Citrus Sinensis ID: 032585

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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
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVILGSYEPQLNLLSKKKLRWFYYCDGGM
Secondary Structure (PSIPRED)
ccccccccEEcccEEEcccccccccEEEcccccccccccccccccccccHHHHHcccccccccEEEEEEcccccccEEEccccccccEEEEEEccHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHEEccccccccEEEEcccccccccEEEEccHHcccccHHHHccccccccccEccEcccccccEEEEccccccccEEHHHHccHHHHHHHHHHHHHHHEcccccccccHHcccccEEEEEEcccc
Coil and Loop (DISEMBL)
mcslqsqhflnspllifpkfndnrkfHLNRTRNFGQRIGALSSVEeflpnatrrkkdslwrggfslgvdlglsrtglalskgfcvrpltVLKLRGEKLELQLLEIAQREVILGSYEPQLNLLSKKKLRWfyycdggm
Flexible Loop (DISEMBL)
mcslqsqhflnspllifPKFNDNRKFHLNRTRNFgqrigalssveeflpnatrrkkdslwrgGFSLGVDLGLSrtglalskgfcvRPLTVLKLRGEKLELQLLEIAqrevilgsyepqlnllskkklrwFYYCDGGM
Low Complexity Region (SEG)
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVILGSYEPQLNLLSKKKLRWFYYCDGGM
Disordered region (IsUnstruct)
********FLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVILGSYEPQLNLLSKKKLRWFYYCD***
Disordered Region (DISOPRED)
*******HFLNSPLLIFPKFNDN***************************************GFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVI**********LSKKKLRWFYYCDGGM
Disordered Region (DISEMBL)
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVILGSYEPQLNLLSKKKLRWFYYCDGGM
Disordered Region (DISPRO)
*C***SQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVILGSYEPQLNLLSKKKLRWFYYCDG**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVILGSYEPQLNLLSKKKLRWFYYCDGGM
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
224129716	254	predicted protein [Populus trichocarpa]	0.700	0.377	0.618	3e-24
297734533	679	unnamed protein product [Vitis vinifera]	0.540	0.108	0.746	1e-22
359489199	229	PREDICTED: putative Holliday junction re	0.540	0.323	0.746	3e-21
297844086	238	DNA binding protein [Arabidopsis lyrata	0.693	0.399	0.504	2e-19
356506432	226	PREDICTED: putative Holliday junction re	0.540	0.327	0.626	3e-19
449431960	235	PREDICTED: putative Holliday junction re	0.496	0.289	0.724	4e-19
79317769	254	putative holliday junction resolvase [Ar	0.467	0.251	0.703	3e-18
255573708	239	hydrolase, acting on ester bonds, putati	0.737	0.422	0.517	1e-17
242035117	214	hypothetical protein SORBIDRAFT_01g02939	0.576	0.369	0.564	7e-14
414867730	235	TPA: holliday junction resolvase [Zea ma	0.525	0.306	0.552	4e-13

>gi|224129716|ref|XP_002328785.1| predicted protein [Populus trichocarpa] gi|222839083|gb|EEE77434.1| predicted protein [Populus trichocarpa]

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/97 (61%), Positives = 74/97 (76%), Gaps = 1/97 (1%)

Query: 15  LIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSR 74
           L+FP F  +    L+  +   +R+ AL S+ E  PNA RRK D LWRGGFSLGVDLGLSR
Sbjct: 42  LLFPNFTTS-SLQLDSDKPCRRRLRALLSIHEIPPNALRRKNDPLWRGGFSLGVDLGLSR 100

Query: 75  TGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVI 111
           +G+ALSKGF VRPLTVL+LRG+KLEL+LLEIA+ E +
Sbjct: 101 SGVALSKGFTVRPLTVLELRGQKLELRLLEIAENEEV 137

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734533|emb|CBI16584.3| unnamed protein product [Vitis vinifera]

 Score =  111 bits (277), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 56/75 (74%), Positives = 63/75 (84%), Gaps = 1/75 (1%)

Query: 37  RIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGE 96
           RI A+S + E LPNA RRK +  W GGFSLGVDLG+SRTGLALSKGF VRPL+VLKLRG+
Sbjct: 485 RIRAVS-LNEILPNALRRKHNPHWTGGFSLGVDLGMSRTGLALSKGFSVRPLSVLKLRGQ 543

Query: 97  KLELQLLEIAQREVI 111
           KLELQLLEIA RE +
Sbjct: 544 KLELQLLEIAGREEV 558

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489199|ref|XP_002275849.2| PREDICTED: putative Holliday junction resolvase [Vitis vinifera]

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 56/75 (74%), Positives = 63/75 (84%), Gaps = 1/75 (1%)

Query: 37  RIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGE 96
           RI A+S + E LPNA RRK +  W GGFSLGVDLG+SRTGLALSKGF VRPL+VLKLRG+
Sbjct: 35  RIRAVS-LNEILPNALRRKHNPHWTGGFSLGVDLGMSRTGLALSKGFSVRPLSVLKLRGQ 93

Query: 97  KLELQLLEIAQREVI 111
           KLELQLLEIA RE +
Sbjct: 94  KLELQLLEIAGREEV 108

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297844086|ref|XP_002889924.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata] gi|297335766|gb|EFH66183.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata]

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 57/113 (50%), Positives = 74/113 (65%), Gaps = 18/113 (15%)

Query: 1   MCSLQS----------QHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPN 50
           MCSL S          Q ++N+PL+  P+ +         +RN    + A +S++E  PN
Sbjct: 1   MCSLHSLSSVAISFRTQKYVNTPLV--PRLSSIG------SRNNPLPLRAATSIDEIPPN 52

Query: 51  ATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLL 103
           A RRK D  WRGGFSLGVDLGLSRTG+A+SKG+ V+PLTVLK RG+KLE +LL
Sbjct: 53  AVRRKIDRDWRGGFSLGVDLGLSRTGVAISKGYTVKPLTVLKSRGQKLETRLL 105

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356506432|ref|XP_003521987.1| PREDICTED: putative Holliday junction resolvase-like [Glycine max]

 Score = 99.8 bits (247), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/75 (62%), Positives = 64/75 (85%), Gaps = 1/75 (1%)

