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= 039424
(203 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2RHM|A Chain A, Crystal Structure Of A Putative Kinase (Caur_3907) From
Chloroflexus Aurantiacus J-10-Fl At 1.70 A Resolution
pdb|2RHM|B Chain B, Crystal Structure Of A Putative Kinase (Caur_3907) From
Chloroflexus Aurantiacus J-10-Fl At 1.70 A Resolution
pdb|2RHM|C Chain C, Crystal Structure Of A Putative Kinase (Caur_3907) From
Chloroflexus Aurantiacus J-10-Fl At 1.70 A Resolution
pdb|2RHM|D Chain D, Crystal Structure Of A Putative Kinase (Caur_3907) From
Chloroflexus Aurantiacus J-10-Fl At 1.70 A Resolution
Length = 193
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 25/32 (78%)
Query: 1 MKGHPGTGKSTLADAIASALKIPLIDKDDVRD 32
+ GHP TGK+TL+ A+A+ L++PL+ KD ++
Sbjct: 10 VTGHPATGKTTLSQALATGLRLPLLSKDAFKE 41
>pdb|3VAA|A Chain A, 1.7 Angstrom Resolution Crystal Structure Of Shikimate
Kinase From Bacteroides Thetaiotaomicron
pdb|3VAA|B Chain B, 1.7 Angstrom Resolution Crystal Structure Of Shikimate
Kinase From Bacteroides Thetaiotaomicron
pdb|3VAA|C Chain C, 1.7 Angstrom Resolution Crystal Structure Of Shikimate
Kinase From Bacteroides Thetaiotaomicron
Length = 199
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 1 MKGHPGTGKSTLADAIASALKIPLIDKD 28
+ G+ G GK+TL A A L +P ID D
Sbjct: 30 LTGYMGAGKTTLGKAFARKLNVPFIDLD 57
>pdb|1ZP6|A Chain A, Crystal Structure Of Atu3015, A Putative Cytidylate
Kinase From Agrobacterium Tumefaciens, Northeast
Structural Genomics Target Atr62
Length = 191
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 20/25 (80%)
Query: 1 MKGHPGTGKSTLADAIASALKIPLI 25
+ GHPG+GKST+A+A+A+ +P +
Sbjct: 14 LSGHPGSGKSTIAEALANLPGVPKV 38
>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh
Length = 257
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 16/25 (64%)
Query: 1 MKGHPGTGKSTLADAIASALKIPLI 25
M G PGTGK+ LA AIA K+P
Sbjct: 50 MVGPPGTGKTLLAKAIAGEAKVPFF 74
>pdb|1L4U|A Chain A, Crystal Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis In Complex With Mgadp And Pt(Ii) At 1.8
Angstrom Resolution
pdb|1L4Y|A Chain A, Crystal Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis In Complex With Mgadp At 2.0 Angstrom
Resolution
pdb|1U8A|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Shikimate Kinase In Complex With Shikimate And Adp At
2.15 Angstrom Resolution
pdb|1WE2|A Chain A, Crystal Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis In Complex With Mgadp And Shikimic Acid
pdb|1ZYU|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Shikimate Kinase In Complex With Shikimate And Amppcp
At 2.85 Angstrom Resolution
pdb|2G1J|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Shikimate Kinase At 2.0 Angstrom Resolution
pdb|2G1J|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis
Shikimate Kinase At 2.0 Angstrom Resolution
pdb|2G1K|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Shikimate Kinase In Complex With Shikimate At 1.75
Angstrom Resolution
pdb|2DFN|A Chain A, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Shikimate At 1.9
Angstrons Of Resolution
pdb|2DFT|A Chain A, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Mg At 2.8 Angstrons
Of Resolution
pdb|2DFT|B Chain B, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Mg At 2.8 Angstrons
Of Resolution
pdb|2DFT|C Chain C, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Mg At 2.8 Angstrons
Of Resolution
pdb|2DFT|D Chain D, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Mg At 2.8 Angstrons
Of Resolution
pdb|3BAF|A Chain A, Crystal Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis In Complex With Amp-Pnp
Length = 176
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKD 28
G PG+GKST+ +A AL + L+D D
Sbjct: 9 GLPGSGKSTIGRRLAKALGVGLLDTD 34
>pdb|2IYQ|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate And Adp
pdb|2IYR|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate
pdb|2IYR|B Chain B, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate
pdb|2IYS|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate, Open Lid (Conf. A)
pdb|2IYT|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Unliganded State, Open Lid (conf. A)
pdb|2IYU|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Adp, Open Lid (Conf. A)
