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= 044788
(483 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 81/333 (24%), Positives = 130/333 (39%), Gaps = 21/333 (6%)
Query: 40 SKKLSLLPLIFLIYFEVAGGPYGEEPAVGAAGPLFAILGFLIFPFIWSIPEALVTAELAT 99
+ K+ L+P+ ++ + G PA AA AI G+L+ I ++ ++V A++++
Sbjct: 7 AHKVGLIPVTLMVSGNIMGSGVFLLPANLAATGGIAIYGWLV-TIIGALALSMVYAKMSS 65
Query: 100 TFPGNGGYVIWAHHAFGPFWGSLMGSWKFLSGVINLASYPILCIDYLKLVFPIFASGFSH 159
P GG +A FGPF G +L+ I + ++ + YL FPI
Sbjct: 66 LDPSPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFFPILKDPLVL 125
Query: 160 YLAIFVVTLVLSFLNYTGLAIVGYTAVTLGVVSLIPFLFLTVIA----IPKIDSIRWISL 215
L V + LN G ++ V++L+P + + V + W
Sbjct: 126 TLTCVAVLWIFVLLNIVGPKMITRVQAVATVLALVPIVGIAVFGWFWFKGETYMAAWNVS 185
Query: 216 GQNGVPKXXXXXXXXXXXXXXXXDNASTLAGEVEQPQRTFPKALFSAGLLTCVAYLLPLL 275
G N ++AS AG V+ P+R P A L+ V Y+L
Sbjct: 186 GMNTF-GAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTT 244
Query: 276 AATGAIPLDQQNWVDGYFAEVAEI----IAGKWLKICIEIGACLSIIG---LYEAQLSNC 328
A G IP F + A + AG + C G CL +G L Q +
Sbjct: 245 AIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAG-CLGSLGGWTLLAGQTAKA 303
Query: 329 AYQILGMTNLGLLPKVFGSRSSWFHTPWVGIFI 361
A + GL P +F +R + TP G+ I
Sbjct: 304 A------ADDGLFPPIF-ARVNKAGTPVAGLLI 329
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 80/333 (24%), Positives = 131/333 (39%), Gaps = 21/333 (6%)
Query: 40 SKKLSLLPLIFLIYFEVAGGPYGEEPAVGAAGPLFAILGFLIFPFIWSIPEALVTAELAT 99
+ K+ L+P+ ++ + G PA A+ AI G+L+ I ++ ++V A+++
Sbjct: 7 AHKVGLIPVTLMVSGNIMGSGVFLLPANLASTGGIAIYGWLV-TIIGALGLSMVYAKMSF 65
Query: 100 TFPGNGGYVIWAHHAFGPFWGSLMGSWKFLSGVINLASYPILCIDYLKLVFPIFASGFSH 159
P GG +A FGPF G +L+ I + ++ + YL FPI
Sbjct: 66 LDPSPGGSYAYARRCFGPFLGYQTNVLYWLACWIGAIAMVVIGVGYLSYFFPILKDPLVL 125
Query: 160 YLAIFVVTLVLSFLNYTGLAIVGYTAVTLGVVSLIPFLFLTVIA----IPKIDSIRWISL 215
+ VV + LN G ++ V++LIP + + V + W ++
Sbjct: 126 TITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGETYMAAW-NV 184
Query: 216 GQNGVPKXXXXXXXXXXXXXXXXDNASTLAGEVEQPQRTFPKALFSAGLLTCVAYLLPLL 275
G ++AS AG V+ P+R P A L+ V Y+L
Sbjct: 185 SGLGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTT 244
Query: 276 AATGAIPLDQQNWVDGYFAEVAEI----IAGKWLKICIEIGACLSIIG---LYEAQLSNC 328
A G IP F + A + AG + C G CL +G L Q +
Sbjct: 245 AIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAG-CLGSLGGWTLLAGQTAKA 303
Query: 329 AYQILGMTNLGLLPKVFGSRSSWFHTPWVGIFI 361
A + GL P +F +R + TP G+ I
Sbjct: 304 A------ADDGLFPPIF-ARVNKAGTPVAGLII 329
>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 = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 80/333 (24%), Positives = 131/333 (39%), Gaps = 21/333 (6%)
Query: 40 SKKLSLLPLIFLIYFEVAGGPYGEEPAVGAAGPLFAILGFLIFPFIWSIPEALVTAELAT 99
+ K+ L+P+ ++ + G PA A+ AI G+L+ I ++ ++V A+++
Sbjct: 7 AHKVGLIPVTLMVSGNIMGSGVFLLPANLASTGGIAIYGWLV-TIIGALGLSMVYAKMSF 65
Query: 100 TFPGNGGYVIWAHHAFGPFWGSLMGSWKFLSGVINLASYPILCIDYLKLVFPIFASGFSH 159
P GG +A FGPF G +L+ I + ++ + YL FPI
Sbjct: 66 LDPSPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFFPILKDPLVL 125
Query: 160 YLAIFVVTLVLSFLNYTGLAIVGYTAVTLGVVSLIPFLFLTVIA----IPKIDSIRWISL 215
+ VV + LN G ++ V++LIP + + V + W ++
Sbjct: 126 TITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGETYMAAW-NV 184
Query: 216 GQNGVPKXXXXXXXXXXXXXXXXDNASTLAGEVEQPQRTFPKALFSAGLLTCVAYLLPLL 275
G ++AS AG V+ P+R P A L+ V Y+L
Sbjct: 185 SGLGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTT 244
Query: 276 AATGAIPLDQQNWVDGYFAEVAEI----IAGKWLKICIEIGACLSIIG---LYEAQLSNC 328
A G IP F + A + AG + C G CL +G L Q +
Sbjct: 245 AIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAG-CLGSLGGWTLLAGQTAKA 303
Query: 329 AYQILGMTNLGLLPKVFGSRSSWFHTPWVGIFI 361
A + GL P +F +R + TP G+ I
Sbjct: 304 A------ADDGLFPPIF-ARVNKAGTPVAGLII 329
>pdb|3L1L|A Chain A, Structure Of Arg-Bound Escherichia Coli Adic
Length = 445
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 80/333 (24%), Positives = 132/333 (39%), Gaps = 21/333 (6%)
Query: 40 SKKLSLLPLIFLIYFEVAGGPYGEEPAVGAAGPLFAILGFLIFPFIWSIPEALVTAELAT 99
+ K+ L+P+ ++ + G PA A+ AI G+L+ I ++ ++V A+++
Sbjct: 7 AHKVGLIPVTLMVSGAIMGSGVFLLPANLASTGGIAIYGWLV-TIIGALGLSMVYAKMSF 65
Query: 100 TFPGNGGYVIWAHHAFGPFWGSLMGSWKFLSGVINLASYPILCIDYLKLVFPIFASGFSH 159
P GG +A FGPF G +L+ I + ++ + YL FPI +
Sbjct: 66 LDPSPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFFPILKDPWVL 125
Query: 160 YLAIFVVTLVLSFLNYTGLAIVGYTAVTLGVVSLIPFLFLTVIA----IPKIDSIRWISL 215
+ VV + LN G ++ V++LIP + + V + W ++
Sbjct: 126 TITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGETYMAAW-NV 184
Query: 216 GQNGVPKXXXXXXXXXXXXXXXXDNASTLAGEVEQPQRTFPKALFSAGLLTCVAYLLPLL 275
G ++AS AG V+ P+R P A L+ V Y+L
Sbjct: 185 SGLGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTT 244
Query: 276 AATGAIPLDQQNWVDGYFAEVAEI----IAGKWLKICIEIGACLSIIG---LYEAQLSNC 328
A G IP F + A + AG + C G CL +G L Q +
Sbjct: 245 AIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAG-CLGSLGGWTLLAGQTAKA 303
Query: 329 AYQILGMTNLGLLPKVFGSRSSWFHTPWVGIFI 361
A + GL P +F +R + TP G+ I
Sbjct: 304 A------ADDGLFPPIF-ARVNKAGTPVAGLII 329
>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 = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 58/125 (46%), Gaps = 6/125 (4%)
Query: 240 NASTLAGEVEQPQRTFPKALFSAGLLTCVAYLLPLLAATGAIPLDQQ-NWVDGYFAEVAE 298
NAS +E P++ P+A+F + L+ Y+ ++A G +P+D+ + A A+
Sbjct: 209 NASE---HIENPKKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAK 265
Query: 299 IIAGKWLKICIEIGACLSIIGLYEAQLSNCAYQILGMTNLGLLPKVFGSRSSWFHTPWVG 358
