Citrus Sinensis ID: 032606

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
MAGAKLCGGDTAFLLRSHSHSHSHFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICLSRSVCNSLRFEEPFSD
Secondary Structure (PSIPRED)
ccccEEEcccEEEEEEccccccHHHHHHHHHHccccccccccccccccccccEEEEEEEEccccccccccccccccccEEEEEEcccccccccHHHHHHHHHcccEEEEcccccEEEEEEccccHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccHEEEccccEEEEEccccccccccccccccccccccccccccccccccccEEEEEEEEEccccccEEccccccccccEEEEEEccccccHccHHHHHHHHHcccEEEEEcccEEEEEEHccHHHHHHccccccccc
Coil and Loop (DISEMBL)
magaklcggdtafllrshshshsHFLEAAtrraapfpgrvssvspnpkpsrYRILAMTVkrspkrlkysapqftkegglmyveadpsgadswklEPVVELLKEgavgviptdtLYATAICLSRsvcnslrfeepfsd
Flexible Loop (DISEMBL)
MAGAKLCGGDTAFLLRSHSHSHSHFLEAATrraapfpgrvssvspnpkpsryRILAmtvkrspkrlkysapqftkeggLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICLSRSVCNSLRFEEPFSD
Low Complexity Region (SEG)
MAGAKLCGGDTAFLLRshshshshFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICLSRSVCNSLRFEEPFSD
Disordered region (IsUnstruct)
***********AFL**************************************************************GGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICLSRSVCNSLR*******
Disordered Region (DISOPRED)
*******GGDTAFLLRSHSH***********************************************************MYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICLSRSVCNSLRFEEP***
Disordered Region (DISEMBL)
MAGAKLCGGDTAFLLRSHSHSHSHFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICLSRSVCNSLRFEEPFSD
Disordered Region (DISPRO)
*AGAKLCGGDTAFLLRSH********EAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICLSRSVCNSLRFEE****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAGAKLCGGDTAFLLRSHSHSHSHFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICLSRSVCNSLRFEEPFSD
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	137
118489827	313	unknown [Populus trichocarpa x Populus d	0.751	0.329	0.632	9e-28
224055737	322	predicted protein [Populus trichocarpa]	0.751	0.319	0.632	9e-28
255536893	326	sua5, putative [Ricinus communis] gi|223	0.700	0.294	0.656	2e-24
147841978	329	hypothetical protein VITISV_012595 [Viti	0.532	0.221	0.743	5e-24
225451447	306	PREDICTED: uncharacterized protein HI_11	0.532	0.238	0.743	6e-24
6513939	297	hypothetical protein [Arabidopsis thalia	0.846	0.390	0.514	1e-23
22330801	307	putative translation factor [Arabidopsis	0.846	0.377	0.514	2e-23
297832740	305	yrdC family protein [Arabidopsis lyrata	0.598	0.268	0.650	3e-23
449455846	309	PREDICTED: uncharacterized protein HI_11	0.591	0.262	0.617	2e-20
356571525	308	PREDICTED: uncharacterized protein HI_11	0.656	0.292	0.597	8e-20

>gi|118489827|gb|ABK96713.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  128 bits (321), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 67/106 (63%), Positives = 78/106 (73%), Gaps = 3/106 (2%)

Query: 26  LEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEAD 85
           L    R  APFP  VS  +P  KP R R+L+M +KRSPKRLKYSAP+FTKE GL+YVEAD
Sbjct: 21  LTTLRRHVAPFPSLVSFNTP--KPPRLRVLSMAIKRSPKRLKYSAPRFTKEDGLLYVEAD 78

Query: 86  PSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLR 130
             G+D+WKLEPV+ELLK+GAVGVIPTDT+YA    L S S    LR
Sbjct: 79  ELGSDTWKLEPVIELLKQGAVGVIPTDTVYAIVCDLKSNSAIERLR 124

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224055737|ref|XP_002298628.1| predicted protein [Populus trichocarpa] gi|222845886|gb|EEE83433.1| predicted protein [Populus trichocarpa]

 Score =  128 bits (321), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 67/106 (63%), Positives = 78/106 (73%), Gaps = 3/106 (2%)

Query: 26  LEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEAD 85
           L    R  APFP  VS  +P  KP R R+L+M +KRSPKRLKYSAP+FTKE GL+YVEAD
Sbjct: 21  LTTLRRHVAPFPSLVSFNTP--KPPRLRVLSMAIKRSPKRLKYSAPRFTKEDGLLYVEAD 78

Query: 86  PSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLR 130
             G+D+WKLEPV+ELLK+GAVGVIPTDT+YA    L S S    LR
Sbjct: 79  ELGSDTWKLEPVIELLKQGAVGVIPTDTVYAIVCDLKSNSAIERLR 124

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255536893|ref|XP_002509513.1| sua5, putative [Ricinus communis] gi|223549412|gb|EEF50900.1| sua5, putative [Ricinus communis]

