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= 040051
(590 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 62/291 (21%), Positives = 121/291 (41%), Gaps = 19/291 (6%)
Query: 104 KHAGPAIVLSYVASGVSAMLSVFCYTEFAIEIPVAGGSFAYLRIELGDFAAFIT-AGNIL 162
K AG + +++ SG+ A+L + YT+ +I G A++ +GD IT A +IL
Sbjct: 35 KIAGRNLPETFILSGIYALLVAYSYTKLGAKIVSNAGPIAFIHKAIGD--NIITGALSIL 92
Query: 163 L--ESIVGGAAVARAWTSYFTTLLNREPNSLRIHTNLREGYNLLDPXXXXXXXXXXXXXX 220
L ++ A A+ + YF L+N N+ I
Sbjct: 93 LWMSYVISIALFAKGFAGYFLPLINAPINTFNIAIT-----------EIGIVAFFTALNF 141
Query: 221 XXXRKTSVLNWIASAINTVVILFVIIVGFAHADASNLKPFL-PFGSEGIFKAAAVVYFAY 279
+ + + +++ I G S + P L P G+ A+A+ + +Y
Sbjct: 142 FGSKAVGRAEFFIVLVKLLILGLFIFAGLITIHPSYVIPDLAPSAVSGMIFASAIFFLSY 201
Query: 280 GGFDNIATMAEETKNPSRDIPIGLLGSMSMITIIYCLMALSLCVMQPYTDIDPNA--AYS 337
GF I +E +NP +++P + S+ ++ +Y +A+S P ++ + A +
Sbjct: 202 MGFGVITNASEHIENPKKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALA 261
Query: 338 VAFQRVGMKWAKYLVALGALKGMTTVLLVGALGNARYTTHIARAHMIPPWF 388
VA + L+++GAL +++ + G A +A+ +P +F
Sbjct: 262 VAAKPFLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFF 312
>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
Monoclonal Fab Fragment
Length = 444
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 62/291 (21%), Positives = 121/291 (41%), Gaps = 19/291 (6%)
Query: 104 KHAGPAIVLSYVASGVSAMLSVFCYTEFAIEIPVAGGSFAYLRIELGDFAAFIT-AGNIL 162
K AG + +++ SG+ A+L + YT+ +I G A++ +GD IT A +IL
Sbjct: 35 KIAGRNLPETFILSGIYALLVAYSYTKLGAKIVSNAGPIAFIHKAIGD--NIITGALSIL 92
Query: 163 L--ESIVGGAAVARAWTSYFTTLLNREPNSLRIHTNLREGYNLLDPXXXXXXXXXXXXXX 220
L ++ A A+ + YF L+N N+ I
Sbjct: 93 LWMSYVISIALFAKGFAGYFLPLINAPINTFNIAIT-----------EIGIVAFFTALNF 141
Query: 221 XXXRKTSVLNWIASAINTVVILFVIIVGFAHADASNLKPFL-PFGSEGIFKAAAVVYFAY 279
+ + + +++ I G S + P L P G+ A+A+ + +Y
Sbjct: 142 FGSKAVGRAEFFIVLVALLILGLFIFAGLITIHPSYVIPDLAPSAVSGMIFASAIFFLSY 201
Query: 280 GGFDNIATMAEETKNPSRDIPIGLLGSMSMITIIYCLMALSLCVMQPYTDIDPNA--AYS 337
GF I +E +NP +++P + S+ ++ +Y +A+S P ++ + A +
Sbjct: 202 MGFGVITNASEHIENPKKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALA 261
Query: 338 VAFQRVGMKWAKYLVALGALKGMTTVLLVGALGNARYTTHIARAHMIPPWF 388
VA + L+++GAL +++ + G A +A+ +P +F
Sbjct: 262 VAAKPFLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFF 312
>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 = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 65/148 (43%), Gaps = 8/148 (5%)
Query: 258 KPFLP-FGSEGIFKAAAVVYFAYGGFDNIATMAEETKNPSRDIPIGLLGSMSMITIIYCL 316
