Citrus Sinensis ID: 037858

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
Protein Sequence
MKGSLTTLCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVHPNPVSYS
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEHHHHHHccccccEEEEEEEcccccccccEEEEEEEEEccEEEEEEEEccEEEEEEcccccEEEEcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHccccEEEEEEEccccccccccEEEEEEEEccEEEEEEEEEccEEEEEcccccEEcccccccccccccc
Coil and Loop (DISEMBL)
MKGSLTTLCVGFLCGLVIYKIFKRiadddvvsdaetsdhtVTVSVANRLEelyggtayvglripdpetrslqniDIVLVKNGEEVVISVKNFSGlvsinndgswvcmgeavhpnpvsys
Flexible Loop (DISEMBL)
MKGSLTTLCVGFLCGLVIYKIFKRIADDDVVsdaetsdhtvtvsvanrleelyGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEavhpnpvsys
Low Complexity Region (SEG)
MKGSLTTLCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVHPNPVSYS
Disordered region (IsUnstruct)
****LTTLCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAV********
Disordered Region (DISOPRED)
***SLTTLCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDP**RSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVC*************
Disordered Region (DISEMBL)
MKGSLTTLCVGFLCGLVIYKIFKRIADDDV*********TVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVHPNPVSYS
Disordered Region (DISPRO)
***SLTTLCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAV*P******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKGSLTTLCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVHPNPVSYS
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	119
255558079	325	conserved hypothetical protein [Ricinus	0.932	0.341	0.589	1e-29
297840839	319	hypothetical protein ARALYDRAFT_475506 [	0.924	0.344	0.565	2e-29
15220924	319	uncharacterized protein [Arabidopsis tha	0.924	0.344	0.565	2e-29
6227000	259	EST gb|AI998705 comes from this gene, pa	0.924	0.424	0.565	3e-29
110736720	182	hypothetical protein [Arabidopsis thalia	0.924	0.604	0.565	6e-29
224124124	323	predicted protein [Populus trichocarpa]	0.873	0.321	0.581	2e-26
388508826	329	unknown [Lotus japonicus]	0.915	0.331	0.508	1e-25
357481063	322	hypothetical protein MTR_5g007360 [Medic	0.890	0.329	0.513	2e-24
225454722	322	PREDICTED: uncharacterized protein LOC10	0.924	0.341	0.504	2e-24
449460696	321	PREDICTED: uncharacterized protein LOC10	0.907	0.336	0.539	7e-24

>gi|255558079|ref|XP_002520068.1| conserved hypothetical protein [Ricinus communis] gi|223540832|gb|EEF42392.1| conserved hypothetical protein [Ricinus communis]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 69/117 (58%), Positives = 83/117 (70%), Gaps = 6/117 (5%)

Query: 8   LCVGFLCGLVIYKIFK-RIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDP 66
           + V  LCGL+ YK+F+   +D D V + E+SD T   +VANRLE+LYGG  YVGLRIPD 
Sbjct: 1   MWVEILCGLIAYKLFRCFFSDSDDVLELESSDTTALFNVANRLEKLYGGKVYVGLRIPDA 60

Query: 67  ETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAV-----HPNPVSY 118
           +T S QN+D+VLV  GE VVISVKNFSGLVSI  DGSWVC G        HP+PVS+
Sbjct: 61  DTGSRQNVDMVLVTKGEAVVISVKNFSGLVSITGDGSWVCEGHGKHKPEHHPDPVSH 117

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297840839|ref|XP_002888301.1| hypothetical protein ARALYDRAFT_475506 [Arabidopsis lyrata subsp. lyrata] gi|297334142|gb|EFH64560.1| hypothetical protein ARALYDRAFT_475506 [Arabidopsis lyrata subsp. lyrata]

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 65/115 (56%), Positives = 83/115 (72%), Gaps = 5/115 (4%)

Query: 8   LCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPE 67
           + +  +CGLVIYK+ +R   DD  SD ETSD T   SVA+RLE+LYGG AYVGLRIPD +
Sbjct: 1   MWIEIICGLVIYKLVRRFFYDDEFSDVETSDSTALFSVAHRLEKLYGGKAYVGLRIPDAD 60

Query: 68  TRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVH-----PNPVS 117
           T S Q+ID+VLV  GE VVI+VKN SG+V++ +DGSWVC G   H     P+P++
Sbjct: 61  TASRQDIDVVLVTKGEIVVIAVKNLSGIVTVTSDGSWVCEGGKHHTTESFPDPLA 115

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15220924|ref|NP_176682.1| uncharacterized protein [Arabidopsis thaliana] gi|53828515|gb|AAU94367.1| At1g65020 [Arabidopsis thaliana] gi|55167914|gb|AAV43789.1| At1g65020 [Arabidopsis thaliana] gi|332196195|gb|AEE34316.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  132 bits (333), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 65/115 (56%), Positives = 83/115 (72%), Gaps = 5/115 (4%)

Query: 8   LCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPE 67
           + +  +CGLVIYK+ +R   DD  SD ETSD T   SVA+RLE+LYGG AYVGLRIPD +
Sbjct: 1   MWIEIICGLVIYKLVRRFFYDDEFSDVETSDSTALFSVAHRLEKLYGGKAYVGLRIPDAD 60

Query: 68  TRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVH-----PNPVS 117
           T S Q+ID+VLV  G+ VVISVKN SG+V++ +DGSWVC G   H     P+P++
Sbjct: 61  TASRQDIDVVLVTKGDVVVISVKNLSGIVTVTSDGSWVCEGGKHHTTETFPDPLA 115

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6227000|gb|AAF06036.1|AC009360_1 EST gb|AI998705 comes from this gene, partial [Arabidopsis thaliana]

 Score =  132 bits (331), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 65/115 (56%), Positives = 83/115 (72%), Gaps = 5/115 (4%)

Query: 8   LCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPE 67
           + +  +CGLVIYK+ +R   DD  SD ETSD T   SVA+RLE+LYGG AYVGLRIPD +
Sbjct: 1   MWIEIICGLVIYKLVRRFFYDDEFSDVETSDSTALFSVAHRLEKLYGGKAYVGLRIPDAD 60

Query: 68  TRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVH-----PNPVS 117
           T S Q+ID+VLV  G+ VVISVKN SG+V++ +DGSWVC G   H     P+P++
Sbjct: 61  TASRQDIDVVLVTKGDVVVISVKNLSGIVTVTSDGSWVCEGGKHHTTETFPDPLA 115

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|110736720|dbj|BAF00323.1| hypothetical protein [Arabidopsis thaliana]

 Score =  131 bits (329), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 65/115 (56%), Positives = 83/115 (72%), Gaps = 5/115 (4%)

Query: 8   LCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPE 67
           + +  +CGLVIYK+ +R   DD  SD ETSD T   SVA+RLE+LYGG AYVGLRIPD +
Sbjct: 1   MWIEIICGLVIYKLVRRFFYDDEFSDVETSDSTALFSVAHRLEKLYGGKAYVGLRIPDAD 60

Query: 68  TRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVH-----PNPVS 117
           T S Q+ID+VLV  G+ VVISVKN SG+V++ +DGSWVC G   H     P+P++
Sbjct: 61  TASRQDIDVVLVTKGDVVVISVKNLSGIVTVTSDGSWVCEGGKHHTTETFPDPLA 115

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124124|ref|XP_002319251.1| predicted protein [Populus trichocarpa] gi|222857627|gb|EEE95174.1| predicted protein [Populus trichocarpa]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 64/110 (58%), Positives = 77/110 (70%), Gaps = 6/110 (5%)