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 65/99 (65%), Positives = 71/99 (71%), Gaps = 3/99 (3%)

Query: 33  AAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSW 92
            APF  RVS  S   KP R  +LAM  KRSPKRLKYS P+FTKE  L+YVEAD SGADSW
Sbjct: 28  VAPFASRVSFHSR--KPPRLLVLAMATKRSPKRLKYSTPRFTKEDALVYVEADASGADSW 85

Query: 93  KLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLR 130
           KL+PV+ELL EGAVGVIPTDT+YA    L S S    LR
Sbjct: 86  KLDPVIELLNEGAVGVIPTDTVYAMVCHLKSHSAVERLR 124

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147841978|emb|CAN72004.1| hypothetical protein VITISV_012595 [Vitis vinifera]

 Score =  115 bits (288), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 55/74 (74%), Positives = 64/74 (86%), Gaps = 1/74 (1%)

Query: 51  RYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIP 110
           R+R +A+  KRSPKRLKYSAP+F+KE GL+YVEADPSG DSWKLEPV +LLKEGAVGVIP
Sbjct: 64  RFRFVALAAKRSPKRLKYSAPRFSKEDGLLYVEADPSGTDSWKLEPVADLLKEGAVGVIP 123

Query: 111 TDTLYATAICLSRS 124
           TDT+YA  +C  RS
Sbjct: 124 TDTVYAI-VCHLRS 136

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225451447|ref|XP_002273946.1| PREDICTED: uncharacterized protein HI_1198 [Vitis vinifera] gi|296082345|emb|CBI21350.3| unnamed protein product [Vitis vinifera]

 Score =  115 bits (288), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 55/74 (74%), Positives = 64/74 (86%), Gaps = 1/74 (1%)

Query: 51  RYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIP 110
           R+R +A+  KRSPKRLKYSAP+F+KE GL+YVEADPSG DSWKLEPV +LLKEGAVGVIP
Sbjct: 36  RFRFVALAAKRSPKRLKYSAPRFSKEDGLLYVEADPSGTDSWKLEPVADLLKEGAVGVIP 95

Query: 111 TDTLYATAICLSRS 124
           TDT+YA  +C  RS
Sbjct: 96  TDTVYAI-VCHLRS 108

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6513939|gb|AAF14843.1|AC011664_25 hypothetical protein [Arabidopsis thaliana]

 Score =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 69/134 (51%), Positives = 82/134 (61%), Gaps = 18/134 (13%)

Query: 1   MAGAKLCGGDTA---FLLRSHSHSHSHFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAM 57
           MA AKL GG  A    LL     +H        RR +  P   S       P RY I+A+
Sbjct: 1   MAVAKLHGGGMAAMRLLLLPSPMTH--------RRPSTLPSTASL-----SPRRY-IVAL 46

Query: 58  TVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYAT 117
             KRSPKRLKYS P+FTKEG L+Y+E DP G DSWKL+PV++LLK+GAVGVIPTDT+YA 
Sbjct: 47  AAKRSPKRLKYSTPRFTKEGELVYIEVDPCGVDSWKLQPVIDLLKQGAVGVIPTDTVYAI 106

Query: 118 AI-CLSRSVCNSLR 130
           A  C + S    LR
Sbjct: 107 ACDCKNHSAVERLR 120

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330801|ref|NP_566156.2| putative translation factor [Arabidopsis thaliana] gi|6091731|gb|AAF03443.1|AC010797_19 hypothetical protein [Arabidopsis thaliana] gi|19310491|gb|AAL84979.1| At3g1920/F28J7.25 [Arabidopsis thaliana] gi|23505865|gb|AAN28792.1| At3g1920/F28J7.25 [Arabidopsis thaliana] gi|332640214|gb|AEE73735.1| putative translation factor [Arabidopsis thaliana]

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 69/134 (51%), Positives = 84/134 (62%), Gaps = 18/134 (13%)

Query: 1   MAGAKLCGGDTA---FLLRSHSHSHSHFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAM 57
           MA AKL GG  A    LL     +H        RR +  P   +S+SP     R  I+A+
Sbjct: 1   MAVAKLHGGGMAAMRLLLLPSPMTH--------RRPSTLPS-TASLSP-----RRYIVAL 46

Query: 58  TVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYAT 117
             KRSPKRLKYS P+FTKEG L+Y+E DP G DSWKL+PV++LLK+GAVGVIPTDT+YA 
Sbjct: 47  AAKRSPKRLKYSTPRFTKEGELVYIEVDPCGVDSWKLQPVIDLLKQGAVGVIPTDTVYAI 106

Query: 118 AI-CLSRSVCNSLR 130
           A  C + S    LR
Sbjct: 107 ACDCKNHSAVERLR 120

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297832740|ref|XP_002884252.1| yrdC family protein [Arabidopsis lyrata subsp. lyrata] gi|297330092|gb|EFH60511.1| yrdC family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 54/83 (65%), Positives = 65/83 (78%), Gaps = 1/83 (1%)

