Conserved Domains in CDD Database Detected by RPS-BLAST and HHsearch
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
Identity Alignment graph Length
Definition
E-value
Target 86
exodeoxyribonuclease VII small subunit [Candidatus Libe
PRK00977 80
PRK00977, PRK00977, exodeoxyribonuclease VII small subu
3e-14
TIGR01280 67
TIGR01280, xseB, exodeoxyribonuclease VII, small subuni
3e-10
COG1722 81
COG1722, XseB, Exonuclease VII small subunit [DNA repli
9e-09
PRK14069 95
PRK14069, PRK14069, exodeoxyribonuclease VII small subu
8e-08
PRK14063 76
PRK14063, PRK14063, exodeoxyribonuclease VII small subu
1e-05
PRK14068 76
PRK14068, PRK14068, exodeoxyribonuclease VII small subu
3e-05
PRK14064 75
PRK14064, PRK14064, exodeoxyribonuclease VII small subu
4e-05
PRK14066 75
PRK14066, PRK14066, exodeoxyribonuclease VII small subu
5e-05
PRK14067 80
PRK14067, PRK14067, exodeoxyribonuclease VII small subu
0.002
pfam02609 53
pfam02609, Exonuc_VII_S, Exonuclease VII small subunit
3e-11
>gnl|CDD|179195 PRK00977, PRK00977, exodeoxyribonuclease VII small subunit; Provisional
Back Show alignment and domain information
Score = 72.2 bits (178), Expect = 3e-14
Identities = 34/71 (47%), Positives = 51/71 (71%), Gaps = 1/71 (1%)
Query: 14 LPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRD 73
L FEEA++ELE I+ +LE GD+ L+ES++ +ERG AL C+ L AE+R+E++ L+ D
Sbjct: 10 LSFEEALAELEEIVTRLESGDLPLEESLAAFERGVALARQCQKKLQQAEQRVEKL-LDED 68
Query: 74 NKIQSVKPFDE 84
K S++PFD
Sbjct: 69 GKEASLEPFDP 79
>gnl|CDD|162283 TIGR01280, xseB, exodeoxyribonuclease VII, small subunit
Back Show alignment and domain information
Score = 58.9 bits (143), Expect = 3e-10
Identities = 29/60 (48%), Positives = 42/60 (70%)
Query: 14 LPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRD 73
L FEEA+SELE I+ KLE GD+ L+E+++++ERG AL CE L AE+R+ ++ D
Sbjct: 1 LSFEEALSELEQIVQKLESGDLALEEALNLFERGMALARRCEKKLAQAEQRVRKLLKEDD 60
This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides. Length = 67
>gnl|CDD|31908 COG1722, XseB, Exonuclease VII small subunit [DNA replication, recombination, and repair]
Back Show alignment and domain information
Score = 53.8 bits (129), Expect = 9e-09
Identities = 26/67 (38%), Positives = 42/67 (62%)
Query: 10 DLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIK 69
S L FEEA++ELE I+ LE G++ L+E++ +ERG AL C+ L AE+R+E++
Sbjct: 6 PKSALSFEEALAELEEIVESLESGELPLEEALKEFERGMALYKECQEKLQQAEQRVEKLL 65
Query: 70 LNRDNKI 76
+ +
Sbjct: 66 EEDEEED 72
>gnl|CDD|172559 PRK14069, PRK14069, exodeoxyribonuclease VII small subunit; Provisional
Back Show alignment and domain information
Score = 50.8 bits (121), Expect = 8e-08
Identities = 28/58 (48%), Positives = 37/58 (63%)
Query: 9 DDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIE 66
+ S + FE+A+ ELE I KLER D +L+ES+ YERG LK C +L AE +IE
Sbjct: 3 EKKSKISFEDALRELEQIAEKLERQDFSLEESLKAYERGMELKKICSGILDDAEGKIE 60
>gnl|CDD|184483 PRK14063, PRK14063, exodeoxyribonuclease VII small subunit; Provisional
Back Show alignment and domain information
Score = 43.7 bits (103), Expect = 1e-05
Identities = 23/55 (41%), Positives = 40/55 (72%)
Query: 14 LPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQI 68
L FEEA+S+LE++++KLE+GDV L+E+IS ++ G L C+ L + ++++ I
Sbjct: 5 LSFEEAISQLEHLVSKLEQGDVPLEEAISYFKEGMELSKLCDEKLKNVQEQMAVI 59
>gnl|CDD|184485 PRK14068, PRK14068, exodeoxyribonuclease VII small subunit; Provisional
Back Show alignment and domain information
Score = 42.2 bits (99), Expect = 3e-05
Identities = 24/69 (34%), Positives = 42/69 (60%)
