Citrus Sinensis ID: 032215

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-----

MMSLLMNTANPWKRMEHGPDIWNCKQLLLLHIVIYAFIGSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEYSVKKQ

cccccccccccccccccccccccccccEEEEEEEcccccccccccccccEEccccccccccccEEEcccccccHHHHccccccccccccccccccHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHcccccHHHccc

ccHHHHccccHHHHccccccHHHHHHHHHHHHHHHHHHcccccccccccEEccccccccccccEEEEEccccccccccccccccccccccccccccHEEEEEcccccccHHHHHHHHHHccccHHHHHHHHHHHccccccccccc

mmsllmntanpwkrmehgpdiwnCKQLLLLHIVIYAFigsyhdgehyngvrlkedscigsarpiiikadadisaasiqSKTVTSKLKGAAGIINAGSIKLVMagsgcensEKVEEVLLQVGGDVDAAIEFLIAeqgteeysvkkq

MMSLLMNTANPWKRMEHGPDIWNCKQLLLLHIVIYAFIGSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKtvtsklkgaagiINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLiaeqgteeysvkkq

MMSLLMNTANPWKRMEHGPDIWNCKQLLLLHIVIYAFIGSYHDGEHYNGVRLKEDSCIGSARPiiikadadisaasiQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEYSVKKQ

***********WKRMEHGPDIWNCKQLLLLHIVIYAFIGSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE***********

*******TANPWKRMEHGPDIWNCKQLLLLHIVIYAFIGSYHDGEHYNGVRLKEDSCIGSAR***********************************IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL**************

MMSLLMNTANPWKRMEHGPDIWNCKQLLLLHIVIYAFIGSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG*********

**SLLMNTANPWKRMEHGPDIWNCKQLLLLHIVIYAFIGSYHDGEHYNGVRLKEDSCIGSARPIIIKADAD*********************INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ**********

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

ooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MMSLLMNTANPWKRMEHGPDIWNCKQLLLLHIVIYAFIGSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAGIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEYSVKKQ

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		145
356565555		382	PREDICTED: OTU domain-containing protein	0.710	0.269	0.695	1e-33
296082384		385	unnamed protein product [Vitis vinifera]	0.689	0.259	0.725	4e-33
225438775		467	PREDICTED: OTU domain-containing protein	0.689	0.214	0.725	6e-33
147791288		1324	hypothetical protein VITISV_042268 [Viti	0.689	0.075	0.725	9e-33
356514204		383	PREDICTED: uncharacterized protein LOC10	0.703	0.266	0.673	2e-31
255565284		371	OTU domain-containing protein, putative	0.703	0.274	0.663	6e-31
23306370		375	putative protein [Arabidopsis thaliana]	0.682	0.264	0.663	1e-30
30698282		375	SEC-C motif-containing protein / OTU-lik	0.682	0.264	0.663	2e-30
224081718		349	predicted protein [Populus trichocarpa]	0.717	0.297	0.647	2e-30
42573818		374	SEC-C motif-containing protein / OTU-lik	0.682	0.264	0.663	2e-30

>gi\|356565555\|ref\|XP_003551005.1\| PREDICTED: OTU domain-containing protein 3-like [Glycine max]	Back alignment and taxonomy information

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 73/105 (69%), Positives = 84/105 (80%), Gaps = 2/105 (1%)

Query: 40  SYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKTVTSKLKGAAG--IINAGS 97
           SYHDGEHYN VRLK+D C G+ARPI+I+ADAD+S  S Q+K V +K  G AG      GS
Sbjct: 150 SYHDGEHYNSVRLKDDPCDGAARPIVIEADADLSVPSHQTKVVGNKFHGRAGWEAFQPGS 209

Query: 98  IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEYSV 142
           IKLVMAG+GCEN+EKVE++L QV GDVDAAIEFLIAEQGTEE S 
Sbjct: 210 IKLVMAGTGCENAEKVEQILEQVNGDVDAAIEFLIAEQGTEECSA 254