Query: 13  LCGLVIYKIFK-RIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSL 71
           +CGL++YK+ K   +D D V   ++SD     +VAN+LE+LYGG  Y GLRIPD +T S 
Sbjct: 6   VCGLIVYKLCKCFFSDADDVLAVQSSDTNALFNVANKLEKLYGGKVYAGLRIPDADTGSR 65

Query: 72  QNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEA-----VHPNPV 116
           QNIDIVLV  GE VVISVKNFSG VSI+ DGSWVC GE       HP+PV
Sbjct: 66  QNIDIVLVTKGEAVVISVKNFSGFVSISGDGSWVCEGEGRHKSERHPDPV 115

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388508826|gb|AFK42479.1| unknown [Lotus japonicus]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/114 (50%), Positives = 77/114 (67%), Gaps = 5/114 (4%)

Query: 8   LCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPE 67
           +    +CGLVIYK+F+R   DD + D E SD +   SVA+RL++LYGG  +VGLRIPD +
Sbjct: 8   MWAAIICGLVIYKLFRRFMYDDDILDIEGSDSSALFSVADRLKKLYGGKVHVGLRIPDAD 67

Query: 68  TRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVC-----MGEAVHPNPV 116
           + S Q IDIVLV   E  VISVKNFSG+++++ DGSWV        +  HP+PV
Sbjct: 68  SASRQTIDIVLVTKQELAVISVKNFSGILAVHRDGSWVSEKPGKHKQETHPDPV 121

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357481063|ref|XP_003610817.1| hypothetical protein MTR_5g007360 [Medicago truncatula] gi|355512152|gb|AES93775.1| hypothetical protein MTR_5g007360 [Medicago truncatula]

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 57/111 (51%), Positives = 74/111 (66%), Gaps = 5/111 (4%)

Query: 11  GFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRS 70
             +CGL+IYK+FK    DD V D E SD TV  SVANRL++L+GG  +VGLRIPD ++ S
Sbjct: 4   AIICGLIIYKLFKCFFYDDDVLDIEASDSTVLFSVANRLQKLFGGKVFVGLRIPDADSAS 63

Query: 71  LQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVH-----PNPV 116
            Q ID+VL+   E +VISVKNFSG++++  DGSW C     H     P P+
Sbjct: 64  PQTIDLVLLTKRELLVISVKNFSGILTVQGDGSWACEKPGKHKVDRYPEPL 114

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454722|ref|XP_002272266.1| PREDICTED: uncharacterized protein LOC100263053 [Vitis vinifera] gi|297737284|emb|CBI26485.3| unnamed protein product [Vitis vinifera]

 Score =  116 bits (290), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 75/115 (65%), Gaps = 5/115 (4%)

Query: 8   LCVGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPE 67
           +    LCGLVIY++ +    DD V + E +D     SVAN++E+LY G  Y GLRIPD +
Sbjct: 1   MWAELLCGLVIYRVLRYFFSDDDVLEVENTDSGALFSVANKIEKLYDGKVYAGLRIPDAD 60

Query: 68  TRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMG-----EAVHPNPVS 117
           T S +NID+VLV  G  VVISVKNFSG++SI+ DGSWVC          HP+PV+
Sbjct: 61  TGSRENIDMVLVTKGGAVVISVKNFSGIISIDADGSWVCNAGDRHKAERHPDPVA 115

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460696|ref|XP_004148081.1| PREDICTED: uncharacterized protein LOC101217532 [Cucumis sativus] gi|449521866|ref|XP_004167950.1| PREDICTED: uncharacterized protein LOC101224358 [Cucumis sativus]

 Score =  114 bits (285), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 62/115 (53%), Positives = 77/115 (66%), Gaps = 7/115 (6%)

Query: 8   LCVGFLCGLVIYKIFKRI-ADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDP 66
           +    + GL++Y +FK   A DD V + ETSD     +VA+R E+LYGG AYVGLRIPD 
Sbjct: 1   MWFAIVGGLIVYGLFKLFFAGDDDVMEVETSDFNAIFAVASRFEKLYGGNAYVGLRIPDA 60

Query: 67  ETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVH-----PNPV 116
           +T S QNID+V+V   E +VISVKN SG VSIN+DGSWVC  +  H     PNPV
Sbjct: 61  DTGSRQNIDLVVVTKEELLVISVKNLSGFVSINSDGSWVC-DDGKHKAKTLPNPV 114

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	119
TAIR|locus:2014983	319	AT1G65020 "AT1G65020" [Arabido	0.865	0.322	0.611	3.4e-29

TAIR|locus:2014983 AT1G65020 "AT1G65020" [Arabidopsis thaliana (taxid:3702)]

 Score = 324 (119.1 bits), Expect = 3.4e-29, P = 3.4e-29
 Identities = 63/103 (61%), Positives = 77/103 (74%)

Query:    10 VGFLCGLVIYKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETR 69
             +  +CGLVIYK+ +R   DD  SD ETSD T   SVA+RLE+LYGG AYVGLRIPD +T 
Sbjct:     3 IEIICGLVIYKLVRRFFYDDEFSDVETSDSTALFSVAHRLEKLYGGKAYVGLRIPDADTA 62

Query:    70 SLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGEAVH 112
             S Q+ID+VLV  G+ VVISVKN SG+V++ +DGSWVC G   H
Sbjct:    63 SRQDIDVVLVTKGDVVVISVKNLSGIVTVTSDGSWVCEGGKHH 105


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        0.317   0.136   0.397    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      119       119   0.00091  102 3  11 22  0.38    31
                                                     29  0.47    32


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:  560 (60 KB)
  Total size of DFA:  119 KB (2078 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:  12.67u 0.14s 12.81t   Elapsed:  00:00:00
  Total cpu time:  12.67u 0.14s 12.81t   Elapsed:  00:00:00
  Start:  Fri May 10 03:39:48 2013   End:  Fri May 10 03:39:48 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

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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

Fail to connect to STRING server

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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	119
pfam08378	107	pfam08378, NERD, Nuclease-related domain	0.002

>gnl|CDD|219813 pfam08378, NERD, Nuclease-related domain

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 45  VANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSW 104
           VA  L +L     YV L I          ID +++      VI VKN+SG +  + DG W
Sbjct: 9   VAKFLGKLLPDNYYVLLLIDRG--GGTAEIDHLVISPKGIFVIEVKNYSGWIFGDEDGKW 66

