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= 039800
(576 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 = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 77/350 (22%), Positives = 153/350 (43%), Gaps = 29/350 (8%)
Query: 53 RKTLRWYDLVCFGIGGMVGAGVFVTTGRASRLNAGPAIVISYAIAGLCALLSAFCYTEFA 112
K L ++ V +G M+GA +F G +++ AG + ++ ++G+ ALL A+ YT+
Sbjct: 5 NKKLSLWEAVSMAVGVMIGASIFSIFGVGAKI-AGRNLPETFILSGIYALLVAYSYTKLG 63
Query: 113 VDMPVAGGAFSYLRVTFGEFAAFLTGSNLIL---EYVMSNAAVARGFASYFGTAIGVPTA 169
+ G +++ G+ +TG+ IL YV+S A A+GFA YF I P
Sbjct: 64 AKIVSNAGPIAFIHKAIGD--NIITGALSILLWMSYVISIALFAKGFAGYFLPLINAPIN 121
Query: 170 KWRLKVD--GLPDGFNEIDXXXXXXXXXITFVICYSTRDSSVVNMILTVLHILFIAFVIL 227
+ + + G+ F ++ + ++ + ++ +L + I
Sbjct: 122 TFNIAITEIGIVAFFTALN--------------FFGSKAVGRAEFFIVLVKLLILGLFIF 167
Query: 228 MGFWKDPKNPS----GFFPYGAKGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVKDIPXXX 283
G +PS P G+ +A+ +LSY+G+ ++ +E ++NP K++P
Sbjct: 168 AGLITI--HPSYVIPDLAPSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVPRAI 225
Query: 284 XXXXXXXTVLYCLMAASMSMLMPYDMIDAEAPFSGAFSGKSDGWKWVSNVIGVGASFGIL 343
+Y +A S +P D + + + A + K +I +GA F I
Sbjct: 226 FISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAKPFLGNLGFLLISIGALFSIS 285
Query: 344 TSLLVAMLGQARYMCVIGRSSVVPAWFAR-VHPKTSTPVNASAFLGIFTA 392
+++ + G A + + +P +F R V K++ + ++ LG+ A
Sbjct: 286 SAMNATIYGGANVAYSLAKDGELPEFFERKVWFKSTEGLYITSALGVLFA 335
>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
Monoclonal Fab Fragment
Length = 444
Score = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 77/350 (22%), Positives = 153/350 (43%), Gaps = 29/350 (8%)
Query: 53 RKTLRWYDLVCFGIGGMVGAGVFVTTGRASRLNAGPAIVISYAIAGLCALLSAFCYTEFA 112
K L ++ V +G M+GA +F G +++ AG + ++ ++G+ ALL A+ YT+
Sbjct: 5 NKKLSLWEAVSMAVGVMIGASIFSIFGVGAKI-AGRNLPETFILSGIYALLVAYSYTKLG 63
Query: 113 VDMPVAGGAFSYLRVTFGEFAAFLTGSNLIL---EYVMSNAAVARGFASYFGTAIGVPTA 169
+ G +++ G+ +TG+ IL YV+S A A+GFA YF I P
Sbjct: 64 AKIVSNAGPIAFIHKAIGD--NIITGALSILLWMSYVISIALFAKGFAGYFLPLINAPIN 121
Query: 170 KWRLKVD--GLPDGFNEIDXXXXXXXXXITFVICYSTRDSSVVNMILTVLHILFIAFVIL 227
+ + + G+ F ++ + ++ + ++ +L + I
Sbjct: 122 TFNIAITEIGIVAFFTALN--------------FFGSKAVGRAEFFIVLVALLILGLFIF 167
Query: 228 MGFWKDPKNPS----GFFPYGAKGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVKDIPXXX 283
G +PS P G+ +A+ +LSY+G+ ++ +E ++NP K++P
Sbjct: 168 AGLITI--HPSYVIPDLAPSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVPRAI 225
Query: 284 XXXXXXXTVLYCLMAASMSMLMPYDMIDAEAPFSGAFSGKSDGWKWVSNVIGVGASFGIL 343
+Y +A S +P D + + + A + K +I +GA F I
Sbjct: 226 FISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAKPFLGNLGFLLISIGALFSIS 285
Query: 344 TSLLVAMLGQARYMCVIGRSSVVPAWFAR-VHPKTSTPVNASAFLGIFTA 392
+++ + G A + + +P +F R V K++ + ++ LG+ A
Sbjct: 286 SAMNATIYGGANVAYSLAKDGELPEFFERKVWFKSTEGLYITSALGVLFA 335
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 48/193 (24%), Positives = 90/193 (46%), Gaps = 9/193 (4%)
Query: 257 LSYIGYDAVSTMAEEVKNPVKDIPXXXXXXXXXXTVLYCLMAASMSMLMPYDMIDAEA-- 314
LSY+G +A +T E+ NP +D P L + S++M++P + I+ A
Sbjct: 212 LSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGV 271
Query: 315 --PFSGAFSGKSDGWKWVSNVIGVGASFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAR 372
F+ S + +W VI G+L + ++G +R M V + +++PA FA+
Sbjct: 272 MQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAK 331
