MGF-~~~~a~~AL~~t~~nve~A~e~L~~~~~d   50 (63)
T 2dak_A            6 SGPPEDCVTTIVS-MGF-SRDQALKALRATNNSLERAVDWIFSHIDD   50 (63)
T ss_dssp             CCCCHHHHHHHHH-HTC-CHHHHHHHHHHTTSCSHHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHH-cCC-CHHHHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence            4566778888877 465 69999999999999999999999986543

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

Probab=96.54  E-value=0.0028  Score=39.51  Aligned_cols=35  Identities=29%  Similarity=0.139  Sum_probs=31.8

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHH
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEF  169 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~  169 (184)
                      +.|...+.-||+.|....++.|+.++.|++.|+..
T Consensus         7 e~ia~F~~iTG~~d~~~A~~~Lea~nWDLe~Av~~   41 (45)
T 3e21_A            7 MILADFQACTGIENIDEAITLLEQNNWDLVAAING   41 (45)
T ss_dssp             HHHHHHHHHHCCCCHHHHHHHHHHTTTCHHHHHTT
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHcCCcHHHHHHH
Confidence            46789999999999999999999999999999853

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

Probab=96.48  E-value=0.0022  Score=46.59  Aligned_cols=38  Identities=37%  Similarity=0.538  Sum_probs=33.9

Q ss_pred             CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHH
Q 030009          132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL  170 (184)
Q Consensus       132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~L  170 (184)
                      +++..|..||..+||+ ....+++|++|+||+-.||.+|
T Consensus        64 i~~edi~lv~~q~~vs-~~~A~~aL~~~~gDiv~Ai~~L  101 (102)
T 1tr8_A           64 IPEDDIELVMNQTGAS-REDATRALQETGGDLAEAIMRL  101 (102)
T ss_dssp             CCHHHHHHHHHHHCCC-HHHHHHHHHHTTTCHHHHHHHC
T ss_pred             CCHHHHHHHHHHhCCC-HHHHHHHHHHcCCCHHHHHHHh
Confidence            4566799999999996 8999999999999999999876

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

Probab=96.43  E-value=0.0051  Score=41.25  Aligned_cols=43  Identities=19%  Similarity=0.190  Sum_probs=38.3

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE  177 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~  177 (184)
                      +.|++.|.-|||.|....++.|+.+++|++.||...++...+.
T Consensus        20 e~i~qF~~ITg~~d~~~A~~~Le~~~WnLe~Av~~ff~~~~~~   62 (67)
T 2dam_A           20 EKLLQFQDLTGIESMDQCRHTLEQHNWNIEAAVQDRLNEQEGS   62 (67)
T ss_dssp             HHHHHHHHHHCCSCHHHHHHHHHHHTSCHHHHHHHHHHSSCSS
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHcCCCHHHHHHHHHhCCCCC
Confidence            4688999999988999999999999999999999998876543

>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=96.12  E-value=0.0094  Score=40.60  Aligned_cols=41  Identities=20%  Similarity=0.447  Sum_probs=33.8

Q ss_pred             CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      .++.+|++++. -| .+...++++|+.++||++.|+++|+.-.
T Consensus        28 ~~~~~v~~L~~-MG-F~~~~a~~AL~~t~~nve~Ave~L~~~~   68 (73)
T 1wiv_A           28 IDQSSVDTLLS-FG-FAEDVARKALKASGGDIEKATDWVFNNS   68 (73)
T ss_dssp             SCHHHHHHHHH-HT-CCHHHHHHHHHHTTSCHHHHHHHHHHSC
T ss_pred             CCHHHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence            44667877776 36 4799999999999999999999999743

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

Probab=96.10  E-value=0.0066  Score=44.54  Aligned_cols=37  Identities=27%  Similarity=0.470  Sum_probs=31.1

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      .++++.. -|..|.+.++++|+.++||++.||++|+.-
T Consensus        69 qL~qL~e-MGF~d~~~ni~AL~~t~Gdve~AVe~L~~~  105 (108)
T 2cwb_A           69 QLQQLRD-MGIQDDELSLRALQATGGDIQAALELIFAG  105 (108)
T ss_dssp             HHHHHHT-TTCCCHHHHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHHHHH-cCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence            4544444 688899999999999999999999999964

>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=95.82  E-value=0.016  Score=40.58  Aligned_cols=41  Identities=24%  Similarity=0.253  Sum_probs=34.6

Q ss_pred             CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      .+++.|++++. -| .+...++.+|+.++||++.|+++|+.-.
T Consensus        28 ~~ee~I~~Lv~-MG-F~~~~A~~AL~~t~gdve~A~e~L~sh~   68 (83)
T 1veg_A           28 PSQESINQLVY-MG-FDTVVAEAALRVFGGNVQLAAQTLAHHG   68 (83)
T ss_dssp             CCHHHHHHHHH-HS-CCHHHHHHHHHHTTTCHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHH-cC-CCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence            34677888877 36 4899999999999999999999999843

>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=95.78  E-value=0.03  Score=37.01  Aligned_cols=44  Identities=14%  Similarity=0.302  Sum_probs=35.5

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHh-CCCHHHHHHHHHHhcCC
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQV-GGDVDAAIEFLIAEQGT  176 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~-~gdid~Ai~~Ll~~~~~  176 (184)
                      .+++..|++++. -|. +...++++|..+ ++|++.|+++|+.-...
T Consensus         7 ~~~~~~v~~L~~-MGF-~~~~a~~AL~~t~~~nve~A~ewLl~~~~d   51 (64)
T 1whc_A            7 GAELTALESLIE-MGF-PRGRAEKALALTGNQGIEAAMDWLMEHEDD   51 (64)
T ss_dssp             CCCCCHHHHHHT-TTC-CHHHHHHHHHHHTSCCHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHH-cCC-CHHHHHHHHHHhcCCCHHHHHHHHHhCCCC
Confidence            345667888887 464 689999999999 79999999999986543

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

Probab=95.59  E-value=0.022  Score=34.73  Aligned_cols=37  Identities=16%  Similarity=0.280  Sum_probs=33.0

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      +.|++.+.-||| +....++.|+.+++|++.||....+
T Consensus         7 ~~i~~F~~iTg~-~~~~A~~~L~~~~wdle~Ai~~ff~   43 (46)
T 1v92_A            7 DALREFVAVTGA-EEDRARFFLESAGWDLQIALASFYE   43 (46)
T ss_dssp             HHHHHHHHHTCC-CHHHHHHHHHHTTSCSHHHHHHHHH
T ss_pred             HHHHHHHHHhCc-CHHHHHHHHHHcCCCHHHHHHHHHc
Confidence            368899999998 6999999999999999999987765

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

Probab=95.49  E-value=0.027  Score=37.01  Aligned_cols=43  Identities=14%  Similarity=0.279  Sum_probs=36.7

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE  177 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~  177 (184)
                      .+.|++.|.-|||. ....++.|+.+++|++.||...++.....
T Consensus        16 ~e~i~qF~~iTg~~-~~~A~~~Le~~~WnLe~Av~~ff~~~~~~   58 (62)
T 2dal_A           16 KGLIQQFTTITGAS-ESVGKHMLEACNNNLEMAVTMFLDGGGSG   58 (62)
T ss_dssp             HHHHHHHHHHTCCC-HHHHHHHHHTTTSCHHHHHHHHHHSCCCC
T ss_pred             HHHHHHHHHHhCCC-HHHHHHHHHHcCCCHHHHHHHHHcCCCCC
Confidence            34689999999995 99999999999999999999888765443