The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing. Length = 107

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	119
PF08378	115	NERD: Nuclease-related domain; InterPro: IPR011528	99.64
cd00523	123	archeal_HJR Holliday junction resolvases (HJRs) ar	94.41
PF01870	88	Hjc: Archaeal holliday junction resolvase (hjc); I	93.44
PRK14684	120	hypothetical protein; Provisional	93.06
PRK14686	119	hypothetical protein; Provisional	93.05
TIGR00252	119	conserved hypothetical protein TIGR00252. the scor	92.78
PRK14677	107	hypothetical protein; Provisional	92.74
PRK14676	117	hypothetical protein; Provisional	92.64
PRK14679	128	hypothetical protein; Provisional	92.53
PRK14688	121	hypothetical protein; Provisional	92.22
PRK14675	125	hypothetical protein; Provisional	92.14
PRK14689	124	hypothetical protein; Provisional	92.04
PRK14674	133	hypothetical protein; Provisional	91.92
PRK12497	119	hypothetical protein; Reviewed	91.76
PRK14680	134	hypothetical protein; Provisional	91.44
PRK14685	177	hypothetical protein; Provisional	91.28
PRK14678	120	hypothetical protein; Provisional	91.23
PHA01753	121	Holliday junction resolvase	91.1
COG1591	137	Holliday junction resolvase - archaeal type [DNA r	91.04
PRK14681	158	hypothetical protein; Provisional	90.86
PF13635	90	DUF4143: Domain of unknown function (DUF4143)	90.69
PRK14682	117	hypothetical protein; Provisional	90.3
PRK14683	122	hypothetical protein; Provisional	89.22
PF02021	93	UPF0102: Uncharacterised protein family UPF0102; I	88.61
PRK14673	137	hypothetical protein; Provisional	87.35
COG0792	114	Predicted endonuclease distantly related to archae	87.15
PF04471	115	Mrr_cat: Restriction endonuclease; InterPro: IPR00	85.81
PRK14687	173	hypothetical protein; Provisional	84.82
PF08011	105	DUF1703: Protein of unknown function (DUF1703); In	84.26
PF03008	100	DUF234: Archaea bacterial proteins of unknown func	82.73

>PF08378 NERD: Nuclease-related domain; InterPro: IPR011528 The nuclease-related domain (NERD) is found in a broad range of bacterial, as well as single archaeal and plant proteins

Probab=99.64  E-value=4.6e-16  Score=107.23  Aligned_cols=76  Identities=29%  Similarity=0.458  Sum_probs=62.1

Q ss_pred             cchhhHHHHH-hhccC--ceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCceeEEEcCCCCeEEecC-CcCCCC
Q 037858           40 TVTVSVANRL-EELYG--GTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGE-AVHPNP  115 (119)
Q Consensus        40 ~~~~~v~~~L-ekl~~--~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~I~~~~dg~W~q~~~-~~~~nP  115 (119)
                      .++-.++++| +.+..  +.+|+|+++|+ ..+...|||+|++|+++|+|||+|||+|.|+.+.+++|.|. + ..++||
T Consensus         4 ~gE~~~~~~L~~~l~~~~~~v~~~i~~~~-~~~~~~eiD~lvi~~~gi~viE~K~~~g~i~~~~~~~w~~~-~~~~~~nP   81 (115)
T PF08378_consen    4 AGEQRVAERLEKHLPDDEYHVFHNIRLPD-PQGGTREIDHLVITPKGIFVIEVKNWSGKIYGDEDGQWFQE-NKKEFKNP   81 (115)
T ss_pred             HHHHHHHHHHHhhCCcCcEEEEeceEEec-cCCCCceeEEEEEeCCEEEEEEEecccceEEEcCCCcEEEc-CCeecCCH
Confidence            4566788889 44444  47999999987 45567899999999999999999999999998776689997 4 478888


Q ss_pred             CC
Q 037858          116 VS  117 (119)
Q Consensus       116 V~  117 (119)
                      +.
T Consensus        82 ~~   83 (115)
T PF08378_consen   82 LE   83 (115)
T ss_pred             HH
Confidence            74

Most NERD-containing proteins have a single domain, sometimes with additional (predicted) transmembrane helices. In a few instances, proteins containing NERD domains have additional domains (mostly involved in DNA processing), such as the HRDC, the UvrD/REP helicase, the DNA-binding C4 zinc finger, or the serine/threonine and tyrosine protein kinases. In all cases in which a NERD domain is present in multidomain proteins, it is found at the N terminus. The NERD domain is predicted to function in DNA processing, and may have a nuclease function [].

>cd00523 archeal_HJR Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination

Probab=94.41  E-value=0.097  Score=38.49  Aligned_cols=49  Identities=27%  Similarity=0.289  Sum_probs=33.9

Q ss_pred             hhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           42 TVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        42 ~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      +=.+++-|++ .|   |.=+|.|...++...|||+|..-++.++.||||-.++
T Consensus         9 E~~a~~~L~~-~G---~~vlR~~~sG~~~~~eiDIIA~~~~~lvfVEVK~r~~   57 (123)
T cd00523           9 ERELVKILEE-KG---FAVVRAPGSGGGPRPLPDIVAGNGGTYLAIEVKSTKK   57 (123)
T ss_pred             HHHHHHHHHh-CC---CEEEEEcCCCCCCCCceeEEEecCCEEEEEEEEecCC
Confidence            3345555665 34   4444776543333459999999999999999997665

HJR's occur in archaea, bacteria, and in the mitochondria of certain eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations.

>PF01870 Hjc: Archaeal holliday junction resolvase (hjc); InterPro: IPR002732 This entry represents Holliday junction resolvases (hjc gene) and related proteins, primarily from archaeal species []

Probab=93.44  E-value=0.1  Score=36.40  Aligned_cols=43  Identities=23%  Similarity=0.277  Sum_probs=31.9

Q ss_pred             HHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           47 NRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        47 ~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      ++|.++.-.++|+-+|.|...+.     |+|-+-++.+++||+|..+.
T Consensus         4 rel~~~L~~~Gf~v~R~~~Sg~~-----DiiA~~~~~~l~IEvKs~~~   46 (88)
T PF01870_consen    4 RELVKILWERGFAVVRAAGSGGG-----DIIAGKGGRYLAIEVKSTSK   46 (88)
T ss_dssp             HHHHHHHHHTT-EEEEBSCCSSS-----SEEEEETTEEEEEEEEEESS
T ss_pred             HHHHHHHHhCCcEEEEecCCCCc-----CEEEECCCEEEEEEEeeccC
Confidence            34444444578999999875432     99999999999999997663

The Holliday junction is an essential intermediate of homologous recombination. Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. In the presence of divalent cations, these junctions exist predominantly as the stacked-X form in which the double-helical segments are coaxially stacked and twisted by 60 degrees in a right-handed direction across the junction cross-over. In this structure, the stacked arms resemble two adjacent double-helices, but are linked at the junction by two common strands that cross-over between the duplexes []. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.; PDB: 2WJ0_A 2WIZ_B 2WIW_B 2WCW_C 2WCZ_A 1HH1_A 1GEF_D 1IPI_B 2EO0_B 1OB9_A ....

>PRK14684 hypothetical protein; Provisional

Probab=93.06  E-value=0.33  Score=35.49  Aligned_cols=43  Identities=19%  Similarity=0.256  Sum_probs=30.9

Q ss_pred             hHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858           44 SVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS   93 (119)
Q Consensus        44 ~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS   93 (119)
                      .++.-|++ .|+.+.+ |.|-|      .+|||+|....+.+..||||--+
T Consensus        15 ~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~R~   58 (120)
T PRK14684         15 TACRYLQK-QGLSFITKNFRYK------QGEIDLIMSDQSMLVFIEVRYRR   58 (120)
T ss_pred             HHHHHHHH-CCCEEEEEEecCC------CCeEEEEEEeCCEEEEEEEeEcC
Confidence            34444544 5666644 77763      35999999999999999999544

>PRK14686 hypothetical protein; Provisional

Probab=93.05  E-value=0.27  Score=35.73  Aligned_cols=43  Identities=28%  Similarity=0.258  Sum_probs=31.4

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      ++.-|++ .|+++.. |.|-+      .+|||+|..-.+.+..||||--++
T Consensus        15 A~~~L~~-~Gy~il~rN~r~~------~GEIDlIa~~~~~lvFVEVKtR~~   58 (119)
T PRK14686         15 AVEFLIK-KGYTILERNYRFQ------KAEIDIIAQKGNILVIVEVKTRSS   58 (119)
T ss_pred             HHHHHHH-CCCEEEEEEecCC------CCcEEEEECcCCEEEEEEEEecCC
Confidence            3444444 5676654 77763      359999999999999999996543