Query: 37  RIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGE 96
           R+ AL+ ++E  PNA R+K++  WRGGFSLG+DLGL+RTGLALSKGF +RPLTVL+LRG+
Sbjct: 34  RVKALT-LDELPPNALRKKREPQWRGGFSLGLDLGLARTGLALSKGFSIRPLTVLELRGQ 92

Query: 97  KLELQLLEIAQREVI 111
           KLE+Q++ IA+ E +
Sbjct: 93  KLEVQIINIAEEEEV 107

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449431960|ref|XP_004133768.1| PREDICTED: putative Holliday junction resolvase-like [Cucumis sativus] gi|449522992|ref|XP_004168509.1| PREDICTED: putative Holliday junction resolvase-like [Cucumis sativus]

 Score = 99.4 bits (246), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 50/69 (72%), Positives = 58/69 (84%), Gaps = 1/69 (1%)

Query: 41  LSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLEL 100
           +SS+E   PNA RRK D  WRGGFSLGVDLG SRTGLALSKGF  RPLTVL+LRG+KLE 
Sbjct: 50  ISSIE-LPPNALRRKLDPHWRGGFSLGVDLGTSRTGLALSKGFSTRPLTVLELRGQKLEA 108

Query: 101 QLLEIAQRE 109
           +L+EIA++E
Sbjct: 109 KLIEIAEQE 117

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79317769|ref|NP_001031028.1| putative holliday junction resolvase [Arabidopsis thaliana] gi|332190735|gb|AEE28856.1| putative holliday junction resolvase [Arabidopsis thaliana]

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 55/64 (85%)

Query: 40  ALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLE 99
           A++S++E  PNA RRK D  WRGGFSLGVDLGLSRTG+A+SKG+ V+PLTVLK RG+KLE
Sbjct: 58  AVTSIDEIPPNAVRRKIDRNWRGGFSLGVDLGLSRTGIAISKGYTVKPLTVLKSRGQKLE 117

Query: 100 LQLL 103
            +LL
Sbjct: 118 TRLL 121

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573708|ref|XP_002527775.1| hydrolase, acting on ester bonds, putative [Ricinus communis] gi|223532810|gb|EEF34585.1| hydrolase, acting on ester bonds, putative [Ricinus communis]

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/114 (51%), Positives = 72/114 (63%), Gaps = 13/114 (11%)

Query: 1   MCSLQSQHFLNS---PLLI--FPKFNDNRKF------HLNRTRNFGQRIGALSSVEEFLP 49
           MCSL+S    ++   PL I   PK  +   F       +    NF  R  A+ S EE  P
Sbjct: 3   MCSLKSFCIQSTQLFPLSINSLPKVINTSAFLRQSLPQICIHNNFKLR--AVLSTEEVPP 60

Query: 50  NATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLL 103
           NA RR+ D  WRGGFSLG+DLGLSRTGLA+SKGF  +PLTVL+LRG+KLE +LL
Sbjct: 61  NAARRRSDPQWRGGFSLGIDLGLSRTGLAISKGFSFKPLTVLELRGQKLETRLL 114

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242035117|ref|XP_002464953.1| hypothetical protein SORBIDRAFT_01g029390 [Sorghum bicolor] gi|241918807|gb|EER91951.1| hypothetical protein SORBIDRAFT_01g029390 [Sorghum bicolor]

 Score = 82.0 bits (201), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 48/85 (56%), Positives = 61/85 (71%), Gaps = 6/85 (7%)

Query: 35  GQRIGALSSVEEFLPNATRRKKDSLWRGG-FSLGVDLGLSRTGLALSKGFCV-RPLTVLK 92
           G+  GA       LPNA RR +D LW GG FSLGVDLG +RTGLA+ +G  + RPLTVLK
Sbjct: 43  GRTEGAGELPAPLLPNARRRGRDPLWHGGGFSLGVDLGDARTGLAVGRGITLPRPLTVLK 102

Query: 93  LRGEKLELQLLEIAQR----EVILG 113
           LRG+KLEL LL++A++    E+I+G
Sbjct: 103 LRGQKLELTLLDVARQQEADELIIG 127

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414867730|tpg|DAA46287.1| TPA: holliday junction resolvase [Zea mays]

 Score = 79.7 bits (195), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 47/85 (55%), Positives = 59/85 (69%), Gaps = 13/85 (15%)

Query: 49  PNATRRKKDSLWRGG-FSLGVDLGLSRTGLALSKGFC-VRPLTVLKLRGEKLELQLLEIA 106
           PNA RR +D LW GG FSLGVDLG +RTGLA+ +G    RPLTVL+LRG+KLEL LL++A
Sbjct: 57  PNARRRGRDPLWHGGGFSLGVDLGDARTGLAIGRGITFPRPLTVLRLRGQKLELALLDVA 116

Query: 107 QR----EVIL-------GSYEPQLN 120
           ++    E+I+       GS  PQ N
Sbjct: 117 RQQEADELIIGLPVSADGSETPQSN 141

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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:1009023117	254	AT1G12244 [Arabidopsis thalian	0.759	0.409	0.530	9e-22

TAIR|locus:1009023117 AT1G12244 [Arabidopsis thaliana (taxid:3702)]

 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 61/115 (53%), Positives = 76/115 (66%)

Query:     1 MCSLQSQHFLNSPLLIF--PKFNDNRKFHLNRTRNFGQRI----GALSSVEEFLPNATRR 54
             MCSL   H  +S  + F   K+ +    H  R    G R      A++S++E  PNA RR
Sbjct:    18 MCSL---HSFSSVAISFRTQKYVNTSLVH--RLSPIGYRNYPLPWAVTSIDEIPPNAVRR 72

Query:    55 KKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE 109
             K D  WRGGFSLGVDLGLSRTG+A+SKG+ V+PLTVLK RG+KLE +LLEIA+ E
Sbjct:    73 KIDRNWRGGFSLGVDLGLSRTGIAISKGYTVKPLTVLKSRGQKLETRLLEIAEEE 127


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        0.324   0.141   0.429    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       137   0.00091  102 3  11 22  0.38    31
                                                     30  0.45    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:  590 (63 KB)
  Total size of DFA:  137 KB (2085 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:  12.90u 0.14s 13.04t   Elapsed:  00:00:00
  Total cpu time:  12.90u 0.14s 13.04t   Elapsed:  00:00:00
  Start:  Thu May  9 17:07:50 2013   End:  Thu May  9 17:07:50 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA

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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_scaffold_86000044 hypothetical protein (254 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
PF03652	135	UPF0081: Uncharacterised protein family (UPF0081);	99.76
COG0816	141	Predicted endonuclease involved in recombination (	99.74
PRK00109	138	Holliday junction resolvase-like protein; Reviewed	99.72
TIGR00250	130	RNAse_H_YqgF RNAse H-fold protein YqgF. This prote	99.67
smart00732	99	YqgFc Likely ribonuclease with RNase H fold. YqgF	98.27
PRK00039	164	ruvC Holliday junction resolvase; Reviewed	93.96
cd00529	154	RuvC_resolvase Holliday junction resolvases (HJRs)	93.92
PF02075	149	RuvC: Crossover junction endodeoxyribonuclease Ruv	92.78
TIGR00228	156	ruvC crossover junction endodeoxyribonuclease RuvC	85.45
PF04312	138	DUF460: Protein of unknown function (DUF460); Inte	83.5

>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination

Probab=99.76  E-value=1.4e-18  Score=131.02  Aligned_cols=73  Identities=27%  Similarity=0.322  Sum_probs=63.2

Q ss_pred             ceEEEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHH
Q 032585           63 GFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLR  128 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~r  128 (137)
                      +|+||||||+|||||||||  +.+|+|++||...+ ..+++.|.++++++    ||||       +++++++.+++|+++
T Consensus         1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~   80 (135)
T PF03652_consen    1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNREKDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFAEE   80 (135)
T ss_dssp             -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCCCCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHHHH
T ss_pred             CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCchHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHHHH
Confidence            6899999999999999994  77899999999653 35788999999886    9999       899999999999999


Q ss_pred             HHHhcCC
Q 032585          129 WFYYCDG  135 (137)
Q Consensus       129 L~~~~~~  135 (137)
                      |++.+++
T Consensus        81 L~~~~~~   87 (135)
T PF03652_consen   81 LKKRFPG   87 (135)
T ss_dssp             HHHHH-T
T ss_pred             HHHhcCC
Confidence            9998743

The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.

>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B

Probab=99.74  E-value=4.8e-18  Score=130.70  Aligned_cols=73  Identities=27%  Similarity=0.350  Sum_probs=65.4

Q ss_pred             cceEEEeecCCceEEEEeec--ceeeeeeeeEEccch--hHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHH
Q 032585           62 GGFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRGE--KLELQLLEIAQRE----VILG-------SYEPQLNLLSKKK  126 (137)
Q Consensus        62 ~gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~~--~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA  126 (137)
                      ++++||||||+||||||+|+  +.+|+|++||.+.+.  .+++.|.+++++|    ||||       +++++++.+++|+
T Consensus         1 ~~~ilalD~G~KrIGvA~sd~~~~~A~pl~~i~~~~~~~~~~~~l~~li~~~~~~~vVVGlP~~m~g~~~~~~~~~~~f~   80 (141)
T COG0816           1 GMRILALDVGTKRIGVAVSDILGSLASPLETIKRKNGKPQDFNALLKLVKEYQVDTVVVGLPLNMDGTEGPRAELARKFA   80 (141)
T ss_pred             CceEEEEecCCceEEEEEecCCCccccchhhheeccccHhhHHHHHHHHHHhCCCEEEEecCcCCCCCcchhHHHHHHHH
Confidence            47899999999999999996  669999999998654  3788899999886    9999       8999999999999


Q ss_pred             HHHHHhcC
Q 032585          127 LRWFYYCD  134 (137)
Q Consensus       127 ~rL~~~~~  134 (137)
                      ++|++.++
T Consensus        81 ~~L~~r~~   88 (141)
T COG0816          81 ERLKKRFN   88 (141)
T ss_pred             HHHHHhcC
Confidence            99999875

subtilis) [DNA replication, recombination, and repair]

>PRK00109 Holliday junction resolvase-like protein; Reviewed

Probab=99.72  E-value=2.9e-17  Score=124.22  Aligned_cols=72  Identities=25%  Similarity=0.285  Sum_probs=64.5

Q ss_pred             cceEEEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHH
Q 032585           62 GGFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKL  127 (137)
Q Consensus        62 ~gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~  127 (137)
                      .+++||||||+||||||+||  +.+|+|++|+...+ ...++.|.+++.++    ||||       ++++++..|++|++
T Consensus         3 ~~~iLalD~G~kriGvAv~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~   82 (138)
T PRK00109          3 SGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKFAN   82 (138)
T ss_pred             CCcEEEEEeCCCEEEEEEecCCCCEEcCEEEEEcCCCchHHHHHHHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHHHHH
Confidence            46799999999999999995  89999999998754 34678899999886    9999       99999999999999


Q ss_pred             HHHHhc
Q 032585          128 RWFYYC  133 (137)
Q Consensus       128 rL~~~~  133 (137)
                      +|++.+
T Consensus        83 ~L~~~~   88 (138)
T PRK00109         83 RLEGRF   88 (138)
T ss_pred             HHHHHh
Confidence            999876

>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF

Probab=99.67  E-value=2.4e-16  Score=118.23  Aligned_cols=68  Identities=21%  Similarity=0.255  Sum_probs=61.3

Q ss_pred             EEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHHHHH
Q 032585           66 LGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLRWFY  131 (137)
Q Consensus        66 LGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~rL~~  131 (137)
                      ||||||+||||||+||  +.+|+|++|+...+ ...++.|.++++++    ||||       +++++|++|++|+++|++
T Consensus         1 laiD~G~kriGvA~~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~~~~iVvGlP~~~dG~~~~~a~~v~~f~~~L~~   80 (130)
T TIGR00250         1 LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEG   80 (130)
T ss_pred             CeEccCCCeEEEEEECCCCCEEeceEEEEecCCcHHHHHHHHHHHHcCCCEEEEeccCCCCcCcCHHHHHHHHHHHHHHH
Confidence            6999999999999995  88999999998744 45678899999886    9999       999999999999999998


Q ss_pred             hc
Q 032585          132 YC  133 (137)
Q Consensus       132 ~~  133 (137)
                      .+
T Consensus        81 ~~   82 (130)
T TIGR00250        81 RF   82 (130)
T ss_pred             Hh
Confidence            76

This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.