G + I IGA SI A + A + G LP+ F R WF + G
Sbjct: 266 PFLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFF-ERKVWFKSTE-G 323
Query: 359 IFIST 363
++I++
Sbjct: 324 LYITS 328
>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
Monoclonal Fab Fragment
Length = 444
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 58/125 (46%), Gaps = 6/125 (4%)
Query: 240 NASTLAGEVEQPQRTFPKALFSAGLLTCVAYLLPLLAATGAIPLDQQ-NWVDGYFAEVAE 298
NAS +E P++ P+A+F + L+ Y+ ++A G +P+D+ + A A+
Sbjct: 209 NASE---HIENPKKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAK 265
Query: 299 IIAGKWLKICIEIGACLSIIGLYEAQLSNCAYQILGMTNLGLLPKVFGSRSSWFHTPWVG 358
G + I IGA SI A + A + G LP+ F R WF + G
Sbjct: 266 PFLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFF-ERKVWFKSTE-G 323
Query: 359 IFIST 363
++I++
Sbjct: 324 LYITS 328
>pdb|1JCM|P Chain P, Trpc Stability Mutant Containing An Engineered Disulphide
Bridge And In Complex With A Cdrp-Related Substrate
Length = 259
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 123 MGSWKFLSGVINLASYPILCIDYLKLVFPIFASGFSHYLAIFVVTLVLSFLNYTGLAIVG 182
GS+ FL V +A PILC D++ + I+ + + A ++ VL Y LA V
Sbjct: 94 QGSFNFLPIVSQIAPQPILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVA 153
Query: 183 YTAVTLGVVSLI 194
++ + +GV++ +
Sbjct: 154 HS-LEMGVLTEV 164
>pdb|1PII|A Chain A, Three-Dimensional Structure Of The Bifunctional Enzyme
Phosphoribosylanthranilate Isomerase:
Indoleglycerolphosphate Synthase From Escherichia Coli
Refined At 2.0 Angstroms Resolution
Length = 452
Score = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 123 MGSWKFLSGVINLASYPILCIDYLKLVFPIFASGFSHYLAIFVVTLVLSFLNYTGLAIVG 182
GS+ FL V +A PILC D++ + I+ + + A ++ VL Y LA V
Sbjct: 94 QGSFNFLPIVSQIAPQPILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVA 153
Query: 183 YTAVTLGVVSLI 194
++ + +GV++ +
Sbjct: 154 HS-LEMGVLTEV 164
>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 = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 72 PLFAILGF------LIFPFIWSIPEALVTAELATTFP-GNGGYVIWAHHAFGPFWG 120
P FA GF L+ +W IP L AE+AT GG W + GP WG
Sbjct: 33 PTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWG 88
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
0.328 0.143 0.452
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,646,791
Number of Sequences: 62578
Number of extensions: 535881
Number of successful extensions: 960
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 934
Number of HSP's gapped (non-prelim): 25
length of query: 483
length of database: 14,973,337
effective HSP length: 103
effective length of query: 380
effective length of database: 8,527,803
effective search space: 3240565140
effective search space used: 3240565140
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)