Query: 49  PSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGV 108
           P R+ I+A+  KRSPKRLKYS P+FTKEG L+Y+E DP GADSWKL+PV+ELLK+GAVGV
Sbjct: 36  PRRHTIVALAAKRSPKRLKYSTPRFTKEGELVYIEVDPFGADSWKLQPVIELLKQGAVGV 95

Query: 109 IPTDTLYATAI-CLSRSVCNSLR 130
           IPTDT+YA    C + S    LR
Sbjct: 96  IPTDTVYALVCDCKNHSAVERLR 118

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455846|ref|XP_004145661.1| PREDICTED: uncharacterized protein HI_1198-like [Cucumis sativus] gi|449502016|ref|XP_004161520.1| PREDICTED: uncharacterized protein HI_1198-like [Cucumis sativus]

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 55/89 (61%), Positives = 65/89 (73%), Gaps = 8/89 (8%)

Query: 33  AAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSW 92
           A PF G  +S        R ++LAM VKRSPKRLKYSAP+FTKEG L+YV+A+ SG D W
Sbjct: 34  ATPFDGFETS-------RRLQVLAMVVKRSPKRLKYSAPRFTKEGSLIYVKAE-SGEDGW 85

Query: 93  KLEPVVELLKEGAVGVIPTDTLYATAICL 121
           KL+P+V LLKEGAVGVIPTDT+Y     L
Sbjct: 86  KLDPIVNLLKEGAVGVIPTDTVYGIVCDL 114

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571525|ref|XP_003553927.1| PREDICTED: uncharacterized protein HI_1198-like [Glycine max]

 Score =  101 bits (252), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 55/92 (59%), Positives = 67/92 (72%), Gaps = 2/92 (2%)

Query: 41  SSVSPNPKPSRYRILAMTVKRSPKRLKY-SAPQFTKEGGLMYVEADPSGADSWKLEPVVE 99
           + VS  P   R  +++M  KRSPKRLKY SA +FTKE GL+Y+EADPS +DSWKLEP+  
Sbjct: 29  TRVSFCPPRRRSGLVSMVAKRSPKRLKYTSASRFTKEDGLVYIEADPSASDSWKLEPIAN 88

Query: 100 LLKEGAVGVIPTDTLYATAICL-SRSVCNSLR 130
           LLK+GAVGVIPTDT+YA    L S+S    LR
Sbjct: 89  LLKQGAVGVIPTDTMYAIVCDLRSQSAIERLR 120

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	137
TAIR|locus:2078668	307	AT3G01920 [Arabidopsis thalian	0.868	0.387	0.519	4.6e-25

TAIR|locus:2078668 AT3G01920 [Arabidopsis thaliana (taxid:3702)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 68/131 (51%), Positives = 83/131 (63%)

Query:     1 MAGAKLCGGDTAFLLRXXXXXXXXFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVK 60
             MA AKL GG  A  +R              RR +  P   +S+SP     RY I+A+  K
Sbjct:     1 MAVAKLHGGGMA-AMRLLLLPS----PMTHRRPSTLPS-TASLSPR----RY-IVALAAK 49

Query:    61 RSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAI- 119
             RSPKRLKYS P+FTKEG L+Y+E DP G DSWKL+PV++LLK+GAVGVIPTDT+YA A  
Sbjct:    50 RSPKRLKYSTPRFTKEGELVYIEVDPCGVDSWKLQPVIDLLKQGAVGVIPTDTVYAIACD 109

Query:   120 CLSRSVCNSLR 130
             C + S    LR
Sbjct:   110 CKNHSAVERLR 120


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        0.318   0.134   0.398    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      137       129   0.00091  102 3  11 22  0.40    31
                                                     29  0.41    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:  579 (62 KB)
  Total size of DFA:  124 KB (2079 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  13.38u 0.20s 13.58t   Elapsed:  00:00:01
  Total cpu time:  13.38u 0.20s 13.58t   Elapsed:  00:00:01
  Start:  Thu May  9 18:06:19 2013   End:  Thu May  9 18:06:20 2013

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.I.3086.1 hypothetical protein (261 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	137
COG0009	211	COG0009, SUA5, Putative translation factor (SUA5)	7e-04

>gnl|CDD|223088 COG0009, SUA5, Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 12/33 (36%), Positives = 16/33 (48%)

Query: 84  ADPSGADSWKLEPVVELLKEGAVGVIPTDTLYA 116
             P       +E  VE L++G V   PTDT+Y 
Sbjct: 6   IHPENPQPRAIEKAVEALRKGGVVAYPTDTVYG 38

Length = 211

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
PRK11630	206	hypothetical protein; Provisional	99.65
COG0009	211	SUA5 Putative translation factor (SUA5) [Translati	99.61
TIGR00057	201	Sua5/YciO/YrdC/YwlC family protein. partial match	99.59
PRK10634	190	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modif	99.54
TIGR00143	711	hypF [NiFe] hydrogenase maturation protein HypF. A	98.93
KOG3051	261	consensus RNA binding/translational regulation pro	96.63
COG0068	750	HypF Hydrogenase maturation factor [Posttranslatio	91.62
KOG3051	261	consensus RNA binding/translational regulation pro	87.23