>smart00732 YqgFc Likely ribonuclease with RNase H fold

Probab=98.27  E-value=7.8e-06  Score=55.77  Aligned_cols=69  Identities=19%  Similarity=0.193  Sum_probs=49.5

Q ss_pred             ceEEEeecCCceEEEEee--cceeeeeeeeEEc-cchhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHH
Q 032585           63 GFSLGVDLGLSRTGLALS--KGFCVRPLTVLKL-RGEKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLR  128 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVS--dgiiAsPL~tI~~-~~~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~r  128 (137)
                      +++||||+|..+||+|+.  ++-+..++.+... +....++.|.+++.++    |+||       ...+.. . ..|++.
T Consensus         1 ~~ilgiD~Ggt~i~~a~~d~~g~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~i~Ig~pg~v~g~~~~~~-~-~~l~~~   78 (99)
T smart00732        1 KRVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRET-E-EAFAEL   78 (99)
T ss_pred             CcEEEEccCCCeEEEEEECCCCCEecCEEEEEecCcchHHHHHHHHHHHhCCCEEEEeCCcCCCCCcCHHH-H-HHHHHH
Confidence            368999999999999998  4677777766553 2234577888888774    8888       223333 2 788888


Q ss_pred             HHHhc
Q 032585          129 WFYYC  133 (137)
Q Consensus       129 L~~~~  133 (137)
                      |++.+
T Consensus        79 l~~~~   83 (99)
T smart00732       79 LKERF   83 (99)
T ss_pred             HHHhh
Confidence            88765

YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.

>PRK00039 ruvC Holliday junction resolvase; Reviewed

Probab=93.96  E-value=0.21  Score=39.05  Aligned_cols=47  Identities=26%  Similarity=0.336  Sum_probs=30.7

Q ss_pred             ceEEEeecCCceEEEEeec--c--eeeeeeeeEEccc--------hhHHHHHHHHhhcc
Q 032585           63 GFSLGVDLGLSRTGLALSK--G--FCVRPLTVLKLRG--------EKLELQLLEIAQRE  109 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--g--iiAsPL~tI~~~~--------~~~~~~L~eli~ee  109 (137)
                      +|+||||-|+.++|+||-+  +  +..--.++|....        ....+.|.++++++
T Consensus         2 m~iLGIDPgl~~tG~avi~~~~~~~~~~~~G~i~t~~~~~~~~Rl~~I~~~l~~~i~~~   60 (164)
T PRK00039          2 MRILGIDPGLRRTGYGVIEVEGRRLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEY   60 (164)
T ss_pred             CEEEEEccccCceeEEEEEecCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            5899999999999999973  2  2223334665321        12346777777765

>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination

Probab=93.92  E-value=0.22  Score=37.86  Aligned_cols=46  Identities=22%  Similarity=0.270  Sum_probs=29.3

Q ss_pred             eEEEeecCCceEEEEeec--c--eeeeeeeeEEcc-c-------hhHHHHHHHHhhcc
Q 032585           64 FSLGVDLGLSRTGLALSK--G--FCVRPLTVLKLR-G-------EKLELQLLEIAQRE  109 (137)
Q Consensus        64 RiLGlD~GtKRIGVAVSd--g--iiAsPL~tI~~~-~-------~~~~~~L~eli~ee  109 (137)
                      |+||||.|+.++|.||-+  +  +..--.++|+.. +       ....+.|.+++.++
T Consensus         1 rILGIDPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~~i~~~   58 (154)
T cd00529           1 RILGIDPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQF   58 (154)
T ss_pred             CEEEEccCcCceEEEEEEeeCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            689999999999999973  2  111234466543 1       12345666776664

HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.

>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []

Probab=92.78  E-value=0.43  Score=36.39  Aligned_cols=45  Identities=29%  Similarity=0.381  Sum_probs=25.5

Q ss_pred             EEEeecCCceEEEEeec----ceeeeeeeeEEccc-----h---hHHHHHHHHhhcc
Q 032585           65 SLGVDLGLSRTGLALSK----GFCVRPLTVLKLRG-----E---KLELQLLEIAQRE  109 (137)
Q Consensus        65 iLGlD~GtKRIGVAVSd----giiAsPL~tI~~~~-----~---~~~~~L~eli~ee  109 (137)
                      |||||-|+.++|.||-+    .+..--.++|+.+.     +   ...+.|.++++++
T Consensus         1 ILGIDPgl~~tG~avi~~~~~~~~~i~~G~I~t~~~~~~~~Rl~~I~~~l~~li~~~   57 (149)
T PF02075_consen    1 ILGIDPGLSNTGYAVIEEDGGKLRLIDYGTIKTSSKDSLPERLKEIYEELEELIEEY   57 (149)
T ss_dssp             EEEEE--SSEEEEEEEEEETTEEEEEEEEEEE---S--HHHHHHHHHHHHHHHHHHH
T ss_pred             CEEECCCCCCeeEEEEEeeCCEEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            79999999999999972    22223344565422     1   2245666666664

RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.

>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC

Probab=85.45  E-value=1.4  Score=34.75  Aligned_cols=45  Identities=18%  Similarity=0.205  Sum_probs=27.9

Q ss_pred             EEEeecCCceEEEEeec----ceeeeeeeeEEccc-------hhHHHHHHHHhhcc
Q 032585           65 SLGVDLGLSRTGLALSK----GFCVRPLTVLKLRG-------EKLELQLLEIAQRE  109 (137)
Q Consensus        65 iLGlD~GtKRIGVAVSd----giiAsPL~tI~~~~-------~~~~~~L~eli~ee  109 (137)
                      +||||-|+.++|.||-+    .+..--.++|....       ....+.|.+++.++
T Consensus         1 ILGIDPGl~~tG~gvi~~~~~~~~~v~~G~I~t~~~~~~~RL~~I~~~l~~~i~~y   56 (156)
T TIGR00228         1 ILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQF   56 (156)
T ss_pred             CEeECcccccccEEEEEecCCeEEEEEeeEEECCCCCHHHHHHHHHHHHHHHHHHh
Confidence            69999999999999952    22223344554322       12345666666664

Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.

