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= 009185
         (541 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 =  158 bits (399), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 139/518 (26%), Positives = 232/518 (44%), Gaps = 88/518 (16%)

Query: 65  NKYALTGAILASTNSILLGYDIGVMSGAILYIRDNLNITSIQVEVL------------VG 112
           + Y  +  ++A+   +L GYD  V+SG +    ++LN   +  + L            V 
Sbjct: 7   SSYIFSITLVATLGGLLFGYDTAVISGTV----ESLNTVFVAPQNLSESAANSLLGFCVA 62

Query: 113 SLNVCSLIGSLAAGKTSDCIGRRYTIVXXXXXXXXXXXXXXXXPSFLF-----------L 161
           S  +  +IG    G  S+  GRR ++                 P   F            
Sbjct: 63  SALIGCIIGGALGGYCSNRFGRRDSL-KIAAVLFFISGVGSAWPELGFTSINPDNTVPVY 121

Query: 162 MAG--------RVVSGIGVGYSLMIAPVYTTEISPAMTRGFLSSLPEVFINFGILLGYIS 213
           +AG        R++ GIGVG + M++P+Y  E++PA  RG L S  +  I FG LL Y  
Sbjct: 122 LAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCV 181

Query: 214 NY--ALSGLPEHIN---WRLMLGLAALPAIAVAFGVIAMPESPRWLVMKGRFADAKQALI 268
           NY  A SG    +N   WR M     +PA+     +  +PESPRWL+ +G+   A+  L 
Sbjct: 182 NYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILR 241

Query: 269 K------TSDSVEEAEFRLNEMTRTIADLGHAASSNNWQGQGVWKEXXXXXXXXXXXXXX 322
           K       + +V+E +  L+   +T   L          G GV                 
Sbjct: 242 KIMGNTLATQAVQEIKHSLDHGRKTGGRLLMF-------GVGV----------------- 277

Query: 323 AAIGV--NFFMQASGNDAVVYYSPEVFKDAGINSKKQLVGVTVIMGIAKTSFVLISALYL 380
             IGV  + F Q  G + V+YY+PEVFK  G ++   L+  T+I+G+   +F +++ + +
Sbjct: 278 IVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQ-TIIVGVINLTFTVLAIMTV 336

Query: 381 DHFGRRPLLMLGSTGMAVSLAVLGLGSKYLDQSDIKPXXXXXXXXXXXXXXXSFFSIGLG 440
           D FGR+PL ++G+ GMA+ +    LG+ +  Q+                   + F++  G
Sbjct: 337 DKFGRKPLQIIGALGMAIGM--FSLGTAFYTQAP------GIVALLSMLFYVAAFAMSWG 388

Query: 441 PITWVYSSEIFPTKFRAQGSSLAISVNRLVSGIVAMSFLSISRAVTF------GGMFFIL 494
           P+ WV  SEIFP   R +  ++A++   L +  V+ +F  + +          G  ++I 
Sbjct: 389 PVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIY 448

Query: 495 SGITAVGTVFFYFFLPETKGKSLEDIGLLFEDKAHDNH 532
             +  +  +F + F+PETKGK+LE++  L+E +     
Sbjct: 449 GCMGVLAALFMWKFVPETKGKTLEELEALWEPETKKTQ 486


>pdb|3VYW|A Chain A, Crystal Structure Of Mnmc2 From Aquifex Aeolicus
 pdb|3VYW|B Chain B, Crystal Structure Of Mnmc2 From Aquifex Aeolicus
 pdb|3VYW|C Chain C, Crystal Structure Of Mnmc2 From Aquifex Aeolicus
 pdb|3VYW|D Chain D, Crystal Structure Of Mnmc2 From Aquifex Aeolicus
          Length = 308

 Score = 31.2 bits (69), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 169 GIGVGYSLMIAPVYTTEISPAMTRGFLSSLPEVFINFGIL---LGYISNYALSGLPEHIN 225
           G G+GY+L +A  +  E++P +    +S   E+   F IL      I  + L  +PE+  
Sbjct: 104 GFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEG 163

Query: 226 WRLMLGL 232
            RL L +
Sbjct: 164 ERLSLKV 170


  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
   0.322    0.137    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,508,497
Number of Sequences: 62578
Number of extensions: 493221
Number of successful extensions: 968
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 959
Number of HSP's gapped (non-prelim): 14
length of query: 541
length of database: 14,973,337
effective HSP length: 104
effective length of query: 437
effective length of database: 8,465,225
effective search space: 3699303325
effective search space used: 3699303325
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)