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= 018042
         (361 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 = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 76/335 (22%), Positives = 133/335 (39%), Gaps = 59/335 (17%)

Query: 14  NNIYNGKITAFVILSCMMAGMGGVIFGYDIGISGGVTSMEPFLEKFFPEVHRKMKEDTKI 73
           N  YN   ++++    ++A +GG++FGYD  +  G  ++E     F    +        +
Sbjct: 2   NTQYN---SSYIFSITLVATLGGLLFGYDTAVISG--TVESLNTVFVAPQNLSESAANSL 56

Query: 74  SNYCKFDSQLLTSFTSSLYVAGLVASFVASSVTRAFGRKPSVLMXXXXXXXXXXXXX--- 130
             +C           +S  +  ++   +    +  FGR+ S+ +                
Sbjct: 57  LGFC----------VASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPE 106

Query: 131 ---------XXVNVYM------LIFGRXXXXXXXXFANQSVPLYLSEMAPARYRGAINNG 175
                      V VY+       +  R         A+   P+Y++E+APA  RG + + 
Sbjct: 107 LGFTSINPDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSF 166

Query: 176 FQFSIGIGALAANFINYGTEQI-KGGW----GWRVSLALAAVPASILTLGALFLPETPNS 230
            QF+I  G L    +NY   +     W    GWR   A   +PA +  +    +PE+P  
Sbjct: 167 NQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRW 226

Query: 231 LIQRKSDHQKAKLMLQRVRGTNDVEAEFDDLLKASSTAKTINHPFKKIIQRKYRPQLLM- 289
           L+ R    Q A+ +L+++ G             A+   + I H       RK   +LLM 
Sbjct: 227 LMSRGKQEQ-AEGILRKIMGNT----------LATQAVQEIKHSLDH--GRKTGGRLLMF 273

Query: 290 -------AMAIPFFQQVTGINVIAFYAPLLFRTIG 317
                   + +  FQQ  GINV+ +YAP +F+T+G
Sbjct: 274 GVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLG 308


  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    0.138    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,522,040
Number of Sequences: 62578
Number of extensions: 356031
Number of successful extensions: 1082
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1078
Number of HSP's gapped (non-prelim): 2
length of query: 361
length of database: 14,973,337
effective HSP length: 100
effective length of query: 261
effective length of database: 8,715,537
effective search space: 2274755157
effective search space used: 2274755157
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: 52 (24.6 bits)