pdb|2IYV|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Adp, Open Lid (Conf. B)
pdb|2IYW|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Mgatp, Open Lid (Conf. B)
pdb|2IYX|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate And So4
pdb|2IYY|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate-3-Phosphate And So4
pdb|2IYZ|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate-3-Phosphate And Adp
Length = 184
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKD 28
G PG+GKST+ +A AL + L+D D
Sbjct: 9 GLPGSGKSTIGRRLAKALGVGLLDTD 34
>pdb|1VIA|A Chain A, Crystal Structure Of Shikimate Kinase
pdb|1VIA|B Chain B, Crystal Structure Of Shikimate Kinase
Length = 175
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKD 28
G G+GKSTLA A+A L + +D D
Sbjct: 11 GFXGSGKSTLARALAKDLDLVFLDSD 36
>pdb|1ZUH|A Chain A, Structural Basis For Shikimate-Binding Specificity Of
Helicobacter Pylori Shikimate Kinase
pdb|1ZUI|A Chain A, Structural Basis For Shikimate-binding Specificity Of
Helicobacter Pylori Shikimate Kinase
pdb|3HR7|A Chain A, Crystal Structure Of The Shikimate Kinase-Sulfate
Complex From Helicobacter Pylori
pdb|3HR7|B Chain B, Crystal Structure Of The Shikimate Kinase-Sulfate
Complex From Helicobacter Pylori
pdb|3MUF|A Chain A, Shikimate Kinase From Helicobacter Pylori In Complex
With Shikimate-3- Phosphate And Adp
Length = 168
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDV 30
G G+GKS+LA + ALK+ ++D D +
Sbjct: 14 GFMGSGKSSLAQELGLALKLEVLDTDMI 41
>pdb|3MRS|A Chain A, Crystal Structure Of Shikimate Kinase Mutant (R57a) From
Helicobacter Pylori
Length = 168
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDV 30
G G+GKS+LA + ALK+ ++D D +
Sbjct: 14 GFMGSGKSSLAQELGLALKLEVLDTDMI 41
>pdb|3N2E|A Chain A, Crystal Structure Of Helicobactor Pylori Shikimate
Kinase In Complex With Nsc162535
pdb|3N2E|B Chain B, Crystal Structure Of Helicobactor Pylori Shikimate
Kinase In Complex With Nsc162535
pdb|3N2E|C Chain C, Crystal Structure Of Helicobactor Pylori Shikimate
Kinase In Complex With Nsc162535
Length = 168
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDV 30
G G+GKS+LA + ALK+ ++D D +
Sbjct: 8 GFMGSGKSSLAQELGLALKLEVLDTDMI 35
>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|B Chain B, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|C Chain C, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|D Chain D, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|E Chain E, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|F Chain F, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
Length = 499
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 3 GHPGTGKSTLADAIASALKIPLI 25
G PG GK+ LA A+A ++P I
Sbjct: 71 GPPGVGKTHLARAVAGEARVPFI 93
>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|B Chain B, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|C Chain C, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|D Chain D, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|E Chain E, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|F Chain F, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
Length = 508
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 3 GHPGTGKSTLADAIASALKIPLI 25
G PG GK+ LA A+A ++P I
Sbjct: 80 GPPGVGKTHLARAVAGEARVPFI 102
>pdb|1ZIN|A Chain A, Adenylate Kinase With Bound Ap5a
pdb|1ZIO|A Chain A, Phosphotransferase
pdb|1ZIP|A Chain A, Bacillus Stearothermophilus Adenylate Kinase
Length = 217
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 1 MKGHPGTGKSTLADAIASALKIPLIDKDDV 30
+ G PG GK T A+ I +A IP I D+
Sbjct: 5 LMGLPGAGKGTQAEKIVAAYGIPHISTGDM 34
>pdb|3C8U|A Chain A, Crystal Structure Of Putative Fructose Transport System
Kinase (Yp_612366.1) From Silicibacter Sp. Tm1040 At
1.95 A Resolution
Length = 208
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 1 MKGHPGTGKSTLADAIASAL 20
+ G PG+GKSTL++ +A+AL
Sbjct: 27 LSGAPGSGKSTLSNPLAAAL 46
>pdb|2CE7|A Chain A, Edta Treated
pdb|2CE7|B Chain B, Edta Treated
pdb|2CE7|C Chain C, Edta Treated
pdb|2CE7|D Chain D, Edta Treated
pdb|2CE7|E Chain E, Edta Treated
pdb|2CE7|F Chain F, Edta Treated
pdb|2CEA|A Chain A, Cell Division Protein Ftsh
pdb|2CEA|B Chain B, Cell Division Protein Ftsh
