BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy499
(122 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ZTQ|A Chain A, Hexagonal Crystal Form P61 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTQ|B Chain B, Hexagonal Crystal Form P61 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTQ|C Chain C, Hexagonal Crystal Form P61 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTQ|D Chain D, Hexagonal Crystal Form P61 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTQ|E Chain E, Hexagonal Crystal Form P61 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTQ|F Chain F, Hexagonal Crystal Form P61 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTQ|G Chain G, Hexagonal Crystal Form P61 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTQ|H Chain H, Hexagonal Crystal Form P61 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTO|A Chain A, Orthorhombic Crystal Form C222 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTP|A Chain A, Orthorhombic Crystal Form P21212 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTP|C Chain C, Orthorhombic Crystal Form P21212 Of The Aquifex Aeolicus
Nucleoside Diphosphate Kinase
pdb|3ZTR|A Chain A, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|B Chain B, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|C Chain C, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|D Chain D, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|E Chain E, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|F Chain F, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|G Chain G, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|H Chain H, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|I Chain I, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|J Chain J, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|K Chain K, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTR|L Chain L, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (First Stage Of Radiation Damage)
pdb|3ZTS|A Chain A, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|B Chain B, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|C Chain C, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|D Chain D, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|E Chain E, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|F Chain F, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|G Chain G, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|H Chain H, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|I Chain I, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|J Chain J, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|K Chain K, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
pdb|3ZTS|L Chain L, Hexagonal Form P6122 Of The Aquifex Aeolicus Nucleoside
Diphosphate Kinase (Final Stage Of Radiation Damage)
Length = 142
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 26/36 (72%)
Query: 32 ETAKELRPNTIRAMYGRNSVENAVHVTDLPEDAFFE 67
E A+++ PN+IRA +G + +NA+H +D PE A +E
Sbjct: 96 EEARKVAPNSIRAQFGTDKGKNAIHASDSPESAQYE 131
>pdb|3VGS|A Chain A, Wild-Type Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGS|B Chain B, Wild-Type Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGT|A Chain A, Wild-Type Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGT|B Chain B, Wild-Type Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGT|C Chain C, Wild-Type Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGT|D Chain D, Wild-Type Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGT|E Chain E, Wild-Type Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
Length = 141
Score = 32.3 bits (72), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 35 KELRPNTIRAMYGRNSVENAVHVTDLPEDA------FFEFGKQC 72
KE TIRA Y ++ NAVH +D PE A FFE + C
Sbjct: 96 KEAEAGTIRADYAQSIDANAVHGSDSPESAAREIAYFFEESEIC 139
>pdb|3VGU|A Chain A, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGU|B Chain B, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGU|C Chain C, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGU|D Chain D, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGU|E Chain E, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGU|F Chain F, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGU|G Chain G, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGU|H Chain H, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|A Chain A, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|B Chain B, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|C Chain C, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|D Chain D, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|E Chain E, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|F Chain F, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|G Chain G, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|H Chain H, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|I Chain I, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|J Chain J, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|K Chain K, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|L Chain L, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|M Chain M, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|N Chain N, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|O Chain O, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
pdb|3VGV|P Chain P, E134a Mutant Nucleoside Diphosphate Kinase Derived From
Halomonas Sp. 593
Length = 141
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 19/34 (55%)
Query: 35 KELRPNTIRAMYGRNSVENAVHVTDLPEDAFFEF 68
KE TIRA Y ++ NAVH +D PE A E
Sbjct: 96 KEAEAGTIRADYAQSIDANAVHGSDSPESAAREI 129
>pdb|2NQW|A Chain A, Structure Of The Transporter Associated Domain From
Pg_0272, A Cbs Domain Protein From Porphyromonas
Gingivalis
Length = 93
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 47 GRNSVENAVHVTDLPEDAFFEFGKQC 72
G+ S+ + H DLPE+AF E G +
Sbjct: 21 GKTSLSDVRHYLDLPENAFGELGDEV 46
>pdb|3PJ9|A Chain A, Crystal Structure Of A Nucleoside Diphosphate Kinase From
Campylobacter Jejuni
pdb|3PJ9|B Chain B, Crystal Structure Of A Nucleoside Diphosphate Kinase From
Campylobacter Jejuni
pdb|3PJ9|C Chain C, Crystal Structure Of A Nucleoside Diphosphate Kinase From
Campylobacter Jejuni
pdb|3PJ9|D Chain D, Crystal Structure Of A Nucleoside Diphosphate Kinase From
Campylobacter Jejuni
Length = 140
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 35 KELRPNTIRAMYGRNSVENAVHVTDLPEDAFFEF 68
KE + TIRA + + NAVH +D E+A E
Sbjct: 97 KEAKAGTIRADFAESIDANAVHGSDSLENAKIEI 130
>pdb|4DUT|A Chain A, The Structure Of Nucleoside Diphosphate Kinase (Ndk) From
Burkholderia Thailandensis
pdb|4DUT|B Chain B, The Structure Of Nucleoside Diphosphate Kinase (Ndk) From
Burkholderia Thailandensis
pdb|4EK2|A Chain A, The Structure Of Nucleoside Diphosphate Kinase (Ndk) From
Burkholderia Thailandensis Bound To Deoxyadenosine
Monophosphate
pdb|4EK2|B Chain B, The Structure Of Nucleoside Diphosphate Kinase (Ndk) From
Burkholderia Thailandensis Bound To Deoxyadenosine
Monophosphate
pdb|4HR2|A Chain A, Structure Of Nucleoside Diphosphate Kinase (Ndk) From
Burkholderia Thailandensis Bound To Adp
pdb|4HR2|B Chain B, Structure Of Nucleoside Diphosphate Kinase (Ndk) From
Burkholderia Thailandensis Bound To Adp
Length = 145
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 35 KELRPNTIRAMYGRNSVENAVHVTDLPEDAFFEFG 69
K+ TIRA + + NAVH +D PE A E
Sbjct: 100 KKAEKGTIRADFADSIDANAVHGSDAPETARVEIA 134
>pdb|2VU5|A Chain A, Crystal Structure Of Pndk From Bacillus Anthracis
Length = 148
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 36 ELRPNTIRAMYGRNSVENAVHVTDLPEDAFFEFG 69
E P TIR +G +N +H +D E A E G
Sbjct: 95 EAAPGTIRGDFGVTVAKNIIHGSDSLESAEREIG 128
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.137 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,498,565
Number of Sequences: 62578
Number of extensions: 112935
Number of successful extensions: 191
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 184
Number of HSP's gapped (non-prelim): 7
length of query: 122
length of database: 14,973,337
effective HSP length: 84
effective length of query: 38
effective length of database: 9,716,785
effective search space: 369237830
effective search space used: 369237830
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)