Query: 373 VHPKTSTPVN-ASAFLGIFTAAIALFTDLTVLLN---LVSIGTLFVFYMVANAVIYRRYV 428
++ K PV + L I + A+ + T+ N L+++ V Y+ A +++ Y+
Sbjct: 332 MN-KNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYI 390
Query: 429 NLGTTNPQPTLSF 441
L +P +F
Sbjct: 391 VLVLKHPDLKRTF 403
>pdb|3L1L|A Chain A, Structure Of Arg-Bound Escherichia Coli Adic
Length = 445
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 80/339 (23%), Positives = 133/339 (39%), Gaps = 41/339 (12%)
Query: 67 GGMVGAGVFVTTGRASRLNAGPAIVISYAIAGLCALLSAFCYTEFAVDMPVAGGAFSYLR 126
G ++G+GVF+ A+ + G + + + + AL + Y + + P GG+++Y R
Sbjct: 21 GAIMGSGVFLLP--ANLASTGGIAIYGWLVTIIGALGLSMVYAKMSFLDPSPGGSYAYAR 78
Query: 127 VTFGEFAAFLTGSNLILEYVMSNAA---VARGFASYFGTAIGVPTAKWRLKVDGLPDGFN 183
FG F + T L + N A + G+ SYF + P W L +
Sbjct: 79 RCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFFPILKDP---WVLTIT------- 128
Query: 184 EIDXXXXXXXXXITFVICYSTRDSSVVNMILTVLHILFIAFVILMG-FWKDPK------N 236
+ + + V + TVL ++ I + + G FW + N
Sbjct: 129 -----CVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGETYMAAWN 183
Query: 237 PSGFFPYGA-KGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVKDIPXXXXXXXXXXTVLYC 295
SG +GA + N + S+IG ++ S A VKNP +++P V Y
Sbjct: 184 VSGLGTFGAIQSTLN---VTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYV 240
Query: 296 LMAASMSMLMPYDMIDAEA-PFSGAFS---GKSDGWKWVSNVIGVGASFGILTSLLVAML 351
L ++ ++P + A PF A G + G ++ A+ G L SL L
Sbjct: 241 LSTTAIMGMIPNAALRVSASPFGDAARMALGDTAG-----AIVSFCAAAGCLGSLGGWTL 295
Query: 352 GQARYMCVIGRSSVVPAWFARVHPKTSTPVNASAFLGIF 390
+ + P FARV+ K TPV +GI
Sbjct: 296 LAGQTAKAAADDGLFPPIFARVN-KAGTPVAGLIIVGIL 333
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 81/341 (23%), Positives = 134/341 (39%), Gaps = 45/341 (13%)
Query: 67 GGMVGAGVFVTTGRASRLNAGPAIVISYAIAGLCALLSAFCYTEFAVDMPVAGGAFSYLR 126
G ++G+GVF+ A+ + G + + + + AL + Y + + P GG+++Y R
Sbjct: 21 GNIMGSGVFLLP--ANLASTGGIAIYGWLVTIIGALGLSMVYAKMSFLDPSPGGSYAYAR 78
Query: 127 VTFGEFAAFLTGSNLILEYVMSNAA---VARGFASYFGTAIGVPTAKWRLKVDGLPDGFN 183
FG F + T L + N A + G+ SYF P K +
Sbjct: 79 RCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYF-----FPILK------------D 121
Query: 184 EIDXXXXXXXXXITFVIC--YSTRDSSVVNMILTVLHILFIAFVILMG-FWKDPK----- 235
+ FV+ + + V + TVL ++ I + + G FW +
Sbjct: 122 PLVLTITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGETYMAA 181
Query: 236 -NPSGFFPYGA-KGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVKDIPXXXXXXXXXXTVL 293
N SG +GA + N + S+IG ++ S A VKNP +++P V
Sbjct: 182 WNVSGLGTFGAIQSTLN---VTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVC 238
Query: 294 YCLMAASMSMLMPYDMIDAEA-PFSGAFS---GKSDGWKWVSNVIGVGASFGILTSLLVA 349
Y L ++ ++P + A PF A G + G ++ A+ G L SL
Sbjct: 239 YVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAG-----AIVSFCAAAGCLGSLGGW 293
Query: 350 MLGQARYMCVIGRSSVVPAWFARVHPKTSTPVNASAFLGIF 390
L + + P FARV+ K TPV +GI
Sbjct: 294 TLLAGQTAKAAADDGLFPPIFARVN-KAGTPVAGLIIVGIL 333
>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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 81/339 (23%), Positives = 132/339 (38%), Gaps = 41/339 (12%)
Query: 67 GGMVGAGVFVTTGRASRLNAGPAIVISYAIAGLCALLSAFCYTEFAVDMPVAGGAFSYLR 126
G ++G+GVF+ A+ G + + + + AL + Y + + P GG+++Y R
Sbjct: 21 GNIMGSGVFLLP--ANLAATGGIAIYGWLVTIIGALALSMVYAKMSSLDPSPGGSYAYAR 78
Query: 127 VTFGEFAAFLTGSNLILEYVMSNAA---VARGFASYFGTAIGVPTAKWRLKVDGLPDGFN 183
FG F + T L + N A + G+ SYF P K D L
