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= 009538
(532 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter
Length = 524
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 101/440 (22%), Positives = 183/440 (41%), Gaps = 55/440 (12%)
Query: 1 MKSITATTLINIFSGTTNFATLLGAFLSDTYFGRYKTLGFASVASFLGMLVLSLTAAISK 60
++ A + + F F LLG +++D +FG+Y T+ L LSL +
Sbjct: 51 LRGAVAKDVFHSFVIGVYFFPLLGGWIADRFFGKYNTI-----------LWLSLIYCVGH 99
Query: 61 LHPPDCGNQDSGACPGPTPWQLAFLFTGLGLMVIGAGGIRPCNLAFGADQFNPNTESGKQ 120
+ G +TGL L+ +G+GGI+P +F DQF+ + +S Q
Sbjct: 100 AFLAIFEHSVQG------------FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQ 147
Query: 121 GITSFFNWYYFTFTFAMMISLTVIVYVQSDVSWAWGLGIPAFMMFLSCAMFFLGSRLYAK 180
F+ +YFT F + + + + A GIP +MF++ F+LG + Y
Sbjct: 148 ---KAFDMFYFTINFGSFFASLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIH 204
Query: 181 VKPE-GSPLASTVQVFVAAIKKRHLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKA 239
+ PE P + A + K K L L + +P G L A
Sbjct: 205 MPPEPKDPHGFLPVIRSALLTKVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCA 264
Query: 240 AIMTPEDQIKSDGSAINPWRLSSMQ---KVEEVKVLIRVIPIWASAIVYYVALVQQQTYV 296
++ G+++ R V+ V+ ++R++ ++A ++ Q+ +
Sbjct: 265 MVLV--MGFVGAGASLQLERARKSHPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTW 322
Query: 297 VFQALQSDRRVGNTHFKIPAASYAIFSMLGLTIWIPIYDRIIVPRLQRLTKKEGGITILQ 356
+ LQ++ V F+ PA A+ +L + + IP + ++ P ++R+ K +T L+
Sbjct: 323 I---LQANDMVKPQWFE-PAMMQALNPLL-VMLLIPFNNFVLYPAIERMGVK---LTALR 374
Query: 357 RMAIGMILAIFTMIISGIIEDKRRSLALSRPVGLEQRRGAISSLSGLWLIPQLSLIGFSE 416
+M G+ + + I+ G I+ L G S+LS W I +L+ F E
Sbjct: 375 KMGAGIAITGLSWIVVGTIQ-------------LMMDGG--SALSIFWQILPYALLTFGE 419
Query: 417 AFTIIAEVEFYYKQFPENMR 436
+EF Y Q P+ M+
Sbjct: 420 VLVSATGLEFAYSQAPKAMK 439
>pdb|3QPT|A Chain A, Crystal Structure Of The Salmonella Transcriptional
Regulator Slya
Length = 147
Score = 32.0 bits (71), Expect = 0.82, Method: Composition-based stats.
Identities = 30/109 (27%), Positives = 49/109 (44%), Gaps = 14/109 (12%)
Query: 179 AKVKPEGSPLASTVQVFVAAIKKR--HLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCL 236
A P GS LA V+++ A I R L+L + W+TLHN I+ P Q +
Sbjct: 3 AXESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHN------IHQLPPDQSQIQLA 56
Query: 237 DKAAIMTPE-----DQIKSDGSAINPWRLSSMQKVEEVKVLIRVIPIWA 280
I P DQ++ G I+ +S ++ + +K+ + P+ A
Sbjct: 57 KAIGIEQPSLVRTLDQLEDKG-LISRQTCASDRRAKRIKLTEKAEPLIA 104
>pdb|3Q5F|A Chain A, Crystal Structure Of The Salmonella Transcriptional
Regulator Slya In Complex With Dna
pdb|3Q5F|B Chain B, Crystal Structure Of The Salmonella Transcriptional
Regulator Slya In Complex With Dna
Length = 147
Score = 31.6 bits (70), Expect = 1.0, Method: Composition-based stats.
Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 14/105 (13%)
Query: 183 PEGSPLASTVQVFVAAIKKR--HLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAA 240
P GS LA V+++ A I R L+L + W+TLHN I+ P Q +
Sbjct: 7 PLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHN------IHQLPPDQSQIQLAKAIG 60
Query: 241 IMTPE-----DQIKSDGSAINPWRLSSMQKVEEVKVLIRVIPIWA 280
I P DQ++ G I+ +S ++ + +K+ + P+ A
Sbjct: 61 IEQPSLVRTLDQLEDKG-LISRQTCASDRRAKRIKLTEKAEPLIA 104
>pdb|3DEU|A Chain A, Crystal Structure Of Transcription Regulatory Protein Slya
From Salmonella Typhimurium In Complex With Salicylate
Ligands
pdb|3DEU|B Chain B, Crystal Structure Of Transcription Regulatory Protein Slya
From Salmonella Typhimurium In Complex With Salicylate
Ligands
Length = 166
Score = 31.6 bits (70), Expect = 1.0, Method: Composition-based stats.
Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 14/105 (13%)
Query: 183 PEGSPLASTVQVFVAAIKKR--HLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAA 240
P GS LA V+++ A I R L+L + W+TLHN I+ P Q +
Sbjct: 26 PLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHN------IHQLPPDQSQIQLAKAIG 79
Query: 241 IMTPE-----DQIKSDGSAINPWRLSSMQKVEEVKVLIRVIPIWA 280
I P DQ++ G I+ +S ++ + +K+ + P+ A
Sbjct: 80 IEQPSLVRTLDQLEDKG-LISRQTCASDRRAKRIKLTEKAEPLIA 123
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 0.139 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,313,190
Number of Sequences: 62578
Number of extensions: 615262
Number of successful extensions: 1264
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1260
Number of HSP's gapped (non-prelim): 8
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)