254780467

254780467

exodeoxyribonuclease VII small subunit

GeneID in NCBI database:8209455Locus tag:CLIBASIA_01760
Protein GI in NCBI database:254780467Protein Accession:YP_003064880.1
Gene range:+(388736, 388996)Protein Length:86aa
Gene description:exodeoxyribonuclease VII small subunit
COG prediction:[L] Exonuclease VII small subunit
KEGG prediction:exodeoxyribonuclease VII small subunit (EC:3.1.11.6); K03602 exodeoxyribonuclease VII small subunit [EC:3.1.11.6]
SEED prediction:Exodeoxyribonuclease VII small subunit (EC 3.1.11.6)
Pathway involved in KEGG:Mismatch repair [PATH:las03430]
Subsystem involved in SEED:DNA repair, bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80------
MNDDSINLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSVKPFDEKN
cccccccHHHHHHccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccc
ccccccccccHHcccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccc
mnddsinlddlshlpfEEAVSELENIIAKLErgdvtldesISIYERGEALKSHCEFLLCSAEKRIEQIKLnrdnkiqsvkpfdekn
mnddsinlddlshlpFEEAVSELENIIAKlergdvtldESISIYERGEALKSHCEFLLCSAEKRIEQiklnrdnkiqsvkpfdekn
MNDDSINLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSVKPFDEKN
****************EEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIE********************
MNDDSINLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSVKPFDEKN
*****INLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNR**************
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MNDDSINLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSVKPFDEKN
MNDDSINLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSVKPFDEKN
MNDDSINLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSVKPFDEKN

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target86 exodeoxyribonuclease VII small subunit [Candidatus Libe
31512207785 exodeoxyribonuclease VII small subunit [Candidatus Libe 1 5e-31
2382154486 RecName: Full=Exodeoxyribonuclease 7 small subunit; Alt 1 8e-22
15918444884 exodeoxyribonuclease VII small subunit [Agrobacterium t 1 8e-22
11625075085 exodeoxyribonuclease VII small subunit [Rhizobium legum 1 1e-20
20954817583 exodeoxyribonuclease VII small subunit [Rhizobium legum 1 1e-20
32719181283 exodeoxyribonuclease VII small subunit [Rhizobium etli 1 2e-20
19089063083 exodeoxyribonuclease VII protein, small subunit [Rhizob 1 2e-20
22208509883 exodeoxyribonuclease VII, small subunit [Agrobacterium 1 2e-20
21867968483 exodeoxyribonuclease VII small subunit [Rhizobium etli 1 4e-20
8635656283 exodeoxyribonuclease VII small subunit [Rhizobium etli 1 4e-20
>gi|315122077|ref|YP_004062566.1| exodeoxyribonuclease VII small subunit [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 85 Back     alignment and organism information
 Score =  137 bits (345), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 68/81 (83%), Positives = 74/81 (91%)

Query: 3  DDSINLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAE 62
          +D +N +D+S LPFE+AVSELENII KLERGDVTLDESISIYERGEALK HCE LLCSAE
Sbjct: 2  NDLVNKNDISLLPFEQAVSELENIITKLERGDVTLDESISIYERGEALKLHCESLLCSAE 61