>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function

Probab=83.50  E-value=5.3  Score=31.31  Aligned_cols=68  Identities=21%  Similarity=0.242  Sum_probs=47.4

Q ss_pred             ccceEEEeecCCceEEEEeecceeeeeeeeEEccchhHHHHHHHHhhcc---EEEC-CCChhhHHHHHHHHHHHH
Q 032585           61 RGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE---VILG-SYEPQLNLLSKKKLRWFY  131 (137)
Q Consensus        61 ~~gRiLGlD~GtKRIGVAVSdgiiAsPL~tI~~~~~~~~~~L~eli~ee---vVVG-tEgp~A~kVr~FA~rL~~  131 (137)
                      +..-|+|||-|+. +|||+-| +-..+|.+...++ -....+.+|+.++   +||- ...|+-..|++++..+..
T Consensus        30 ~~~lIVGiDPG~t-tgiAild-L~G~~l~l~S~R~-~~~~evi~~I~~~G~PviVAtDV~p~P~~V~Kia~~f~A  101 (138)
T PF04312_consen   30 RRYLIVGIDPGTT-TGIAILD-LDGELLDLKSSRN-MSRSEVIEWISEYGKPVIVATDVSPPPETVKKIARSFNA  101 (138)
T ss_pred             CCCEEEEECCCce-eEEEEEe-cCCcEEEEEeecC-CCHHHHHHHHHHcCCEEEEEecCCCCcHHHHHHHHHhCC
Confidence            4567999999984 8999973 2235665554433 2345677777776   8888 777777888888877654

---

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	Length	Definition	Probability
Query	137
1iv0_A	98	Hypothetical protein; rnaseh-like, YQGF, structura	99.8
1nu0_A	138	Hypothetical protein YQGF; structural genomics, st	99.77
1vhx_A	150	Putative holliday junction resolvase; structural g	99.59
4ep4_A	166	Crossover junction endodeoxyribonuclease RUVC; res	96.47
1hjr_A	158	Holliday junction resolvase (RUVC); site-specific	93.73

>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8

Probab=99.80  E-value=3.9e-20  Score=132.25  Aligned_cols=70  Identities=20%  Similarity=0.105  Sum_probs=62.8

Q ss_pred             ceEEEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHH
Q 032585           63 GFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLR  128 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~r  128 (137)
                      +|+||||||+||||||+||  +++|+|++||.+.+ ..+++.|.+++++|    ||||       +++++++++++|+++
T Consensus         1 mriLglD~G~kriGvAvsd~~~~~A~pl~ti~~~~~~~~~~~l~~li~e~~v~~iVvGlP~~mdGt~~~~~~~~~~f~~~   80 (98)
T 1iv0_A            1 MRVGALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRTDLKESAQAGKVLPLVEA   80 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCSSCCCEEEEECCCHHHHHHHHHHHHHHHTCCEEEEECCCCCCSSSCCCSSTTHHHHHH
T ss_pred             CcEEEEEeCCCEEEEEEEeCCCCeeeeeEEEEccCcHHHHHHHHHHHHHcCCCEEEEeeccCCCCCcCHHHHHHHHHHHH
Confidence            4799999999999999995  88999999997543 45688999999886    9999       999999999999999


Q ss_pred             HHHh
Q 032585          129 WFYY  132 (137)
Q Consensus       129 L~~~  132 (137)
                      |++.
T Consensus        81 L~~~   84 (98)
T 1iv0_A           81 LRAR   84 (98)
T ss_dssp             HHHT
T ss_pred             HhcC
Confidence            9985

>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A

Probab=99.77  E-value=5.1e-19  Score=133.08  Aligned_cols=72  Identities=19%  Similarity=0.201  Sum_probs=63.6

Q ss_pred             ceEEEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHH
Q 032585           63 GFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLR  128 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~r  128 (137)
                      +++||||||+|||||||||  +.+|+|++||.+.+ ..+++.|.++++++    ||||       +++++++++++|+++
T Consensus         3 ~~iLglD~G~kriGvAvsd~~~~~A~pl~ti~~~~~~~~~~~l~~li~e~~v~~iVvGlP~~mdGt~~~~~~~~~~f~~~   82 (138)
T 1nu0_A            3 GTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANR   82 (138)
T ss_dssp             CEEEEEECCSSEEEEEEEETTTTEEEEEEEEEEETTEECHHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCEEEEEEEcCCCCEEeeEEEEEcCCcchHHHHHHHHHHHcCCCEEEEecccCCCcCcCHHHHHHHHHHHH
Confidence            5899999999999999995  78999999998643 34678888888885    9999       999999999999999


Q ss_pred             HHHhcC
Q 032585          129 WFYYCD  134 (137)
Q Consensus       129 L~~~~~  134 (137)
                      |++.++
T Consensus        83 L~~~~~   88 (138)
T 1nu0_A           83 IHGRFG   88 (138)
T ss_dssp             HHHHHC
T ss_pred             HHHHhC
Confidence            998763

>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8

Probab=99.59  E-value=3.1e-15  Score=113.14  Aligned_cols=71  Identities=23%  Similarity=0.259  Sum_probs=63.2

Q ss_pred             ceEEEeecCCceEEEEeec--ceeeeeeeeEEccc---hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHH
Q 032585           63 GFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRG---EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKK  126 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~---~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA  126 (137)
                      +|+||||+|++|||+||+|  +.+++|++||...+   ..+++.|.+++++|    ||||       ++++++.+++.|+
T Consensus         3 mriLGiDpG~~riGvAv~d~~g~~a~p~~~I~~~~~r~~~~~~~l~~li~~~~~~~ivVGlP~~~nGt~~~~~~~ar~f~   82 (150)
T 1vhx_A            3 LRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNMNGTVGPRGEASQTFA   82 (150)
T ss_dssp             EEEEEEEECSSEEEEEEECTTSSSEEEEEEEECBGGGTBCCHHHHHHHHTTSEEEEEEEECCCCBTTBCCHHHHHHHHHH
T ss_pred             CEEEEEEccCCEEEEEEEECCCCEEeeEEEEEcCCcchHHHHHHHHHHHHHcCCCEEEEeeeecCCcchhHHHHHHHHHH
Confidence            6899999999999999995  88999999998543   34688999999996    9999       8999999999999


Q ss_pred             HHHHHhc
Q 032585          127 LRWFYYC  133 (137)
Q Consensus       127 ~rL~~~~  133 (137)
                      ..|.+.+
T Consensus        83 ~~L~~~~   89 (150)
T 1vhx_A           83 KVLETTY   89 (150)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhh
Confidence            9998764

>4ep4_A Crossover junction endodeoxyribonuclease RUVC; resolvase, hydrolase; 1.28A {Thermus thermophilus} PDB: 4ep5_A

