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= 007398
(605 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
Monoclonal Fab Fragment
Length = 444
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 56/235 (23%), Positives = 93/235 (39%), Gaps = 18/235 (7%)
Query: 69 EMK-KTLTWWDLXXXXXXXXXXXXXXXLTGQEARQEAGPAVVLSFVVSGLSAMLSVFCYT 127
E+K K L+ W+ + G A+ AG + +F++SG+ A+L + YT
Sbjct: 2 ELKNKKLSLWEAVSMAVGVMIGASIFSIFGVGAKI-AGRNLPETFILSGIYALLVAYSYT 60
Query: 128 EFAVEIPVAGGSFAYLRVELGDFVAFVAAGNILL--EYVIGGAAVARSWTSYFATLCNKQ 185
+ +I G A++ +GD + A +ILL YVI A A+ + YF L N
Sbjct: 61 KLGAKIVSNAGPIAFIHKAIGDNI-ITGALSILLWMSYVISIALFAKGFAGYFLPLINAP 119
Query: 186 PEDFRIIVHSMPEDYGQLDPIAVGVSAVICILAVVSTKGSSRFNYXXXXXXXXXXXXXXX 245
F I + +G+ A L +K R +
Sbjct: 120 INTFNIAITE------------IGIVAFFTALNFFGSKAVGRAEFFIVLVALLILGLFIF 167
Query: 246 XXXXNAD-TKNYKAFAPFGTRGVFKASAVLFFAYIGFDAVSTMAEETKNPAKDIP 299
+ AP G+ ASA+ F +Y+GF ++ +E +NP K++P
Sbjct: 168 AGLITIHPSYVIPDLAPSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVP 222
>pdb|3GI9|C Chain C, Crystal Structure Of Apct Transporter Bound To 7f11
Monoclonal Fab Fragment
pdb|3GIA|A Chain A, Crystal Structure Of Apct Transporter
Length = 444
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 56/235 (23%), Positives = 93/235 (39%), Gaps = 18/235 (7%)
Query: 69 EMK-KTLTWWDLXXXXXXXXXXXXXXXLTGQEARQEAGPAVVLSFVVSGLSAMLSVFCYT 127
E+K K L+ W+ + G A+ AG + +F++SG+ A+L + YT
Sbjct: 2 ELKNKKLSLWEAVSMAVGVMIGASIFSIFGVGAKI-AGRNLPETFILSGIYALLVAYSYT 60
Query: 128 EFAVEIPVAGGSFAYLRVELGDFVAFVAAGNILL--EYVIGGAAVARSWTSYFATLCNKQ 185
+ +I G A++ +GD + A +ILL YVI A A+ + YF L N
Sbjct: 61 KLGAKIVSNAGPIAFIHKAIGDNI-ITGALSILLWMSYVISIALFAKGFAGYFLPLINAP 119
Query: 186 PEDFRIIVHSMPEDYGQLDPIAVGVSAVICILAVVSTKGSSRFNYXXXXXXXXXXXXXXX 245
F I + +G+ A L +K R +
Sbjct: 120 INTFNIAITE------------IGIVAFFTALNFFGSKAVGRAEFFIVLVKLLILGLFIF 167
Query: 246 XXXXNAD-TKNYKAFAPFGTRGVFKASAVLFFAYIGFDAVSTMAEETKNPAKDIP 299
+ AP G+ ASA+ F +Y+GF ++ +E +NP K++P
Sbjct: 168 AGLITIHPSYVIPDLAPSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVP 222
>pdb|3LRB|A Chain A, Structure Of E. Coli Adic
pdb|3LRB|B Chain B, Structure Of E. Coli Adic
pdb|3LRC|A Chain A, Structure Of E. Coli Adic (P1)
pdb|3LRC|B Chain B, Structure Of E. Coli Adic (P1)
pdb|3LRC|C Chain C, Structure Of E. Coli Adic (P1)
pdb|3LRC|D Chain D, Structure Of E. Coli Adic (P1)
Length = 445
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 40/145 (27%), Positives = 64/145 (44%), Gaps = 3/145 (2%)
Query: 262 FGTRGVFKASA-VLFFAYIGFDAVSTMAEETKNPAKDIPIGLVGSMAVTTXXXXXXXXXX 320
GT G +++ V +++IG ++ S A KNP +++PI +G + +
Sbjct: 187 LGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAI 246
Query: 321 XXMQPYYAINVDA-PFSVAFEAVGWDWAKYVVAFGALKGMTTVLLVSAVGQARYLTHIAR 379
M P A+ V A PF A D A +V+F A G L + + A
Sbjct: 247 MGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAAD 306
Query: 380 THMMPPWLAQVHGKTGTPVNATIVM 404
+ PP A+V+ K GTPV I++
Sbjct: 307 DGLFPPIFARVN-KAGTPVAGLIIV 330
>pdb|3OB6|A Chain A, Structure Of Adic(N101a) In The Open-To-Out Arg+ Bound
Conformation
pdb|3OB6|B Chain B, Structure Of Adic(N101a) In The Open-To-Out Arg+ Bound
Conformation
Length = 445
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 40/145 (27%), Positives = 64/145 (44%), Gaps = 3/145 (2%)
Query: 262 FGTRGVFKASA-VLFFAYIGFDAVSTMAEETKNPAKDIPIGLVGSMAVTTXXXXXXXXXX 320
GT G +++ V +++IG ++ S A KNP +++PI +G + +
Sbjct: 187 LGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAI 246
Query: 321 XXMQPYYAINVDA-PFSVAFEAVGWDWAKYVVAFGALKGMTTVLLVSAVGQARYLTHIAR 379
M P A+ V A PF A D A +V+F A G L + + A
Sbjct: 247 MGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAAD 306