>PRK11630 hypothetical protein; Provisional

Probab=99.65  E-value=1.1e-16  Score=126.85  Aligned_cols=55  Identities=20%  Similarity=0.348  Sum_probs=51.9

Q ss_pred             EEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           81 YVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        81 ~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      ++++++++++.+.+++++++|++||+|+|||||+||||||+ |++|++|||++|+-
T Consensus         4 ~~~~~~~~~~~~~i~~a~~~L~~G~vi~~PTdTvYgL~~d~~n~~Av~~l~~lK~R   59 (206)
T PRK11630          4 FFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQL   59 (206)
T ss_pred             eEecCCCCCCHHHHHHHHHHHHCCCEEEEeCCChHhhhcCCCCHHHHHHHHHHcCC
Confidence            67789999998889999999999999999999999999999 99999999999974

>COG0009 SUA5 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]

Probab=99.61  E-value=6.5e-16  Score=124.89  Aligned_cols=56  Identities=23%  Similarity=0.290  Sum_probs=52.6

Q ss_pred             EEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCCC
Q 032606           81 YVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPFS  136 (137)
Q Consensus        81 ~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~~  136 (137)
                      ++.+++.+++.+.++++++.|++|++|+|||||||||||++ |++|++|||++|+.+
T Consensus         3 ~~~~~~~~~~~~~~~~a~~~l~~G~vVa~PTeTVYGLg~~~~~~~Av~~i~~~K~Rp   59 (211)
T COG0009           3 IFMIHPENPQPRAIEKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYEIKQRP   59 (211)
T ss_pred             eeecCccccchHHHHHHHHHHHcCCEEEEEccchheeecCCCCHHHHHHHHHHhCCC
Confidence            56788888888999999999999999999999999999999 999999999999864

>TIGR00057 Sua5/YciO/YrdC/YwlC family protein

Probab=99.59  E-value=6.6e-16  Score=121.48  Aligned_cols=53  Identities=23%  Similarity=0.342  Sum_probs=49.5

Q ss_pred             ecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCCC
Q 032606           84 ADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPFS  136 (137)
Q Consensus        84 vdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~~  136 (137)
                      +|+++++.+.+++++++|++||||+|||||+|||+|++ |++|++|||++|+-+
T Consensus         1 ~~~~~~~~~~i~~a~~~L~~G~ii~~PTdTvYgL~~~~~~~~av~ri~~iK~R~   54 (201)
T TIGR00057         1 IHPENPSQRGIEQAVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYRIKGRP   54 (201)
T ss_pred             CCcCCCCHHHHHHHHHHHHCCCEEEEeCCCHHHhhcCCCCHHHHHHHHHHhCCC
Confidence            57888888889999999999999999999999999999 999999999999743

partial match to sua5, which is involved in regulation of translation initiation. 3' end of sua5 has matches to sua5, BS3690, and weakly to AF0781 and BB0734.

>PRK10634 tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; Provisional

Probab=99.54  E-value=3.9e-15  Score=116.85  Aligned_cols=48  Identities=17%  Similarity=0.146  Sum_probs=44.5

Q ss_pred             CCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCCC
Q 032606           89 ADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPFS  136 (137)
Q Consensus        89 pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~~  136 (137)
                      ++.+.++++++.|++||||+|||||||||||++ |++|++|||++|+-+
T Consensus         5 ~~~~~i~~a~~~L~~G~vv~~PTdTvYgL~~~~~n~~Av~ri~~iK~R~   53 (190)
T PRK10634          5 LQGDAIAAAVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRP   53 (190)
T ss_pred             ccHHHHHHHHHHHHCCCEEEEeCCchhhhhcCCCCHHHHHHHHHHhCCC
Confidence            456789999999999999999999999999999 999999999999743

>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF

Probab=98.93  E-value=2.2e-09  Score=99.26  Aligned_cols=44  Identities=23%  Similarity=0.180  Sum_probs=42.0

Q ss_pred             cccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCC
Q 032606           91 SWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEP  134 (137)
Q Consensus        91 ~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~  134 (137)
                      .+.++++++.|++|+||++||||+|||+||+ |++||+|||++|+
T Consensus       162 ~~~i~~aa~~L~~G~IVaipt~ggy~L~cda~n~~AV~rLr~~K~  206 (711)
T TIGR00143       162 DDALLEAAKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKN  206 (711)
T ss_pred             hHHHHHHHHHHhCCCEEEEEcCCcceeecCCCCHHHHHHHHHHhC
Confidence            4679999999999999999999999999999 9999999999986

A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.