Query: 63 KRIEQIKLNRDNKIQSVKPFD 83
          KRIEQIKLNRDNKIQ V+PFD
Sbjct: 62 KRIEQIKLNRDNKIQGVEPFD 82


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|23821544|sp|Q8UHD5|EX7S_AGRT5 RecName: Full=Exodeoxyribonuclease 7 small subunit; AltName: Full=Exodeoxyribonuclease VII small subunit; Short=Exonuclease VII small subunit Length = 86 Back     alignment and organism information
>gi|159184448|ref|NP_353771.2| exodeoxyribonuclease VII small subunit [Agrobacterium tumefaciens str. C58] Length = 84 Back     alignment and organism information
>gi|116250750|ref|YP_766588.1| exodeoxyribonuclease VII small subunit [Rhizobium leguminosarum bv. viciae 3841] Length = 85 Back     alignment and organism information
>gi|209548175|ref|YP_002280092.1| exodeoxyribonuclease VII small subunit [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 83 Back     alignment and organism information
>gi|327191812|gb|EGE58811.1| exodeoxyribonuclease VII small subunit [Rhizobium etli CNPAF512] Length = 83 Back     alignment and organism information
>gi|190890630|ref|YP_001977172.1| exodeoxyribonuclease VII protein, small subunit [Rhizobium etli CIAT 652] Length = 83 Back     alignment and organism information
>gi|222085098|ref|YP_002543628.1| exodeoxyribonuclease VII, small subunit [Agrobacterium radiobacter K84] Length = 83 Back     alignment and organism information
>gi|218679684|ref|ZP_03527581.1| exodeoxyribonuclease VII small subunit [Rhizobium etli CIAT 894] Length = 83 Back     alignment and organism information
>gi|86356562|ref|YP_468454.1| exodeoxyribonuclease VII small subunit [Rhizobium etli CFN 42] Length = 83 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target86 exodeoxyribonuclease VII small subunit [Candidatus Libe
PRK0097780 PRK00977, PRK00977, exodeoxyribonuclease VII small subu 3e-14
TIGR0128067 TIGR01280, xseB, exodeoxyribonuclease VII, small subuni 3e-10
COG172281 COG1722, XseB, Exonuclease VII small subunit [DNA repli 9e-09
PRK1406995 PRK14069, PRK14069, exodeoxyribonuclease VII small subu 8e-08
PRK1406376 PRK14063, PRK14063, exodeoxyribonuclease VII small subu 1e-05
PRK1406876 PRK14068, PRK14068, exodeoxyribonuclease VII small subu 3e-05
PRK1406475 PRK14064, PRK14064, exodeoxyribonuclease VII small subu 4e-05
PRK1406675 PRK14066, PRK14066, exodeoxyribonuclease VII small subu 5e-05
PRK1406780 PRK14067, PRK14067, exodeoxyribonuclease VII small subu 0.002
pfam0260953 pfam02609, Exonuc_VII_S, Exonuclease VII small subunit 3e-11
>gnl|CDD|179195 PRK00977, PRK00977, exodeoxyribonuclease VII small subunit; Provisional Back     alignment and domain information
>gnl|CDD|162283 TIGR01280, xseB, exodeoxyribonuclease VII, small subunit Back     alignment and domain information
>gnl|CDD|31908 COG1722, XseB, Exonuclease VII small subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|172559 PRK14069, PRK14069, exodeoxyribonuclease VII small subunit; Provisional Back     alignment and domain information
>gnl|CDD|184483 PRK14063, PRK14063, exodeoxyribonuclease VII small subunit; Provisional Back     alignment and domain information
>gnl|CDD|184485 PRK14068, PRK14068, exodeoxyribonuclease VII small subunit; Provisional Back     alignment and domain information
>gnl|CDD|172554 PRK14064, PRK14064, exodeoxyribonuclease VII small subunit; Provisional Back     alignment and domain information
>gnl|CDD|172556 PRK14066, PRK14066, exodeoxyribonuclease VII small subunit; Provisional Back     alignment and domain information
>gnl|CDD|172557 PRK14067, PRK14067, exodeoxyribonuclease VII small subunit; Provisional Back     alignment and domain information
>gnl|CDD|145648 pfam02609, Exonuc_VII_S, Exonuclease VII small subunit Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 86 exodeoxyribonuclease VII small subunit [Candidatus Libe
PRK0097782 exodeoxyribonuclease VII small subunit; Provisional 99.74
TIGR0128069 xseB exodeoxyribonuclease VII, small subunit; InterPro: 99.7
COG172281 XseB Exonuclease VII small subunit [DNA replication, re 99.59
pfam0260953 Exonuc_VII_S Exonuclease VII small subunit. This family 99.44
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional Back     alignment and domain information
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit; InterPro: IPR003761 Exonuclease VII 3 Back     alignment and domain information
>COG1722 XseB Exonuclease VII small subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>pfam02609 Exonuc_VII_S Exonuclease VII small subunit Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target86 exodeoxyribonuclease VII small subunit [Candidatus Libe
1vp7_A100 Crystal Structure Of Exodeoxyribonuclease Vii Small 5e-10
>gi|56554311|pdb|1VP7|A Chain A, Crystal Structure Of Exodeoxyribonuclease Vii Small Subunit (Np_881400.1) From Bordetella Pertussis At 2.40 A Resolution Length = 100 Back     alignment and structure
 Score = 67.8 bits (165), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 8/85 (9%)

