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= 035554
         (562 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 = 65.9 bits (159), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 100/440 (22%), Positives = 164/440 (37%), Gaps = 61/440 (13%)

Query: 70  NAEASNTFSRWMGSLYLSSLMGAFLSDSYLGRYLTCVTFQAFSIIGLLGLSFATQSFLLR 129
            A A + F  ++  +Y   L+G +++D + G+Y T +       +G              
Sbjct: 53  GAVAKDVFHSFVIGVYFFPLLGGWIADRFFGKYNTILWLSLIYCVG-------------- 98

Query: 130 PHGCGKIGQLCDPHSPAETAIFYISIYLFALGIGAPEPALATFGADQFDEEDPKEKKSKT 189
            H    I +    HS      FY  ++L ALG G  +P +++F  DQFD+ +   K    
Sbjct: 99  -HAFLAIFE----HS---VQGFYTGLFLIALGSGGIKPLVSSFMGDQFDQSN---KSLAQ 147

Query: 190 SFYSYFYIALNLGCLF-SETVLVYAENMGYWVLGFWICAGCDILAFSSLLSGTLRYRHFK 248
             +  FY  +N G  F S ++ +  +N G   + F I      +A      G  RY H  
Sbjct: 148 KAFDMFYFTINFGSFFASLSMPLLLKNFGA-AVAFGIPGVLMFVATVFFWLGRKRYIHMP 206

Query: 249 PSGNPLSRFSQVIVASLR-------KINLEMPTNGGGLFEVHVREYEANGTRRILHTNDF 301
           P       F  VI ++L         I L +   GG      +      G    L     
Sbjct: 207 PEPKDPHGFLPVIRSALLTKVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMV 266

Query: 302 KFLDRAAIMTSADITTNEDQNPNQWRLCTVTQVEEMLSLFV---------EQGAAM---- 348
             +       S  +      +P+   +  V  V  +L LF          +Q A+     
Sbjct: 267 LVMGFVGAGASLQLERARKSHPDA-AVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQ 325

Query: 349 -NTGVSNFQIPPASMTAFDIVSTTAFILLYDKLIVPLYLKVAKRRPKTPSELQRVGIGLA 407
            N  V      PA M A + +     I   + ++ P      +R     + L+++G G+A
Sbjct: 326 ANDMVKPQWFEPAMMQALNPLLVMLLIPFNNFVLYP----AIERMGVKLTALRKMGAGIA 381

Query: 408 IATVAMIIAGIVEQRRLKYASFGGEETSSLSIFWQTPQYVLLGVSEAFVYVAQMEFFASQ 467
           I  ++ I+ G ++           +  S+LSIFWQ   Y LL   E  V    +EF  SQ
Sbjct: 382 ITGLSWIVVGTIQLMM--------DGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQ 433

Query: 468 IPNGLKSLGIALSMSSTAIG 487
            P  +K   ++    S  +G
Sbjct: 434 APKAMKGTIMSFWTLSVTVG 453


>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 = 32.0 bits (71), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 30/114 (26%), Positives = 50/114 (43%), Gaps = 18/114 (15%)

Query: 66  LRQTNAEASNTFSRWMGSLYLSSLMGAFLSDS---------------YLGRYLTCVTFQA 110
           L  T A A++  + +   +YLS  +G F++D                 LG  +  + F A
Sbjct: 49  LHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGA 108

Query: 111 FSIIGLLGLSFATQSFLLRPHGCGKIGQLCDPHSPAETAIFYISIYLFALGIGA 164
            ++ G + L      F L+P+    +G L D H     A F  SI++F + +GA
Sbjct: 109 SALFGSIILIIIGTGF-LKPNVSTLVGTLYDEHDRRRDAGF--SIFVFGINLGA 159


  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
   0.323    0.137    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,727,554
Number of Sequences: 62578
Number of extensions: 628454
Number of successful extensions: 1011
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1005
Number of HSP's gapped (non-prelim): 6
length of query: 562
length of database: 14,973,337
effective HSP length: 104
effective length of query: 458
effective length of database: 8,465,225
effective search space: 3877073050
effective search space used: 3877073050
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)