>KOG3051 consensus RNA binding/translational regulation protein of the SUA5 family [Translation, ribosomal structure and biogenesis]

Probab=96.63  E-value=0.00049  Score=58.51  Aligned_cols=43  Identities=12%  Similarity=0.087  Sum_probs=36.3

Q ss_pred             cHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           93 KLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        93 ~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      .++.+.-+-+.++.+++||||+||+|+++ +..++.+||.+|..
T Consensus        18 ~~~aa~~~r~~~~~va~pT~t~yg~g~~~~~~~av~~v~~~K~r   61 (261)
T KOG3051|consen   18 LYDAALIVRRTDKRVAFPTETVYGLGASAYNEVAVLRLYKLKNR   61 (261)
T ss_pred             hhhhhhheeccCCceecCchhhhhhhhhhhccccchhhhhhhcC
Confidence            34444556678999999999999999999 99999999998763

>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]

Probab=91.62  E-value=0.3  Score=46.97  Aligned_cols=42  Identities=19%  Similarity=0.156  Sum_probs=39.3

Q ss_pred             cHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCC
Q 032606           93 KLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEP  134 (137)
Q Consensus        93 ~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~  134 (137)
                      .+.++++.|+.|++|++--=-.|.|+||+ |.++|++|++-++
T Consensus       199 ai~~a~klL~~G~IvAIKGiGGFhLaCda~~~eaV~~LR~rk~  241 (750)
T COG0068         199 AIRKAAKLLKVGKIVAIKGIGGFHLACDARNEEAVAKLRKRKN  241 (750)
T ss_pred             HHHHHHHHHhhCCEEEEeecCceeeeecCCchHHHHHHHHhcC
Confidence            67899999999999999999999999999 9999999998654

>KOG3051 consensus RNA binding/translational regulation protein of the SUA5 family [Translation, ribosomal structure and biogenesis]

Probab=87.23  E-value=0.047  Score=46.71  Aligned_cols=68  Identities=19%  Similarity=0.126  Sum_probs=61.9

Q ss_pred             CceeeeeeeeccCcccccccccceeecCceEEEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEe
Q 032606           50 SRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYAT  117 (137)
Q Consensus        50 ~r~~~~~~~~~r~~krlky~~~~~~~~~~~~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGL  117 (137)
                      +++...+.++++..|+.+|.++++.+..+..|.+.++..-..|+...+.+.|.-+-.-+.+++++|..
T Consensus        16 ~~~~~aa~~~r~~~~~va~pT~t~yg~g~~~~~~~av~~v~~~K~rP~~~pL~~~~~s~~~~~~v~~~   83 (261)
T KOG3051|consen   16 PALYDAALIVRRTDKRVAFPTETVYGLGASAYNEVAVLRLYKLKNRPADNPLIVHVSSVDQLKRVVAI   83 (261)
T ss_pred             hhhhhhhhheeccCCceecCchhhhhhhhhhhccccchhhhhhhcCccccchhhccccHHHHHHHHhh
Confidence            56677999999999999999999999988889999999999999999999999999999999999876

---

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	137
1k7j_A	206	Protein YCIO, protein TF1; structural genomics, X-	2e-04

>1k7j_A Protein YCIO, protein TF1; structural genomics, X-RAY crystallography, putative translation factor, PSI, protein structure initiative; 1.40A {Escherichia coli} SCOP: d.115.1.1 PDB: 1kk9_A Length = 206

 Score = 38.2 bits (90), Expect = 2e-04
 Identities = 11/36 (30%), Positives = 18/36 (50%)

Query: 81  YVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYA 116
           +    P       +   VE++++G V V PTD+ YA
Sbjct: 4   FFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYA 39

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
1k7j_A	206	Protein YCIO, protein TF1; structural genomics, X-	99.64
1jcu_A	208	Conserved protein MTH1692; mixed alpha-beta struct	99.64
2eqa_A	352	Hypothetical protein ST1526; YRDC/RIBB fold, YRDC	99.57
1hru_A	188	YRDC gene product; protein folding, structural gen	99.51
3l7v_A	295	Putative uncharacterized protein SMU.1377C; transc	99.15
3vth_A	761	Hydrogenase maturation factor; carbamoyltransfer,	99.06
3ttc_A	657	HYPF, transcriptional regulatory protein; Zn finge	99.02
4g9i_A	772	Hydrogenase maturation protein HYPF; zinc finger,	98.67

>1k7j_A Protein YCIO, protein TF1; structural genomics, X-RAY crystallography, putative translation factor, PSI, protein structure initiative; 1.40A {Escherichia coli} SCOP: d.115.1.1 PDB: 1kk9_A

Probab=99.64  E-value=1.6e-16  Score=124.31  Aligned_cols=56  Identities=20%  Similarity=0.336  Sum_probs=53.4