>TIGR00252 conserved hypothetical protein TIGR00252

Probab=92.78  E-value=0.36  Score=35.20  Aligned_cols=43  Identities=21%  Similarity=0.292  Sum_probs=31.0

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      ++.-|++ .|+.+.+ |.|-|      .+|||+|....+.+..||||--++
T Consensus        16 A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~R~~   59 (119)
T TIGR00252        16 ARAWLEQ-KGLKFIAANWNSP------WGEIDLIMHDTKTIAFVEVRTRSG   59 (119)
T ss_pred             HHHHHHH-CCCEEeEEEecCC------CCcEEEEEeeCCEEEEEEEEecCC
Confidence            4444444 5666654 67763      359999999999999999996543

the scores for Mycobacterium tuberculosis and Treponema pallidum are low considering the alignment

>PRK14677 hypothetical protein; Provisional

Probab=92.74  E-value=0.41  Score=34.35  Aligned_cols=40  Identities=28%  Similarity=0.287  Sum_probs=29.6

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecC
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKN   91 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKN   91 (119)
                      ++.-|++ .|+.+.. |.|-|      .+|||+|....+.+..||||-
T Consensus        10 A~~~L~~-~Gy~Il~rN~r~~------~GEIDlIa~~~~~lvFVEVK~   50 (107)
T PRK14677         10 ACKFLKK-KGYKILERNYRTK------YGEIDIVARDGREIVFVEVKS   50 (107)
T ss_pred             HHHHHHH-CCCEEEEEEecCC------CceeeEEEEECCEEEEEEEec
Confidence            4444544 5666644 67764      259999999999999999994

>PRK14676 hypothetical protein; Provisional

Probab=92.64  E-value=0.36  Score=35.12  Aligned_cols=39  Identities=26%  Similarity=0.278  Sum_probs=29.4

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEec
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVK   90 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvK   90 (119)
                      ++.-|++ .|+.+.. |.|-|      .+|||+|....+.+..||||
T Consensus        17 A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVK   56 (117)
T PRK14676         17 VARIYDR-SGRPVAARRWRGV------SGEIDLIAREGAEVIFIEVK   56 (117)
T ss_pred             HHHHHHH-CCCEEeeeecCCC------CCeEEEEEeeCCEEEEEEEe
Confidence            4444554 5676654 67764      35999999999999999999

>PRK14679 hypothetical protein; Provisional

Probab=92.53  E-value=0.38  Score=35.65  Aligned_cols=43  Identities=16%  Similarity=0.139  Sum_probs=30.5

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      ++.-|+ ..|+.+.. |.|-+      .+|||+|.--.+.+..||||--++
T Consensus        25 A~~~L~-~~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVKtR~~   68 (128)
T PRK14679         25 ALLALM-LKGYRPLARRFAAA------GGEIDLIVRRGRTIAFVEVKARAT   68 (128)
T ss_pred             HHHHHH-HCCCEEEeeeccCC------CCeEEEEEEeCCEEEEEEEEecCC
Confidence            344444 35666643 66653      359999999999999999996543

>PRK14688 hypothetical protein; Provisional

Probab=92.22  E-value=0.49  Score=34.66  Aligned_cols=44  Identities=27%  Similarity=0.233  Sum_probs=31.7

Q ss_pred             hHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           44 SVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        44 ~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      .++.-|++ .|+.+.. |.|-|      .+|||+|.-..+.+..||||--++
T Consensus        15 ~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVK~R~~   59 (121)
T PRK14688         15 LAAEYLKG-MGYSIIQTNCRLP------EGEIDIVGQDGEYLVFIEVRTKRR   59 (121)
T ss_pred             HHHHHHHH-CCCEEEEEEeeCC------CCcEeEEEeeCCEEEEEEEEecCC
Confidence            34444544 5666654 77764      359999999999999999995443

>PRK14675 hypothetical protein; Provisional

Probab=92.14  E-value=0.58  Score=34.32  Aligned_cols=49  Identities=16%  Similarity=0.068  Sum_probs=35.6

Q ss_pred             hhHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCceeEEE
Q 037858           43 VSVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSI   98 (119)
Q Consensus        43 ~~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~I~~   98 (119)
                      -.++.-|++ .|+++.. |.|.|      .+|||+|..-.+.+.+||||-.++.-..
T Consensus        16 ~~A~~~L~~-~G~~il~rn~r~~------~GEIDlIa~d~~~lvFVEVK~R~~~~~g   65 (125)
T PRK14675         16 SIAVTYLKG-LRYKIVERNFRCR------CGEIDIIARDGKTLVFVEVKTRKNYAYG   65 (125)
T ss_pred             HHHHHHHHH-CCCEEEEEEEeCC------CCeEEEEEEeCCEEEEEEEEeccCCCCc
Confidence            344555555 5666654 67774      3599999999999999999987765443

>PRK14689 hypothetical protein; Provisional

Probab=92.04  E-value=0.36  Score=35.75  Aligned_cols=43  Identities=23%  Similarity=0.217  Sum_probs=31.0

Q ss_pred             hHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858           44 SVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS   93 (119)
Q Consensus        44 ~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS   93 (119)
                      .++.-|++ .|+.+.+ |.|-+      .+|||+|..-.+.+..||||--+
T Consensus        17 ~Aa~~L~~-~Gy~Il~rN~r~~------~GEIDIIa~~~~~lVFVEVKtR~   60 (124)
T PRK14689         17 RVLRLLQR-RGWRLLDRNWSCR------WGELDLVLEKQQRLLVVEVKGRR   60 (124)
T ss_pred             HHHHHHHH-CCCEEEEEecCCC------CCcccEEeeeCCEEEEEEEEECC
Confidence            34455554 5666654 67763      35999999999999999999543

>PRK14674 hypothetical protein; Provisional

Probab=91.92  E-value=0.52  Score=35.15  Aligned_cols=43  Identities=14%  Similarity=0.172  Sum_probs=31.7

Q ss_pred             hHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858           44 SVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS   93 (119)
Q Consensus        44 ~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS   93 (119)
                      .++.-|++ .|+++.. |.|-|      .+|||+|.-..+.+..||||--+
T Consensus        14 ~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~LVFVEVK~R~   57 (133)
T PRK14674         14 TALKLLKE-QNYEWVASNYHSR------RGEVDLIVKRGNELIFVEVKARG   57 (133)
T ss_pred             HHHHHHHH-CCCEEeEEeeecC------CCCEeEEEEeCCEEEEEEEEecC
Confidence            34444444 6777765 78763      35999999999999999999544

>PRK12497 hypothetical protein; Reviewed

Probab=91.76  E-value=0.5  Score=34.06  Aligned_cols=45  Identities=22%  Similarity=0.203  Sum_probs=32.7

Q ss_pred             hHHHHHhhccCceeE-EEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858           44 SVANRLEELYGGTAY-VGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL   95 (119)
Q Consensus        44 ~v~~~Lekl~~~kiy-~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~   95 (119)
                      -++.-|++ .|+.+. .|.|-|      .+|||+|..-.+.+..||||-.++.
T Consensus        15 ~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~R~~~   60 (119)
T PRK12497         15 LAARYLES-KGLRILARNFRCR------FGEIDLIARDGDTLVFVEVKTRRSD   60 (119)
T ss_pred             HHHHHHHH-CCCEEEcceecCC------CCcEeeeEEeCCEEEEEEEEeccCC
Confidence            34444543 566665 477764      3599999999999999999977654

