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= 010323
(513 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 = 136 bits (342), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 130/516 (25%), Positives = 221/516 (42%), Gaps = 80/516 (15%)
Query: 14 DYNGKITSFVVLSCIVAATGGLIFGYDLG-ISGGVTSMEPFLEKFFPKVYRKMKEDTHIS 72
YN +S++ +VA GGL+FGYD ISG V S+ P+ + E
Sbjct: 4 QYN---SSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVA--PQ---NLSESA--- 52
Query: 73 NYCKFDSQLLTSFTSSLYIAGLIASLFASSVTRAFGRRASIXXXXXXXXXXXXXXX---- 128
+ LL +S I +I + FGRR S+
Sbjct: 53 -----ANSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPEL 107
Query: 129 --------XXXNIYM------LIFGRVLLGVGIGFANQASSVPLYLSEMAPPRHRGAFNI 174
+Y+ + R++ G+G+G A+ S P+Y++E+AP RG
Sbjct: 108 GFTSINPDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLS--PMYIAELAPAHIRGKLVS 165
Query: 175 GYELCTAIGILAASLINYGTQKI-KGGW----GWRISLAMAAAPALILTLGALFLPETPN 229
+ G L +NY + W GWR A PAL+ + +PE+P
Sbjct: 166 FNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPR 225
Query: 230 SIIQRSNDLQRAKQMLQRIRGTDDVEAEFDDLIKASSIAKTVNHPFKKIIQRKYRPQLVM 289
++ R ++A+ +L++I G A+ + + H RK +L+M
Sbjct: 226 WLMSRGKQ-EQAEGILRKIMGNT----------LATQAVQEIKHSLDH--GRKTGGRLLM 272
Query: 290 --------AILIPFFLQVTGINVIGFYAPVLFRTIKLSESTSLLMSAVVTGGIGTLSTII 341
+++ F Q GINV+ +YAP +F+T+ S +LL + ++ G I T++
Sbjct: 273 FGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQT-IIVGVINLTFTVL 331
Query: 342 SMILVDKLGRKVLFLVGGIQMLAAQVMIGSIMENQLGDQGGFSKGNAYLILVLICVYVAG 401
+++ VDK GRK L ++G + M +G+ +++ + L+ + YVA
Sbjct: 332 AIMTVDKFGRKPLQIIGALGMAIGMFSLGTAF---------YTQAPGIVALLSMLFYVAA 382
Query: 402 FAVSWGPLGFLVPSEIFPLEIRSAGQSINVAVGFLFTFLIAQTFLAM------LCHFKAG 455
FA+SWGP+ +++ SEIFP IR +I VA +L + ++ TF M + HF G
Sbjct: 383 FAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNG 442
Query: 456 IXXXXXXXXXXXXXXXHF-FLPETKNVPIEQMDEVW 490
+ F+PETK +E+++ +W
Sbjct: 443 FSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALW 478
>pdb|1ZXX|A Chain A, The Crystal Structure Of Phosphofructokinase From
Lactobacillus Delbrueckii
Length = 319
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 378 GDQGGFSKGNAYLILVLICVYVAGFAVSWGPLGFLVPSEIFPLEIRSAGQSINVAVGFLF 437
GD G + + V I + F + +G G LV +IFPLE INV+ FL+
Sbjct: 11 GDAPGMNAAVRAVTRVAIANGLEVFGIRYGFAG-LVAGDIFPLESEDVAHLINVSGTFLY 69
Query: 438 T 438
+
Sbjct: 70 S 70
>pdb|4A17|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 239
Score = 28.5 bits (62), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 26/128 (20%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 223 FLPETPNSIIQRSNDLQRAKQMLQRIRGTDDVEAEFDDLIKASSIAKTVNHPFKKIIQRK 282
F+PE + R L++AK ++ + + + + KA A KKI+ K
Sbjct: 4 FVPENVQKKLARDEKLRKAKAEQRKASSAQMKQRKAEWISKAQKYAAEYEAAEKKIVDEK 63
Query: 283 YRPQLVMAILIP------FFLQVTGINVIGFYAPVLFRTIKLSESTSLLMSAVVTGGIGT 336
+ + A +P F +++ G+N + P + R ++L L A +
Sbjct: 64 RKARKTGAFYVPAEAKVAFAIRIRGVNQLH---PDVKRVLRLFRLRQLHNGAFFRVNKAS 120
Query: 337 LSTIISMI 344
L+ I ++
Sbjct: 121 LNMIKRVL 128
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 0.140 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,721,196
Number of Sequences: 62578
Number of extensions: 460625
Number of successful extensions: 1279
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1272
Number of HSP's gapped (non-prelim): 4
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
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)