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= 019329
(342 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3R20|A Chain A, Crystal Structure Of Cytidylate Kinase From Mycobacterium
Smegmatis
Length = 233
Score = 32.0 bits (71), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 149 GVGFTPHV-ITVKAGEDVSSKIMSFSQNGPRAVCILSANGAISNVTL---RQAATSGGTV 204
GVG P V AGEDVSS+I + G AV +SA A+ + R+ AT GG V
Sbjct: 74 GVGSDPDVDAAFLAGEDVSSEIRGDAVTG--AVSAVSAVPAVRTRLVDIQRKLATEGGRV 131
Query: 205 TYEGR 209
EGR
Sbjct: 132 VVEGR 136
>pdb|2HX0|A Chain A, Three-Dimensional Structure Of The Hypothetical Protein
From Salmonella Cholerae-Suis (Aka Salmonella Enterica)
At The Resolution 1.55 A. Northeast Structural Genomics
Target Scr59
Length = 154
Score = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 32/111 (28%), Positives = 50/111 (45%), Gaps = 18/111 (16%)
Query: 162 GEDVSSKIMSF-SQNGPRAVCILSANGAISNVTLR---QAATSGGTVTYEGRXXXXXXXX 217
G++V S++ +F QN RA I G++++V LR Q AT+ T T+E
Sbjct: 28 GQEVFSQLHAFVQQNQLRAAWIAGCTGSLTDVALRYAGQEATTSLTGTFE---------- 77
Query: 218 XXXXXXXXXQRSRTG-GLSVSLSGPDGRVLGGSVAGLLTAATPVQVVVGSF 267
TG L +++S P G LGG T T +++V+G
Sbjct: 78 ---VISLNGTLELTGEHLHLAVSDPYGVXLGGHXXPGCTVRTTLELVIGEL 125
>pdb|2NMU|A Chain A, Crystal Structure Of The Hypothetical Protein From
Salmonella Typhimurium Lt2. Northeast Structural
Genomics Consortium Target Str127
Length = 156
Score = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 32/111 (28%), Positives = 50/111 (45%), Gaps = 18/111 (16%)
Query: 162 GEDVSSKIMSF-SQNGPRAVCILSANGAISNVTLR---QAATSGGTVTYEGRXXXXXXXX 217
G++V S++ +F QN RA I G++++V LR Q AT+ T T+E
Sbjct: 28 GQEVFSQLHAFVQQNQLRAAWIAGCTGSLTDVALRYAGQEATTSLTGTFE---------- 77
Query: 218 XXXXXXXXXQRSRTG-GLSVSLSGPDGRVLGGSVAGLLTAATPVQVVVGSF 267
TG L +++S P G LGG T T +++V+G
Sbjct: 78 ---VISLNGTLELTGEHLHLAVSDPYGVXLGGHXXPGCTVRTTLELVIGEL 125
>pdb|2A79|B Chain B, Mammalian Shaker Kv1.2 Potassium Channel- Beta Subunit
Complex
Length = 499
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 243 GRVLGG--SVAGLLTAATPVQVVVGSFLADGRKESKSSHRMESLPV 286
G+++G ++AG+LT A PV V+V +F +E++ + + L V
Sbjct: 387 GKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQYLQV 432
>pdb|3LUT|B Chain B, A Structural Model For The Full-Length Shaker Potassium
Channel Kv1.2
Length = 499
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 243 GRVLGG--SVAGLLTAATPVQVVVGSFLADGRKESKSSHRMESLPV 286
G+++G ++AG+LT A PV V+V +F +E++ + + L V
Sbjct: 387 GKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQYLQV 432
>pdb|3LNM|B Chain B, F233w Mutant Of The Kv2.1 Paddle-Kv1.2 Chimera Channel
pdb|3LNM|D Chain D, F233w Mutant Of The Kv2.1 Paddle-Kv1.2 Chimera Channel
Length = 514
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 243 GRVLGG--SVAGLLTAATPVQVVVGSFLADGRKESKSSHRMESLPV 286
G+++G ++AG+LT A PV V+V +F +E++ + + L V
Sbjct: 402 GKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQYLQV 447
>pdb|2R9R|B Chain B, Shaker Family Voltage Dependent Potassium Channel
(Kv1.2-Kv2.1 Paddle Chimera Channel) In Association With
Beta Subunit
pdb|2R9R|H Chain H, Shaker Family Voltage Dependent Potassium Channel
(Kv1.2-Kv2.1 Paddle Chimera Channel) In Association With
Beta Subunit
Length = 514
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 243 GRVLGG--SVAGLLTAATPVQVVVGSFLADGRKESKSSHRMESLPV 286
G+++G ++AG+LT A PV V+V +F +E++ + + L V
Sbjct: 402 GKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQYLQV 447
>pdb|3BWL|A Chain A, Crystal Structure Of Pas Domain Of Htr-Like Protein From
Haloarcula Marismortui
pdb|3BWL|B Chain B, Crystal Structure Of Pas Domain Of Htr-Like Protein From
Haloarcula Marismortui
pdb|3BWL|C Chain C, Crystal Structure Of Pas Domain Of Htr-Like Protein From
Haloarcula Marismortui
pdb|3BWL|D Chain D, Crystal Structure Of Pas Domain Of Htr-Like Protein From
Haloarcula Marismortui
Length = 126
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 160 KAGEDVSSKIMSFSQNGPRAVCILSANGAISNVTLRQAATSG 201
K E+ SS++ + +N P + +L A+G I V R A G
Sbjct: 10 KRLEETSSRLEALFENSPDXIDVLDADGTICEVNQRFCAELG 51
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
0.310 0.127 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,495,256
Number of Sequences: 62578
Number of extensions: 254752
Number of successful extensions: 395
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 394
Number of HSP's gapped (non-prelim): 8
length of query: 342
length of database: 14,973,337
effective HSP length: 100
effective length of query: 242
effective length of database: 8,715,537
effective search space: 2109159954
effective search space used: 2109159954
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)