>PRK14680 hypothetical protein; Provisional

Probab=91.44  E-value=0.61  Score=34.76  Aligned_cols=44  Identities=23%  Similarity=0.185  Sum_probs=31.4

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL   95 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~   95 (119)
                      ++.-|++ .|+.+.. |.|-|      .+|||+|......+..||||-.++.
T Consensus        16 A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVKtR~~~   60 (134)
T PRK14680         16 AAALLQR-TGHRILARNWRHG------GLELDIVCEDGDTIVFVEVKTRAAH   60 (134)
T ss_pred             HHHHHHH-CCCEEEEeecCCC------CCeEEEEEEeCCEEEEEEEEecCCC
Confidence            3444443 5666644 67763      3599999999999999999976654

>PRK14685 hypothetical protein; Provisional

Probab=91.28  E-value=0.55  Score=37.00  Aligned_cols=35  Identities=20%  Similarity=0.254  Sum_probs=26.9

Q ss_pred             cCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858           53 YGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS   93 (119)
Q Consensus        53 ~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS   93 (119)
                      .|+.|.. |.|-|      .+|||+|.-..+.+..||||--+
T Consensus        59 ~Gy~IL~RN~R~~------~GEIDIIA~dg~~LVFVEVKtR~   94 (177)
T PRK14685         59 QGLRPLARNLRCR------AGEIDLAMRDGEVLVLVEVRARA   94 (177)
T ss_pred             CCCEEeEeeecCC------CCcEEEEEecCCEEEEEEEeECC
Confidence            4666644 67764      35999999999999999999543

>PRK14678 hypothetical protein; Provisional

Probab=91.23  E-value=0.59  Score=34.11  Aligned_cols=43  Identities=28%  Similarity=0.283  Sum_probs=30.7

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      ++.-|++ .|+.+.. |.|-|      .+|||+|..-.+.+..||||--++
T Consensus        16 A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVKtR~~   59 (120)
T PRK14678         16 AAAYLER-CGYTIIARNWRCR------AGEIDIVAREGDQLVFVEVRTRRD   59 (120)
T ss_pred             HHHHHHH-CCCEEeeeeecCC------CCCEeeeEEeCCEEEEEEEEECCC
Confidence            3444444 5666643 67763      359999999999999999995543

>PHA01753 Holliday junction resolvase

Probab=91.10  E-value=0.42  Score=35.54  Aligned_cols=52  Identities=29%  Similarity=0.262  Sum_probs=35.5

Q ss_pred             CcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           39 HTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        39 ~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      +..+-.+++-|++    ++|+=++-|-...+...|||+|....+.++.||||--++
T Consensus         8 ~~~E~~a~~~L~~----~G~~il~rn~~~~~~~GEiDIIA~~~~~lvfVEVKtR~~   59 (121)
T PHA01753          8 KYYEYKTLEILES----NGFKALRIPVSGTGKQALPDIIATKNNTIYPIEVKSTSK   59 (121)
T ss_pred             HHHHHHHHHHHHH----CCCEEEEeccccCCCCCCccEEEeeCCEEEEEEEEeCCC
Confidence            3344445556655    456666665443223579999999999999999996554

>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]

Probab=91.04  E-value=0.37  Score=36.70  Aligned_cols=58  Identities=17%  Similarity=0.173  Sum_probs=43.7

Q ss_pred             hhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee-EEEc
Q 037858           42 TVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL-VSIN   99 (119)
Q Consensus        42 ~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~-I~~~   99 (119)
                      +-+..++|-+..-.++|+-+|.|....+++-..|+|-..+..+++||+|--++. |..+
T Consensus         6 G~~~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA~~g~~~l~iE~K~~~~~kiYl~   64 (137)
T COG1591           6 GSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVAGNGGVYLAIEVKSRRETKIYLD   64 (137)
T ss_pred             cchHHHHHHHHHHhcCceEEEcccCCCCCCCCCCEEecCCCEEEEEEEEeccCCcEEEc
Confidence            344556666665568999999998763455579999999999999999965543 6654

>PRK14681 hypothetical protein; Provisional

Probab=90.86  E-value=0.76  Score=35.33  Aligned_cols=43  Identities=28%  Similarity=0.250  Sum_probs=29.9

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeC-CeEEEEEecCCce
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKN-GEEVVISVKNFSG   94 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~-~~IlVIEvKNwSG   94 (119)
                      ++.-|++ .|+++.. |.|-|      .+|||+|..-. +.+..||||--++
T Consensus        53 Aa~~L~~-~Gy~IL~rN~R~~------~GEIDIIa~d~~~~LVFVEVKtR~~   97 (158)
T PRK14681         53 AAAWLEE-HGWTTLSRNWHCR------YGELDIVALNPEYTIVFVEVKTRRS   97 (158)
T ss_pred             HHHHHHH-CCCEEEEEEEeCC------CCcEEEEEEcCCceEEEEEEEeccC
Confidence            3444443 5666654 77763      35999999886 5899999996543

>PF13635 DUF4143: Domain of unknown function (DUF4143)

Probab=90.69  E-value=0.44  Score=32.03  Aligned_cols=48  Identities=25%  Similarity=0.266  Sum_probs=30.4

Q ss_pred             CcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEec
Q 037858           39 HTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVK   90 (119)
Q Consensus        39 ~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvK   90 (119)
                      .-.+--|+.+|.+.... .+. +..=. +..+ .|||+|+-+.+.++.||||
T Consensus        41 ~l~En~V~~eL~~~~~~-~~~-l~y~r-~~~~-~EVDfv~~~~~~~~~IEVK   88 (90)
T PF13635_consen   41 ALFENFVAQELLKRLRE-GYE-LYYWR-DKSG-QEVDFVIENGGRIIPIEVK   88 (90)
T ss_pred             HHHHHHHHHHHHHhcCC-Cce-EEEEE-CCCC-CEEEEEEEeCCEEEEEEEE
Confidence            33445678888877411 111 22211 1123 3999999999999999999

>PRK14682 hypothetical protein; Provisional

Probab=90.30  E-value=1.1  Score=32.62  Aligned_cols=45  Identities=22%  Similarity=0.269  Sum_probs=32.8

Q ss_pred             hHHHHHhhccCceeEE-EEE-ecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858           44 SVANRLEELYGGTAYV-GLR-IPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL   95 (119)
Q Consensus        44 ~v~~~Lekl~~~kiy~-gLR-IPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~   95 (119)
                      .++.-|++ .|+.+.. |.| .|      .+|||+|..-.+.+..||||-.++.
T Consensus        13 ~A~~~L~~-~Gy~Il~rN~r~~~------~GEIDiIa~~~~~lvFVEVKtR~~~   59 (117)
T PRK14682         13 QACKFLHT-QALEILAHNFKALP------YGEIDIIALDKDTLVFIEVKYRSKT   59 (117)
T ss_pred             HHHHHHHH-CCCEEeeeeEECCC------CCcEEEEEeeCCEEEEEEEEecCCC
Confidence            44555555 5666654 777 44      2599999999999999999976643

>PRK14683 hypothetical protein; Provisional

Probab=89.22  E-value=0.54  Score=34.66  Aligned_cols=40  Identities=30%  Similarity=0.183  Sum_probs=28.1