K F P F G +Y G + AT E NP RD P+ +L M + +
Sbjct: 192 KTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSV 251
Query: 317 MALSLCVMQPYTDIDPNAA----YSVAFQRVG--MKWAKYLVALGALKGMTTVLLVGALG 370
LS+ ++ P +I+ +A ++V V ++W +++ L G+ + +G
Sbjct: 252 GGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVG 311
Query: 371 NARYTTHIARAHMIPPWFALVHPKTGTP 398
+R A+ +++P FA ++ K G P
Sbjct: 312 PSRGMYVTAQKNLLPAAFAKMN-KNGVP 338
>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 = 36.2 bits (82), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 70/294 (23%), Positives = 119/294 (40%), Gaps = 53/294 (18%)
Query: 128 YTEFAIEIPVAGGSFAYLRIELGDFAAFITAGNIL--LESIVGGAA---VARAWTSYFTT 182
Y + + P GGS+AY R G F + T N+L L +G A + + SYF
Sbjct: 60 YAKMSFLDPSPGGSYAYARRCFGPFLGYQT--NVLYWLACWIGAIAMVVIGVGYLSYFFP 117
Query: 183 LLNREPNSLRIHTN----LREGYNLLDPXXXXXXXXXXXXXXXXXRKTSVLNWIASAINT 238
+L ++P L I + N++ P + + + +A+ +
Sbjct: 118 IL-KDPLVLTITCVVVLWIFVLLNIVGP-----------------KMITRVQAVATVLAL 159
Query: 239 VVILFVIIVGF------AHADASNLKPFLPFGSEGIFKAAAVVYFAYGGFDNIATMAEET 292
+ I+ + + G+ + A N+ FG+ I V +++ G ++ + A
Sbjct: 160 IPIVGIAVFGWFWFRGETYMAAWNVSGLGTFGA--IQSTLNVTLWSFIGVESASVAAGVV 217
Query: 293 KNPSRDIPIGLLGSMSMITIIYCLMALSLCVMQPYTDIDPNA-----AYSVAFQRVGMKW 347
KNP R++PI +G + + + Y L ++ M P + +A A +A
Sbjct: 218 KNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAGAI 277
Query: 348 AKYLVA---LGALKGMTTVLLVGALGNARYTTHIARAHMIPPWFALVHPKTGTP 398
+ A LG+L G T LL G A A + PP FA V+ K GTP
Sbjct: 278 VSFCAAAGCLGSLGGWT--LLAGQTAKAA-----ADDGLFPPIFARVN-KAGTP 323
>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 = 36.2 bits (82), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 70/294 (23%), Positives = 119/294 (40%), Gaps = 53/294 (18%)
Query: 128 YTEFAIEIPVAGGSFAYLRIELGDFAAFITAGNIL--LESIVGGAA---VARAWTSYFTT 182
Y + + P GGS+AY R G F + T N+L L +G A + + SYF
Sbjct: 60 YAKMSFLDPSPGGSYAYARRCFGPFLGYQT--NVLYWLACWIGNIAMVVIGVGYLSYFFP 117
Query: 183 LLNREPNSLRIHTN----LREGYNLLDPXXXXXXXXXXXXXXXXXRKTSVLNWIASAINT 238
+L ++P L I + N++ P + + + +A+ +
Sbjct: 118 IL-KDPLVLTITCVVVLWIFVLLNIVGP-----------------KMITRVQAVATVLAL 159
Query: 239 VVILFVIIVGF------AHADASNLKPFLPFGSEGIFKAAAVVYFAYGGFDNIATMAEET 292
+ I+ + + G+ + A N+ FG+ I V +++ G ++ + A
Sbjct: 160 IPIVGIAVFGWFWFRGETYMAAWNVSGLGTFGA--IQSTLNVTLWSFIGVESASVAAGVV 217
Query: 293 KNPSRDIPIGLLGSMSMITIIYCLMALSLCVMQPYTDIDPNA-----AYSVAFQRVGMKW 347
KNP R++PI +G + + + Y L ++ M P + +A A +A
Sbjct: 218 KNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAGAI 277