Probab=96.47  E-value=0.0072  Score=46.43  Aligned_cols=51  Identities=27%  Similarity=0.411  Sum_probs=33.7

Q ss_pred             ceEEEeecCCceEEEEeec--ce---eeeee--eeEEccc--------hhHHHHHHHHhhcc----EEEC
Q 032585           63 GFSLGVDLGLSRTGLALSK--GF---CVRPL--TVLKLRG--------EKLELQLLEIAQRE----VILG  113 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--gi---iAsPL--~tI~~~~--------~~~~~~L~eli~ee----vVVG  113 (137)
                      +||||||.|+.++|.+|-+  +-   ..+.+  ++|....        ....+.|.++++++    ++|-
T Consensus         1 MrILGIDPGl~~tG~gvi~~~g~~~~~~~~v~~G~I~t~~~~~~~~RL~~I~~~l~~~i~~~~Pd~vaiE   70 (166)
T 4ep4_A            1 MVVAGIDPGITHLGLGVVAVEGKGALKARLLHGEVVKTSPQEPAKERVGRIHARVLEVLHRFRPEAVAVE   70 (166)
T ss_dssp             CEEEEEECCSSEEEEEEEEECSSSSSCEEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHHHHCCSEEEEE
T ss_pred             CEEEEEccccCceEEEEEEecCCccceEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEe
Confidence            5899999999999999973  33   23333  6776432        12346666666664    6665

>1hjr_A Holliday junction resolvase (RUVC); site-specific recombinase; 2.50A {Escherichia coli} SCOP: c.55.3.6

Probab=93.73  E-value=0.13  Score=38.84  Aligned_cols=47  Identities=19%  Similarity=0.227  Sum_probs=29.2

Q ss_pred             ceEEEeecCCceEEEEeec--ceee--eeeeeEEccc-------hhHHHHHHHHhhcc
Q 032585           63 GFSLGVDLGLSRTGLALSK--GFCV--RPLTVLKLRG-------EKLELQLLEIAQRE  109 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--giiA--sPL~tI~~~~-------~~~~~~L~eli~ee  109 (137)
                      +|+||||-|+.++|.||-+  +-..  --.++|+...       ....+.|.+++.++
T Consensus         1 m~ILGIDPGl~~tG~gvi~~~g~~~~~v~~G~i~t~~~~~~~Rl~~i~~~l~~~i~~~   58 (158)
T 1hjr_A            1 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQF   58 (158)
T ss_dssp             CEEEEEECCSSEEEEEEEEEETTEEEEEEEEEEECCCSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEccCCCCeeEEEEEecCCeEEEEEeeEEECCCCCHHHHHHHHHHHHHHHHHHc
Confidence            5899999999999999983  3211  2223454331       12345566666664

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	137
d1iv0a_	98	Hypothetical protein, YqgF homologue {Thermus ther	99.8
d1nu0a_	138	Hypothetical protein YqgF (RuvX) {Escherichia coli	99.75
d1vhxa_	140	Hypothetical protein YrrK (RuvX) {Bacillus subtili	99.71
d1hjra_	158	RuvC resolvase {Escherichia coli [TaxId: 562]}	92.85
d3bzka5	149	Transcriptional accessory factor Tex {Pseudomonas	92.54
d1bupa1	185	Heat shock protein 70kDa, ATPase fragment {Cow (Bo	91.67
d1dkgd1	183	Heat shock protein 70kDa, ATPase fragment {Escheri	90.09
d2ap1a2	117	Putative regulator protein YcfX {Salmonella typhim	83.67
d1jcea1	137	Prokaryotic actin homolog MreB {Thermotoga maritim	83.41
d2aa4a1	119	N-acetylmannosamine kinase NanK {Escherichia coli	81.16
d2gupa1	114	Hypothetical protein SP2142 {Streptococcus pneumon	80.8

>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein, YqgF homologue
species: Thermus thermophilus [TaxId: 274]

Probab=99.80  E-value=2.7e-20  Score=131.19  Aligned_cols=70  Identities=20%  Similarity=0.105  Sum_probs=63.0

Q ss_pred             ceEEEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHH
Q 032585           63 GFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLR  128 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~r  128 (137)
                      +|+||||||+||||||+||  +.+|+|++|+.+.+ ..+++.|.+++++|    ||||       +++++++++++|+++
T Consensus         1 MriLglD~G~kriGiAisd~~~~~a~pl~~i~~~~~~~~~~~l~~ii~e~~i~~iVvGlP~~~dG~~~~~~~~v~~f~~~   80 (98)
T d1iv0a_           1 MRVGALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRTDLKESAQAGKVLPLVEA   80 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCSSCCCEEEEECCCHHHHHHHHHHHHHHHTCCEEEEECCCCCCSSSCCCSSTTHHHHHH
T ss_pred             CcEEEEEcCCCEEEEEEecCCCCeEcceEEEECCCchHHHHHHHHHHHhhccceeEcccccccCCCcCHHHHHHHHHHHH
Confidence            6899999999999999995  88999999998755 35688999999986    9999       899999999999999


Q ss_pred             HHHh
Q 032585          129 WFYY  132 (137)
Q Consensus       129 L~~~  132 (137)
                      |++.
T Consensus        81 L~~~   84 (98)
T d1iv0a_          81 LRAR   84 (98)
T ss_dssp             HHHT
T ss_pred             HhhC
Confidence            9753

>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YqgF (RuvX)
species: Escherichia coli [TaxId: 562]

Probab=99.75  E-value=8.7e-19  Score=129.31  Aligned_cols=72  Identities=19%  Similarity=0.198  Sum_probs=64.5

Q ss_pred             ceEEEeecCCceEEEEeec--ceeeeeeeeEEccch-hHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHH
Q 032585           63 GFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRGE-KLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLR  128 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~~-~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~r  128 (137)
                      ||+||||||+|||||||||  +.+|+|+.|+...+. .+++.|.+++.+|    ||||       +++++++.+++|++.
T Consensus         3 griLgiD~G~kriGvAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~i~~e~~~~~iVvG~P~~~~g~~~~~~~~v~~f~~~   82 (138)
T d1nu0a_           3 GTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANR   82 (138)
T ss_dssp             CEEEEEECCSSEEEEEEEETTTTEEEEEEEEEEETTEECHHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCEEEEEEeCCCCCccccceeeecccchhhHHHHHHHhhccCccEEEeecccccccchHHHHHHHHHHHHH
Confidence            8999999999999999994  889999999997543 4688888888886    9999       899999999999999