Q ss_pred             EEEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           80 MYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        80 ~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      +++++|+++++.+.++++++.|++||||+|||||+|||+||+ |++|++|||++|+-
T Consensus         3 ~~~~~~~~~~~~~~i~~a~~~L~~G~iva~pTdtvygL~~da~n~~Av~rl~~~K~R   59 (206)
T 1k7j_A            3 QFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQL   59 (206)
T ss_dssp             EEEECCSSSCCHHHHHHHHHHHHTTCCEEEEETTEEEEEEETTCHHHHHHHHHHHTC
T ss_pred             ceEecCCCCCCHHHHHHHHHHHHCCCEEEEECCCEEEEEEeCCCHHHHHHHHHHcCC
Confidence            578999999999999999999999999999999999999999 99999999999863

>1jcu_A Conserved protein MTH1692; mixed alpha-beta structure, structural genomics; NMR {Methanothermobacterthermautotrophicus} SCOP: d.115.1.1

Probab=99.64  E-value=7.8e-17  Score=126.39  Aligned_cols=57  Identities=16%  Similarity=0.256  Sum_probs=53.8

Q ss_pred             eEEEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           79 LMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        79 ~~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      |+++++++++++.+.+++++++|++||||+|||||+|||+||+ |++|++|||++|+-
T Consensus         1 ~~~~~~~~~~~~~~~i~~a~~~L~~G~vVa~pTdtvygL~~da~n~~Av~rl~~~K~R   58 (208)
T 1jcu_A            1 MLIRKITRKNPSPDVLEEAISVMEGGGIVIYPTDTIYGLGVNALDEDAVRRLFRVKGR   58 (208)
T ss_dssp             CCSCCCCSSCCCCHHHHHHHHHHHTTCEEECCCSSSCEEEEETTSHHHHHHHHHHCCS
T ss_pred             CeEEEecCCCCCHHHHHHHHHHHHCCCEEEEECCCEEEEEEeCCCHHHHHHHHHHhCC
Confidence            4677899999999999999999999999999999999999999 99999999999963

>2eqa_A Hypothetical protein ST1526; YRDC/RIBB fold, YRDC domain, SUA5 domain, structural genomics, NPPSFA; HET: AMP; 1.80A {Sulfolobus tokodaii} PDB: 3aje_A* 4e1b_A*

Probab=99.57  E-value=2e-15  Score=128.13  Aligned_cols=56  Identities=16%  Similarity=0.317  Sum_probs=53.1

Q ss_pred             EEEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           80 MYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        80 ~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      .+++++|+|++.+.+++++++|++||+|+||||||||||||+ |++||+|||++|+-
T Consensus         3 ~~~~i~~~~~~~~~i~~aa~~L~~G~iVa~PTeTvYGLg~da~n~~AV~rI~~~K~R   59 (352)
T 2eqa_A            3 QIIKIDPLNPEIDKIKIAADVIRNGGTVAFPTETVYGLGANAFDGNACLKIFQAKNR   59 (352)
T ss_dssp             EEEECCSSSCCHHHHHHHHHHHHTTCCEEECCSSSCEEEEETTCHHHHHHHHHHHTC
T ss_pred             eEEEeCCCCCCHHHHHHHHHHHHcCCEEEEECCCEeEEEEeCCCHHHHHHHHHHcCC
Confidence            477999999999999999999999999999999999999999 99999999999863

>1hru_A YRDC gene product; protein folding, structural genomics, RNA, SUA5, PSI, protein structure initiative, midwest center for structural genomics; 2.00A {Escherichia coli} SCOP: d.115.1.1

Probab=99.51  E-value=5e-15  Score=113.98  Aligned_cols=50  Identities=14%  Similarity=0.134  Sum_probs=45.8

Q ss_pred             CCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           86 PSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        86 p~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      +++++.+.+++++++|++||||+|||||+|||+||+ |++|++|||++|+-
T Consensus         2 ~~~~~~~~i~~a~~~L~~G~iva~ptdt~ygL~~da~~~~av~rl~~~K~R   52 (188)
T 1hru_A            2 NNNLQRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQR   52 (188)
T ss_dssp             -CHHHHHHHHHHHHHHHTTCCEEEECSSSEEEEECTTCHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHHCCCEEEEeCCCEeeeEEcCCCHHHHHHHHHHcCC
Confidence            456777889999999999999999999999999999 99999999999863

>3l7v_A Putative uncharacterized protein SMU.1377C; transcription; 2.26A {Streptococcus mutans}

Probab=99.15  E-value=2e-11  Score=101.94  Aligned_cols=43  Identities=21%  Similarity=0.081  Sum_probs=40.0

Q ss_pred             ccHHHHHHHHh-cCCeEEeccCCeeEeeecCCHHHHHHHHhcCCC
Q 032606           92 WKLEPVVELLK-EGAVGVIPTDTLYATAICLSRSVCNSLRFEEPF  135 (137)
Q Consensus        92 ~~l~~aa~~Lr-~GgVVa~PTDTVYGLgcdan~~AVerIy~I~~~  135 (137)
                      ..+++|+++|+ +||||+|||||+|||+| .|++||+|||++|+-
T Consensus        44 ~~i~~Aa~~L~~~GgIVa~PTdTvYGL~c-~n~~AV~rL~~iK~R   87 (295)
T 3l7v_A           44 NLSQEGFEIVKGEGGVIVCPTKVGYIIMT-SDKKGLERKFEAKKR   87 (295)
T ss_dssp             SCCHHHHHHHHSTTCEEEEEETTEEEEEE-SSHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCEEEEEE-cCHHHHHHHHHHcCC
Confidence            35889999999 99999999999999999 799999999999864

