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= 009990
         (520 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 53/222 (23%), Positives = 96/222 (43%), Gaps = 36/222 (16%)

Query: 73  FIFGNEMAERMAYFGLSVNMVTFMFYVMHKSFAD------SSNAVNNFLGISQASSVLGG 126
           +I  +E  ER +++G+   +  F+   +  S  +      + +  ++F+       +LGG
Sbjct: 16  YIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGG 75

Query: 127 FLADAYLGRYWTIAIFTTIYLAGLTGITLCATMKVFMPNQDNCDRISQLLGSCEPAKSWQ 186
           ++AD + G+Y TI   + IY  G       A + +F  +                     
Sbjct: 76  WIADRFFGKYNTILWLSLIYCVG------HAFLAIFEHSVQG------------------ 111

Query: 187 MLYLYTVLYITGFGAAGIRPCVSSFGADQFDERSKDYKTHLDRFFNFFYLSVTVGAIVAF 246
               YT L++   G+ GI+P VSSF  DQFD+ +K       + F+ FY ++  G+  A 
Sbjct: 112 ---FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLA---QKAFDMFYFTINFGSFFAS 165

Query: 247 TLVVYIQMEHGWGSAFGALAIAMGISNMLFFIGTPLYRHRLP 288
             +  +    G   AFG   + M ++ + F++G   Y H  P
Sbjct: 166 LSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPP 207


>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation.
 pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation
          Length = 491

 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 52/211 (24%), Positives = 90/211 (42%), Gaps = 37/211 (17%)

Query: 74  IFGNEMAERMAYFGLSVNMVTFMFYV-----MHKSFADSSNAVNNFLGISQASSVLGGFL 128
           +F  EM ER +Y+G+   ++ +M+++     +H + A +++ +  +  +   S  +GGF+
Sbjct: 18  LFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFV 77

Query: 129 ADAYLGRYWTIAIFTTIYLAGLTGITLCATMKVFMPNQDNCDRISQLLGSCEPAKSWQML 188
           AD  +G     A+F    L  L  I L                 S L GS          
Sbjct: 78  ADRIIGA--RPAVFWGGVLIMLGHIVLALPFGA-----------SALFGSI--------- 115

Query: 189 YLYTVLYITGFGAAGIRPCVSSFGADQFDERSKDYKTHLDRFFNFFYLSVTVGAIVAFTL 248
               +L I G G   ++P VS+     +DE  +      D  F+ F   + +GA +A  +
Sbjct: 116 ----ILIIIGTGF--LKPNVSTLVGTLYDEHDR----RRDAGFSIFVFGINLGAFIAPLI 165

Query: 249 VVYIQMEHGWGSAFGALAIAMGISNMLFFIG 279
           V   Q   G+  AF   AI M I  ++++ G
Sbjct: 166 VGAAQEAAGYHVAFSLAAIGMFIGLLVYYFG 196


  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    0.136    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,172,008
Number of Sequences: 62578
Number of extensions: 551631
Number of successful extensions: 936
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 930
Number of HSP's gapped (non-prelim): 8
length of query: 520
length of database: 14,973,337
effective HSP length: 103
effective length of query: 417
effective length of database: 8,527,803
effective search space: 3556093851
effective search space used: 3556093851
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)