Q ss_pred             HHHhcC
Q 032585          129 WFYYCD  134 (137)
Q Consensus       129 L~~~~~  134 (137)
                      |++.++
T Consensus        83 L~~~~~   88 (138)
T d1nu0a_          83 IHGRFG   88 (138)
T ss_dssp             HHHHHC
T ss_pred             HhhccC
Confidence            998763

>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YrrK (RuvX)
species: Bacillus subtilis [TaxId: 1423]

Probab=99.71  E-value=1.5e-17  Score=122.84  Aligned_cols=72  Identities=22%  Similarity=0.254  Sum_probs=63.5

Q ss_pred             ceEEEeecCCceEEEEeec--ceeeeeeeeEEccch---hHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHH
Q 032585           63 GFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRGE---KLELQLLEIAQRE----VILG-------SYEPQLNLLSKKK  126 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~~---~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA  126 (137)
                      +|+||||||+||||||+||  +.+|+|+.||.....   ..+..|.+++++|    ||||       +++++++.+++|+
T Consensus         2 mriLgiD~G~kriGvAisd~~~~~a~pl~~i~~~~~~~~~~~~~l~~ii~e~~i~~iViGlP~~~dg~~~~~~~~~~~f~   81 (140)
T d1vhxa_           2 LRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNMNGTVGPRGEASQTFA   81 (140)
T ss_dssp             EEEEEEEECSSEEEEEEECTTSSSEEEEEEEECBGGGTBCCHHHHHHHHTTSEEEEEEEECCCCBTTBCCHHHHHHHHHH
T ss_pred             ceEEEEEeCCCEEEEEEecCCCCcccceeeEeecccccchHHHHHHHHHHhhccceEEEecccccCCcchhHHHHHHHHH
Confidence            6899999999999999995  889999999975432   2478999999997    9999       8999999999999


Q ss_pred             HHHHHhcC
Q 032585          127 LRWFYYCD  134 (137)
Q Consensus       127 ~rL~~~~~  134 (137)
                      +.|++.++
T Consensus        82 ~~l~~~~~   89 (140)
T d1vhxa_          82 KVLETTYN   89 (140)
T ss_dssp             HHHHHHHC
T ss_pred             HHhccCCC
Confidence            99998753

>d1hjra_ c.55.3.6 (A:) RuvC resolvase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: RuvC resolvase
domain: RuvC resolvase
species: Escherichia coli [TaxId: 562]

Probab=92.85  E-value=0.084  Score=37.58  Aligned_cols=45  Identities=20%  Similarity=0.215  Sum_probs=27.5

Q ss_pred             EEEeecCCceEEEEeec--cee--eeeeeeEEccch-------hHHHHHHHHhhcc
Q 032585           65 SLGVDLGLSRTGLALSK--GFC--VRPLTVLKLRGE-------KLELQLLEIAQRE  109 (137)
Q Consensus        65 iLGlD~GtKRIGVAVSd--gii--AsPL~tI~~~~~-------~~~~~L~eli~ee  109 (137)
                      |||||-|+.++|.||-+  +-.  .--.++|+....       ...+.|.+++.++
T Consensus         3 ILGIDPGl~~~G~avid~~~~~~~~v~~g~i~t~~~~~~~Rl~~i~~~l~~li~~~   58 (158)
T d1hjra_           3 ILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQF   58 (158)
T ss_dssp             EEEEECCSSEEEEEEEEEETTEEEEEEEEEEECCCSCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEccCCCceEEEEEEeeCCEEEEEEeeEEeCCCCChHHHHHHHHHHHHHHHhcc
Confidence            79999999999999963  211  112245553221       2345666777664

>d3bzka5 c.55.3.13 (A:325-473) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Tex RuvX-like domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.54  E-value=0.39  Score=34.24  Aligned_cols=71  Identities=13%  Similarity=0.090  Sum_probs=47.0

Q ss_pred             ccceEEEeecC-CceEEEEeec--ceeeeeeeeEEc-----cchhHHHHHHHHhhcc----EEECCCChhhHHHHHHHHH
Q 032585           61 RGGFSLGVDLG-LSRTGLALSK--GFCVRPLTVLKL-----RGEKLELQLLEIAQRE----VILGSYEPQLNLLSKKKLR  128 (137)
Q Consensus        61 ~~gRiLGlD~G-tKRIGVAVSd--giiAsPL~tI~~-----~~~~~~~~L~eli~ee----vVVGtEgp~A~kVr~FA~r  128 (137)
                      .+.++||||-| .-=.++|+-|  |-.-- ..+|..     +.+...+.|.++++++    ||||..+ .++.+++|...
T Consensus         3 ~~~~vlg~DPg~r~gck~AvlD~~G~vld-~~viyp~~~~~~~~~a~~~l~~li~k~~p~vIaIGNgT-asre~~~~v~~   80 (149)
T d3bzka5           3 GPRATLGLDPGLRTGVKVAVVDATGKLLD-TATVYPHAPKNQWDQTLAVLAALCAKHQVELIAIGNGT-ASRETDKLAGE   80 (149)
T ss_dssp             CSCCEEEEECCSTTCEEEEEECTTSCEEE-EEEECCSTTTCCHHHHHHHHHHHHHHTTCCEEEEESST-THHHHHHHHHH
T ss_pred             CCceEEEECCCcccccEEEEECCCCCEEE-EEEEecCCcHHHHHHHHHHHHHHHHHcCCeEEEECCCc-cHHHHHHHHHH
Confidence            46799999999 5668899884  32221 234421     1123456788888886    8899333 46888888888


Q ss_pred             HHHhc
Q 032585          129 WFYYC  133 (137)
Q Consensus       129 L~~~~  133 (137)
                      |-+..
T Consensus        81 l~~~~   85 (149)
T d3bzka5          81 LIKKY   85 (149)
T ss_dssp             HHHHC
T ss_pred             HHHhC
Confidence            87654

>d1bupa1 c.55.1.1 (A:4-188) Heat shock protein 70kDa, ATPase fragment {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: Actin/HSP70
domain: Heat shock protein 70kDa, ATPase fragment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.67  E-value=0.042  Score=38.91  Aligned_cols=18  Identities=28%  Similarity=0.540  Sum_probs=17.0