Sbjct: 79 RCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYF-----FPILK-----DPLVLTLT 128
Query: 184 EIDXXXXXXXXXITFVICYSTRDSSVVNMILTVLHILFIAFVILMG-FWKDPK------N 236
+ I + + V + TVL ++ I + + G FW + N
Sbjct: 129 CVAVLWIFVLLNIV-----GPKMITRVQAVATVLALVPIVGIAVFGWFWFKGETYMAAWN 183
Query: 237 PSGFFPYGA-KGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVKDIPXXXXXXXXXXTVLYC 295
SG +GA + N + S+IG ++ S A VKNP +++P V Y
Sbjct: 184 VSGMNTFGAIQSTLN---VTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYV 240
Query: 296 LMAASMSMLMPYDMIDAEA-PFSGAFS---GKSDGWKWVSNVIGVGASFGILTSLLVAML 351
L ++ ++P + A PF A G + G ++ A+ G L SL L
Sbjct: 241 LSTTAIMGMIPNAALRVSASPFGDAARMALGDTAG-----AIVSFCAAAGCLGSLGGWTL 295
Query: 352 GQARYMCVIGRSSVVPAWFARVHPKTSTPVNASAFLGIF 390
+ + P FARV+ K TPV +G+
Sbjct: 296 LAGQTAKAAADDGLFPPIFARVN-KAGTPVAGLLIVGVL 333
>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 = 37.7 bits (86), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 81/343 (23%), Positives = 135/343 (39%), Gaps = 49/343 (14%)
Query: 67 GGMVGAGVFVTTGRASRLNAGPAIVISYAIAGLCALLSAFCYTEFAVDMPVAGGAFSYLR 126
G ++G+GVF+ A+ + G + + + + AL + Y + + P GG+++Y R
Sbjct: 21 GNIMGSGVFLLP--ANLASTGGIAIYGWLVTIIGALGLSMVYAKMSFLDPSPGGSYAYAR 78
Query: 127 VTFGEFAAFLTGSNLILEYVMSNAAVAR-----GFASYFGTAIGVPTAKWRLKVDGLPDG 181
FG F + T N++ A+A G+ SYF P K
Sbjct: 79 RCFGPFLGYQT--NVLYWLACWIGAIAMVVIGVGYLSYF-----FPILK----------- 120
Query: 182 FNEIDXXXXXXXXXITFVI--CYSTRDSSVVNMILTVLHILFIAFVILMG-FWKDPK--- 235
+ + FV+ + + V + TVL ++ I + + G FW +
Sbjct: 121 -DPLVLTITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGETYM 179
Query: 236 ---NPSGFFPYGA-KGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVKDIPXXXXXXXXXXT 291
N SG +GA + N + S+IG ++ S A VKNP +++P
Sbjct: 180 AAWNVSGLGTFGAIQSTLN---VTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAA 236
Query: 292 VLYCLMAASMSMLMPYDMIDAEA-PFSGAFS---GKSDGWKWVSNVIGVGASFGILTSLL 347
V Y L ++ ++P + A PF A G + G ++ A+ G L SL
Sbjct: 237 VCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAG-----AIVSFCAAAGCLGSLG 291
Query: 348 VAMLGQARYMCVIGRSSVVPAWFARVHPKTSTPVNASAFLGIF 390
L + + P FARV+ K TPV +GI
Sbjct: 292 GWTLLAGQTAKAAADDGLFPPIFARVN-KAGTPVAGLIIVGIL 333
>pdb|1PA2|A Chain A, Arabidopsis Thaliana Peroxidase A2
pdb|1QO4|A Chain A, Arabidopsis Thaliana Peroxidase A2 At Room Temperature
Length = 306
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 24/104 (23%), Positives = 46/104 (44%), Gaps = 6/104 (5%)
Query: 348 VAMLGQARYMCVIGRSSVVPAWFARVHPKTSTPVNASAFLGIFTAAIALFTDLTVLLNLV 407
V++ G + ++GR + A A + +P+ + + + +A+ L T+ +LV
Sbjct: 110 VSLAGGPSWTVLLGRRDSLTANLAGANSSIPSPIESLSNITFKFSAVGLNTN-----DLV 164
Query: 408 SIGTLFVFYMVANAVIYRRYVNL-GTTNPQPTLSFLFLFSVTSI 450
++ F V R N GT NP PTL+ L ++ +
Sbjct: 165 ALSGAHTFGRARCGVFNNRLFNFSGTGNPDPTLNSTLLSTLQQL 208
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
0.326 0.138 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,081,979
Number of Sequences: 62578
Number of extensions: 560055
Number of successful extensions: 1318
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1295
Number of HSP's gapped (non-prelim): 24
length of query: 576
length of database: 14,973,337
effective HSP length: 104
effective length of query: 472
effective length of database: 8,465,225
effective search space: 3995586200
effective search space used: 3995586200
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)