Query: 380 THMMPPWLAQVHGKTGTPVNATIVM 404
+ PP A+V+ K GTPV I++
Sbjct: 307 DGLFPPIFARVN-KAGTPVAGLIIV 330
>pdb|3L1L|A Chain A, Structure Of Arg-Bound Escherichia Coli Adic
Length = 445
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 40/145 (27%), Positives = 64/145 (44%), Gaps = 3/145 (2%)
Query: 262 FGTRGVFKASA-VLFFAYIGFDAVSTMAEETKNPAKDIPIGLVGSMAVTTXXXXXXXXXX 320
GT G +++ V +++IG ++ S A KNP +++PI +G + +
Sbjct: 187 LGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAI 246
Query: 321 XXMQPYYAINVDA-PFSVAFEAVGWDWAKYVVAFGALKGMTTVLLVSAVGQARYLTHIAR 379
M P A+ V A PF A D A +V+F A G L + + A
Sbjct: 247 MGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAAD 306
Query: 380 THMMPPWLAQVHGKTGTPVNATIVM 404
+ PP A+V+ K GTPV I++
Sbjct: 307 DGLFPPIFARVN-KAGTPVAGLIIV 330
>pdb|3NCY|A Chain A, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
pdb|3NCY|B Chain B, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
pdb|3NCY|C Chain C, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
pdb|3NCY|D Chain D, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
Length = 445
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 76/177 (42%), Gaps = 9/177 (5%)
Query: 273 VLFFAYIGFDAVSTMAEETKNPAKDIPIGLVGSMAVTTXXXXXXXXXXXXMQPYYAINVD 332
V +++IG ++ S A KNP +++PI +G + + M P A+ V
Sbjct: 199 VTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVS 258
Query: 333 A-PFSVAFEAVGWDWAKYVVAFGALKGMTTVLLVSAVGQARYLTHIARTHMMPPWLAQVH 391
A PF A D A +V+F A G L + + A + PP A+V+
Sbjct: 259 ASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVN 318
Query: 392 GKTGTPVNATIVMLTATAIIAFFT-------KLNVLSNLLSISTLFIFMLVAVALLV 441
K GTPV +++ I F + + ++S++ I TL ++ ALL+
Sbjct: 319 -KAGTPVAGLLIVGVLMTIFQFSSMSPNAAKEFGLVSSVSVIFTLVPYLYTCAALLL 374
>pdb|4DJI|A Chain A, Structure Of Glutamate-Gaba Antiporter Gadc
pdb|4DJI|B Chain B, Structure Of Glutamate-Gaba Antiporter Gadc
pdb|4DJK|A Chain A, Structure Of Glutamate-Gaba Antiporter Gadc
pdb|4DJK|B Chain B, Structure Of Glutamate-Gaba Antiporter Gadc
Length = 511
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 43/166 (25%), Positives = 72/166 (43%), Gaps = 11/166 (6%)
Query: 252 DTKNY-KAFAPFGTRGVFKASAVLFFAYIGFDAVSTMAEETKNPAKDIPIGLVGSMAVTT 310
D+K + F+ GT VF A +Y+G +A +T E NP +D P+ ++ M
Sbjct: 190 DSKTFFPDFSKVGTLVVFVA---FILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAI 246
Query: 311 XXXXXXXXXXXXMQPYYAINVDA----PFSVAFEAVG--WDWAKYVVAFGALKGMTTVLL 364
+ P IN+ A F+V V +W V++ L G+ +
Sbjct: 247 CLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIA 306
Query: 365 VSAVGQARYLTHIARTHMMPPWLAQVHGKTGTPVNATIVMLTATAI 410
VG +R + A+ +++P A+++ K G PV I L T+I
Sbjct: 307 SWIVGPSRGMYVTAQKNLLPAAFAKMN-KNGVPVTLVISQLVITSI 351
>pdb|4E4U|A Chain A, Crystal Structure Of A Putative Mandelate RacemaseMUCONATE
Lactonizing Enzyme (Target Psi-200780) From Burkholderia
Sar-1
Length = 412
Score = 29.3 bits (64), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 16 SCTKNDFLPEESFRSWGNYVQALKATPLRLKD 47
+CT N FL +ES +WG + + TP+R +D
Sbjct: 325 TCTPN-FLIQESIMTWGGFHAEVVKTPIRWED 355
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 0.135 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,504,656
Number of Sequences: 62578
Number of extensions: 553460
Number of successful extensions: 1131
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1114
Number of HSP's gapped (non-prelim): 16
length of query: 605
length of database: 14,973,337
effective HSP length: 104
effective length of query: 501
effective length of database: 8,465,225
effective search space: 4241077725
effective search space used: 4241077725
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)