Q ss_pred             ceEEEeecCCceEEEEee
Q 032585           63 GFSLGVDLGLSRTGLALS   80 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVS   80 (137)
                      |.++||||||..+.||+.
T Consensus         1 g~vvGIDfGTt~s~va~~   18 (185)
T d1bupa1           1 GPAVGIDLGSTYSCVGVF   18 (185)
T ss_dssp             CCCEEEEECSSEEEEEEE
T ss_pred             CCEEEEEcChhcEEEEEE
Confidence            679999999999999998

>d1dkgd1 c.55.1.1 (D:3-185) Heat shock protein 70kDa, ATPase fragment {Escherichia coli, gene dnaK [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: Actin/HSP70
domain: Heat shock protein 70kDa, ATPase fragment
species: Escherichia coli, gene dnaK [TaxId: 562]

Probab=90.09  E-value=0.062  Score=37.88  Aligned_cols=17  Identities=29%  Similarity=0.556  Sum_probs=15.9

Q ss_pred             eEEEeecCCceEEEEee
Q 032585           64 FSLGVDLGLSRTGLALS   80 (137)
Q Consensus        64 RiLGlD~GtKRIGVAVS   80 (137)
                      |++||||||..+.||+.
T Consensus         1 ~VvGIDfGTt~s~va~~   17 (183)
T d1dkgd1           1 KIIGIDLGTTNSCVAIM   17 (183)
T ss_dssp             CCCEEECCSSEEEEEEE
T ss_pred             CEEEEEcChhcEEEEEE
Confidence            68999999999999987

>d2ap1a2 c.55.1.10 (A:1-117) Putative regulator protein YcfX {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: Putative regulator protein YcfX
species: Salmonella typhimurium [TaxId: 90371]

Probab=83.67  E-value=0.87  Score=28.92  Aligned_cols=17  Identities=24%  Similarity=0.444  Sum_probs=15.5

Q ss_pred             EEEeecCCceEEEEeec
Q 032585           65 SLGVDLGLSRTGLALSK   81 (137)
Q Consensus        65 iLGlD~GtKRIGVAVSd   81 (137)
                      |+|||+|...|=+|+.|
T Consensus         2 yiGiDiGgT~i~~~l~d   18 (117)
T d2ap1a2           2 YYGFDIGGTKIALGVFD   18 (117)
T ss_dssp             EEEEEECSSEEEEEEEE
T ss_pred             EEEEEECcceEEEEEEe
Confidence            69999999999999983

>d1jcea1 c.55.1.1 (A:4-140) Prokaryotic actin homolog MreB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: Actin/HSP70
domain: Prokaryotic actin homolog MreB
species: Thermotoga maritima [TaxId: 2336]

Probab=83.41  E-value=0.34  Score=32.24  Aligned_cols=18  Identities=33%  Similarity=0.471  Sum_probs=16.0

Q ss_pred             eEEEeecCCceEEEEeec
Q 032585           64 FSLGVDLGLSRTGLALSK   81 (137)
Q Consensus        64 RiLGlD~GtKRIGVAVSd   81 (137)
                      |.+||||||..+-||+-+
T Consensus         1 ~~iGIDlGTtns~va~~~   18 (137)
T d1jcea1           1 KDIGIDLGTANTLVFLRG   18 (137)
T ss_dssp             CEEEEEECSSEEEEEETT
T ss_pred             CeEEEEcChhhEEEEEeC
Confidence            579999999999999873

>d2aa4a1 c.55.1.10 (A:1-119) N-acetylmannosamine kinase NanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: N-acetylmannosamine kinase NanK
species: Escherichia coli [TaxId: 562]

Probab=81.16  E-value=2.2  Score=27.23  Aligned_cols=46  Identities=20%  Similarity=0.121  Sum_probs=27.7

Q ss_pred             ceEEEeecCCceEEEEeec---ceeeeeeeeEEc-cc-hhHHHHHHHHhhc
Q 032585           63 GFSLGVDLGLSRTGLALSK---GFCVRPLTVLKL-RG-EKLELQLLEIAQR  108 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd---giiAsPL~tI~~-~~-~~~~~~L~eli~e  108 (137)
                      +.+||||+|...|=+|+.|   .+..+--.-.+. .. +...+.+.+++++
T Consensus         1 M~~lgiDiGgT~i~~~l~d~~G~i~~~~~~~~~~~~~~~~~~~~i~~~i~~   51 (119)
T d2aa4a1           1 MTTLAIDIGGTKLAAALIGADGQIRDRRELPTPASQTPEALRDALSALVSP   51 (119)
T ss_dssp             CCEEEEEECSSEEEEEEECTTCCEEEEEEEECCSSCCHHHHHHHHHHHHTT
T ss_pred             CeEEEEEeCcCEEEEEEEcCCCCEEEeEEEeccccCcHHHHHHHHHHHHHH
Confidence            4689999999999999984   333311111111 11 2345677777766

>d2gupa1 c.55.1.10 (A:1-114) Hypothetical protein SP2142 {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: Hypothetical protein SP2142
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=80.80  E-value=1.6  Score=28.19  Aligned_cols=45  Identities=16%  Similarity=0.028  Sum_probs=28.9

Q ss_pred             ceEEEeecCCceEEEEeec---ceeeeeeeeEEccc--hhHHHHHHHHhhcc
Q 032585           63 GFSLGVDLGLSRTGLALSK---GFCVRPLTVLKLRG--EKLELQLLEIAQRE  109 (137)
Q Consensus        63 gRiLGlD~GtKRIGVAVSd---giiAsPL~tI~~~~--~~~~~~L~eli~ee  109 (137)
                      +.++|||+|...|=+|+.+   .+..+  ..++...  ++..+.|.+.+.++
T Consensus         1 M~i~~iDiGgT~i~~~l~d~~g~i~~~--~~~~t~~~~~~~~~~i~~~~~~~   50 (114)
T d2gupa1           1 MTIATIDIGGTGIKFASLTPDGKILDK--TSISTPENLEDLLAWLDQRLSEQ   50 (114)
T ss_dssp             CCEEEEEEETTEEEEEEECTTCCEEEE--EEECCCSSHHHHHHHHHHHHTTS
T ss_pred             CeEEEEEeCcccEEEEEEcCCCCEEEE--EEEcccccHHHHHHHHHHHhhhc
Confidence            5789999999999999994   33332  2232211  34456677776664