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= 047115
         (522 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 =  100 bits (248), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/302 (27%), Positives = 137/302 (45%), Gaps = 39/302 (12%)

Query: 223 GWRISLAMAAVPASILTIGSLFLPETPNSIIQRNKDHQKAEEILQIVRNTT-------DV 275
           GWR   A   +PA +  +    +PE+P  ++ R K  Q AE IL+ +   T       ++
Sbjct: 198 GWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQ-AEGILRKIMGNTLATQAVQEI 256

Query: 276 KAELDDIIRASSKIIHRIYRPQLVMAILIPFQQVTRVNVISFNAPVLFMTIKVRKSTSLL 335
           K  LD   +   +++       ++  +L  FQQ   +NV+ + AP +F T+      +LL
Sbjct: 257 KHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALL 316

Query: 336 MSAVVPDGIGTVSTILPMILADKLGRTVLFLLGGIQILVSQVMIRSIMAAQLGDHGGFNI 395
            + +V   I    T+L ++  DK GR  L ++G + + +                G F++
Sbjct: 317 QTIIV-GVINLTFTVLAIMTVDKFGRKPLQIIGALGMAI----------------GMFSL 359

Query: 396 GYAY-------LILFLICVYKAGFAFSRGPLGWLVPSEIFPLEIRSAGQSITVAVDLLFT 448
           G A+       + L  +  Y A FA S GP+ W++ SEIFP  IR    +I VA   L  
Sbjct: 360 GTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLAN 419

Query: 449 FLVAQTFLAM------LCHFKAGV-FFCFGGWVAFMTTFVHFFLPETKYMPIEFMDKVWR 501
           + V+ TF  M      + HF  G  ++ +G        F+  F+PETK   +E ++ +W 
Sbjct: 420 YFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479

Query: 502 EH 503
             
Sbjct: 480 PE 481


>pdb|1QX6|A Chain A, Crystal Structure Of Sortase B Complexed With E-64
          Length = 214

 Score = 34.3 bits (77), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 3/54 (5%)

Query: 17  LIFGYDIGVSGGVTLMEPFLKKCFLEVYKKMKEDPKISNYGKFDSQLLAAFTSS 70
           +++G+ +G +    ++E +LK+ F E +K ++ D K   YGK+  Q+ +A+ ++
Sbjct: 96  ILYGHHVGDNTXFDVLEDYLKQSFYEKHKIIEFDNK---YGKYQLQVFSAYKTT 146


>pdb|1NG5|A Chain A, 2.0 A Crystal Structure Of Staphylococcus Aureus Sortase B
 pdb|1NG5|B Chain B, 2.0 A Crystal Structure Of Staphylococcus Aureus Sortase B
          Length = 215

 Score = 33.5 bits (75), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 15/56 (26%), Positives = 35/56 (62%), Gaps = 3/56 (5%)

Query: 15  SGLIFGYDIGVSGGVTLMEPFLKKCFLEVYKKMKEDPKISNYGKFDSQLLAAFTSS 70
           + +++G+ +G +    ++E +LK+ F E +K ++ D K   YGK+  Q+ +A+ ++
Sbjct: 95  NTILYGHHVGDNTMFDVLEDYLKQSFYEKHKIIEFDNK---YGKYQLQVFSAYKTT 147


>pdb|1QWZ|A Chain A, Crystal Structure Of Sortase B From S. Aureus Complexed
           With Mtset
 pdb|1QXA|A Chain A, Crystal Structure Of Sortase B Complexed With Gly3
          Length = 235

 Score = 33.5 bits (75), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 3/54 (5%)

Query: 17  LIFGYDIGVSGGVTLMEPFLKKCFLEVYKKMKEDPKISNYGKFDSQLLAAFTSS 70
           +++G+ +G +    ++E +LK+ F E +K ++ D K   YGK+  Q+ +A+ ++
Sbjct: 117 ILYGHHVGDNTMFDVLEDYLKQSFYEKHKIIEFDNK---YGKYQLQVFSAYKTT 167


>pdb|3DL8|G Chain G, Structure Of The Complex Of Aquifex Aeolicus Secyeg And
           Bacillus Subtilis Seca
 pdb|3DL8|H Chain H, Structure Of The Complex Of Aquifex Aeolicus Secyeg And
           Bacillus Subtilis Seca
          Length = 429

 Score = 28.9 bits (63), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 26/112 (23%), Positives = 49/112 (43%), Gaps = 19/112 (16%)

Query: 322 LFMTIKVRKSTSLLMSAVVPDGI--------GTVSTILPMILADKLGRTVLFLLGGIQIL 373
           L M +  R  + + +  + P+ +        G+V  +  +     LGR  +F LG +  +
Sbjct: 22  LLMFVIYRLGSHIPIPGINPEALRDFLKAFEGSVFALYDIFSGGNLGRLTVFALGVMPYI 81

Query: 374 VSQVMIRSI---------MAAQLGDHGGFNIG--YAYLILFLICVYKAGFAF 414
            + +M++ +         +A + GD+G + I     YL LF+  V   G AF
Sbjct: 82  SASIMMQLLTVAIPSLQRLAKEEGDYGRYKINEYTKYLTLFVATVQSLGIAF 133


  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
   0.328    0.141    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,723,493
Number of Sequences: 62578
Number of extensions: 461898
Number of successful extensions: 1291
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1285
Number of HSP's gapped (non-prelim): 6
length of query: 522
length of database: 14,973,337
effective HSP length: 103
effective length of query: 419
effective length of database: 8,527,803
effective search space: 3573149457
effective search space used: 3573149457
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)