Query: 2  NDDSINLDDLSHL--PFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLC 59
          +  +    D   L   FE A++ELE++++  E G + L++S+S Y RG  L   C+  L 
Sbjct: 16 SKQADPQTDARPLPQDFETALAELESLVSAXENGTLPLEQSLSAYRRGVELARVCQDRLA 75

Query: 60 SAEKRIEQIKLNRDNKIQSVKPFDE 84
           AE++++ ++ +       ++P D 
Sbjct: 76 QAEQQVKVLEGDL------LRPLDP 94


Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target86 exodeoxyribonuclease VII small subunit [Candidatus Libe
1vp7_A100 Exodeoxyribonuclease VII small subunit; NP_881400.1, st 1e-12
>1vp7_A Exodeoxyribonuclease VII small subunit; NP_881400.1, structural genomics, joint center for structural genomics, JCSG, PSI; 2.40A {Bordetella pertussis tohama I} SCOP: a.7.13.1 Length = 100 Back     alignment and structure
 Score = 66.4 bits (162), Expect = 1e-12
 Identities = 21/69 (30%), Positives = 41/69 (59%)

Query: 16  FEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNK 75
           FE A++ELE++++ +E G + L++S+S Y RG  L   C+  L  AE++++ ++ +    
Sbjct: 32  FETALAELESLVSAMENGTLPLEQSLSAYRRGVELARVCQDRLAQAEQQVKVLEGDLLRP 91

Query: 76  IQSVKPFDE 84
           +      DE
Sbjct: 92  LDPAALDDE 100


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target86 exodeoxyribonuclease VII small subunit [Candidatus Libe
1vp7_A100 Exodeoxyribonuclease VII small subunit; NP_881400.1, st 99.66
>1vp7_A Exodeoxyribonuclease VII small subunit; NP_881400.1, structural genomics, joint center for structural genomics, JCSG, PSI; 2.40A {Bordetella pertussis tohama I} SCOP: a.7.13.1 Back     alignment and structure
Probab=99.66  E-value=2e-16  Score=127.48  Aligned_cols=69  Identities=29%  Similarity=0.521  Sum_probs=61.1

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             8999999999999999877999999999999999999999999999999999999831588733468999
Q gi|254780467|r   14 LPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSVKPFD   83 (86)
Q Consensus        14 ~sfEea~~~Le~Iv~~LE~g~l~Lees~~~ye~G~~L~~~C~~~L~~ae~ki~~l~~~~~~~~~~~~p~d   83 (86)
                      .|||++|.+|++||.+||+|++|||+|+++|++|+.|+++|+++|+.|++||++|..+..+.. ...|+|
T Consensus        30 ~SFEeal~~LE~IV~~LE~g~l~Leesl~lye~G~~L~k~C~~~L~~aE~kV~~L~~~~~~~~-~~~~~d   98 (100)
T 1vp7_A           30 QDFETALAELESLVSAMENGTLPLEQSLSAYRRGVELARVCQDRLAQAEQQVKVLEGDLLRPL-DPAALD   98 (100)
T ss_dssp             CSHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-------
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCC
T ss_conf             799999999999999996699899999999999999999999999999999999974767888-989988




Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 86 exodeoxyribonuclease VII small subunit [Candidatus Libe
d1vp7a_68 a.7.13.1 (A:) Exonuclease VII small subunit XseB {Borde 2e-12
>d1vp7a_ a.7.13.1 (A:) Exonuclease VII small subunit XseB {Bordetella pertussis [TaxId: 520]} Length = 68 Back     information, alignment and structure

class: All alpha proteins
fold: Spectrin repeat-like
superfamily: XseB-like
family: XseB-like
domain: Exonuclease VII small subunit XseB
species: Bordetella pertussis [TaxId: 520]
 Score = 64.7 bits (158), Expect = 2e-12
 Identities = 19/56 (33%), Positives = 38/56 (67%)

Query: 16 FEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLN 71
          FE A++ELE++++ +E G + L++S+S Y RG  L   C+  L  AE++++ ++ +
Sbjct: 8  FETALAELESLVSAMENGTLPLEQSLSAYRRGVELARVCQDRLAQAEQQVKVLEGD 63


Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target86 exodeoxyribonuclease VII small subunit [Candidatus Libe
d1vp7a_68 Exonuclease VII small subunit XseB {Bordetella pertussi 99.58
>d1vp7a_ a.7.13.1 (A:) Exonuclease VII small subunit XseB {Bordetella pertussis [TaxId: 520]} Back     information, alignment and structure
class: All alpha proteins
fold: Spectrin repeat-like
superfamily: XseB-like
family: XseB-like
domain: Exonuclease VII small subunit XseB
species: Bordetella pertussis [TaxId: 520]
Probab=99.58  E-value=3.6e-15  Score=117.80  Aligned_cols=60  Identities=32%  Similarity=0.571  Sum_probs=57.0

Q ss_pred             HCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             289999999999999998779999999999999999999999999999999999998315
Q gi|254780467|r   13 HLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNR   72 (86)
Q Consensus        13 ~~sfEea~~~Le~Iv~~LE~g~l~Lees~~~ye~G~~L~~~C~~~L~~ae~ki~~l~~~~   72 (86)
                      ..|||++|.+||+||++||+|++|||+|+++|++|++|+++|+++|+.|++||++|..+.
T Consensus         5 p~sfEe~l~~LE~IV~~LE~g~l~Leesl~~ye~G~~L~~~C~~~L~~ae~ki~~l~~~~   64 (68)
T d1vp7a_           5 PQDFETALAELESLVSAMENGTLPLEQSLSAYRRGVELARVCQDRLAQAEQQVKVLEGDL   64 (68)
T ss_dssp             CCSHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             979999999999999998679998999999999999999999999999999999997256



Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 86 exodeoxyribonuclease VII small subunit [Candidatus
1vp7_A_100 (A:) Exodeoxyribonuclease VII small subunit; NP_88 7e-12
>1vp7_A (A:) Exodeoxyribonuclease VII small subunit; NP_881400.1, structural genomics, joint center for structural genomics, JCSG, PSI; 2.40A {Bordetella pertussis tohama I}Length = 100 Back     alignment and structure
 Score = 64.0 bits (156), Expect = 7e-12
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 14 LPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRD 73
            FE A++ELE++++  E G + L++S+S Y RG  L   C+  L  AE++++ +     
Sbjct: 30 QDFETALAELESLVSAXENGTLPLEQSLSAYRRGVELARVCQDRLAQAEQQVKVL-EGDL 88

Query: 74 NKIQSVKPFDE 84
           +       D+
Sbjct: 89 LRPLDPAALDD 99


Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target86 exodeoxyribonuclease VII small subunit [Candidatus Libe
1vp7_A_100 Exodeoxyribonuclease VII small subunit; NP_881400. 99.69
>1vp7_A (A:) Exodeoxyribonuclease VII small subunit; NP_881400.1, structural genomics, joint center for structural genomics, JCSG, PSI; 2.40A {Bordetella pertussis tohama I} Back     alignment and structure
Probab=99.69  E-value=8.2e-17  Score=131.06  Aligned_cols=75  Identities=25%  Similarity=0.400  Sum_probs=66.5

Q ss_pred             CCCHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             568101662899999999999999987799999999999999999999999999999999999983158873346
Q gi|254780467|r    5 SINLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSV   79 (86)
Q Consensus         5 ~~~~~~~~~~sfEea~~~Le~Iv~~LE~g~l~Lees~~~ye~G~~L~~~C~~~L~~ae~ki~~l~~~~~~~~~~~   79 (86)
                      .......+.+|||++|.+||+||++||+|++||++|+++|++|++|+++|+++|+.|+++|++|..+..+.....
T Consensus        21 ~~~~~~~~~~sfEeal~~LE~IV~~LE~g~l~Leesl~~ye~G~~L~k~C~~~L~~aE~ki~~L~~~~~~~~~~~   95 (100)
T 1vp7_A           21 PQTDARPLPQDFETALAELESLVSAXENGTLPLEQSLSAYRRGVELARVCQDRLAQAEQQVKVLEGDLLRPLDPA   95 (100)
T ss_dssp             ----CCCBCCSHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC---
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             988889999799999999999999996699889999999999999999999999999999999973767889988