pdb|2CEA|C Chain C, Cell Division Protein Ftsh
pdb|2CEA|D Chain D, Cell Division Protein Ftsh
pdb|2CEA|E Chain E, Cell Division Protein Ftsh
pdb|2CEA|F Chain F, Cell Division Protein Ftsh
Length = 476
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 3 GHPGTGKSTLADAIASALKIPLI 25
G PGTGK+ LA A+A +P
Sbjct: 56 GPPGTGKTLLARAVAGEANVPFF 78
>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus
Thermophilus
Length = 278
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 3 GHPGTGKSTLADAIASALKIPLI 25
G PG GK+ LA A+A ++P I
Sbjct: 80 GPPGVGKTHLARAVAGEARVPFI 102
>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus
Thermophilus
pdb|1IY0|A Chain A, Crystal Structure Of The Ftsh Atpase Domain With Amp-Pnp
From Thermus Thermophilus
pdb|1IY1|A Chain A, Crystal Structure Of The Ftsh Atpase Domain With Adp
From Thermus Thermophilus
Length = 254
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 3 GHPGTGKSTLADAIASALKIPLI 25
G PG GK+ LA A+A ++P I
Sbjct: 56 GPPGVGKTHLARAVAGEARVPFI 78
>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh
pdb|2R62|B Chain B, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh
pdb|2R65|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|B Chain B, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|C Chain C, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|D Chain D, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|E Chain E, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
Length = 268
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 3 GHPGTGKSTLADAIASALKIPLI 25
G PGTGK+ LA A+A +P
Sbjct: 51 GPPGTGKTLLAKAVAGEAHVPFF 73
>pdb|1US8|A Chain A, The Rad50 Signature Motif: Essential To Atp Binding And
Biological Function
Length = 147
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDVRD 32
G G+GKS+L DAI L PL KD +D
Sbjct: 30 GQNGSGKSSLLDAILVGLYWPLRIKDIKKD 59
>pdb|1F2T|A Chain A, Crystal Structure Of Atp-free Rad50 Abc-atpase
pdb|1F2U|A Chain A, Crystal Structure Of Rad50 Abc-Atpase
pdb|1F2U|C Chain C, Crystal Structure Of Rad50 Abc-Atpase
Length = 149
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDVRD 32
G G+GKS+L DAI L PL KD +D
Sbjct: 30 GQNGSGKSSLLDAILVGLYWPLRIKDIKKD 59
>pdb|3QKT|A Chain A, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|B Chain B, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|C Chain C, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|D Chain D, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
Length = 339
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDVRD 32
G G+GKS+L DAI L PL KD +D
Sbjct: 30 GQNGSGKSSLLDAILVGLYWPLRIKDIKKD 59
>pdb|1II8|A Chain A, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
Length = 195
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDVRD 32
G G+GKS+L DAI L PL KD +D
Sbjct: 30 GQNGSGKSSLLDAILVGLYWPLRIKDIKKD 59
>pdb|3QKU|A Chain A, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
pdb|3QKU|B Chain B, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
Length = 359
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDVRD 32
G G+GKS+L DAI L PL KD +D
Sbjct: 30 GQNGSGKSSLLDAILVGLYWPLRIKDIKKD 59
>pdb|3QKR|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
pdb|3QKS|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
Length = 203
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 3 GHPGTGKSTLADAIASALKIPLIDKDDVRD 32
G G+GKS+L DAI L PL KD +D
Sbjct: 30 GQNGSGKSSLLDAILVGLYWPLRIKDIKKD 59
>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp
Length = 262
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 3 GHPGTGKSTLADAIASALKIPLI 25
G PG GK+ LA A+A+ ++P +
Sbjct: 46 GPPGCGKTLLAKAVATEAQVPFL 68
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
0.318 0.136 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,019,408
Number of Sequences: 62578
Number of extensions: 151863
Number of successful extensions: 540
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 513
Number of HSP's gapped (non-prelim): 28
length of query: 203
length of database: 14,973,337
effective HSP length: 94
effective length of query: 109
effective length of database: 9,091,005
effective search space: 990919545
effective search space used: 990919545
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)