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= psy6067
(584 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 = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 52/192 (27%), Positives = 94/192 (48%), Gaps = 18/192 (9%)
Query: 245 APFGLNGIIVGAAKCFFGFVGFDCIATTGEESKNPKRDIPLSILLSLFIVFVCYLAIAIV 304
AP ++G+I +A F ++GF I E +NPK+++P +I +S+ IV Y+ +AI
Sbjct: 183 APSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVPRAIFISILIVMFVYVGVAIS 242
Query: 305 LTLIIPYYE---------QDAEAPFPHIFDSLGWPVMKWLVTVGSLFALLTAMFGALFPL 355
+P E A PF +LG+ L+++G+LF++ +AM ++
Sbjct: 243 AIGNLPIDELIKASENALAVAAKPF---LGNLGF----LLISIGALFSISSAMNATIYGG 295
Query: 356 PRILYAMSLDGLLYDCFSYVSPRTKTPVLSSLLTGALTAVLSAVFKLDQLVDMLSIGTLL 415
+ Y+++ DG L + F T L +T AL + + +F ++ + + S ++
Sbjct: 296 ANVAYSLAKDGELPEFFERKVWFKSTEGL--YITSALGVLFALLFNMEGVASITSAVFMV 353
Query: 416 AYTIVALSVLIL 427
Y V LS IL
Sbjct: 354 IYLFVILSHYIL 365
>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
Monoclonal Fab Fragment
Length = 444
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 52/192 (27%), Positives = 94/192 (48%), Gaps = 18/192 (9%)
Query: 245 APFGLNGIIVGAAKCFFGFVGFDCIATTGEESKNPKRDIPLSILLSLFIVFVCYLAIAIV 304
AP ++G+I +A F ++GF I E +NPK+++P +I +S+ IV Y+ +AI
Sbjct: 183 APSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVPRAIFISILIVMFVYVGVAIS 242
Query: 305 LTLIIPYYE---------QDAEAPFPHIFDSLGWPVMKWLVTVGSLFALLTAMFGALFPL 355
+P E A PF +LG+ L+++G+LF++ +AM ++
Sbjct: 243 AIGNLPIDELIKASENALAVAAKPF---LGNLGF----LLISIGALFSISSAMNATIYGG 295
Query: 356 PRILYAMSLDGLLYDCFSYVSPRTKTPVLSSLLTGALTAVLSAVFKLDQLVDMLSIGTLL 415
+ Y+++ DG L + F T L +T AL + + +F ++ + + S ++
Sbjct: 296 ANVAYSLAKDGELPEFFERKVWFKSTEGL--YITSALGVLFALLFNMEGVASITSAVFMV 353
Query: 416 AYTIVALSVLIL 427
Y V LS IL
Sbjct: 354 IYLFVILSHYIL 365
>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 = 0.11, Method: Compositional matrix adjust.
Identities = 41/187 (21%), Positives = 76/187 (40%), Gaps = 9/187 (4%)
Query: 260 FFGFVGFDCIATTGEESKNPKRDIPLSILLSLFIVFVCYLAIAIVLTLIIPYYEQDAEA- 318
+ F+G + + KNPKR++P++ + + I VCY+ + +IP A
Sbjct: 201 LWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSAS 260
Query: 319 PFPHIFDSLGWPVMKWLVTVGSLFALLTAMFGALFPLPRILYAMSLDGLLYDCFSYVSPR 378
PF +V+ + L ++ G + A + DGL F+ V+ +
Sbjct: 261 PFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVN-K 319
Query: 379 TKTPVLSSLLTGALTAVL-------SAVFKLDQLVDMLSIGTLLAYTIVALSVLILRYSE 431
TPV L+ G L + +A + + + I TL+ Y ++L+L +
Sbjct: 320 AGTPVAGLLIVGVLMTIFQFSSMSPNAAKEFGLVSSVSVIFTLVPYLYTCAALLLLGHGH 379
Query: 432 DGADTPI 438
G P+
Sbjct: 380 FGKARPL 386
>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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 48/106 (45%), Gaps = 5/106 (4%)
Query: 244 FAPFGLNGIIVGAAKCFFGFVGFDCIATTGEESKNPKRDIPLSILLSLFIVFVCYLAI-A 302
F F G +V ++G + AT E NP RD PL++LL L + +C ++
Sbjct: 195 FPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLL-LMVAAICLSSVGG 253
Query: 303 IVLTLIIPYYEQDAEAPFPHIFDSLG---WPVMKWLVTVGSLFALL 345
+ + ++IP E + A F L P ++W V V S LL
Sbjct: 254 LSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLL 299
>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 = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 17/190 (8%)
Query: 260 FFGFVGFDCIATTGEESKNPKRDIPLSILLSLFIVFVCYLAIAIVLTLIIPYYEQDAEA- 318
+ F+G + + KNPKR++P++ + + I VCY+ + +IP A
Sbjct: 201 LWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSAS 260
Query: 319 PFPHIFDSLGWPVMKWLVTVGSLFALLTAMFGALFPLPRILYAMSLDGLLYDCFSYVSPR 378
PF +V+ + L ++ G + A + DGL F+ V+ +
Sbjct: 261 PFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVN-K 319
Query: 379 TKTPVLSSLLTGALTAVLSAVFKLDQ----------LVDMLS-IGTLLAYTIVALSVLIL 427
TPV ++ G +L +F+L LV +S I TL+ Y ++L+L
Sbjct: 320 AGTPVAGLIIVG----ILMTIFQLSSISPNATKEFGLVSSVSVIFTLVPYLYTCAALLLL 375