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

Probab=95.43  E-value=0.036  Score=37.74  Aligned_cols=44  Identities=11%  Similarity=0.277  Sum_probs=36.1

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCC-CHHHHHHHHHHhcCC
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGG-DVDAAIEFLIAEQGT  176 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~g-did~Ai~~Ll~~~~~  176 (184)
                      .+++..|++++. -|. +...++++|..++| |++.|+++|+.-...
T Consensus         7 ~~~e~~v~~L~~-MGF-~~~~a~~AL~~t~n~~ve~A~ewL~~~~~d   51 (74)
T 2dag_A            7 GLDESVIIQLVE-MGF-PMDACRKAVYYTGNSGAEAAMNWVMSHMDD   51 (74)
T ss_dssp             SSCHHHHHHHHH-HSC-CHHHHHHHHHHHTSCCHHHHHHHHHHHTTS
T ss_pred             CCCHHHHHHHHH-cCC-CHHHHHHHHHHhCCCCHHHHHHHHHhCCCC
Confidence            356778888877 364 68999999999997 899999999986554

>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=95.40  E-value=0.0067  Score=37.87  Aligned_cols=40  Identities=18%  Similarity=0.214  Sum_probs=32.6

Q ss_pred             CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      .+..+|+.++. -| .+...++++|.+|++|.+.|..+|++-
T Consensus         3 ~e~eaI~rL~~-mG-F~~~~a~~Al~a~~~n~e~A~~~Lf~~   42 (47)
T 1dv0_A            3 QEKEAIERLKA-LG-FPESLVIQAYFACEKNENLAANFLLSQ   42 (47)
T ss_dssp             CCHHHHTTTTT-TT-CCHHHHHHHHTTTTSCHHHHHHHTTSC
T ss_pred             chHHHHHHHHH-cC-CCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            44567776665 35 579999999999999999999999864

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

Probab=95.27  E-value=0.03  Score=34.53  Aligned_cols=39  Identities=26%  Similarity=0.443  Sum_probs=31.5

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      ..++..|++++. -|. +.+.++++|..+ ||++.|+++|+.
T Consensus         7 ~~~~~~v~~L~~-MGF-~~~~a~~AL~~~-~n~e~A~~~L~~   45 (47)
T 2ekk_A            7 GVNQQQLQQLMD-MGF-TREHAMEALLNT-STMEQATEYLLT   45 (47)
T ss_dssp             SSCHHHHHHHHH-HHC-CHHHHHHHHHHS-CSHHHHHHHHHT
T ss_pred             CCCHHHHHHHHH-cCC-CHHHHHHHHHHc-CCHHHHHHHHHc
Confidence            345677887776 364 679999999999 599999999985

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

Probab=95.19  E-value=0.046  Score=38.11  Aligned_cols=44  Identities=16%  Similarity=0.239  Sum_probs=36.3

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT  176 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~  176 (184)
                      .+++..|++++. -| .+...++++|..++||++.|+++|+.-...
T Consensus        27 ~~~e~~i~~L~~-MG-F~~~~a~~AL~~t~~nve~A~ewL~~~~~d   70 (83)
T 2dai_A           27 RVDEAALRQLTE-MG-FPENRATKALQLNHMSVPQAMEWLIEHAED   70 (83)
T ss_dssp             SCCHHHHHHHHH-HT-CCHHHHHHHHHHTTSCHHHHHHHHHHGGGC
T ss_pred             CCCHHHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHHHCCCC
Confidence            356778888877 46 468999999999999999999999986543

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

Probab=95.16  E-value=0.038  Score=37.86  Aligned_cols=42  Identities=17%  Similarity=0.384  Sum_probs=35.8

Q ss_pred             HHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCCc
Q 030009          137 IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE  178 (184)
Q Consensus       137 v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~~  178 (184)
                      +.+.-.-||..|.....++|++-+||+..||.+|-+++-.+.
T Consensus        28 LnQLrEITGiqD~~~L~~ALkas~Gdl~~AV~~LT~~~~~~P   69 (80)
T 1vdl_A           28 LNQLREITGINDAQILQQALKDSNGNLELAVAFLTAKNAKTP   69 (80)
T ss_dssp             HHHHHHHSCCCCHHHHHHHHHHHTSCHHHHHHHHHTTSCCCC
T ss_pred             HHHHHHHhCCCcHHHHHHHHHhccCCHHHHHHHHhcccccCC
Confidence            344445799999999999999999999999999998866554

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

Probab=94.99  E-value=0.021  Score=37.84  Aligned_cols=40  Identities=20%  Similarity=0.402  Sum_probs=31.9

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      +..|..+++ -| ...+.++.+|++++||+|+|++.|+.-..
T Consensus        20 ~e~V~~Lvs-MG-Fs~~qA~kALKat~~NvErAaDWLFSH~D   59 (63)
T 1wgn_A           20 RQCVETVVN-MG-YSYECVLRAMKKKGENIEQILDYLFAHSG   59 (63)
T ss_dssp             HHHHHHHHH-HH-CCHHHHHHHHHHHCSCHHHHHHHHHHHSC
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            445776665 35 56899999999999999999999987543

>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=94.91  E-value=0.033  Score=36.86  Aligned_cols=41  Identities=17%  Similarity=0.464  Sum_probs=33.5

Q ss_pred             CChhHHHHHHhcCCCCChHHHHHHHHHhCC-CHHHHHHHHHHhc
Q 030009          132 INAGSIKLVMAGSGCENSEKVEEVLLQVGG-DVDAAIEFLIAEQ  174 (184)
Q Consensus       132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~g-did~Ai~~Ll~~~  174 (184)
                      .++..|++++. -|. +...++++|..++| |++.|+++|+.-.
T Consensus        18 ~~e~~i~~L~~-MGF-~~~~a~~AL~~t~~~nve~A~ewL~~~~   59 (64)
T 2cpw_A           18 KHGSALDVLLS-MGF-PRARAQKALASTGGRSVQTACDWLFSHS   59 (64)
T ss_dssp             SCCCHHHHHHH-HTC-CHHHHHHHHHHTTTSCHHHHHHHHHSCC
T ss_pred             CCHHHHHHHHH-cCC-CHHHHHHHHHHcCCCCHHHHHHHHHhCC
Confidence            34557877776 364 68999999999999 9999999999744

>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=94.59  E-value=0.11  Score=34.40  Aligned_cols=45  Identities=13%  Similarity=0.147  Sum_probs=36.3

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCC-CHHHHHHHHHHhcCCC
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGG-DVDAAIEFLIAEQGTE  177 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~g-did~Ai~~Ll~~~~~~  177 (184)
                      ..++..|++++. -| .+.+.++++|..+++ |++.|+++|++-....
T Consensus         7 ~~~e~~v~~L~~-MG-F~~~~a~~AL~~t~n~~~e~A~~wL~~h~~d~   52 (64)
T 2crn_A            7 GSSPSLLEPLLA-MG-FPVHTALKALAATGRKTAEEALAWLHDHCNDP   52 (64)
T ss_dssp             CCSCSSHHHHHH-TS-CCHHHHHHHHHHHTSCCHHHHHHHHHHHSSST
T ss_pred             CCCHHHHHHHHH-cC-CCHHHHHHHHHHhCCCCHHHHHHHHHhCCCCc
Confidence            445667888877 46 468999999999987 9999999999876543