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|296082384\|emb\|CBI21389.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225438775\|ref\|XP_002278347.1\| PREDICTED: OTU domain-containing protein 3-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147791288\|emb\|CAN65606.1\| hypothetical protein VITISV_042268 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356514204\|ref\|XP_003525796.1\| PREDICTED: uncharacterized protein LOC100782446 [Glycine max]	Back alignment and taxonomy information

>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]	Back alignment and taxonomy information

>gi\|23306370\|gb\|AAN17412.1\| putative protein [Arabidopsis thaliana] gi\|25084238\|gb\|AAN72203.1\| putative protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>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]	Back alignment and taxonomy information

>gi\|224081718\|ref\|XP_002306480.1\| predicted protein [Populus trichocarpa] gi\|222855929\|gb\|EEE93476.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>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]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		145
TAIR\|locus:2155588		375	AT5G67170 [Arabidopsis thalian	0.682	0.264	0.584	3.6e-25

TAIR\|locus:2155588 AT5G67170 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 286 (105.7 bits), Expect = 3.6e-25, P = 3.6e-25
 Identities = 59/101 (58%), Positives = 69/101 (68%)

Query:    40 SYHDGEHYNGVRLKEDSCIGSARPXXXXXXXXXXXXXXQSKTVTSKLKGAAGI--INAGS 97
             SYHDGEHYN VR KED+C G ARP              Q+K   SK K  A    +NAG+
Sbjct:   148 SYHDGEHYNSVRSKEDACGGPARPVVIEADAKVSAASKQAKATESKSKNKADKCHVNAGA 207

Query:    98 IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 138
             IK+VM+GS C+N+EK E+VLLQV GDVDAAIEFLIA+QG E
Sbjct:   208 IKVVMSGSCCDNTEKAEQVLLQVNGDVDAAIEFLIADQGME 248


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.133   0.391    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      145       131   0.00091  102 3  11 22  0.43    31
                                                     29  0.42    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  575 (61 KB)
  Total size of DFA:  136 KB (2085 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:01
  No. of threads or processors used:  24
  Search cpu time:  10.53u 0.12s 10.65t   Elapsed:  00:00:00
  Total cpu time:  10.53u 0.12s 10.65t   Elapsed:  00:00:01
  Start:  Fri May 10 21:30:35 2013   End:  Fri May 10 21:30:36 2013

GO:0005634 "nucleus" evidence=ISM

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		145
PF00627		37	UBA: UBA/TS-N domain; InterPro: IPR000449 UBA doma	97.27
PF14555		43	UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A	97.24
PF02845		42	CUE: CUE domain; InterPro: IPR003892 This domain m	97.13
TIGR00264		116	alpha-NAC-related protein. This hypothetical prote	96.75
PRK06369		115	nac nascent polypeptide-associated complex protein	96.72
cd00194		38	UBA Ubiquitin Associated domain. The UBA domain is	96.39
smart00546		43	CUE Domain that may be involved in binding ubiquit	96.16
smart00165		37	UBA Ubiquitin associated domain. Present in Rad23,	95.74
PRK12332		198	tsf elongation factor Ts; Reviewed	94.3
TIGR00116		290	tsf translation elongation factor Ts. This protein	94.2
PRK09377		290	tsf elongation factor Ts; Provisional	94.07
CHL00098		200	tsf elongation factor Ts	93.85
COG1308		122	EGD2 Transcription factor homologous to NACalpha-B	92.95
COG0264		296	Tsf Translation elongation factor Ts [Translation,	91.45
PF06972		60	DUF1296: Protein of unknown function (DUF1296); In	86.51
PF05861		358	PhnI: Bacterial phosphonate metabolism protein (Ph	83.76
PF03474		39	DMA: DMRTA motif; InterPro: IPR005173 This region	82.31

>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 []	Back alignment and domain information

Probab=97.27  E-value=0.00063  Score=41.16  Aligned_cols=35  Identities=26%  Similarity=0.497  Sum_probs=30.1

