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= psy8697
         (508 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 = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 75/317 (23%), Positives = 140/317 (44%), Gaps = 55/317 (17%)

Query: 61  SFVIITSPVGSTVIGPIMDY----IGRKWSLILVCVPYIISSLLTILAD-------PGNI 109
            F + ++ +G  + G +  Y     GR+ SL +  V + IS + +   +       P N 
Sbjct: 58  GFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNT 117

Query: 110 ELLYLS---------KICAGIGGGM-STVAMVYVSEICHENFRPAILCLNSVFISCGILL 159
             +YL+         +I  GIG G+ S ++ +Y++E+   + R  ++  N   I  G LL
Sbjct: 118 VPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLL 177

Query: 160 TTILNLYL------------DWRSL--SYCFLALVLISGLVLICFAPESPHWLINMDRTA 205
              +N ++             WR +  S C  AL+    L+L+   PESP WL++     
Sbjct: 178 VYCVNYFIARSGDASWLNTDGWRYMFASECIPALLF---LMLLYTVPESPRWLMS----- 229

Query: 206 NVNKRMAKAEKSLKFLNRNPEIFEKEWRVLCQVRTRYDETRNKKALWRQILTTRECYKPL 265
               +  +AE  L+ +  N        + + +++   D  R      R ++        +
Sbjct: 230 --RGKQEQAEGILRKIMGN----TLATQAVQEIKHSLDHGRKTGG--RLLMFGVGV---I 278

Query: 266 ILLVILFTLQQFTGVYPVIFYAMQLFKEVGTEIDES-HALVFLGIIRFGMSVVTTVLARG 324
           ++ V+L   QQF G+  V++YA ++FK +G   D +    + +G+I    +V+  +    
Sbjct: 279 VIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDK 338

Query: 325 FGRKQLLIVSAAGLGVS 341
           FGRK L I+ A G+ + 
Sbjct: 339 FGRKPLQIIGALGMAIG 355



 Score = 40.4 bits (93), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 7/84 (8%)

Query: 428 WTMISELLPSYARGVCSGLMISYGYVCMFFMVKAFPFAIHSS-VIGTFN------VFGLV 480
           W ++SE+ P+  RG    + ++  ++  +F+   FP    +S ++  F+      ++G +
Sbjct: 392 WVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCM 451

Query: 481 SFTLVGFVYFYLPETKGKTFVEIE 504
                 F++ ++PETKGKT  E+E
Sbjct: 452 GVLAALFMWKFVPETKGKTLEELE 475


>pdb|3EFY|A Chain A, Structure Of The Cyclomodulin Cif From Pathogenic
           Escherichia Coli
 pdb|3EFY|B Chain B, Structure Of The Cyclomodulin Cif From Pathogenic
           Escherichia Coli
          Length = 195

 Score = 30.0 bits (66), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 14/23 (60%)

Query: 154 SCGILLTTILNLYLDWRSLSYCF 176
           SCG+    I+ L+LD    SYCF
Sbjct: 9   SCGVTANAIMKLFLDKDGFSYCF 31


  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
   0.329    0.142    0.441 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,522,442
Number of Sequences: 62578
Number of extensions: 514059
Number of successful extensions: 1254
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1246
Number of HSP's gapped (non-prelim): 6
length of query: 508
length of database: 14,973,337
effective HSP length: 103
effective length of query: 405
effective length of database: 8,527,803
effective search space: 3453760215
effective search space used: 3453760215
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (25.4 bits)