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= 004956
(722 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XQ2|B Chain B, Structure Of The K294a Mutant Of Vsglt
Length = 593
Score = 36.6 bits (83), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 27/40 (67%)
Query: 399 AVTSAGSSELIAVSSLCTYDIYRTYINPDASGEKILKVSR 438
A+ S+ +S L + +++ T DIY+ YI+PD+ K++ V R
Sbjct: 361 AIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGR 400
>pdb|3DH4|A Chain A, Crystal Structure Of SodiumSUGAR SYMPORTER WITH BOUND
GALACTOSE FROM Vibrio Parahaemolyticus
pdb|3DH4|B Chain B, Crystal Structure Of SodiumSUGAR SYMPORTER WITH BOUND
GALACTOSE FROM Vibrio Parahaemolyticus
pdb|3DH4|C Chain C, Crystal Structure Of SodiumSUGAR SYMPORTER WITH BOUND
GALACTOSE FROM Vibrio Parahaemolyticus
pdb|3DH4|D Chain D, Crystal Structure Of SodiumSUGAR SYMPORTER WITH BOUND
GALACTOSE FROM Vibrio Parahaemolyticus
Length = 530
Score = 36.6 bits (83), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 27/40 (67%)
Query: 399 AVTSAGSSELIAVSSLCTYDIYRTYINPDASGEKILKVSR 438
A+ S+ +S L + +++ T DIY+ YI+PD+ K++ V R
Sbjct: 332 AIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGR 371
>pdb|2XQ2|A Chain A, Structure Of The K294a Mutant Of Vsglt
Length = 593
Score = 36.6 bits (83), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 27/40 (67%)
Query: 399 AVTSAGSSELIAVSSLCTYDIYRTYINPDASGEKILKVSR 438
A+ S+ +S L + +++ T DIY+ YI+PD+ K++ V R
Sbjct: 361 AIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGR 400
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 37/185 (20%), Positives = 87/185 (47%), Gaps = 7/185 (3%)
Query: 38 LNQGVGYSVILGFGAFFAVFTSFLVWLEKRYVGSRHTSEWFNTAGRNVKTGLIASVIVSQ 97
+ G+ + I+ F + A+ +W+ + G++ ++E + AG+++ + + +++
Sbjct: 4 IEHGLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAA 63
Query: 98 WTWAATILQSSNVAWEYGVS-GPFWYASGATIQVLLFGVMAIEIKRKASHAHTVCEIVKA 156
A + S + G++ + + S T+ ++ + I I++ +T+ E V+
Sbjct: 64 NISAEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEK---GIYTIPEFVEK 120
Query: 157 RWGTAAHLVFLAFCFLTNIIV--TAMLLLGGSAVVNALTGVNIYAASFLIPLGVIVYTLA 214
R+ + F I V T++L LGG A + + G+ + + + L +VY++
Sbjct: 121 RFNKKLKTILAVFWISLYIFVNLTSVLYLGGLA-LETILGIPLMYSILGLALFALVYSIY 179
Query: 215 GGLKA 219
GGL A
Sbjct: 180 GGLSA 184
>pdb|2NYB|A Chain A, Crystal Structure Of E.Coli Iron Superoxide Dismutase Q69e
At 1.1 Angstrom Resolution
pdb|2NYB|B Chain B, Crystal Structure Of E.Coli Iron Superoxide Dismutase Q69e
At 1.1 Angstrom Resolution
pdb|2NYB|C Chain C, Crystal Structure Of E.Coli Iron Superoxide Dismutase Q69e
At 1.1 Angstrom Resolution
pdb|2NYB|D Chain D, Crystal Structure Of E.Coli Iron Superoxide Dismutase Q69e
At 1.1 Angstrom Resolution
pdb|2BKB|A Chain A, Q69e-Fesod
pdb|2BKB|B Chain B, Q69e-Fesod
pdb|2BKB|C Chain C, Q69e-Fesod
pdb|2BKB|D Chain D, Q69e-Fesod
Length = 192
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 411 VSSLCTYDIYRTYINPDASGEKILKVSRAVILGFGCFMGFLAVILNKA--GVSLGWMYL 467
+ + + Y + P+A GE KV+ A+ FG F F A + A GW +L
Sbjct: 67 AAEVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWL 125
>pdb|1ISA|A Chain A, Structure-Function In E. Coli Iron Superoxide Dismutase:
Comparisons With The Manganese Enzyme From T.
Thermophilus
pdb|1ISA|B Chain B, Structure-Function In E. Coli Iron Superoxide Dismutase:
Comparisons With The Manganese Enzyme From T.
Thermophilus
pdb|1ISB|A Chain A, Structure-Function In E. Coli Iron Superoxide Dismutase:
Comparisons With The Manganese Enzyme From T.
Thermophilus
pdb|1ISB|B Chain B, Structure-Function In E. Coli Iron Superoxide Dismutase:
Comparisons With The Manganese Enzyme From T.
Thermophilus
pdb|1ISC|A Chain A, Structure-Function In E. Coli Iron Superoxide Dismutase:
Comparisons With The Manganese Enzyme From T.
Thermophilus
pdb|1ISC|B Chain B, Structure-Function In E. Coli Iron Superoxide Dismutase:
Comparisons With The Manganese Enzyme From T.
Thermophilus
Length = 192
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 411 VSSLCTYDIYRTYINPDASGEKILKVSRAVILGFGCFMGFLAVILNKA--GVSLGWMYL 467
+ + + Y + P+A GE KV+ A+ FG F F A + A GW +L
Sbjct: 67 AAQVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWL 125
>pdb|1ZA5|A Chain A, Q69h-Fesod
pdb|1ZA5|B Chain B, Q69h-Fesod
Length = 192
Score = 30.4 bits (67), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 416 TYDIYRTYINPDASGEKILKVSRAVILGFGCFMGFLAVILNKA--GVSLGWMYL 467
+ Y + P+A GE KV+ A+ FG F F A + A GW +L
Sbjct: 72 NHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWL 125
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
0.324 0.137 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,124,006
Number of Sequences: 62578
Number of extensions: 715953
Number of successful extensions: 1759
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1749
Number of HSP's gapped (non-prelim): 12
length of query: 722
length of database: 14,973,337
effective HSP length: 106
effective length of query: 616
effective length of database: 8,340,069
effective search space: 5137482504
effective search space used: 5137482504
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.8 bits)