Q ss_pred             hhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHH
Q 032215           95 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL  131 (145)
Q Consensus        95 ~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~L  131 (145)
                      ++.|++++.- |.+ .+.++++|..++||+|.||+||
T Consensus         3 ~~~v~~L~~m-Gf~-~~~~~~AL~~~~~nve~A~~~L   37 (37)
T PF00627_consen    3 EEKVQQLMEM-GFS-REQAREALRACNGNVERAVDWL   37 (37)
T ss_dssp             HHHHHHHHHH-TS--HHHHHHHHHHTTTSHHHHHHHH
T ss_pred             HHHHHHHHHc-CCC-HHHHHHHHHHcCCCHHHHHHhC
Confidence            4678888888 866 6699999999999999999997

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	Back alignment and domain information

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

>TIGR00264 alpha-NAC-related protein	Back alignment and domain information

>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed	Back alignment and domain information

>cd00194 UBA Ubiquitin Associated domain	Back alignment and domain information

>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs)	Back alignment and domain information

>smart00165 UBA Ubiquitin associated domain	Back alignment and domain information

>PRK12332 tsf elongation factor Ts; Reviewed	Back alignment and domain information

>TIGR00116 tsf translation elongation factor Ts	Back alignment and domain information

>PRK09377 tsf elongation factor Ts; Provisional	Back alignment and domain information

>CHL00098 tsf elongation factor Ts	Back alignment and domain information

>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]	Back alignment and domain information

>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>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	Back alignment and domain information

>PF05861 PhnI: Bacterial phosphonate metabolism protein (PhnI); InterPro: IPR008773 This family consists of several proteobacterial phosphonate metabolism protein (PhnI) sequences	Back alignment and domain information