Q ss_pred             HHHHHhhccCcee-EEEEEecCCCCCCceeeeEEEEeCCeEEEEEecC
Q 037858           45 VANRLEELYGGTA-YVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKN   91 (119)
Q Consensus        45 v~~~Lekl~~~ki-y~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKN   91 (119)
                      ++.-|++ .|+.+ =.|.|-      +.+|||+|.--.+.+..||||-
T Consensus        23 A~~~L~~-~Gy~Il~rN~r~------~~GEIDIIa~~~~~lVFVEVKt   63 (122)
T PRK14683         23 IILFLKC-KLYHIIKHRYRC------PLGEIDIIAHKNKQLVFIEVKT   63 (122)
T ss_pred             HHHHHHH-CCCEEEeeecCC------CCCcEEEEEEeCCEEEEEEEee
Confidence            3444444 45544 344554      3469999999999999999994

>PF02021 UPF0102: Uncharacterised protein family UPF0102; InterPro: IPR003509 The proteins in this entry are functionally uncharacterised

Probab=88.61  E-value=2.4  Score=29.35  Aligned_cols=46  Identities=26%  Similarity=0.175  Sum_probs=30.1

Q ss_pred             HHHHHhhccCcee-EEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCceeEE
Q 037858           45 VANRLEELYGGTA-YVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVS   97 (119)
Q Consensus        45 v~~~Lekl~~~ki-y~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~I~   97 (119)
                      ++.-|++ .|+.+ =.|.|-|.      +|||+|....+.+..||||=.++.-.
T Consensus         6 A~~~L~~-~G~~IL~rN~r~~~------GEIDiIa~~~~~lvfVEVK~R~~~~~   52 (93)
T PF02021_consen    6 AARYLER-KGYRILERNWRCRR------GEIDIIARDGDTLVFVEVKTRSSSSF   52 (93)
T ss_dssp             HHHHHHH-TT-EEEEEEEEETT------EEEEEEEEETTEEEEEEEEE------
T ss_pred             HHHHHHH-CCCEEeeeeecCCC------CcEeEEEEEcccEEEEEEEEeecccc
Confidence            3444554 56655 56788843      59999999999999999998776544

; PDB: 3FOV_A.

>PRK14673 hypothetical protein; Provisional

Probab=87.35  E-value=0.61  Score=35.09  Aligned_cols=43  Identities=19%  Similarity=0.186  Sum_probs=29.7

Q ss_pred             HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCC-eEEEEEecCCce
Q 037858           45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNG-EEVVISVKNFSG   94 (119)
Q Consensus        45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~-~IlVIEvKNwSG   94 (119)
                      ++.-|++ .|+.+.. |.|-|      .+|||+|.--++ .+..||||--++
T Consensus        36 A~~~L~~-~Gy~IL~rN~r~~------~GEIDLIa~~~~~~lVFVEVKtR~~   80 (137)
T PRK14673         36 ALAFLQR-AGLALVARNYRCR------GGEIDLVMRERDGTLVFVEVRARAS   80 (137)
T ss_pred             HHHHHHH-CCCEEeEeEecCC------CCccCHHHccCCcEEEEEEEEeCCC
Confidence            3444443 5666654 67763      359999988766 888999996543

>COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=87.15  E-value=0.64  Score=34.14  Aligned_cols=25  Identities=20%  Similarity=0.206  Sum_probs=21.6

Q ss_pred             ceeeeEEEEeCCeEEEEEecCCcee
Q 037858           71 LQNIDIVLVKNGEEVVISVKNFSGL   95 (119)
Q Consensus        71 ~~EIDlVIVT~~~IlVIEvKNwSG~   95 (119)
                      .+|||+|.--.+-|..||||--++.
T Consensus        32 ~GEIDlIa~~~~~ivFVEVK~R~~~   56 (114)
T COG0792          32 YGEIDLIARDGDTVVFVEVKYRRND   56 (114)
T ss_pred             CCceEEEEecCCEEEEEEEEeeccC
Confidence            3599999999999999999976654

>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV

Probab=85.81  E-value=1.6  Score=28.89  Aligned_cols=39  Identities=21%  Similarity=0.409  Sum_probs=22.7

Q ss_pred             eEEEEEecCCCCCCceeeeEEEEeCC---eEEEEEecCCceeEE
Q 037858           57 AYVGLRIPDPETRSLQNIDIVLVKNG---EEVVISVKNFSGLVS   97 (119)
Q Consensus        57 iy~gLRIPd~~~~~~~EIDlVIVT~~---~IlVIEvKNwSG~I~   97 (119)
                      .|.+++....  ++...+|+++-...   .-++||.|+|++.+.
T Consensus        21 g~~~v~~~~~--~~d~giDi~~~~~~~~~~~~~vqcK~~~~~v~   62 (115)
T PF04471_consen   21 GYTDVEVTGG--SGDGGIDIIAEKDDLGKERILVQCKRYKKKVD   62 (115)
T ss_dssp             T-EEEEEE-S--SSEEEEEEEEEETT---EEEEEEE---S-EE-
T ss_pred             CCccEEEecc--CCCCCEEEEEEEcccCceEEEEEEEEeccccc
Confidence            3446666432  24468999988754   688999999987655

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.

>PRK14687 hypothetical protein; Provisional

Probab=84.82  E-value=1.1  Score=35.18  Aligned_cols=46  Identities=20%  Similarity=0.301  Sum_probs=29.2

Q ss_pred             hhhHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCC----eEEEEEecCCc
Q 037858           42 TVSVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNG----EEVVISVKNFS   93 (119)
Q Consensus        42 ~~~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~----~IlVIEvKNwS   93 (119)
                      +--++.-|++ .|+.+.+ |.|-+     ..+|||+|...++    .+..||||--+
T Consensus        37 E~~Aa~~L~~-kGy~IL~RN~R~~-----r~GEIDIIA~d~~~~~~~LVFVEVKtR~   87 (173)
T PRK14687         37 EQLACEFLQE-QGLILIARNWQQP-----KVGELDLVMLEKGQAWSTLVFAEVRQRK   87 (173)
T ss_pred             HHHHHHHHHH-CCCEEeeecccCC-----CCccEEEEEecCCCCCCEEEEEEEeECC
Confidence            3334444544 4555543 56642     2359999998774    89999999544

>PF08011 DUF1703: Protein of unknown function (DUF1703); InterPro: IPR012547 This family contains many hypothetical bacterial proteins

Probab=84.26  E-value=1.3  Score=30.72  Aligned_cols=21  Identities=29%  Similarity=0.295  Sum_probs=18.9

Q ss_pred             CceeeeEEEE----eCCeEEEEEec
Q 037858           70 SLQNIDIVLV----KNGEEVVISVK   90 (119)
Q Consensus        70 ~~~EIDlVIV----T~~~IlVIEvK   90 (119)
                      +.+-+|+++.    +...++|+|+|
T Consensus        29 ~~Gr~Dl~l~~~~~~~~~~~IiElK   53 (105)
T PF08011_consen   29 GKGRIDLVLEPPKPTPKYIYIIELK   53 (105)
T ss_pred             CCCeEEEEEEEccCCCCeEEEEEEE
Confidence            4457999999    99999999999

>PF03008 DUF234: Archaea bacterial proteins of unknown function; InterPro: IPR004256 This represents a C-terminal domain of unknown function, usually fused to a prokaryotic putative DEXX-box ATPase domain (IPR011579 from INTERPRO) []