>3vth_A Hydrogenase maturation factor; carbamoyltransfer, maturation of [NIFE]-hydrogenase, carbamoylphosphate, iron, HYPE; HET: APC AP2; 2.00A {Thermoanaerobacter tengcongensis} PDB: 3vti_A

Probab=99.06  E-value=1.3e-10  Score=106.50  Aligned_cols=49  Identities=18%  Similarity=0.125  Sum_probs=44.5

Q ss_pred             cCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCC
Q 032606           85 DPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEP  134 (137)
Q Consensus        85 dp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~  134 (137)
                      +.++ +...+++++++|++||||+|||||+|||+||+ |++||+|||++|+
T Consensus       197 ~~~~-~~~~i~~aa~~L~~G~IVa~pt~t~YgL~cda~n~~AV~rL~~~K~  246 (761)
T 3vth_A          197 GEGC-FDDEIKCVAKALKEGKIVAIKGIGGFHLAVNALDDEAVATLRRRKK  246 (761)
T ss_dssp             SSCC-CSCHHHHHHHHHHTTCCEEEECSSSEEEECBTTCHHHHHHHHHHHT
T ss_pred             CCCC-chHHHHHHHHHHHcCCEEEEECCcEEEEEecCCCHHHHHHHHHHhC
Confidence            4444 55679999999999999999999999999999 9999999999986

>3ttc_A HYPF, transcriptional regulatory protein; Zn finger, nucleotide binding, hydrogenase maturation factor transferase; HET: ADP; 1.86A {Escherichia coli} PDB: 3tsp_A* 3tsu_A* 3ttf_A* 3ttd_A 3tsq_A

Probab=99.02  E-value=1.8e-10  Score=104.41  Aligned_cols=45  Identities=18%  Similarity=0.111  Sum_probs=42.2

Q ss_pred             cccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           91 SWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        91 ~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      .+.+++++++|++||||+|||||+|||+||+ |++||+|||++|+-
T Consensus       111 ~~~i~~aa~~L~~G~IVa~pt~ggYgL~cda~n~~AV~rL~~~K~R  156 (657)
T 3ttc_A          111 EAALQAAIAQLKMGNIVAIKGIGGFHLACDARNSNAVATLRARKHR  156 (657)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECSSSEEEEEETTCHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHHcCCEEEEECCceeEEEeecCCHHHHHHHHHHhCC
Confidence            3469999999999999999999999999999 99999999999973

>4g9i_A Hydrogenase maturation protein HYPF; zinc finger, ATP binding, carbamoyla transferase; 4.50A {Thermococcus kodakarensis}

Probab=98.67  E-value=1.8e-08  Score=92.39  Aligned_cols=44  Identities=20%  Similarity=0.070  Sum_probs=41.7

Q ss_pred             cccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCC
Q 032606           91 SWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEP  134 (137)
Q Consensus        91 ~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~  134 (137)
                      ...+++++++|++|++|++||+|+|+|+||+ |++||++|++.|+
T Consensus       200 ~~~i~~a~~~l~~G~iva~kg~ggy~L~cda~n~~aV~~lr~~K~  244 (772)
T 4g9i_A          200 GDPLRKAAELIDKGYIVAIKGIGGIHLACDAANEEVVAELRRRTF  244 (772)
T ss_dssp             THHHHHHHHHHTTSCCEEECCSSSBEEECCTTCHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHcCCEEEEecCCeeEEEEecCCHHHHHHHHHhhC
Confidence            3479999999999999999999999999999 9999999999986

---

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	137
d1k7ja_	206	d.115.1.1 (A:) Hypothetical protein YciO {Escheric	5e-05
d1jcua_	208	d.115.1.1 (A:) Hypothetical protein MTH1692 {Archa	1e-04
d1hrua_	186	d.115.1.1 (A:) Hypothetical protein YrdC {Escheric	0.002

>d1k7ja_ d.115.1.1 (A:) Hypothetical protein YciO {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a+b)
fold: YrdC/RibB
superfamily: YrdC/RibB
family: YrdC-like
domain: Hypothetical protein YciO
species: Escherichia coli [TaxId: 562]

 Score = 39.1 bits (90), Expect = 5e-05
 Identities = 11/36 (30%), Positives = 18/36 (50%)

Query: 81  YVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYA 116
           +    P       +   VE++++G V V PTD+ YA
Sbjct: 4   FFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYA 39