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

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		145
3phu_A		219	RNA-directed RNA polymerase L; OTU domain, DE-ubiq	97.62
3phx_A		185	RNA-directed RNA polymerase L; OTU domain, DE-ubiq	97.46
2cp9_A		64	EF-TS, EF-TSMT, elongation factor TS, mitochondria	97.3
1wj7_A		104	Hypothetical protein (RSGI RUH-015); UBA domain, u	97.03
2dhy_A		67	CUE domain-containing protein 1; structural genomi	96.91
1wgl_A		59	TOLL-interacting protein; CUE domain, structural g	96.88
2bwb_A		46	Ubiquitin-like protein DSK2; UBA, signaling protei	96.75
2dah_A		54	Ubiquilin-3; UBA domain, structural genomics, NPPS	96.61
3e21_A		45	HFAF1, FAS-associated factor 1; UBA, alternative s	96.58
1wr1_B		58	Ubiquitin-like protein DSK2; UBA domain, UBA-ubiqu	96.57
1z96_A		40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	96.44
2knz_A		53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	96.31
1tr8_A		102	Conserved protein (MTH177); chaperones, nascent po	96.31
1vej_A		74	Riken cDNA 4931431F19; UBA domain, three helix bun	96.24
2dam_A		67	ETEA protein; KIAA0887, UBA-like domain, structura	96.21
3pfy_A		185	OTU domain-containing protein 5; structural genomi	96.17
1wji_A		63	Tudor domain containing protein 3; UBA domain, str	96.15
2g3q_A		43	Protein YBL047C; endocytosis, solution structure,	96.12
1v92_A		46	NSFL1 cofactor P47; 3-helix bundle, recombination;	96.05
2jy5_A		52	Ubiquilin-1; UBA, alternative splicing, cytoplasm,	96.0
1vg5_A		73	RSGI RUH-014, rhomboid family protein; UBA domain,	95.83
2dal_A		62	Protein KIAA0794; FAS associted factor 1, UBA-like	95.83
2dna_A		67	Unnamed protein product; ubiquitin associated doma	95.78
1ify_A		49	HHR23A, UV excision repair protein RAD23 homolog A	95.74
2dak_A		63	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	95.71
1p3q_Q		54	VPS9P, vacuolar protein sorting-associated protein	95.59
1otr_A		49	Protein CUE2; protein-protein complex, cell cycle;	95.26
3by4_A		212	OTU1, ubiquitin thioesterase OTU1; ubiquitin hydro	95.19
1wiv_A		73	UBP14, ubiquitin-specific protease 14; ubiquitin a	95.12
1whc_A		64	RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain	94.79
2cwb_A		108	Chimera of immunoglobulin G binding protein G and	94.78
1veg_A		83	NEDD8 ultimate buster-1; ubiquitin associated doma	94.49
2dag_A		74	Ubiquitin carboxyl-terminal hydrolase 5; isopeptid	94.33
2dai_A		83	Ubadc1, ubiquitin associated domain containing 1;	94.27
2cp8_A		54	NEXT to BRCA1 gene 1 protein; UBA domain, structur	94.12
2ekk_A		47	UBA domain from E3 ubiquitin-protein ligase HUWE1;	94.06
1aip_C		196	EF-TS, elongation factor TS; nucleotide exchange,	93.8
1xb2_B		291	EF-TS, elongation factor TS, mitochondrial, EF-TSM	93.63
2dzl_A		66	Protein FAM100B; UBA-like domain, structural genom	93.62
1vdl_A		80	Ubiquitin carboxyl-terminal hydrolase 25; UBA doma	93.39
2dkl_A		85	Trinucleotide repeat containing 6C protein; TNRC6C	93.34
4ae4_A		118	Ubiquitin-associated protein 1; protein transport,	93.17
2crn_A		64	Ubash3A protein; compact three-helix bundle, struc	93.05
1wgn_A		63	UBAP1, ubiquitin associated protein; ubiquitin ass	92.65
1dv0_A		47	DNA repair protein HHR23A; helical bundle, DNA bin	91.78
2cpw_A		64	CBL-interacting protein STS-1 variant; ubiquitin a	91.76
2lbc_A		126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	91.34
2lva_A		129	Ubiquitin carboxyl-terminal hydrolase 28; UIM, ubi	90.2
1vek_A		84	UBP14, ubiquitin-specific protease 14, putative; U	90.72
1ufz_A		83	Hypothetical protein BAB28515; HBS1-like domain, s	86.46
1tff_A		234	Ubiquitin thiolesterase protein OTUB2; hydrolase;	85.87
2lbc_A		126	Ubiquitin carboxyl-terminal hydrolase 13; tandem U	85.1
2di0_A		71	Activating signal cointegrator 1 complex subunit 2	81.28
2qsf_X		171	RAD23, UV excision repair protein RAD23; alpha-bet	80.2

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

Probab=97.62  E-value=4.8e-06  Score=67.48  Aligned_cols=30  Identities=10%  Similarity=0.086  Sum_probs=27.2

Q ss_pred             HHHHHhcCCCCCCccccCCCCCCCCCceee
Q 032215           36 AFIGSYHDGEHYNGVRLKEDSCIGSARPII   65 (145)
Q Consensus        36 ~LHISYH~GEHYnSVRri~DnsegPA~~~i   65 (145)
                      .+||+||+|+||||||.+.|+++.|+.|+-
T Consensus       143 ~I~L~Y~g~~HYdSL~~~~d~~~~~~~~~~  172 (219)
T 3phu_A          143 AVNLLHSGQTHFDALRILPQFETDTREALS  172 (219)
T ss_dssp             SEEEEEETTTEEEEEEECTTTCCSCCCCCC
T ss_pred             eEEEEECCCcCchhheECCCCCCCCCcchh
Confidence            578999999999999999999999998843

PyMOL of 3phu

>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	Back alignment and structure

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

>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	Back alignment and structure

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

>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	Back alignment and structure

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

>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	Back alignment and structure

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

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

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

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

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

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

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

>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*	Back alignment and structure

>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	Back alignment and structure

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

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

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

>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	Back alignment and structure

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

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

>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	Back alignment and structure

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

>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	Back alignment and structure

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

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

>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	Back alignment and structure

