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= 004673
(738 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 106 bits (265), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 78/236 (33%), Positives = 118/236 (50%), Gaps = 35/236 (14%)
Query: 7 VAIAATIGNFLQGWDNATIAGAI-----VYIKKDLNL----GTTVEGLVVAMSLIGATAI 57
+ + AT+G L G+D A I+G + V++ NL ++ G VA +LIG
Sbjct: 13 ITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQ-NLSESAANSLLGFCVASALIGCIIG 71
Query: 58 TTCSGPISDWLGRRPMLILSSVLYFVSGLVMLW--------SPN----VYV------LCI 99
G S+ GRR L +++VL+F+SG+ W +P+ VY+ I
Sbjct: 72 GALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVI 131
Query: 100 ARLLDGFGVGLAVTLVPLYISETAPSEIRGRLNTLPQFTGSGGMFLAYCMVFGM------ 153
R++ G GVGLA L P+YI+E AP+ IRG+L + QF G L YC+ + +
Sbjct: 132 YRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDA 191
Query: 154 SLLASPSWRLMLGVLSIPXXXXXXXXXXXXPESPRWLVSKGKMLEAKQVLQRLRGR 209
S L + WR M IP PESPRWL+S+GK +A+ +L+++ G
Sbjct: 192 SWLNTDGWRYMFASECIP-ALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGN 246
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 69/271 (25%), Positives = 118/271 (43%), Gaps = 23/271 (8%)
Query: 458 YDVPEEGEYIQAAALVSQPALYSKELMDQHPVGPAMVHPSETASKG-PSWAALLEAGVKR 516
Y VPE ++ + Q +++M A+ + G + LL GV
Sbjct: 218 YTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGVG- 276
Query: 517 ALLVGVGIQILQQFSGINGVLYYTPQILEQAGVEVLLSNLGISSESASFLISAFTTFLML 576
+++GV + I QQF GIN VLYY P++ + G +S + L + + L
Sbjct: 277 VIVIGVMLSIFQQFVGINVVLYYAPEVFKTLG----------ASTDIALLQTIIVGVINL 326
Query: 577 PCIGVAMKLMDVAGRRKXXXXXXXXXXXXXXXXXXXXXXQLISPVLKAGISTACVIIYFC 636
+A+ +D GR+ Q +P + A +S ++ Y
Sbjct: 327 TFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQ--APGIVALLS---MLFYVA 381
Query: 637 CFVAAYGPIPNILCAEIFPTKVRGICIAICAMAYWICDIIVTYTLPVMLSSIGLAGAFG- 695
F ++GP+ +L +EIFP +RG +AI A W+ + V++T P+M + L F
Sbjct: 382 AFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHN 441
Query: 696 -----VYAVVCFISWVFVFLRVPETKGMPLE 721
+Y + ++ +F++ VPETKG LE
Sbjct: 442 GFSYWIYGCMGVLAALFMWKFVPETKGKTLE 472
>pdb|2GFP|A Chain A, Structure Of The Multidrug Transporter Emrd From
Escherichia Coli
pdb|2GFP|B Chain B, Structure Of The Multidrug Transporter Emrd From
Escherichia Coli
Length = 375
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 10/78 (12%)
Query: 28 AIVYIKKDLNLGTTVEGLVVAMSLIGATAIT-----TCSGPISDWLGRRPMLILSSVLYF 82
AI + +DLN+ EG V S++GA +T GPISD +GRRP++++ ++
Sbjct: 22 AIADMARDLNVR---EGAV--QSVMGAYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFM 76
Query: 83 VSGLVMLWSPNVYVLCIA 100
++ LV + + ++ VL A
Sbjct: 77 LATLVAVTTSSLTVLIAA 94
>pdb|1PAF|A Chain A, The 2.5 Angstroms Structure Of Pokeweed Antiviral Protein
pdb|1PAF|B Chain B, The 2.5 Angstroms Structure Of Pokeweed Antiviral Protein
pdb|1PAG|A Chain A, The 2.5 Angstroms Structure Of Pokeweed Antiviral Protein
pdb|1PAG|B Chain B, The 2.5 Angstroms Structure Of Pokeweed Antiviral Protein
pdb|1QCG|A Chain A, Low Temperature Structure Of Pokeweed Antiviral Protein
pdb|1QCG|B Chain B, Low Temperature Structure Of Pokeweed Antiviral Protein
pdb|1QCI|A Chain A, Low Temperature Structure Of Pokeweed Antiviral Protein
Complexed With Adenine
pdb|1QCI|B Chain B, Low Temperature Structure Of Pokeweed Antiviral Protein
Complexed With Adenine
pdb|1QCJ|A Chain A, Low Temperature Complex Of Pokeweed Antiviral Protein With
Pteoric Acid
pdb|1QCJ|B Chain B, Low Temperature Complex Of Pokeweed Antiviral Protein With
Pteoric Acid
pdb|1D6A|A Chain A, Structure Of Pokeweed Antiviral Protein Complexed With
Guanine
pdb|1D6A|B Chain B, Structure Of Pokeweed Antiviral Protein Complexed With
Guanine
Length = 262
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 5/56 (8%)
Query: 511 EAGVKRALLVGVGIQILQQFSG-INGVLYYTPQILEQAGVEVLLSNLGISSESASF 565
+AGVK V +GIQIL G I+GV+ +T E+ E LL + + SE+A F
Sbjct: 129 KAGVKSRSQVQLGIQILDSNIGKISGVMSFT----EKTEAEFLLVAIQMVSEAARF 180
>pdb|2YWD|A Chain A, Crystal Structure Of Glutamine Amidotransferase
Length = 191
Score = 28.9 bits (63), Expect = 9.5, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 41/91 (45%), Gaps = 12/91 (13%)
Query: 190 LVSKGKMLEAKQVLQRL-------RGREDVSGEMALLVEGLGIGGETSIEEYIIGPGDEL 242
L +G E K+ L+RL R +E + G AL+V G G T+I + G E
Sbjct: 8 LALQGDFREHKEALKRLGIEAKEVRKKEHLEGLKALIVPG---GESTTIGKLAREYGIE- 63
Query: 243 ADGEEPTDEKDKIRLYGPEEGLSWVAKPVTG 273
D E+ + L+G G W+AK + G
Sbjct: 64 -DEVRKRVEEGSLALFGTCAGAIWLAKEIVG 93
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
0.320 0.137 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,186,579
Number of Sequences: 62578
Number of extensions: 803194
Number of successful extensions: 1721
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1710
Number of HSP's gapped (non-prelim): 9
length of query: 738
length of database: 14,973,337
effective HSP length: 106
effective length of query: 632
effective length of database: 8,340,069
effective search space: 5270923608
effective search space used: 5270923608
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)