Query: 348 AKYLVA---LGALKGMTTVLLVGALGNARYTTHIARAHMIPPWFALVHPKTGTP 398
+ A LG+L G T LL G A A + PP FA V+ K GTP
Sbjct: 278 VSFCAAAGCLGSLGGWT--LLAGQTAKAA-----ADDGLFPPIFARVN-KAGTP 323
>pdb|3L1L|A Chain A, Structure Of Arg-Bound Escherichia Coli Adic
Length = 445
Score = 35.8 bits (81), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 70/294 (23%), Positives = 119/294 (40%), Gaps = 53/294 (18%)
Query: 128 YTEFAIEIPVAGGSFAYLRIELGDFAAFITAGNIL--LESIVGGAA---VARAWTSYFTT 182
Y + + P GGS+AY R G F + T N+L L +G A + + SYF
Sbjct: 60 YAKMSFLDPSPGGSYAYARRCFGPFLGYQT--NVLYWLACWIGNIAMVVIGVGYLSYFFP 117
Query: 183 LLNREPNSLRIHTN----LREGYNLLDPXXXXXXXXXXXXXXXXXRKTSVLNWIASAINT 238
+L ++P L I + N++ P + + + +A+ +
Sbjct: 118 IL-KDPWVLTITCVVVLWIFVLLNIVGP-----------------KMITRVQAVATVLAL 159
Query: 239 VVILFVIIVGF------AHADASNLKPFLPFGSEGIFKAAAVVYFAYGGFDNIATMAEET 292
+ I+ + + G+ + A N+ FG+ I V +++ G ++ + A
Sbjct: 160 IPIVGIAVFGWFWFRGETYMAAWNVSGLGTFGA--IQSTLNVTLWSFIGVESASVAAGVV 217
Query: 293 KNPSRDIPIGLLGSMSMITIIYCLMALSLCVMQPYTDIDPNA-----AYSVAFQRVGMKW 347
KNP R++PI +G + + + Y L ++ M P + +A A +A
Sbjct: 218 KNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAGAI 277
Query: 348 AKYLVA---LGALKGMTTVLLVGALGNARYTTHIARAHMIPPWFALVHPKTGTP 398
+ A LG+L G T LL G A A + PP FA V+ K GTP
Sbjct: 278 VSFCAAAGCLGSLGGWT--LLAGQTAKAA-----ADDGLFPPIFARVN-KAGTP 323
>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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 16/133 (12%)
Query: 274 VVYFAYGGFDNIATMAEETKNPSRDIPIGLLGSMSMITIIYCLMALSLCVMQPYTDIDPN 333
V +++ G ++ + A KNP R++PI +G + + + Y L ++ M P + +
Sbjct: 199 VTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVS 258
Query: 334 A-----AYSVAFQRVGMKWAKYLVA---LGALKGMTTVLLVGALGNARYTTHIARAHMIP 385
A A +A + A LG+L G T LL G A A + P
Sbjct: 259 ASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWT--LLAGQTAKAA-----ADDGLFP 311
Query: 386 PWFALVHPKTGTP 398
P FA V+ K GTP
Sbjct: 312 PIFARVN-KAGTP 323
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 0.138 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,695,003
Number of Sequences: 62578
Number of extensions: 573042
Number of successful extensions: 1299
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: 1282
Number of HSP's gapped (non-prelim): 16
length of query: 590
length of database: 14,973,337
effective HSP length: 104
effective length of query: 486
effective length of database: 8,465,225
effective search space: 4114099350
effective search space used: 4114099350
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)