>2lva_A Ubiquitin carboxyl-terminal hydrolase 28; UIM, ubiquitin interacting motif, UBA domain, NESG, northeas structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=93.32  E-value=0.0078  Score=45.07  Aligned_cols=39  Identities=23%  Similarity=0.341  Sum_probs=33.7

Q ss_pred             HHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009          139 LVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE  177 (184)
Q Consensus       139 ~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~  177 (184)
                      +.-.-||..|...+.++|++++||+..||.+|-+.+..+
T Consensus        24 QLrEITGIqD~~~L~~ALkAsnGdl~qAV~~LT~~~~~~   62 (129)
T 2lva_A           24 QLREITGIQDPSFLHEALKASNGDITQAVSLLTDERVKE   62 (129)
Confidence            444469999999999999999999999999998875544

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

Probab=94.03  E-value=0.14  Score=32.71  Aligned_cols=37  Identities=24%  Similarity=0.233  Sum_probs=32.1

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      +.|++.|. -| +|.+.+.++|...+||++-|-..||+-
T Consensus        13 ~~Ia~Lm~-mG-Fsr~~ai~AL~~a~nnve~AaniLlef   49 (52)
T 2ooa_A           13 AKIAKLMG-EG-YAFEEVKRALEIAQNNVEVARSILREF   49 (52)
T ss_dssp             HHHHHHHH-TT-CCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHHHh
Confidence            56888887 25 689999999999999999999999874

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

Probab=94.01  E-value=0.071  Score=37.28  Aligned_cols=44  Identities=23%  Similarity=0.207  Sum_probs=35.4

Q ss_pred             cCC-hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009          131 IIN-AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT  176 (184)
Q Consensus       131 ~~~-~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~  176 (184)
                      +|. +.+|++++. -|. +...++++|..+++|++.|+++|+.-...
T Consensus        18 ~~~n~~~I~qL~~-MGF-~~~~a~~AL~~~n~n~e~A~ewL~~h~~D   62 (85)
T 2dkl_A           18 AWIMSRLIKQLTD-MGF-PREPAEEALKSNNMNLDQAMSALLEKKVD   62 (85)
T ss_dssp             HHHHHHHHHHHHH-HTC-CHHHHHHHHHHTTSCHHHHHHHHHTTSCC
T ss_pred             cccCHHHHHHHHH-cCC-CHHHHHHHHHHcCCCHHHHHHHHHHCcCC
Confidence            443 567777777 475 68999999999999999999999985543

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

Probab=93.42  E-value=0.24  Score=31.68  Aligned_cols=39  Identities=15%  Similarity=0.290  Sum_probs=32.4

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      ++.|++.|. -| +|.+.+.++|...+||+|.|-..|+.--
T Consensus        10 e~~I~~L~~-lG-F~r~~ai~AL~~a~nnve~Aa~iL~ef~   48 (53)
T 2d9s_A           10 SSEIERLMS-QG-YSYQDIQKALVIAHNNIEMAKNILREFS   48 (53)
T ss_dssp             HHHHHHHHH-HT-CCHHHHHHHHHHTTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHHHHhcCCHHHHHHHHHHhc
Confidence            346777777 24 6899999999999999999999998653

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

Probab=92.77  E-value=0.15  Score=33.96  Aligned_cols=40  Identities=15%  Similarity=0.332  Sum_probs=34.5

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      +.|++.|.-||| +....++.|+.+++|++.||....+...
T Consensus        19 ~~i~qF~~iTg~-~~~~A~~~Le~~~WdLe~Al~~ff~~~~   58 (66)
T 2dzl_A           19 VMINQFVLAAGC-AADQAKQLLQAAHWQFETALSTFFQETN   58 (66)
T ss_dssp             HHHHHHHHHHCC-CHHHHHHHHHTTTTCHHHHHHHHHTCSC
T ss_pred             HHHHHHHHHcCC-CHHHHHHHHHHcCCCHHHHHHHHHcCCC
Confidence            458899999998 6788999999999999999999886543

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

Probab=92.73  E-value=0.11  Score=38.40  Aligned_cols=37  Identities=30%  Similarity=0.329  Sum_probs=29.8

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      .|.+.+. -| .+.+.|+.+|..++||+|.|++.|+...
T Consensus        79 ~v~~L~e-MG-F~~~~a~~AL~~~~nd~erAlewL~~~~  115 (118)
T 4ae4_A           79 LMSKFKE-MG-FELKDIKEVLLLHNNDQDNALEDLMARA  115 (118)
T ss_dssp             HHHHHHH-TT-CCHHHHHHHHHHTTTCHHHHHHHHHHHC
T ss_pred             HHHHHHH-cC-CCHHHHHHHHHHcCCCHHHHHHHHHHhc
Confidence            3444444 46 5799999999999999999999999754

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

Probab=92.51  E-value=0.17  Score=37.38  Aligned_cols=42  Identities=7%  Similarity=0.270  Sum_probs=34.6

Q ss_pred             CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      .++..|++++. -|+ +...++++|..++||++.|+++|+.-..
T Consensus        77 ~~e~~v~~L~~-MGF-~~~~a~~AL~~~~~~~e~A~e~L~~~~~  118 (126)
T 2lbc_A           77 PPEEIVAIITS-MGF-QRNQAIQALRATNNNLERALDWIFSHPE  118 (126)
T ss_dssp             CCHHHHHHHHH-HTS-CHHHHHHHHHHHTSCHHHHHHHHHTCCS
T ss_pred             cCHHHHHHHHH-cCC-CHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence            34667887777 475 5999999999999999999999997543

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

Probab=91.41  E-value=0.48  Score=32.84  Aligned_cols=44  Identities=11%  Similarity=0.317  Sum_probs=35.1

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhC-CCHHHHHHHHHHhcCC
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVG-GDVDAAIEFLIAEQGT  176 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~-gdid~Ai~~Ll~~~~~  176 (184)
                      .+++.+|++++. -|. +...++++|...+ +|++.|+++|+.-...
T Consensus        27 ~~~e~~v~~L~~-MGF-~~~~a~~AL~~t~n~n~e~A~ewL~~h~~d   71 (84)
T 1vek_A           27 VANEEIVAQLVS-MGF-SQLHCQKAAINTSNAGVEEAMNWLLSHMDD   71 (84)
T ss_dssp             CCCHHHHHHHHH-HTC-CHHHHHHHHHHTTTCCHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHH-cCC-CHHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Confidence            345778888877 464 6899999999885 7999999999986543

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

Probab=91.04  E-value=0.62  Score=28.84  Aligned_cols=37  Identities=16%  Similarity=0.290  Sum_probs=30.3

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      .+|...|. -| +|.+.++++|...++||+.|-..|++-
T Consensus         6 ~~I~~L~s-~G-f~~~~~~rAL~ia~Nnie~A~nIL~ef   42 (46)
T 2oo9_A            6 SEIENLMS-QG-YSYQDIQKALVIAQNNIEMAKNILREF   42 (46)
T ss_dssp             HHHHHHHH-TT-BCHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHH-cC-CCHHHHHHHHHHhhccHHHHHHHHHHh
Confidence            34566665 24 799999999999999999999999864

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

Probab=90.59  E-value=0.5  Score=31.96  Aligned_cols=39  Identities=15%  Similarity=-0.053  Sum_probs=29.6