Query: 16 FEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNK 75
FEE + ELE I+ KL+ V+L+ES+ +Y+RG L + C+ L +AEK++ +
Sbjct: 8 FEEMMQELEQIVQKLDNETVSLEESLDLYQRGMKLSAACDTTLKNAEKKVNDLIKEEAED 67
Query: 76 IQSVKPFDE 84
+++ + DE
Sbjct: 68 VKNDESTDE 76
>gnl|CDD|172554 PRK14064, PRK14064, exodeoxyribonuclease VII small subunit; Provisional
Back Show alignment and domain information
Score = 41.7 bits (97), Expect = 4e-05
Identities = 23/53 (43%), Positives = 37/53 (69%)
Query: 16 FEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQI 68
FEEA++ELE I+ LE G +L++S+ +Y++G L C+ L SAEKR+ ++
Sbjct: 8 FEEAIAELETIVEALENGSASLEDSLDMYQKGIELTKLCQDKLQSAEKRMAKV 60
>gnl|CDD|172556 PRK14066, PRK14066, exodeoxyribonuclease VII small subunit; Provisional
Back Show alignment and domain information
Score = 41.4 bits (97), Expect = 5e-05
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 16 FEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNK 75
FE A+ +LE ++ KLE G+++LD+S+ +E G + C L AE+R+E + +D
Sbjct: 6 FETALKKLEEVVKKLEGGELSLDDSLKAFEEGVKHAAFCSKKLDEAERRVEVLLKQKDGS 65
Query: 76 IQSVKPFDEKN 86
+PF +
Sbjct: 66 F-VREPFRLDD 75
>gnl|CDD|172557 PRK14067, PRK14067, exodeoxyribonuclease VII small subunit; Provisional
Back Show alignment and domain information
Score = 36.3 bits (84), Expect = 0.002
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 16 FEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRI 65
FE+ ++ L+ I+ LE GD+ L+ES+++Y+ G L C L A I
Sbjct: 9 FEQQLARLQEIVDALEGGDLPLEESVALYKEGLGLARACREQLAKARNEI 58
>gnl|CDD|145648 pfam02609, Exonuc_VII_S, Exonuclease VII small subunit
Back Show alignment and domain information
Score = 62.5 bits (153), Expect = 3e-11
Identities = 26/53 (49%), Positives = 39/53 (73%)
Query: 16 FEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQI 68
FEEA++ELE I+ KLE G+++L+ES+ +YE G L HC+ L AE++IE +
Sbjct: 1 FEEALAELEEIVEKLESGELSLEESLKLYEEGVKLLKHCQKKLEEAEQKIEIL 53
This family consist of exonuclease VII, small subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones. Length = 53
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity Alignment graph Length
Definition
Probability
Target
86
exodeoxyribonuclease VII small subunit [Candidatus Libe
PRK00977 82
exodeoxyribonuclease VII small subunit; Provisional
99.74
TIGR01280 69
xseB exodeoxyribonuclease VII, small subunit; InterPro:
99.7
COG1722 81
XseB Exonuclease VII small subunit [DNA replication, re
99.59
pfam02609 53
Exonuc_VII_S Exonuclease VII small subunit. This family
99.44
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Back Show alignment and domain information
Probab=99.74 E-value=1.8e-17 Score=135.81 Aligned_cols=78 Identities=41% Similarity=0.737 Sum_probs=70.4
Q ss_pred CHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 81016628999999999999999877999999999999999999999999999999999999831588733468999998
Q gi|254780467|r 7 NLDDLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKIQSVKPFDEKN 86 (86)
Q Consensus 7 ~~~~~~~~sfEea~~~Le~Iv~~LE~g~l~Lees~~~ye~G~~L~~~C~~~L~~ae~ki~~l~~~~~~~~~~~~p~d~~~ 86 (86)
T Consensus 4 ~~~~~~~lsFE~al~~LE~IV~~LE~g~l~Leesl~~fE~G~~L~~~C~~~L~~Ae~kI~~l~~~~~~~--~~~~f~~~~ 81 (82)
T PRK00977 4 STSDVAPLSFEEALAELEEIVTRLENGDLSLEESLAAYERGEALARRCQKKLQQAEQRVEILLQDDEEA--PLEPFPPDT 81 (82)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC--CCCCCCCCC
T ss_conf 778866589999999999999998579998999999999999999999999999999999999748999--899999888
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit; InterPro: IPR003761 Exonuclease VII 3
Back Show alignment and domain information