Probab=82.73  E-value=1.6  Score=30.10  Aligned_cols=23  Identities=26%  Similarity=0.173  Sum_probs=19.8

Q ss_pred             ceeeeEEEEeCCe--EEEEEecCCc
Q 037858           71 LQNIDIVLVKNGE--EVVISVKNFS   93 (119)
Q Consensus        71 ~~EIDlVIVT~~~--IlVIEvKNwS   93 (119)
                      ..|||+|.+..++  +++.|+|--+
T Consensus        67 ~~EIDiva~~~~~~~~~~gEcKw~~   91 (100)
T PF03008_consen   67 NEEIDIVAVDEDGKRILFGECKWTN   91 (100)
T ss_pred             CccEEEEEECCCCCEEEEEEEEeCC
Confidence            3499999999999  9999999543

---

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	119
1y88_A	199	Hypothetical protein AF1548; APC5567, structural g	94.48
1ob8_A	135	Holliday-junction resolvase; hydrolase, enzyme, ho	93.31
2wcw_A	139	HJC; type II restriction endonuclease, hydrolase,	92.08
1hh1_A	143	Holliday junction resolving enzyme HJC; holliday j	91.04
2eo0_A	147	Hypothetical protein ST1444; holliday junction res	90.42
3fov_A	134	UPF0102 protein RPA0323; structural genomics, APC7	89.96
1gef_A	123	Holliday junction resolvase; HJC, hydrolase; 2.00A	88.12

>1y88_A Hypothetical protein AF1548; APC5567, structural genomics, protein structure INIT PSI, midwest center for structural genomics center, MCSG; 1.85A {Archaeoglobus fulgidus} SCOP: a.60.4.3 c.52.1.30

Probab=94.48  E-value=0.11  Score=39.94  Aligned_cols=47  Identities=30%  Similarity=0.323  Sum_probs=36.0

Q ss_pred             hHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858           44 SVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS   93 (119)
Q Consensus        44 ~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS   93 (119)
                      -++.-|++ .|+.+..+.++.-  ..+.+|||+|.-..+.+++||+|.|+
T Consensus        23 ~va~~L~~-~Gy~i~~~v~v~~--r~~dggIDIIA~k~~~~v~VEvK~r~   69 (199)
T 1y88_A           23 MVARLLEE-HGFETKTNVIVQG--NCVEQEIDVVAERDGERYMIECKFHN   69 (199)
T ss_dssp             HHHHHHHT-TTCEEEEEEEEEC--SSSEEEEEEEEEETTEEEEEEECCCS
T ss_pred             HHHHHHHH-CCCEEEEeecccC--CCCCCcEEEEEEECCEEEEEEecccc
Confidence            46666766 4677776666643  23567999999999999999999998

>1ob8_A Holliday-junction resolvase; hydrolase, enzyme, homologous recombination, holliday junction resolving enzyme, nuclease, archaea; 1.8A {Sulfolobus solfataricus} SCOP: c.52.1.18 PDB: 1ob9_A

Probab=93.31  E-value=0.094  Score=38.13  Aligned_cols=50  Identities=22%  Similarity=0.166  Sum_probs=32.9

Q ss_pred             chhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           41 VTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        41 ~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      .+=.+++-|++. |..+.   |-|....++..|||+|....+.++.||||--++
T Consensus         9 ~E~~A~~~L~~~-G~~il---r~~~~g~~~~gEiDIIA~~g~~lVfVEVKtR~~   58 (135)
T 1ob8_A            9 AERELVSILRGE-GFNAV---RIPTSNSSPNPLPDIFATKGNTLLSIECKSTWE   58 (135)
T ss_dssp             HHHHHHHHHHHT-TCEEE---ECCC-----CCSCSEEEEETTEEEEEEEEEESS
T ss_pred             HHHHHHHHHHHC-CCEEE---EEcccCCCCCCCceEEEeECCEEEEEEEEEcCC
Confidence            344566777775 44554   555322335569999999999999999995554

>2wcw_A HJC; type II restriction endonuclease, hydrolase, DNA binding protein, holliday junction resolvase; 1.58A {Archaeoglobus fulgidus} PDB: 2wcz_A 2wiw_A 2wiz_A 2wj0_A

Probab=92.08  E-value=0.12  Score=37.61  Aligned_cols=49  Identities=16%  Similarity=0.157  Sum_probs=34.8

Q ss_pred             hhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           42 TVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        42 ~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      +=.+++.|++.    +|.=+|.|........|||+|....+.++.||||--++
T Consensus        12 E~~a~~~L~~~----Gy~ilR~~~sg~~~~~eiDIIA~~~~~lv~IEVKtr~~   60 (139)
T 2wcw_A           12 ERDLLVELWKA----GFAAIRVAGAGVSPFPCPDIVAGNGRTYLAIEVKMRKE   60 (139)
T ss_dssp             HHHHHHHHHHT----TCEEEEBTTSSSCSSCCCSEEEECSSCEEEEEEEECSS
T ss_pred             HHHHHHHHHhC----CcEEEEecCCCCCCCCCCCEEEeECCEEEEEEEEECCC
Confidence            34456666653    44445667665445669999999999999999996554

>1hh1_A Holliday junction resolving enzyme HJC; holliday junction resolvase, homologous recombination, nuclease domain, archaea; 2.15A {Sulfolobus solfataricus} SCOP: c.52.1.18

Probab=91.04  E-value=0.29  Score=35.72  Aligned_cols=53  Identities=26%  Similarity=0.376  Sum_probs=33.2

Q ss_pred             CcchhhHHHHHhhccCceeEEEEEecCCC-CCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858           39 HTVTVSVANRLEELYGGTAYVGLRIPDPE-TRSLQNIDIVLVKNGEEVVISVKNFSGL   95 (119)
Q Consensus        39 ~~~~~~v~~~Lekl~~~kiy~gLRIPd~~-~~~~~EIDlVIVT~~~IlVIEvKNwSG~   95 (119)
                      +..+=.+++-|++. |..+.   |-|-.. .....|||+|....+.++.||||--++.
T Consensus         9 ~~~E~~a~~~L~~~-G~~il---r~~~sg~~~~~gEiDIIA~~~~~lvfVEVK~R~~~   62 (143)
T 1hh1_A            9 SAVERNIVSRLRDK-GFAVV---RAPASGSKRKDPIPDIIALKNGVIILIEMKSRKDI   62 (143)
T ss_dssp             CHHHHHHHHHHHHT-TCEEE---ECCC-------CCCSEEEEETTEEEEEEECCEECT
T ss_pred             HHHHHHHHHHHHHC-CCEEE---EEcCcCCcCCCCCceEEEEECCEEEEEEEEECCCC
Confidence            34445566677764 44444   444322 2345699999999999999999966543

>2eo0_A Hypothetical protein ST1444; holliday junction resolvase, DNA binding protein, structural genomics, NPPSFA; 2.40A {Sulfolobus tokodaii}

Probab=90.42  E-value=0.28  Score=35.92  Aligned_cols=52  Identities=27%  Similarity=0.363  Sum_probs=33.7