Q ss_pred             HHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          137 IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       137 v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      |++|..-..-.-..-|+++|..+++|+|.+|.+||+.+-
T Consensus        17 I~qV~DLfPdLG~gfi~~~L~~y~~nvE~vin~LLE~~L   55 (71)
T 2di0_A           17 ISQVKDLLPDLGEGFILACLEYYHYDPEQVINNILEERL   55 (71)
T ss_dssp             HHHHHHHCCSSCHHHHHHHHHHTTTCHHHHHHHHHTTCC
T ss_pred             HHHHHHHcccCCHHHHHHHHHHhCCCHHHHHHHHHccCC
Confidence            334443333344789999999999999999999998754

>3dkb_A Tumor necrosis factor, alpha-induced protein 3; OTU domain, DUB domain, apoptosis, cytoplasm, DNA-binding, hydrolase, metal-binding, nucleus; 2.50A {Homo sapiens} PDB: 2vfj_A

Probab=90.31  E-value=0.37  Score=42.18  Aligned_cols=55  Identities=11%  Similarity=0.151  Sum_probs=38.0

Q ss_pred             HHHHHHHHhhcCccEEEEEcc-------CCceE---Eee-c-----c--cCCCcEEEEEEccCCcccceeccCC
Q 030009           39 HMELQAASLVTHSNICIHRHM-------SPRWY---IRN-F-----D--YHEARMIHLSYHDGEHYNGVRLKED   94 (184)
Q Consensus        39 ~iEL~Ala~~~~v~I~V~~~~-------~~~~~---i~~-~-----~--~~~~~~i~L~Y~~g~HYdSV~~~~~   94 (184)
                      ++.+-+||.++++||+|+...       +..+-   ..+ |     +  .=.+.+|.|+|..| ||.++....+
T Consensus       213 eiHIFvLAhVLRRPIIV~~d~~lr~~~~Ge~~~Pi~f~GIYLPLlwpp~~C~rsPI~LgY~s~-HFsaLV~me~  285 (390)
T 3dkb_A          213 EIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPAQECYRYPIVLGYDSH-HFVPLVTLKD  285 (390)
T ss_dssp             HHHHHHHHHHTTSCEEEEECCCCTTCCCC----CCCCCEEECCTTSCTTSSCSSCEEEEECSS-CEEEEEEBCS
T ss_pred             HHHHHHHHHHhcCCEEEEechhhccccCCCccCcCccCceecCCcCCHHHccCCceEEEeccC-ceeeeeeccc
Confidence            789999999999999999522       11110   011 1     1  11467999999885 9999999864

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

Probab=90.12  E-value=0.46  Score=37.73  Aligned_cols=37  Identities=27%  Similarity=0.284  Sum_probs=30.9

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      ++.|++.+. -| .|...++++|..+++|++.|+++|+.
T Consensus       164 eekV~~l~~-MG-f~~~~a~~AL~~~~wd~~~A~e~L~~  200 (201)
T 3k9o_A          164 TKKIENLCA-MG-FDRNAVIVALSSKSWDVETATELLLS  200 (201)
T ss_dssp             HHHHHHHHT-TT-CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            356776666 35 58999999999999999999999986

>3zrh_A Ubiquitin thioesterase zranb1; hydrolase, deubiquitinating enzyme, WNT signaling, ovarian T domain; 2.23A {Homo sapiens}

Probab=90.12  E-value=0.78  Score=40.86  Aligned_cols=73  Identities=11%  Similarity=0.152  Sum_probs=51.9

Q ss_pred             CHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCc------e---EEee-c-------ccCCCcEEEEEEccCC
Q 030009           22 PFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPR------W---YIRN-F-------DYHEARMIHLSYHDGE   84 (184)
Q Consensus        22 ~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~------~---~i~~-~-------~~~~~~~i~L~Y~~g~   84 (184)
                      .|+.-+..-+.||.==-++.+-+||+++++||.|+......      +   ...+ |       ..=.+.+|.|+|..| 
T Consensus       263 EW~~iv~~As~Pg~sLEeiHIFvLAhVLRRPIIV~~d~~lrs~~Ge~l~pi~f~GIYLPLlwpp~~C~rsPIvLgY~~g-  341 (454)
T 3zrh_A          263 DWAFILSLASQPGASLEQTHIFVLAHILRRPIIVYGVKYYKSFRGETLGYTRFQGVYLPLLWEQSFCWKSPIALGYTRG-  341 (454)
T ss_dssp             HHHHHHHHTTSTTCCCCHHHHHHHHHHTTSCEEEEECSSCC-----CCCCCCCCEEECCTTSCGGGSCSCCEEEEEETT-
T ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHHHhcCCeEEeccccccccCCCcCCCcccceeeccCcCCHHHhcCCceEEEeccc-
Confidence            56666666677887667899999999999999999853211      0   0000 1       111467999999887 


Q ss_pred             cccceeccCCC
Q 030009           85 HYNGVRLKEDS   95 (184)
Q Consensus        85 HYdSV~~~~~~   95 (184)
                      ||.++....+.
T Consensus       342 HFsaLV~~~~~  352 (454)
T 3zrh_A          342 HFSALVAMEND  352 (454)
T ss_dssp             EEEEEEEBCCC
T ss_pred             ceeeeeecccc
Confidence            99999998653

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

Probab=90.04  E-value=0.64  Score=29.87  Aligned_cols=39  Identities=13%  Similarity=0.188  Sum_probs=32.2

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      ++.|...|.  -.+|.+.++++|...++||+.|-..||+--
T Consensus         8 e~~Ia~L~s--mGfsr~da~~AL~ia~Ndv~~AtNiLlEf~   46 (56)
T 2juj_A            8 SSEIENLMS--QGYSYQDIQKALVIAQNNIEMAKNILREFV   46 (56)
T ss_dssp             HHHHHHHHT--TTCCHHHHHHHHHHTTTCSHHHHHHHHHSC
T ss_pred             hHHHHHHHH--cCCCHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            345677776  337999999999999999999999998754

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

Probab=86.30  E-value=1.6  Score=31.91  Aligned_cols=41  Identities=15%  Similarity=0.260  Sum_probs=32.5

Q ss_pred             ChhHHHHHHhcCCCCChHHHHHHHHHhCC-CHHHHHHHHHHhcC
Q 030009          133 NAGSIKLVMAGSGCENSEKVEEVLLQVGG-DVDAAIEFLIAEQG  175 (184)
Q Consensus       133 ~~~~v~~v~~~tG~~d~~~i~~~L~~~~g-did~Ai~~Ll~~~~  175 (184)
                      ++..+++.+. -| .....++++|..+++ |++.|++.|+.-..
T Consensus         3 d~~~l~~L~~-MG-F~~~~a~~AL~~t~n~~~e~A~~wL~~~~~   44 (126)
T 2lbc_A            3 DESSVMQLAE-MG-FPLEACRKAVYFTGNMGAEVAFNWIIVHME   44 (126)
T ss_dssp             CTHHHHHHHT-TS-SCCHHHHHHHHHHTSCCHHHHHHHHHHGGG
T ss_pred             CHHHHHHHHH-cC-CCHHHHHHHHHHcCCCCHHHHHHHHHHhcc
Confidence            4556776666 46 468999999999966 99999999998654

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

Probab=85.28  E-value=1.7  Score=30.12  Aligned_cols=39  Identities=18%  Similarity=0.385  Sum_probs=27.9