Probab=99.70 E-value=9.1e-17 Score=131.20 Aligned_cols=64 Identities=44% Similarity=0.761 Sum_probs=60.4
Q ss_pred HCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 2899999999999999987799999999999999999999999999999999999983158873
Q gi|254780467|r 13 HLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNKI 76 (86)
Q Consensus 13 ~~sfEea~~~Le~Iv~~LE~g~l~Lees~~~ye~G~~L~~~C~~~L~~ae~ki~~l~~~~~~~~ 76 (86)
T Consensus 2 ~~sFE~~l~eLE~iV~~LE~G~~~LE~al~~ferG~~L~~~C~~kL~~Ae~~v~~l~~~~~~~~ 65 (69)
T TIGR01280 2 DISFEEALSELEQIVQKLESGDLALEEALNLFERGMALSRACEKKLEQAEQKVEKLLKENDEAV 65 (69)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 8768889999999998773589767889999888899999988999999999999852445656
1.11.6 from EC is composed of two non-identical subunits; one large subunit and 4 small ones . Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex.
>COG1722 XseB Exonuclease VII small subunit [DNA replication, recombination, and repair]
Back Show alignment and domain information
Probab=99.59 E-value=1.2e-14 Score=117.32 Aligned_cols=66 Identities=39% Similarity=0.644 Sum_probs=60.5
Q ss_pred HHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 166289999999999999998779999999999999999999999999999999999998315887
Q gi|254780467|r 10 DLSHLPFEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQIKLNRDNK 75 (86)
Q Consensus 10 ~~~~~sfEea~~~Le~Iv~~LE~g~l~Lees~~~ye~G~~L~~~C~~~L~~ae~ki~~l~~~~~~~ 75 (86)
T Consensus 6 ~~~~~sfE~~l~eLE~IV~~LE~Gel~Le~sl~~~erG~~L~k~c~~~L~~Ae~~v~~l~~~~~~~ 71 (81)
T COG1722 6 PKSALSFEEALAELEEIVESLESGELPLEEALKEFERGMALYKECQEKLQQAEQRVEKLLEEDEEE 71 (81)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 865000999999999999999857565999999999999999999999999999999999832345
>pfam02609 Exonuc_VII_S Exonuclease VII small subunit
Back Show alignment and domain information
Probab=99.44 E-value=2.6e-13 Score=108.56 Aligned_cols=53 Identities=49% Similarity=0.829 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999877999999999999999999999999999999999999
Q gi|254780467|r 16 FEEAVSELENIIAKLERGDVTLDESISIYERGEALKSHCEFLLCSAEKRIEQI 68 (86)
Q Consensus 16 fEea~~~Le~Iv~~LE~g~l~Lees~~~ye~G~~L~~~C~~~L~~ae~ki~~l 68 (86)
T Consensus 1 fEeal~~Le~Iv~~LE~~~l~Le~sl~~ye~G~~L~~~c~~~L~~ae~~v~~l 53 (53)
T pfam02609 1 FEEALAELEEIVEKLESGELSLEESLKLYEEGVKLLKHCQKKLEEAEQKIEIL 53 (53)
T ss_pred CHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 97789999999999847999899999999999999999999999999987659
This family consist of exonuclease VII, small subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones.
Homologous Domains in SCOP and MMDB Database Detected by RPS-BLAST and HHsearch
Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
Identity Alignment graph Length
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 Hide 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
Original result of HHsearch against SCOP70(version1.75) database
Identity Alignment graph Length
Definition
Probability
Target 86
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 Hide 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
Original result of RPS-BLAST against MMDB70 database
Identity Alignment graph Length
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 Hide 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
Original result of HHsearch against MMDB70 database
Identity Alignment graph Length
Definition
Probability
Target 86
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 Hide 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