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= 009563
         (532 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 = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 102/450 (22%), Positives = 177/450 (39%), Gaps = 85/450 (18%)

Query: 129 VGLVQALFFFGCMIGAGVFGHLSDSRLGRKGSLTVVCMMNAVFGC--------LTAFSPN 180
           +G   A    GC+IG  + G+ S+ R GR+ SL +  ++  + G          T+ +P+
Sbjct: 57  LGFCVASALIGCIIGGALGGYCSN-RFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPD 115

Query: 181 YST----------YVVLRMLTGFSTGGVGLCAFVLATEPVGPSKRGAAGMSTFYFFSTGI 230
            +           +V+ R++ G   G   + + +   E      RG   + +F  F+   
Sbjct: 116 NTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGK--LVSFNQFAIIF 173

Query: 231 ALL-----------SGIAYIFQT--WRALYIAXXXXXXXXXXXXXXXXXXXXRWYLVRGK 277
             L           SG A    T  WR ++ A                    RW + RGK
Sbjct: 174 GQLLVYCVNYFIARSGDASWLNTDGWRYMF-ASECIPALLFLMLLYTVPESPRWLMSRGK 232

Query: 278 LNEAMKIMRAIAKSNGRHLPDGVVLMLDDEQENDASNGKQNYKEELATKEAVTGSVIDVI 337
             +A  I+R I    G  L    V     E ++   +G++     L     + G  + VI
Sbjct: 233 QEQAEGILRKIM---GNTLATQAV----QEIKHSLDHGRKTGGRLL-----MFGVGVIVI 280

Query: 338 KSPLTRIRLFLAVTINFLCSVVYY--------GISLNVVNLQTNLYLNVLVNAVAEMPAF 389
              L+  + F+ + +     V+YY        G S ++  LQT      ++  V  +  F
Sbjct: 281 GVMLSIFQQFVGINV-----VLYYAPEVFKTLGASTDIALLQT------IIVGVINL-TF 328

Query: 390 TITAVL-LDKLGRKPMT-IGTLWFS-GFFCLLGSL-VKNNGIWKIVRMICGVMGIFGVAG 445
           T+ A++ +DK GRKP+  IG L  + G F L  +   +  GI  ++ M+  V       G
Sbjct: 329 TVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWG 388

Query: 446 TYNLLFIYTTELFPTVVRNAALGCATQAAQLGAILAPFVVVL---GGWL--------PFA 494
              + ++  +E+FP  +R  AL  A  A  L      +   +     WL         + 
Sbjct: 389 P--VCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYW 446

Query: 495 VFAACGIIGGLFAF-YLPETLNKPLYDTMA 523
           ++   G++  LF + ++PET  K L +  A
Sbjct: 447 IYGCMGVLAALFMWKFVPETKGKTLEELEA 476


>pdb|2O14|A Chain A, X-Ray Crystal Structure Of Protein Yxim_bacsu From
           Bacillus Subtilis. Northeast Structural Genomics
           Consortium Target Sr595
          Length = 375

 Score = 29.3 bits (64), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 25/42 (59%)

Query: 372 TNLYLNVLVNAVAEMPAFTITAVLLDKLGRKPMTIGTLWFSG 413
           T+  LN+LV       AFT++A+ + KL  +P+T  T++  G
Sbjct: 128 TDGQLNLLVTEGKAGTAFTLSALKIKKLSDQPVTNRTIYVGG 169


  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    0.140    0.439 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,385,293
Number of Sequences: 62578
Number of extensions: 619844
Number of successful extensions: 1701
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1678
Number of HSP's gapped (non-prelim): 23
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
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)