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT  176 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~  176 (184)
                      .++.|+.- -|+ -..++++..++++|++.|++++|.....
T Consensus        40 ~iR~VlGd-sV~-e~~Lv~ailk~dfD~ekALd~vL~~~~~   78 (83)
T 1ufz_A           40 HMREVLGD-AVP-DDILTEAILKHKFDVQKALSVVLEQDGS   78 (83)
T ss_dssp             HHHHHTTT-TSC-HHHHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHcc-cCC-HHHHHHHHHHhcCCHHHHHHHHHhcccc
Confidence            34555552 344 5555667788999999999999987653

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

Probab=84.86  E-value=0.42  Score=41.68  Aligned_cols=39  Identities=21%  Similarity=0.291  Sum_probs=33.0

Q ss_pred             ChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          133 NAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       133 ~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      .+.+|+.+|. -| ++.+.|+.+|++.+||+|.|+++|+.-
T Consensus       168 ~~~~i~~l~~-MG-f~~~~~~~AL~a~~nn~~~A~e~L~~g  206 (368)
T 1oqy_A          168 YETMLTEIMS-MG-YERERVVAALRASYNNPHRAVEYLLTG  206 (368)
T ss_dssp             HHHHHHHHHT-TT-CCSHHHHHHHHHSCSSTTHHHHTTTTS
T ss_pred             hHHHHHHHHH-cC-CCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence            3567888887 24 789999999999999999999999753

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

Probab=82.95  E-value=1.5  Score=32.18  Aligned_cols=38  Identities=18%  Similarity=0.372  Sum_probs=30.8

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      +.|++++. -| +....++.+|..+++|++.|+++|++-+
T Consensus        10 ~~v~~l~~-MG-Fp~~~~~kAl~~~g~~~e~amewL~~h~   47 (118)
T 4ae4_A           10 QCVETVVN-MG-YSYECVLRAMKAAGANIEQILDYLFAHG   47 (118)
T ss_dssp             HHHHHHHH-TT-CCHHHHHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHH-cC-CCHHHHHHHHHHHCcCHHHHHHHHHHhc
Confidence            35666655 34 5799999999999999999999999853

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

Probab=82.16  E-value=2.1  Score=35.42  Aligned_cols=36  Identities=28%  Similarity=0.303  Sum_probs=30.2

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      +.|++.+.- | .|.+.++++|..+++|.+.|+++|+.
T Consensus       217 ~~v~~l~~m-g-f~~~~~~~al~~~nWd~~~A~e~L~~  252 (253)
T 3e46_A          217 KKIENLCAA-G-FDRNAVIVALSSKSWDVETATELLLS  252 (253)
T ss_dssp             HHHHHHHHT-T-CCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHc-C-CCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            456666662 5 58999999999999999999999986

---

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	184
d1tffa_	228	d.3.1.11 (A:) Ubiquitin thiolesterase protein OTUB	8e-17
d2dnaa1	50	a.5.2.1 (A:12-61) Ubiquilin-like protein Ubqlnl {M	0.002

>d1tffa_ d.3.1.11 (A:) Ubiquitin thiolesterase protein OTUB2 (Otubain-2) {Human (Homo sapiens) [TaxId: 9606]} Length = 228

class: Alpha and beta proteins (a+b)
fold: Cysteine proteinases
superfamily: Cysteine proteinases
family: Ubiquitin thiolesterase protein OTUB2 (Otubain-2)
domain: Ubiquitin thiolesterase protein OTUB2 (Otubain-2)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.1 bits (179), Expect = 8e-17
 Identities = 16/96 (16%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 1   MVVQYIVKNRETFEPFIEDDVPFDEYCQS-METDGTWAGHMELQAASLVTHSNICIHRHM 59
           +   +I    + F  FI++++   ++C   +E   T   H+++ A S      + +    
Sbjct: 132 LTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVD 191

Query: 60  SPRWYIRNFDYHE--ARMIHLSYHDGEHYNGVRLKE 93
                + +  + E     ++L Y    HYN +   +
Sbjct: 192 EMDTALNHHVFPEAATPSVYLLYKTS-HYNILYAAD 226

>d2dnaa1 a.5.2.1 (A:12-61) Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

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]

 Score = 32.7 bits (75), Expect = 0.002
 Identities = 11/31 (35%), Positives = 15/31 (48%)

Query: 145 GCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 175
           G  N     + L+   GD +AAI  L + QG
Sbjct: 19  GFVNYNANLQALIATDGDTNAAIYKLKSSQG 49

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	184
d1tffa_	228	Ubiquitin thiolesterase protein OTUB2 (Otubain-2)	99.78
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	97.39
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	97.22
d2daha1	41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	97.2
d2bwba1	44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	97.17
d1mn3a_	54	Vacuolar protein sorting-associated protein vps9 {	97.11
d2dnaa1	50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	97.08
d1wj7a1	91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	97.07
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	96.9
d1veja1	61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	96.89
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	96.89
d1wjia_	63	Tudor domain containing protein 3, TDRD3 {Human (H	96.73
d1efub3	54	Elongation factor Ts (EF-Ts), N-terminal domain {E	96.65
d1v92a_	46	NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {	96.64
d1wiva_	73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	96.64
d2g3qa1	43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	96.57
d1xb2b1	56	Elongation factor Ts (EF-Ts), N-terminal domain {C	96.46
d1aipc1	52	Elongation factor Ts (EF-Ts), N-terminal domain {T	95.99
d1whca_	64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	95.35
d1vdla_	80	Ubiquitin carboxyl-terminal hydrolase 25 {Mouse (M	94.3
d2cpwa1	51	Cbl-interacting protein p70, STS1 {Human (Homo sap	94.13
d2crna1	51	Suppressor of T-cell receptor signaling 2 (STS-2)	89.73
d1veka_	84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	89.5
d2cp8a1	41	Migration-inducing protein 19 NBR1 {Human (Homo sa	84.72
d2di0a1	63	Activating signal cointegrator 1 complex subunit 2	83.52
d1ufza_	83	HBS1-like protein {Mouse (Mus musculus) [TaxId: 10	82.13
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	80.27

>d1tffa_ d.3.1.11 (A:) Ubiquitin thiolesterase protein OTUB2 (Otubain-2) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Cysteine proteinases
superfamily: Cysteine proteinases
family: Ubiquitin thiolesterase protein OTUB2 (Otubain-2)
domain: Ubiquitin thiolesterase protein OTUB2 (Otubain-2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=9.3e-20  Score=148.82  Aligned_cols=92  Identities=17%  Similarity=0.315  Sum_probs=77.3

Q ss_pred             ChHHHHHhCccccccccCCCCCHHHHHHh-hhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEE--eecccCCCcEEE
Q 030009            1 MVVQYIVKNRETFEPFIEDDVPFDEYCQS-METDGTWAGHMELQAASLVTHSNICIHRHMSPRWYI--RNFDYHEARMIH   77 (184)
Q Consensus         1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~-m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i--~~~~~~~~~~i~   77 (184)
                      |++.||+.|++.|.||++++.++++||.+ |.++++||||+||+|||++|+++|.|+.++.+...+  ..+++...++|+
T Consensus       132 l~s~~i~~~~~~y~~Fi~~~~~~~~yc~~~v~~~~~e~d~ieI~aLa~al~v~I~V~~~d~~~~~~~~~~~~~~~~~~I~  211 (228)
T d1tffa_         132 LTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVY  211 (228)
T ss_dssp             HHHHHHHHTHHHHGGGSCTTSCHHHHHHHHTSSTTCCCCHHHHHHHHHHHTCCEEEEECC-------CCCCCCCSSCSEE
T ss_pred             HHHHHHHHCHHHHHhHhcCCccHHHHHHHHHccccccCCcHHHHHHHHHhCCCEEEEEecCCCCccccccCCCCCCCEEE
Confidence            47899999999999999988899999986 999999999999999999999999999987754444  235556678899