>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	Back alignment and structure

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

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

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

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

>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	Back alignment and structure

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

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

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

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

>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	Back alignment and structure

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

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

>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	Back alignment and structure

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

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

>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	Back alignment and structure

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

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

>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	Back alignment and structure

>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	Back alignment and structure

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

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

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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		145
d2dnaa1		50	a.5.2.1 (A:12-61) Ubiquilin-like protein Ubqlnl {M	0.002

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


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 = 32.3 bits (74), Expect = 0.002
 Identities = 11/31 (35%), Positives = 15/31 (48%)

Query: 106 GCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 136
           G  N     + L+   GD +AAI  L + QG
Sbjct: 19  GFVNYNANLQALIATDGDTNAAIYKLKSSQG 49

PyMOL of d2dnaa1

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		145
d1efub3		54	Elongation factor Ts (EF-Ts), N-terminal domain {E	97.2
d1xb2b1		56	Elongation factor Ts (EF-Ts), N-terminal domain {C	96.85
d1wj7a1		91	Ubiquitin-associated protein 2-like Ubap2l {Mouse	96.7
d1vg5a_		73	Rhomboid family protein At3g58460 {Thale cress (Ar	96.63
d1v92a_		46	NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {	96.6
d1wiva_		73	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	96.47
d1aipc1		52	Elongation factor Ts (EF-Ts), N-terminal domain {T	96.36
d1oqya1		41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	96.34
d1wgla_		59	Toll-interacting protein {Human (Homo sapiens) [Ta	96.31
d1wgna_		63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	96.28
d2dnaa1		50	Ubiquilin-like protein Ubqlnl {Mouse (Mus musculus	96.2
d1mn3a_		54	Vacuolar protein sorting-associated protein vps9 {	96.19
d2daha1		41	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	96.19
d1wjia_		63	Tudor domain containing protein 3, TDRD3 {Human (H	96.19
d2bwba1		44	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	96.09
d1veja1		61	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	95.56
d1whca_		64	UBA/UBX 33.3 kDa protein {Mouse (Mus musculus) [Ta	94.99
d1vdla_		80	Ubiquitin carboxyl-terminal hydrolase 25 {Mouse (M	92.22
d2cpwa1		51	Cbl-interacting protein p70, STS1 {Human (Homo sap	89.6
d1veka_		84	Ubiquitin isopeptidase T {Thale cress (Arabidopsis	86.71
d2g3qa1		43	Endocytic protein Ede1, YBL047C {Saccharomyces cer	86.64
d2crna1		51	Suppressor of T-cell receptor signaling 2 (STS-2)	84.15
d1ufza_		83	HBS1-like protein {Mouse (Mus musculus) [TaxId: 10	81.54

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

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

Probab=97.20  E-value=0.00024  Score=45.46  Aligned_cols=41  Identities=24%  Similarity=0.352  Sum_probs=36.7

Q ss_pred             CchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHH
Q 032215           93 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE  134 (145)
Q Consensus        93 ~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~  134 (145)
                      +....|++....||+. +.-.+++|++.+||+|.||++|-..
T Consensus         3 is~~~iK~LR~~Tgag-~~dCKkAL~e~~gD~ekA~e~Lr~k   43 (54)
T d1efub3           3 ITASLVKELRERTGAG-MMDCKKALTEANGDIELAIENMRKS   43 (54)
T ss_dssp             CCHHHHHHHHHHHCCC-HHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCCC-HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            4557899999999998 8899999999999999999999643

PyMOL of d1efub3

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

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

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

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

>d1wiva_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

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

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

>d1wgla_ a.5.2.4 (A:) Toll-interacting protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

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

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

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

>d2daha1 a.5.2.1 (A:8-48) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

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

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

>d1veja1 a.5.2.1 (A:8-68) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

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

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

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

>d1veka_ a.5.2.1 (A:) Ubiquitin isopeptidase T {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

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

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

>d1ufza_ a.5.9.1 (A:) HBS1-like protein {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure