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= 010659
(505 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 = 69.3 bits (168), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 52/192 (27%), Positives = 101/192 (52%), Gaps = 8/192 (4%)
Query: 89 PFGVNGMLAGSATVFFAFIGFDAVASTAEEVKNPQRDLPLGIGTALSICCALYMLVSIVI 148
P V+GM+ SA F +++GF + + +E ++NP++++P I ++ I +Y+ V+I
Sbjct: 184 PSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVPRAIFISILIVMFVYVGVAISA 243
Query: 149 VGLVPYYEMDPDTPISSAFASHGM--HWASYVITIGAVTALCSTLMGSILPQPRILMAMA 206
+G +P E+ + + A A+ + +I+IGA+ ++ S + +I + ++A
Sbjct: 244 IGNLPIDELIKASENALAVAAKPFLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLA 303
Query: 207 RDGLLPPFFSDVNKTTQVPVKSTIVTGIVAAALAFFMDVSALAGMVSVGTLLAFTMVAIS 266
+DG LP FF +V KST I +A F + + G+ S+ T F ++ +
Sbjct: 304 KDGELPEFFER-----KVWFKSTEGLYITSALGVLFALLFNMEGVASI-TSAVFMVIYLF 357
Query: 267 VLILRYVPPDEV 278
V++ Y+ DEV
Sbjct: 358 VILSHYILIDEV 369
>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
Monoclonal Fab Fragment
Length = 444
Score = 69.3 bits (168), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 52/192 (27%), Positives = 101/192 (52%), Gaps = 8/192 (4%)
Query: 89 PFGVNGMLAGSATVFFAFIGFDAVASTAEEVKNPQRDLPLGIGTALSICCALYMLVSIVI 148
P V+GM+ SA F +++GF + + +E ++NP++++P I ++ I +Y+ V+I
Sbjct: 184 PSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVPRAIFISILIVMFVYVGVAISA 243
Query: 149 VGLVPYYEMDPDTPISSAFASHGM--HWASYVITIGAVTALCSTLMGSILPQPRILMAMA 206
+G +P E+ + + A A+ + +I+IGA+ ++ S + +I + ++A
Sbjct: 244 IGNLPIDELIKASENALAVAAKPFLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLA 303
Query: 207 RDGLLPPFFSDVNKTTQVPVKSTIVTGIVAAALAFFMDVSALAGMVSVGTLLAFTMVAIS 266
+DG LP FF +V KST I +A F + + G+ S+ T F ++ +
Sbjct: 304 KDGELPEFFER-----KVWFKSTEGLYITSALGVLFALLFNMEGVASI-TSAVFMVIYLF 357
Query: 267 VLILRYVPPDEV 278
V++ Y+ DEV
Sbjct: 358 VILSHYILIDEV 369
>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 = 58.5 bits (140), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 63/232 (27%), Positives = 103/232 (44%), Gaps = 23/232 (9%)
Query: 23 IIVDP------CAAILVLIVTGLLCVGIKESTIAQAIVTTANVLAMLFVIIAGSYLGFKT 76
I+ DP C A+L + V L VG K T QA+ T VLA++ ++ +
Sbjct: 118 ILKDPLVLTLTCVAVLWIFVL-LNIVGPKMITRVQAVAT---VLALVPIVGIAVF----- 168
Query: 77 GWSGYELPTGYFPFGVNGMLAGSA------TVFFAFIGFDAVASTAEEVKNPQRDLPLGI 130
GW ++ T + V+GM A ++FIG ++ + A VKNP+R++P+
Sbjct: 169 GWFWFKGETYMAAWNVSGMNTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIAT 228
Query: 131 GTALSICCALYMLVSIVIVGLVPYYEMD-PDTPISSAFASHGMHWASYVITIGAVTALCS 189
+ I Y+L + I+G++P + +P A A +++ A
Sbjct: 229 IGGVLIAAVCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLG 288
Query: 190 TLMGSILPQPRILMAMARDGLLPPFFSDVNKTTQVPVKSTIVTGIVAAALAF 241
+L G L + A A DGL PP F+ VNK PV ++ G++ F
Sbjct: 289 SLGGWTLLAGQTAKAAADDGLFPPIFARVNK-AGTPVAGLLIVGVLMTIFQF 339
>pdb|3L1L|A Chain A, Structure Of Arg-Bound Escherichia Coli Adic
Length = 445
Score = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 62/226 (27%), Positives = 100/226 (44%), Gaps = 23/226 (10%)
Query: 23 IIVDP------CAAILVLIVTGLLCVGIKESTIAQAIVTTANVLAMLFVIIAGSYLGFKT 76
I+ DP C +L + V L VG K T QA+ T VLA++ ++ +
Sbjct: 118 ILKDPWVLTITCVVVLWIFVL-LNIVGPKMITRVQAVAT---VLALIPIVGIAVF----- 168
Query: 77 GWSGYELPTGYFPFGVNGMLAGSA------TVFFAFIGFDAVASTAEEVKNPQRDLPLGI 130
GW + T + V+G+ A ++FIG ++ + A VKNP+R++P+
Sbjct: 169 GWFWFRGETYMAAWNVSGLGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIAT 228
Query: 131 GTALSICCALYMLVSIVIVGLVPYYEMD-PDTPISSAFASHGMHWASYVITIGAVTALCS 189
+ I Y+L + I+G++P + +P A A +++ A
Sbjct: 229 IGGVLIAAVCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLG 288
Query: 190 TLMGSILPQPRILMAMARDGLLPPFFSDVNKTTQVPVKSTIVTGIV 235
+L G L + A A DGL PP F+ VNK PV I+ GI+
Sbjct: 289 SLGGWTLLAGQTAKAAADDGLFPPIFARVNK-AGTPVAGLIIVGIL 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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 64/134 (47%), Gaps = 2/134 (1%)
Query: 103 FFAFIGFDAVASTAEEVKNPQRDLPLGIGTALSICCALYMLVSIVIVGLVPYYEMD-PDT 161
++FIG ++ + A VKNP+R++P+ + I Y+L + I+G++P + +
Sbjct: 201 LWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSAS 260
Query: 162 PISSAFASHGMHWASYVITIGAVTALCSTLMGSILPQPRILMAMARDGLLPPFFSDVNKT 221
P A A +++ A +L G L + A A DGL PP F+ VNK
Sbjct: 261 PFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVNK- 319
Query: 222 TQVPVKSTIVTGIV 235
PV I+ GI+
Sbjct: 320 AGTPVAGLIIVGIL 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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 64/134 (47%), Gaps = 2/134 (1%)
Query: 103 FFAFIGFDAVASTAEEVKNPQRDLPLGIGTALSICCALYMLVSIVIVGLVPYYEMD-PDT 161
++FIG ++ + A VKNP+R++P+ + I Y+L + I+G++P + +
Sbjct: 201 LWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSAS 260
Query: 162 PISSAFASHGMHWASYVITIGAVTALCSTLMGSILPQPRILMAMARDGLLPPFFSDVNKT 221
P A A +++ A +L G L + A A DGL PP F+ VNK
Sbjct: 261 PFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVNK- 319
Query: 222 TQVPVKSTIVTGIV 235
PV I+ GI+
Sbjct: 320 AGTPVAGLIIVGIL 333
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 39/143 (27%), Positives = 63/143 (44%), Gaps = 11/143 (7%)
Query: 98 GSATVFFAFI----GFDAVASTAEEVKNPQRDLPLGIGTALSICCALYMLVSIVIVGLVP 153
G+ VF AFI G +A A+ E+ NP RD PL + + L + + I ++P
Sbjct: 202 GTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIP 261
Query: 154 YYEMDPDTPISSAFA---SH---GMHWASYVITIGAVTALCSTLMGSILPQPRILMAMAR 207
E++ + F SH + W VI+ + + + + I+ R + A+
Sbjct: 262 GNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQ 321
Query: 208 DGLLPPFFSDVNKTTQVPVKSTI 230
LLP F+ +NK VPV I
Sbjct: 322 KNLLPAAFAKMNK-NGVPVTLVI 343
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 0.140 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,897,630
Number of Sequences: 62578
Number of extensions: 477621
Number of successful extensions: 1201
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1186
Number of HSP's gapped (non-prelim): 8
length of query: 505
length of database: 14,973,337
effective HSP length: 103
effective length of query: 402
effective length of database: 8,527,803
effective search space: 3428176806
effective search space used: 3428176806
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)