Q ss_pred             EEEccCCcccceeccC
Q 030009           78 LSYHDGEHYNGVRLKE   93 (184)
Q Consensus        78 L~Y~~g~HYdSV~~~~   93 (184)
                      |+|.+| |||+|++.+
T Consensus       212 Lly~pg-HYdiLY~~~  226 (228)
T d1tffa_         212 LLYKTS-HYNILYAAD  226 (228)
T ss_dssp             EEEETT-EEEEEEECC
T ss_pred             EEeCCC-CcccCccCC
Confidence            999765 999999875

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

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

Probab=97.39  E-value=0.00011  Score=46.91  Aligned_cols=41  Identities=24%  Similarity=0.219  Sum_probs=35.0

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT  176 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~  176 (184)
                      .++.+..-.+--|.+.|+.+|++++||+|.||+.||++...
T Consensus        12 ~i~~LkeMFP~~D~~vI~~VL~a~~G~vd~aid~LL~Msd~   52 (59)
T d1wgla_          12 DLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLLQMGEE   52 (59)
T ss_dssp             HHHHHHHHCSSSCHHHHHHHHTTTTTCHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence            46666666666799999999999999999999999998654

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

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

Probab=97.22  E-value=0.00026  Score=46.92  Aligned_cols=43  Identities=26%  Similarity=0.416  Sum_probs=35.9

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      .+++..|++++. -| .+.+.++++|+.|+||+|.|+++||..+.
T Consensus        27 ~~~ee~i~~L~~-MG-F~~~~a~~AL~~~~~n~e~A~~~Ll~~~~   69 (73)
T d1vg5a_          27 AASEEQIQKLVA-MG-FDRTQVEVALAAADDDLTVAVEILMSQSG   69 (73)
T ss_dssp             CCCHHHHHHHHT-TT-CCHHHHHHHHHHHTSCHHHHHHHHHTCSC
T ss_pred             CcCHHHHHHHHH-hC-CCHHHHHHHHHHhCCCHHHHHHHHHhCCC
Confidence            345677888877 36 48999999999999999999999998654

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

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

Probab=97.20  E-value=0.00021  Score=42.36  Aligned_cols=32  Identities=41%  Similarity=0.522  Sum_probs=28.9

Q ss_pred             HhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          141 MAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       141 ~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      +..-|..|.+...++|...+|||++||+.|+.
T Consensus         9 L~~MGF~d~~~Ni~AL~~t~Gdv~~Aie~Ll~   40 (41)
T d2daha1           9 LRSMGFLNREANLQALIATGGDVDAAVEKLRQ   40 (41)
T ss_dssp             HHHHTCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHcCCCCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            44458999999999999999999999999985

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

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

Probab=97.17  E-value=0.00023  Score=42.82  Aligned_cols=34  Identities=21%  Similarity=0.321  Sum_probs=30.2

Q ss_pred             HHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          139 LVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       139 ~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      .-|..-|..|.+...++|+..+|||.+||+.||.
T Consensus        10 ~qL~~MGF~d~~~Ni~AL~~t~GdV~~Aie~Ll~   43 (44)
T d2bwba1          10 RQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN   43 (44)
T ss_dssp             HHHHHTTCCCHHHHHHHHHHHTTCHHHHHHHHHC
T ss_pred             HHHHHcCCCcHHHHHHHHHHcCCCHHHHHHHHhC
Confidence            3455679999999999999999999999999984

>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=97.11  E-value=0.00027  Score=44.25  Aligned_cols=39  Identities=8%  Similarity=0.160  Sum_probs=32.8

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      +++.+..-.+--|.+.|+-+|++++||+|+||+.||++.
T Consensus        15 ~~~~Lk~MFP~~D~~VI~~VL~a~~G~vd~aidaLL~Ms   53 (54)
T d1mn3a_          15 TLNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLSLS   53 (54)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHSCSSCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHhcc
Confidence            345555556667999999999999999999999999975

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

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

Probab=97.08  E-value=0.00029  Score=43.41  Aligned_cols=36  Identities=28%  Similarity=0.288  Sum_probs=31.3

Q ss_pred             HHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          139 LVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       139 ~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      ..|..-|..|.+...++|..++|||++||+.|+.-.
T Consensus        13 ~qL~~MGF~d~~~Ni~AL~~t~GdV~~Aie~Ll~~~   48 (50)
T d2dnaa1          13 ECLQAMGFVNYNANLQALIATDGDTNAAIYKLKSSQ   48 (50)
T ss_dssp             HHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHHCC
T ss_pred             HHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHHhcC
Confidence            344556999999999999999999999999999753

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

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

Probab=97.07  E-value=0.00039  Score=47.75  Aligned_cols=40  Identities=23%  Similarity=0.361  Sum_probs=35.3

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      ...|++||.-|||+ .+-+.=+|-+|+||++.||.+||+..
T Consensus        33 ~~kVkql~e~T~rs-ede~~~ALhDcn~D~~~AIn~lLEg~   72 (91)
T d1wj7a1          33 EEKVKQLIDITGKN-QDECVIALHDCNGDVNRAINVLLEGN   72 (91)
T ss_dssp             HHHHHHHHHHTCCC-HHHHHHHHHHHTSCHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHhCCC-HHHHHHHHhcCCccHHHHHHHHHhcC
Confidence            35789999999997 77777799999999999999999654

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

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

Probab=96.90  E-value=0.00021  Score=42.30  Aligned_cols=37  Identities=22%  Similarity=0.326  Sum_probs=31.3

Q ss_pred             hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      +.+|++++. -| .+.+.++++|+.++||+|.|+++||.
T Consensus         5 e~~i~~L~~-MG-F~~~~a~~AL~~~~~N~e~A~~~LlS   41 (41)
T d1oqya1           5 ETMLTEIMS-MG-YERERVVAALRASYNNPHRAVEYLLT   41 (41)
T ss_dssp             HHHHHHHHT-TT-CCSHHHHHHHHHSCSSTTHHHHTTTT
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence            346777777 45 58999999999999999999999973

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

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

Probab=96.89  E-value=0.00045  Score=44.23  Aligned_cols=34  Identities=29%  Similarity=0.456  Sum_probs=30.0

Q ss_pred             HHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          139 LVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       139 ~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      ..|..-|..|.+...++|+..+|||++||++||.
T Consensus        27 ~qL~eMGF~d~~~Nl~AL~~t~Gdv~~Aie~Ll~   60 (61)
T d1veja1          27 EELKALGFANRDANLQALVATDGDIHAAIEMLLG   60 (61)
T ss_dssp             HHHHHHTCCCHHHHHHHHHHTTSCHHHHHHHHHT
T ss_pred             HHHHHcCCCCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            3444569999999999999999999999999985

>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=96.89  E-value=0.00034  Score=45.07  Aligned_cols=42  Identities=17%  Similarity=0.303  Sum_probs=34.7

