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= 007827
(588 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 = 86.7 bits (213), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 109/479 (22%), Positives = 199/479 (41%), Gaps = 61/479 (12%)
Query: 24 KSMPFVIGNETFEKLGTTGTSSNLLVYLTTIF------NMKSITATTLINIFSGTTNFAT 77
+ +P++I +E E+ G + L +L T ++ A + + F F
Sbjct: 12 RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFP 71
Query: 78 LLGAFLSDTYFGRYKTLGFASVASFLGMLVLSLTAAISKLHPPDCGNQDSGACPGPTPWQ 137
LLG +++D +FG+Y T+ L LSL + + G
Sbjct: 72 LLGGWIADRFFGKYNTI-----------LWLSLIYCVGHAFLAIFEHSVQG--------- 111
Query: 138 LAFLFTGLGLMVIGAGGIRPCNLAFGADQFNPNTESGKQGITSFFNWYYFTFTFAMMISL 197
+TGL L+ +G+GGI+P +F DQF+ + +S Q F+ +YFT F +
Sbjct: 112 ---FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQ---KAFDMFYFTINFGSFFAS 165
Query: 198 TVIVYVQSDVSWAWGLGIPAFMMFLSCAMFFLGSRLYAKVKPE-GSPLASTVQVFVAAIK 256
+ + + A GIP +MF++ F+LG + Y + PE P + A +
Sbjct: 166 LSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLT 225
Query: 257 KRHLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAAIMTPEDQIKSDGSAINPWRL 316
K K L L + +P G L A ++ G+++ R
Sbjct: 226 KVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLV--MGFVGAGASLQLERA 283
Query: 317 SSMQ---KVEEVKVLIRVIPIWASAIVYYVALVQQQTYVVFQALQSDRRVGNTHFKIPAA 373
V+ V+ ++R++ ++A ++ Q+ + + LQ++ V F+ PA
Sbjct: 284 RKSHPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWI---LQANDMVKPQWFE-PAM 339
Query: 374 SYAIFSMLGLTIWIPIYDRIIVPRLQRLTKKEGGITILQRMAIGMILAIFTMIISGIIED 433
A+ +L + + IP + ++ P ++R+ K +T L++M G+ + + I+ G I+
Sbjct: 340 MQALNPLL-VMLLIPFNNFVLYPAIERMGVK---LTALRKMGAGIAITGLSWIVVGTIQ- 394
Query: 434 KRRSLALSRPVGLEQRRGAISSLSGLWLIPQLSLIGFSEAFTIIAEVEFYYKQFPENMR 492
L G S+LS W I +L+ F E +EF Y Q P+ M+
Sbjct: 395 ------------LMMDGG--SALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMK 439
>pdb|3QPT|A Chain A, Crystal Structure Of The Salmonella Transcriptional
Regulator Slya
Length = 147
Score = 32.0 bits (71), Expect = 0.92, Method: Composition-based stats.
Identities = 30/109 (27%), Positives = 49/109 (44%), Gaps = 14/109 (12%)
Query: 235 AKVKPEGSPLASTVQVFVAAIKKR--HLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCL 292
A P GS LA V+++ A I R L+L + W+TLHN I+ P Q +
Sbjct: 3 AXESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHN------IHQLPPDQSQIQLA 56
Query: 293 DKAAIMTPE-----DQIKSDGSAINPWRLSSMQKVEEVKVLIRVIPIWA 336
I P DQ++ G I+ +S ++ + +K+ + P+ A
Sbjct: 57 KAIGIEQPSLVRTLDQLEDKG-LISRQTCASDRRAKRIKLTEKAEPLIA 104
>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
An Inward Open Conformation.
pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
An Inward Open Conformation
Length = 491
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 63/347 (18%), Positives = 129/347 (37%), Gaps = 71/347 (20%)
Query: 32 NETFEKLGTTGTSSNLLVYL-----TTIFNMKSITATTLINIFSGTTNFATLLGAFLSDT 86
E +E+ G + LL Y+ T ++ TA +++ I++ + +G F++D
Sbjct: 21 TEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADR 80
Query: 87 YFGRYKTLGFASVASFLGMLVLSLTAAISKLHPPDCGNQDSGACPGPTPWQLAFLFTGLG 146
G + + V LG +VL+L P+ + LF +
Sbjct: 81 IIGARPAVFWGGVLIMLGHIVLAL------------------------PFGASALFGSII 116
Query: 147 LMVIGAGGIRPCNLAFGADQFNPNTESGKQGITSFFNWYYFTFTFAMMISLTVIVYVQSD 206
L++IG G ++P ++ + G F+ + F I+ ++ Q
Sbjct: 117 LIIIGTGFLKPNVSTLVGTLYDEHDRRRDAG----FSIFVFGINLGAFIAPLIVGAAQEA 172
Query: 207 VSWAWGLGIPAFMMFLSCAMFFLGSRLYAK---VKP-------EGSPLASTVQVFVAAIK 256
+ + A MF+ +++ G + ++P E PL V + VA
Sbjct: 173 AGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFI 232
Query: 257 KRHLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAAIMTPEDQIKSDGSAINPWRL 316
+ + W +L +I L AI P W +
Sbjct: 233 AIIVVMNLVGWNSLPAYI---------------NLLTIVAIAIPVFYFA--------WMI 269
Query: 317 SSMQ--KVEEVKVLIRVIPIWASAIVYYVALVQQQTYVVFQALQSDR 361
SS++ E ++V + IP++ +A++++ +++Q VV ++R
Sbjct: 270 SSVKVTSTEHLRV-VSYIPLFIAAVLFWA--IEEQGSVVLATFAAER 313
>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 = 1.2, Method: Composition-based stats.
Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 14/105 (13%)
Query: 239 PEGSPLASTVQVFVAAIKKR--HLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAA 296
P GS LA V+++ A I R L+L + W+TLHN I+ P Q +
Sbjct: 7 PLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHN------IHQLPPDQSQIQLAKAIG 60
Query: 297 IMTPE-----DQIKSDGSAINPWRLSSMQKVEEVKVLIRVIPIWA 336
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 = 1.2, Method: Composition-based stats.
Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 14/105 (13%)
Query: 239 PEGSPLASTVQVFVAAIKKR--HLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAA 296
P GS LA V+++ A I R L+L + W+TLHN I+ P Q +
Sbjct: 26 PLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHN------IHQLPPDQSQIQLAKAIG 79
Query: 297 IMTPE-----DQIKSDGSAINPWRLSSMQKVEEVKVLIRVIPIWA 336
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
0.323 0.138 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,921,482
Number of Sequences: 62578
Number of extensions: 680295
Number of successful extensions: 1094
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: 1090
Number of HSP's gapped (non-prelim): 8
length of query: 588
length of database: 14,973,337
effective HSP length: 104
effective length of query: 484
effective length of database: 8,465,225
effective search space: 4097168900
effective search space used: 4097168900
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)