Query: 428 RYSEDGADTP 437
+ G P
Sbjct: 376 GHGHFGKARP 385
>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 = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 17/190 (8%)
Query: 260 FFGFVGFDCIATTGEESKNPKRDIPLSILLSLFIVFVCYLAIAIVLTLIIPYYEQDAEA- 318
+ F+G + + KNPKR++P++ + + I VCY+ + +IP A
Sbjct: 201 LWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSAS 260
Query: 319 PFPHIFDSLGWPVMKWLVTVGSLFALLTAMFGALFPLPRILYAMSLDGLLYDCFSYVSPR 378
PF +V+ + L ++ G + A + DGL F+ V+ +
Sbjct: 261 PFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVN-K 319
Query: 379 TKTPVLSSLLTGALTAVLSAVFKLDQ----------LVDMLS-IGTLLAYTIVALSVLIL 427
TPV ++ G +L +F+L LV +S I TL+ Y ++L+L
Sbjct: 320 AGTPVAGLIIVG----ILMTIFQLSSISPNATKEFGLVSSVSVIFTLVPYLYTCAALLLL 375
Query: 428 RYSEDGADTP 437
+ G P
Sbjct: 376 GHGHFGKARP 385
>pdb|3L1L|A Chain A, Structure Of Arg-Bound Escherichia Coli Adic
Length = 445
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 17/190 (8%)
Query: 260 FFGFVGFDCIATTGEESKNPKRDIPLSILLSLFIVFVCYLAIAIVLTLIIPYYEQDAEA- 318
+ F+G + + KNPKR++P++ + + I VCY+ + +IP A
Sbjct: 201 LWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSAS 260
Query: 319 PFPHIFDSLGWPVMKWLVTVGSLFALLTAMFGALFPLPRILYAMSLDGLLYDCFSYVSPR 378
PF +V+ + L ++ G + A + DGL F+ V+ +
Sbjct: 261 PFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVN-K 319
Query: 379 TKTPVLSSLLTGALTAVLSAVFKLDQ----------LVDMLS-IGTLLAYTIVALSVLIL 427
TPV ++ G +L +F+L LV +S I TL+ Y ++L+L
Sbjct: 320 AGTPVAGLIIVG----ILMTIFQLSSISPNATKEFGLVSSVSVIFTLVPYLYTCAALLLL 375
Query: 428 RYSEDGADTP 437
+ G P
Sbjct: 376 GHGHFGKARP 385
>pdb|1OLZ|A Chain A, The Ligand-Binding Face Of The Semaphorins Revealed By The
High Resolution Crystal Structure Of Sema4d
pdb|1OLZ|B Chain B, The Ligand-Binding Face Of The Semaphorins Revealed By The
High Resolution Crystal Structure Of Sema4d
pdb|3OL2|A Chain A, Receptor-Ligand Structure Of Human Semaphorin 4d With
Plexin B1
Length = 663
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 42/164 (25%), Positives = 72/164 (43%), Gaps = 10/164 (6%)
Query: 366 GLLYDCFSYVSPRTKTPVLSSLLTGALTAV-LSAV--FKLDQLVDMLSIGTLLAYTIVAL 422
+L D F SP K PV +L T L V LSAV + L ++ S G + T V
Sbjct: 270 NVLRDVFVLRSPGLKVPVFYALFTPQLNNVGLSAVCAYNLSTAEEVFSHGKYMQSTTVEQ 329
Query: 423 S-VLILRYSEDGADTPIKGTSCAEKETKSSSFAEKDINAKNFSVNALPEETLDPNSQSAL 481
S +RY +G + +C + E +++++ +N + ++ + + L +S + +
Sbjct: 330 SHTKWVRY--NGPVPKPRPGACIDSEARAANYTS-SLNLPDKTLQFVKDHPLMDDSVTPI 386
Query: 482 TGGP---VPTSDCTSALQYATFTLLGLVYTVVFVCLARQNQNRA 522
P + T + T L G VY V+FV R ++A
Sbjct: 387 DNRPRLIKKDVNYTQIVVDRTQALDGTVYDVMFVSTDRGALHKA 430
>pdb|1JPA|A Chain A, Crystal Structure Of Unphosphorylated Ephb2 Receptor
Tyrosine Kinase And Juxtamembrane Region
pdb|1JPA|B Chain B, Crystal Structure Of Unphosphorylated Ephb2 Receptor
Tyrosine Kinase And Juxtamembrane Region
Length = 312
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 16/86 (18%)
Query: 438 IKGTSCAEKETKSSSFAEKDINAKNFSVNA--------------LPEETLDPNSQSALTG 483
++G + K ++ +D+ A+N VN+ L ++T DP SAL G
Sbjct: 141 LRGIAAGMKYLADMNYVHRDLAARNILVNSNLVCKVSDFGLSRFLEDDTSDPTYTSAL-G 199
Query: 484 GPVPTS-DCTSALQYATFTLLGLVYT 508
G +P A+QY FT V++
Sbjct: 200 GKIPIRWTAPEAIQYRKFTSASDVWS 225
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
0.325 0.139 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,892,577
Number of Sequences: 62578
Number of extensions: 555506
Number of successful extensions: 1362
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 1355
Number of HSP's gapped (non-prelim): 38
length of query: 584
length of database: 14,973,337
effective HSP length: 104
effective length of query: 480
effective length of database: 8,465,225
effective search space: 4063308000
effective search space used: 4063308000
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)