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ  174 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~  174 (184)
                      +.++.+|+++|. -| .+.+.++++|+.++||++.|+++||.-.
T Consensus        17 ~~de~~v~~L~~-MG-F~~~~a~~AL~~~~~n~e~A~~~Lls~~   58 (63)
T d1wgna_          17 PSERQCVETVVN-MG-YSYECVLRAMKKKGENIEQILDYLFAHS   58 (63)
T ss_dssp             HHHHHHHHHHHH-HH-CCHHHHHHHHHHHCSCHHHHHHHHHHHS
T ss_pred             chhHHHHHHHHH-cC-CCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence            445667887777 24 4799999999999999999999999854

>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=96.73  E-value=0.0028  Score=40.44  Aligned_cols=47  Identities=17%  Similarity=0.343  Sum_probs=38.6

Q ss_pred             CcCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCCc
Q 030009          130 GIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE  178 (184)
Q Consensus       130 ~~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~~  178 (184)
                      ...++..|+++|.- | .+...++++|+.+++|++.|+++|+.-....+
T Consensus         6 ~~~d~~~v~~L~~M-G-F~~~~a~~AL~~~~~~~e~A~~wL~~~~~~~~   52 (63)
T d1wjia_           6 SGVDEKALKHITEM-G-FSKEASRQALMDNGNNLEAALNVLLTSNKQKP   52 (63)
T ss_dssp             CSSCHHHHHHHHTT-T-CCHHHHHHHHHHTTSCHHHHHHHHHHHSSCCC
T ss_pred             CccCHHHHHHHHHc-C-CCHHHHHHHHHHhCCCHHHHHHHHHHCCCCCC
Confidence            34567788888873 5 57999999999999999999999999765443

>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=96.65  E-value=0.0014  Score=40.90  Aligned_cols=40  Identities=23%  Similarity=0.327  Sum_probs=34.8

Q ss_pred             ChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          133 NAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       133 ~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      ....|+++-..||.. +...+++|++++||+|.||++|-..
T Consensus         4 s~~~iK~LR~~Tgag-~~dCKkAL~e~~gD~ekA~e~Lr~k   43 (54)
T d1efub3           4 TASLVKELRERTGAG-MMDCKKALTEANGDIELAIENMRKS   43 (54)
T ss_dssp             CHHHHHHHHHHHCCC-HHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhCCC-HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            345688888999986 9999999999999999999999643

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

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

Probab=96.64  E-value=0.0015  Score=39.34  Aligned_cols=38  Identities=16%  Similarity=0.296  Sum_probs=34.0

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      +.|++.|.-||| +.+..++.|+.+++|++.||..-.+.
T Consensus         7 ~lI~qF~~iTg~-~~~~A~~~Le~~~w~Le~Ai~~yfe~   44 (46)
T d1v92a_           7 DALREFVAVTGA-EEDRARFFLESAGWDLQIALASFYED   44 (46)
T ss_dssp             HHHHHHHHHTCC-CHHHHHHHHHHTTSCSHHHHHHHHHT
T ss_pred             HHHHHHHHHHCc-CHHHHHHHHHHcCCcHHHHHHHHHhc
Confidence            468999999999 69999999999999999999877653

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

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

Probab=96.64  E-value=0.0018  Score=42.66  Aligned_cols=43  Identities=21%  Similarity=0.448  Sum_probs=35.7

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      +.++.+|++++. -| .+.+.++++|+.++||++.||++||.-..
T Consensus        27 ~~d~~~i~~L~~-MG-F~~~~a~~AL~~~~~n~e~Av~~Lls~~~   69 (73)
T d1wiva_          27 DIDQSSVDTLLS-FG-FAEDVARKALKASGGDIEKATDWVFNNSG   69 (73)
T ss_dssp             SSCHHHHHHHHH-HT-CCHHHHHHHHHHTTSCHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHh-cC-CCHHHHHHHHHHcCCCHHHHHHHHHcCCC
Confidence            455677888876 46 57999999999999999999999997543

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

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

Probab=96.57  E-value=0.0023  Score=37.76  Aligned_cols=36  Identities=22%  Similarity=0.319  Sum_probs=31.2

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      .+|++++. -| .+.+..+++|+++++|.++|.-+||+
T Consensus         6 ~ai~eL~~-MG-F~e~~A~~AL~k~~wnleaAtN~LLd   41 (43)
T d2g3qa1           6 LAVEELSG-MG-FTEEEAHNALEKCNWDLEAATNFLLD   41 (43)
T ss_dssp             HHHHHHHT-TT-SCHHHHHHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHHHHHh-cC-CCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            46888776 34 57999999999999999999999996

>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=96.46  E-value=0.0018  Score=40.69  Aligned_cols=38  Identities=18%  Similarity=0.249  Sum_probs=33.5

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      ..|++.-..||.. +...+.+|++++||+|.||+.|...
T Consensus         6 ~lvk~LRe~Tga~-~~dcKkAL~e~~gD~ekA~e~Lrkk   43 (56)
T d1xb2b1           6 ELLMKLRRKTGYS-FINCKKALETCGGDLKQAESWLHKQ   43 (56)
T ss_dssp             HHHHHHHHHHCCC-HHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCC-HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            4578888899985 9999999999999999999999754

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

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

Probab=95.99  E-value=0.0043  Score=38.28  Aligned_cols=36  Identities=25%  Similarity=0.319  Sum_probs=31.6

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009          136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA  172 (184)
Q Consensus       136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~  172 (184)
                      .|++.-..||-. +...+++|++++||+|.|++.|-.
T Consensus         5 lvK~LR~~Tga~-~~dcKkAL~e~~gD~ekA~e~Lr~   40 (52)
T d1aipc1           5 LIKKLREATGAG-MMDVKRALEDAGWDEEKAVQLLRE   40 (52)
T ss_dssp             HHHHHHHHHCCC-HHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCC-HHHHHHHHHHcCCCHHHHHHHHHH
Confidence            577777889864 999999999999999999999964

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

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

Probab=95.35  E-value=0.026  Score=35.82  Aligned_cols=46  Identities=15%  Similarity=0.343  Sum_probs=37.4

Q ss_pred             CcCChhHHHHHHhcCCCCChHHHHHHHHHhCC-CHHHHHHHHHHhcCCC
Q 030009          130 GIINAGSIKLVMAGSGCENSEKVEEVLLQVGG-DVDAAIEFLIAEQGTE  177 (184)
Q Consensus       130 ~~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~g-did~Ai~~Ll~~~~~~  177 (184)
                      ...|+.+|++++. -|+ +.+.++++|..+++ ++++|+++|++-....
T Consensus         6 s~~d~~~l~~L~~-MGF-~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~d~   52 (64)
T d1whca_           6 SGAELTALESLIE-MGF-PRGRAEKALALTGNQGIEAAMDWLMEHEDDP   52 (64)
T ss_dssp             CCCCCCHHHHHHT-TTC-CHHHHHHHHHHHTSCCHHHHHHHHHHHTTCS
T ss_pred             CccCHHHHHHHHH-cCC-CHHHHHHHHHHhCCCCHHHHHHHHHHCCCCC
Confidence            4456778999887 465 69999999999977 8999999999865543

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

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

Probab=94.30  E-value=0.039  Score=36.17  Aligned_cols=42  Identities=17%  Similarity=0.384  Sum_probs=35.6