Q ss_pred             CcchhhHHHHHhhccCceeEEEEEecCCC-CCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           39 HTVTVSVANRLEELYGGTAYVGLRIPDPE-TRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        39 ~~~~~~v~~~Lekl~~~kiy~gLRIPd~~-~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      +..+=.+++-|++. |..+.   |-|... .....|||+|....+.++.||||--++
T Consensus        12 ~~~E~~a~~~L~~~-G~~il---r~~~sgg~~~~gEiDIIA~~~~~lvfVEVK~R~~   64 (147)
T 2eo0_A           12 SSVERYIVSRLRDK-GFAVI---RAPASGSKRKDHVPDIIALKSGVIILIEVKSRKN   64 (147)
T ss_dssp             CHHHHHHHHHHHHT-TCEEE---CC-----CCGGGSCSEEEEETTEEEEEEEEECCC
T ss_pred             HHHHHHHHHHHHHC-CCEEE---EEcccCCcCCCCCceEEEEeCCEEEEEEEEECCC
Confidence            44555667777775 44444   444322 234559999999999999999995544

>3fov_A UPF0102 protein RPA0323; structural genomics, APC7380, PSI-2, protein structure initi midwest center for structural genomics, MCSG; 1.88A {Rhodopseudomonas palustris}

Probab=89.96  E-value=0.97  Score=32.70  Aligned_cols=47  Identities=21%  Similarity=0.213  Sum_probs=33.3

Q ss_pred             chhhHHHHHhhccCcee-EEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858           41 VTVSVANRLEELYGGTA-YVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG   94 (119)
Q Consensus        41 ~~~~v~~~Lekl~~~ki-y~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG   94 (119)
                      ++--++.-|++ .|+.+ =.|.|-|      .+|||+|....+.+..||||--++
T Consensus        26 gE~~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~LVFVEVKtR~~   73 (134)
T 3fov_A           26 AEASAADYLER-QGYRILARRFKTR------CGEIDLVAQRDALVAFVEVKARGN   73 (134)
T ss_dssp             HHHHHHHHHHH-TTCEEEEEEEEET------TEEEEEEEEETTEEEEEEEEEC--
T ss_pred             HHHHHHHHHHH-CCCEEEeccccCC------CCcEEEEEEECCEEEEEEEEEccC
Confidence            34445555554 46655 5678874      369999999999999999997766

>1gef_A Holliday junction resolvase; HJC, hydrolase; 2.00A {Pyrococcus furiosus} SCOP: c.52.1.18 PDB: 1ipi_A

Probab=88.12  E-value=0.38  Score=34.15  Aligned_cols=43  Identities=19%  Similarity=0.147  Sum_probs=30.6

Q ss_pred             hhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858           42 TVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS   93 (119)
Q Consensus        42 ~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS   93 (119)
                      +-.+++-|++. |+.+..|.|-        +|||+|..-.+.++.||||--+
T Consensus         9 E~~A~~~L~~~-Gy~ilrn~r~--------~EIDIIA~~~~~lvfVEVK~R~   51 (123)
T 1gef_A            9 ERELIKLLEKH-GFAVVRSAGS--------KKVDLVAGNGKKYLCIEVKVTK   51 (123)
T ss_dssp             HHHHHHHHHHT-TCEEEEBGGG--------SSCSEEEECSSCEEEEEEEEES
T ss_pred             HHHHHHHHHHC-CCEEEEecCC--------CCceEEEEeCCEEEEEEEEeCC
Confidence            44566667764 6666644332        2999999999999999999444

---

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	119
d1y88a2	125	Hypothetical protein AF1548, N-terminal domain {Ar	96.41
d1ob8a_	124	Holliday-junction resolvase SSO1176 {Sulfolobus so	94.4
d1hh1a_	132	Archaeal Holliday junction resolvase Hjc {Archaeon	91.79

>d1y88a2 c.52.1.30 (A:3-127) Hypothetical protein AF1548, N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: MRR-like
domain: Hypothetical protein AF1548, N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.41  E-value=0.0053  Score=41.11  Aligned_cols=51  Identities=29%  Similarity=0.269  Sum_probs=40.9

Q ss_pred             HHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCceeEEE
Q 037858           45 VANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSI   98 (119)
Q Consensus        45 v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~I~~   98 (119)
                      ||.-|++ .|+++..+.++..  .++..+||++..-.+..++||.|+|+..+..
T Consensus         9 va~ll~~-~Gy~v~~~v~v~g--~~~d~gvDiia~~~~~~~~VQcK~~~~~~~~   59 (125)
T d1y88a2           9 VARLLEE-HGFETKTNVIVQG--NCVEQEIDVVAERDGERYMIECKFHNIPVYT   59 (125)
T ss_dssp             HHHHHHT-TTCEEEEEEEEEC--SSSEEEEEEEEEETTEEEEEEECCCSSSCEE
T ss_pred             HHHHHHH-cCCceeccEEEee--ccccceEEEEEEcCCcEEEEEEEEeccCCCC
Confidence            4555665 5788888999953  3456799999999999999999999986554

>d1ob8a_ c.52.1.18 (A:) Holliday-junction resolvase SSO1176 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: Hjc-like
domain: Holliday-junction resolvase SSO1176
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=94.40  E-value=0.012  Score=41.03  Aligned_cols=52  Identities=21%  Similarity=0.275  Sum_probs=33.9

Q ss_pred             HHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee-EEE
Q 037858           47 NRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL-VSI   98 (119)
Q Consensus        47 ~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~-I~~   98 (119)
                      ++|-+..-.+.|+-+|.|...++++.-+|+|.+.++.+++||+|--++. |..
T Consensus         6 Relv~~l~~~gf~vvR~~gSGs~~~~~pDllA~~~~~~~~IEvKst~~~kiyi   58 (124)
T d1ob8a_           6 RELVSILRGEGFNAVRIPTSNSSPNPLPDIFATKGNTLLSIECKSTWENKVKV   58 (124)
T ss_dssp             HHHHHHHHHTTCEEEECCC-----CCSCSEEEEETTEEEEEEEEEESSSEEEE
T ss_pred             HHHHHHHHhCCceEEEeccCCCCCCCCCCEEEeCCCeEEEEEEEeccCCeEEE
Confidence            3444433346788899998766554458999999999999999954433 444

>d1hh1a_ c.52.1.18 (A:) Archaeal Holliday junction resolvase Hjc {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: Hjc-like
domain: Archaeal Holliday junction resolvase Hjc
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=91.79  E-value=0.056  Score=37.88  Aligned_cols=53  Identities=17%  Similarity=0.277  Sum_probs=35.6

Q ss_pred             HHHhhccCceeEEEEEecCCCCCC-ceeeeEEEEeCCeEEEEEecCCce---eEEEc
Q 037858           47 NRLEELYGGTAYVGLRIPDPETRS-LQNIDIVLVKNGEEVVISVKNFSG---LVSIN   99 (119)
Q Consensus        47 ~~Lekl~~~kiy~gLRIPd~~~~~-~~EIDlVIVT~~~IlVIEvKNwSG---~I~~~   99 (119)
                      ++|-+..-.+.|+-+|.|...+.+ +--+|+|-.-++.+++||+|--++   .|..+
T Consensus         5 Rel~~~l~~~gFavvRapgSGs~~~~~~pDlvA~~~~~~~~IEvKst~~~~~~iyi~   61 (132)
T d1hh1a_           5 RNIVSRLRDKGFAVVRAPASGSKRKDPIPDIIALKNGVIILIEMKSRKDIEGKIYVR   61 (132)
T ss_dssp             HHHHHHHHHTTCEEEECCC-------CCCSEEEEETTEEEEEEECCEECTTSCEEEC
T ss_pred             HHHHHHHHhCCceEEEeccCCCCCCCCCCcEEeccCCEEEEEEEEeecCCcccEEEC
Confidence            444444434789999998765432 224899999999999999997664   46654