>d1jcua_ d.115.1.1 (A:) Hypothetical protein MTH1692 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 208

class: Alpha and beta proteins (a+b)
fold: YrdC/RibB
superfamily: YrdC/RibB
family: YrdC-like
domain: Hypothetical protein MTH1692
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 37.6 bits (86), Expect = 1e-04
 Identities = 8/38 (21%), Positives = 18/38 (47%)

Query: 79  LMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYA 116
           ++  +          LE  + +++ G + + PTDT+Y 
Sbjct: 1   MLIRKITRKNPSPDVLEEAISVMEGGGIVIYPTDTIYG 38

>d1hrua_ d.115.1.1 (A:) Hypothetical protein YrdC {Escherichia coli [TaxId: 562]} Length = 186

class: Alpha and beta proteins (a+b)
fold: YrdC/RibB
superfamily: YrdC/RibB
family: YrdC-like
domain: Hypothetical protein YrdC
species: Escherichia coli [TaxId: 562]

 Score = 34.5 bits (78), Expect = 0.002
 Identities = 5/23 (21%), Positives = 12/23 (52%)

Query: 94  LEPVVELLKEGAVGVIPTDTLYA 116
           +   +++L E  V   PT+ ++ 
Sbjct: 8   IAAAIDVLNEERVIAYPTEAVFG 30

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	137
d1k7ja_	206	Hypothetical protein YciO {Escherichia coli [TaxId	99.73
d1jcua_	208	Hypothetical protein MTH1692 {Archaeon Methanobact	99.71
d1hrua_	186	Hypothetical protein YrdC {Escherichia coli [TaxId	99.58

>d1k7ja_ d.115.1.1 (A:) Hypothetical protein YciO {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: YrdC/RibB
superfamily: YrdC/RibB
family: YrdC-like
domain: Hypothetical protein YciO
species: Escherichia coli [TaxId: 562]

Probab=99.73  E-value=1.2e-18  Score=133.48  Aligned_cols=56  Identities=20%  Similarity=0.336  Sum_probs=53.5

Q ss_pred             EEEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           80 MYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        80 ~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      .|+.+||++||.+.++++++.|++||||+|||||+|||+||+ |++|++|||++|+-
T Consensus         3 ~~~~~~~~~p~~~~i~~a~~~L~~G~vv~~PTdTvYgl~~da~~~~av~~i~~iK~R   59 (206)
T d1k7ja_           3 QFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQL   59 (206)
T ss_dssp             EEEECCSSSCCHHHHHHHHHHHHTTCCEEEEETTEEEEEEETTCHHHHHHHHHHHTC
T ss_pred             ceEEeCCCCCCHHHHHHHHHHHHcCCEEEEECCceeEEEEeCCChHHHHHHHHhhcc
Confidence            478999999999999999999999999999999999999999 99999999999864

>d1jcua_ d.115.1.1 (A:) Hypothetical protein MTH1692 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: YrdC/RibB
superfamily: YrdC/RibB
family: YrdC-like
domain: Hypothetical protein MTH1692
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=99.71  E-value=2.1e-18  Score=132.26  Aligned_cols=57  Identities=16%  Similarity=0.256  Sum_probs=54.2

Q ss_pred             eEEEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           79 LMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        79 ~~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      ||+..++++|++++.+++|++.|++||||+|||||+|||+|++ |++|++|||++|+-
T Consensus         1 m~i~~i~~~n~~~~~i~~a~~~L~~Ggivi~PTdtvYgl~c~a~~~~av~~i~~lK~R   58 (208)
T d1jcua_           1 MLIRKITRKNPSPDVLEEAISVMEGGGIVIYPTDTIYGLGVNALDEDAVRRLFRVKGR   58 (208)
T ss_dssp             CCSCCCCSSCCCCHHHHHHHHHHHTTCEEECCCSSSCEEEEETTSHHHHHHHHHHCCS
T ss_pred             CEEEEcCCCCcCHHHHHHHHHHHHcCCEEEEEcCceeeeEEeCCCcHHHHHHHHhhcc
Confidence            4677899999999999999999999999999999999999999 99999999999974

>d1hrua_ d.115.1.1 (A:) Hypothetical protein YrdC {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: YrdC/RibB
superfamily: YrdC/RibB
family: YrdC-like
domain: Hypothetical protein YrdC
species: Escherichia coli [TaxId: 562]

Probab=99.58  E-value=2.1e-16  Score=117.74  Aligned_cols=49  Identities=14%  Similarity=0.143  Sum_probs=44.8

Q ss_pred             CCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606           87 SGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF  135 (137)
Q Consensus        87 ~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~  135 (137)
                      +|.+.+.+++|++.|++||||+|||||+|||+|++ |++|++|||++|+-
T Consensus         1 ~n~~~d~i~~a~~~L~~G~iv~~PTdt~Ygl~~~~~~~~av~~i~~~K~R   50 (186)
T d1hrua_           1 NNLQRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQR   50 (186)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEECSSSEEEEECTTCHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHHcCCEEEEECCceeEEEEeCCChHHHHHHHHhhhh
Confidence            35567789999999999999999999999999999 99999999999753