Q ss_pred             HHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCCc
Q 030009          137 IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE  178 (184)
Q Consensus       137 v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~~  178 (184)
                      +.+.-.-||..|....-++|.+-+||+..||.+|-+.+-.+.
T Consensus        28 LNQLrEITGIqD~q~L~~ALkas~Gdl~~AV~~LT~~~~~~P   69 (80)
T d1vdla_          28 LNQLREITGINDAQILQQALKDSNGNLELAVAFLTAKNAKTP   69 (80)
T ss_dssp             HHHHHHHSCCCCHHHHHHHHHHHTSCHHHHHHHHHTTSCCCC
T ss_pred             HHHHHHHhCCCcHHHHHHHHHhcCCCHHHHHHHHhcCCCCCC
Confidence            345555799999999999999999999999999988775543

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

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

Probab=94.13  E-value=0.045  Score=33.22  Aligned_cols=38  Identities=18%  Similarity=0.486  Sum_probs=30.7

Q ss_pred             ChhHHHHHHhcCCCCChHHHHHHHHHhCC-CHHHHHHHHHH
Q 030009          133 NAGSIKLVMAGSGCENSEKVEEVLLQVGG-DVDAAIEFLIA  172 (184)
Q Consensus       133 ~~~~v~~v~~~tG~~d~~~i~~~L~~~~g-did~Ai~~Ll~  172 (184)
                      ++.+|++++. -| .+.+..+++|...++ |++.|++.||+
T Consensus        12 ~~~~l~~L~~-MG-F~~~~a~~AL~~t~n~~ve~A~~WLl~   50 (51)
T d2cpwa1          12 HGSALDVLLS-MG-FPRARAQKALASTGGRSVQTACDWLFS   50 (51)
T ss_dssp             CCCHHHHHHH-HT-CCHHHHHHHHHHTTTSCHHHHHHHHHS
T ss_pred             CHHHHHHHHH-cC-CCHHHHHHHHHHHCCCCHHHHHHHHHc
Confidence            3556777766 35 579999999999887 99999999985

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

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

Probab=89.73  E-value=0.41  Score=28.62  Aligned_cols=42  Identities=14%  Similarity=0.199  Sum_probs=31.8

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhC-CCHHHHHHHHHHhcCCCc
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVG-GDVDAAIEFLIAEQGTEE  178 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~-gdid~Ai~~Ll~~~~~~~  178 (184)
                      ..|++++. -| .+....+++|...+ +|+++|++.|++-....+
T Consensus         4 ~~v~~L~~-MG-F~~~~a~~Al~~t~n~~ve~A~~Wl~~h~~d~d   46 (51)
T d2crna1           4 SLLEPLLA-MG-FPVHTALKALAATGRKTAEEALAWLHDHCNDPS   46 (51)
T ss_dssp             SSHHHHHH-TS-CCHHHHHHHHHHHTSCCHHHHHHHHHHHSSSTT
T ss_pred             HHHHHHHH-cC-CCHHHHHHHHHHHCCCCHHHHHHHHHHcCCCcC
Confidence            35666665 35 56899999999875 599999999998765443

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

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

Probab=89.50  E-value=0.42  Score=31.53  Aligned_cols=46  Identities=11%  Similarity=0.297  Sum_probs=35.6

Q ss_pred             cCChhHHHHHHhcCCCCChHHHHHHHHHh-CCCHHHHHHHHHHhcCCCc
Q 030009          131 IINAGSIKLVMAGSGCENSEKVEEVLLQV-GGDVDAAIEFLIAEQGTEE  178 (184)
Q Consensus       131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~-~gdid~Ai~~Ll~~~~~~~  178 (184)
                      ..++..|++++. -| .+...++++|... ++|++.|+++|++-....+
T Consensus        27 ~~d~~~v~~L~~-MG-F~~~~a~~AL~~t~n~~~e~A~~Wl~~h~~d~d   73 (84)
T d1veka_          27 VANEEIVAQLVS-MG-FSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPD   73 (84)
T ss_dssp             CCCHHHHHHHHH-HT-CCHHHHHHHHHHTTTCCHHHHHHHHHHHTTCST
T ss_pred             CCCHHHHHHHHH-cC-CCHHHHHHHHHHHcCCCHHHHHHHHHHcCCCCC
Confidence            356778887776 35 4699999999885 5699999999998665544

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

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

Probab=84.72  E-value=0.55  Score=26.80  Aligned_cols=31  Identities=10%  Similarity=0.016  Sum_probs=27.9

Q ss_pred             cCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009          143 GSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  173 (184)
Q Consensus       143 ~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~  173 (184)
                      .-|..|..+=.+.|..+++|+..+|--||+.
T Consensus        11 EMGF~DR~lNq~LL~KH~~nl~~vV~eLlq~   41 (41)
T d2cp8a1          11 EMGFCDRQLNLRLLKKHNYNILQVVTELLQL   41 (41)
T ss_dssp             HHTCCCHHHHHHHHTTTTTCHHHHHHHHHHH
T ss_pred             HhCcchhHHHHHHHHHccCcHHHHHHHHHcC
Confidence            3477899999999999999999999999974

>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=83.52  E-value=0.81  Score=28.61  Aligned_cols=38  Identities=16%  Similarity=0.137  Sum_probs=30.4

Q ss_pred             hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009          135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG  175 (184)
Q Consensus       135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~  175 (184)
                      +.|+.++.-.|   ..-|+++|+..++|.|.+|..||+.+-
T Consensus        11 ~qV~Dl~PdLG---~GFi~~~L~~Y~~n~E~vI~~lLe~~L   48 (63)
T d2di0a1          11 SQVKDLLPDLG---EGFILACLEYYHYDPEQVINNILEERL   48 (63)
T ss_dssp             HHHHHHCCSSC---HHHHHHHHHHTTTCHHHHHHHHHTTCC
T ss_pred             HHHHHHcCCCc---HHHHHHHHHHhCCCHHHHHHHHHccCC
Confidence            34566666433   678999999999999999999999763

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

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

Probab=82.13  E-value=1.3  Score=29.00  Aligned_cols=40  Identities=18%  Similarity=0.366  Sum_probs=28.9

Q ss_pred             HHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCCc
Q 030009          137 IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE  178 (184)
Q Consensus       137 v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~~  178 (184)
                      ++.|+.- -|. -..++++..++++|++.|++++|.......
T Consensus        41 mR~VvGD-svp-e~~lv~avlk~dydvekALd~vL~~~~~~p   80 (83)
T d1ufza_          41 MREVLGD-AVP-DDILTEAILKHKFDVQKALSVVLEQDGSGP   80 (83)
T ss_dssp             HHHHTTT-TSC-HHHHHHHHHHTTSCHHHHHHHHHHHHHTSS
T ss_pred             HHHHHcc-cCC-HHHHHHHHHHccCCHHHHHHHHHhccCCCC
Confidence            4455542 344 556666888999999999999998876544

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

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

Probab=80.27  E-value=0.76  Score=28.01  Aligned_cols=23  Identities=13%  Similarity=0.174  Sum_probs=20.1

Q ss_pred             ChHHHHHHHHHhCCCHHHHHHHH
Q 030009          148 NSEKVEEVLLQVGGDVDAAIEFL  170 (184)
Q Consensus       148 d~~~i~~~L~~~~gdid~Ai~~L  170 (184)
                      ..+.|.++|+.|+||+-.|...|
T Consensus        21 Er~~I~~aL~~~~gn~~~aA~~L   43 (60)
T d1umqa_          21 RWEHIQRIYEMCDRNVSETARRL   43 (60)
T ss_dssp             HHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCcHHHHHHHH
Confidence            36789999999999999998766