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= 008096
(577 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter
Length = 524
Score = 82.0 bits (201), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 116/497 (23%), Positives = 204/497 (41%), Gaps = 78/497 (15%)
Query: 19 MPFIFANEVCEKLAVVGFHANMISYLTTQLHMPLTK------AANTLTNFGGTGSLTPLI 72
+P+I A+E CE+ + G + +L T L + + + A + +F PL+
Sbjct: 14 IPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLL 73
Query: 73 GAFVADTYAGRFWTITVASIIYQIGMFSLTLSAILPQLRPPPCQGDQVCKEADTXXXXXX 132
G ++AD + G++ TI S+IY +G L AI QG
Sbjct: 74 GGWIADRFFGKYNTILWLSLIYCVGHAFL---AIFEH----SVQG--------------F 112
Query: 133 XXXXXXXXXXXXXXRPCVVAFGADQFDETDPKQATKTWKYFNWYYFVMGXXXXXXXXXXX 192
+P V +F DQFD+++ A K F+ +YF +
Sbjct: 113 YTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFASLSMP 169
Query: 193 YIQDNVGWNWGLGIPTVAMFLSIIAFVFGYPLYRNLNPAGSPFVRLMQVCVAAFR----- 247
+ N G GIP V MF++ + F G Y ++ P + V +A
Sbjct: 170 LLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKVEG 229
Query: 248 KRNLDMV-------SDPNVLYQNEELD--ASICLDGKLLHTKHMKFLDKAAIVTEEDDIK 298
K N+ +V S L L A +C L+ M F+ A + E K
Sbjct: 230 KGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLV----MGFVGAGASLQLERARK 285
Query: 299 S-PNLWRLNTVHRVEELKSVIRMGPIWASGILLITAYAQQGTFSLQQAKSMDRHLTKSFQ 357
S P+ V+ ++SV+R+ ++A + + Q+ + + QA M + + F+
Sbjct: 286 SHPD-------AAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDMVK--PQWFE 336
Query: 358 IPAGSMSVFTMVSMLSTIALYDRIIIPVARKFTGLDRGITFLHRMGIGFVISVLATLVAG 417
PA ++ ++ ML I + ++ P + + +T L +MG G I+ L+ +V G
Sbjct: 337 -PAMMQALNPLLVML-LIPFNNFVLYPAIER---MGVKLTALRKMGAGIAITGLSWIVVG 391
Query: 418 FVEMKRKQAALAHGLVDKPHIIIPISVLWLVPQYSLHGIAEAFMSVGHLEFLYDQAPESM 477
+++ + +S+ W + Y+L E +S LEF Y QAP++M
Sbjct: 392 TIQLMMDGGS-------------ALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAM 438
Query: 478 RSTATALFWTAN-SIGN 493
+ T + FWT + ++GN
Sbjct: 439 KGTIMS-FWTLSVTVGN 454
>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
An Inward Open Conformation.
pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
An Inward Open Conformation
Length = 491
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 13/94 (13%)
Query: 1 MEEKGGSHVNRKKGGIITMPFIFANEVCEKLAVVGFHANMISYL-----TTQLHMPLTKA 55
ME+KG + + G + +F E+ E+ + G A ++ Y+ T LH+ A
Sbjct: 1 MEDKGKTFFGQPLG----LSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATA 56
Query: 56 ANTLTNFGGTGSLTPLIGAFVADTYAGR----FW 85
A+ + + L+ IG FVAD G FW
Sbjct: 57 ASIMAIYASMVYLSGTIGGFVADRIIGARPAVFW 90
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 35/61 (57%)
Query: 442 ISVLWLVPQYSLHGIAEAFMSVGHLEFLYDQAPESMRSTATALFWTANSIGNYVSTLLVT 501
+S LWLV ++L + E +S L AP++ S ++++ ++S+G+ ++ LVT
Sbjct: 384 VSPLWLVGSWALVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGSALNAQLVT 443
Query: 502 L 502
L
Sbjct: 444 L 444
>pdb|3H2H|A Chain A, Crystal Structure Of G231f Mutant Of The Rice Cell Wall
Degrading Esterase Lipa From Xanthomonas Oryzae
Length = 397
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 12/52 (23%), Positives = 29/52 (55%)
Query: 307 TVHRVEELKSVIRMGPIWASGILLITAYAQQGTFSLQQAKSMDRHLTKSFQI 358
T+ + +SV++ SG ++++ Y+Q G ++ + ++ HL+K F +
Sbjct: 148 TIDAMRAARSVLQHLKTPLSGKVMLSGYSQGGHTAMATQREIEAHLSKEFHL 199
>pdb|3IYG|Q Chain Q, Ca Model Of Bovine TricCCT DERIVED FROM A 4.0 ANGSTROM
Cryo-Em Map
Length = 512
Score = 28.9 bits (63), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 15/70 (21%)
Query: 22 IFANEVCEKLAVVGFHANMISYLTTQLHMPLTKAANTLTNFGGTGSLTPLIGAFVADTYA 81
+ ANEV KL V N L + +P K ++ A V DTY
Sbjct: 442 VKANEVISKLYAVHQEGNKNVGLDIEAEVPAVK---------------DMLEAGVLDTYL 486
Query: 82 GRFWTITVAS 91
G++W I +A+
Sbjct: 487 GKYWAIKLAT 496
>pdb|3H2G|A Chain A, Crystal Structure Of A Rice Cell Wall Degrading Esterase
Lipa From Xanthomonas Oryzae
pdb|3H2J|A Chain A, Crystal Structure Of The Rice Cell Wall Degrading Esterase
Lipa From Xanthomonas Oryzae
pdb|3H2K|A Chain A, Crystal Structure Of A Ligand-Bound Form Of The Rice Cell
Wall Degrading Esterase Lipa From Xanthomonas Oryzae
Length = 397
Score = 28.9 bits (63), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 12/52 (23%), Positives = 29/52 (55%)
Query: 307 TVHRVEELKSVIRMGPIWASGILLITAYAQQGTFSLQQAKSMDRHLTKSFQI 358
T+ + +SV++ SG ++++ Y+Q G ++ + ++ HL+K F +
Sbjct: 148 TIDAMRAARSVLQHLKTPLSGKVMLSGYSQGGHTAMATQREIEAHLSKEFHL 199
>pdb|3H2I|A Chain A, Crystal Structure Of N228w Mutant Of The Rice Cell Wall
Degrading Esterase Lipa From Xanthomonas Oryzae
Length = 397
Score = 28.5 bits (62), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/52 (23%), Positives = 29/52 (55%)
Query: 307 TVHRVEELKSVIRMGPIWASGILLITAYAQQGTFSLQQAKSMDRHLTKSFQI 358
T+ + +SV++ SG ++++ Y+Q G ++ + ++ HL+K F +
Sbjct: 148 TIDAMRAARSVLQHLKTPLSGKVMLSGYSQGGHTAMATQREIEAHLSKEFHL 199
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 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,135,555
Number of Sequences: 62578
Number of extensions: 628580
Number of successful extensions: 1608
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1595
Number of HSP's gapped (non-prelim): 12
length of query: 577
length of database: 14,973,337
effective HSP length: 104
effective length of query: 473
effective length of database: 8,465,225
effective search space: 4004051425
effective search space used: 4004051425
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)