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= 009129
         (543 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 =  136 bits (342), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 127/500 (25%), Positives = 208/500 (41%), Gaps = 90/500 (18%)

Query: 7   PLISGNECCERLAYYGMSTNLVNYLQKQL------NQGNVTASNNVTNWSGTCYITPLIG 60
           P I  +E CER ++YGM   L  +L   L            A +   ++    Y  PL+G
Sbjct: 15  PYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLG 74

Query: 61  AFLADSYMGRFWTIASFSIIYCLGMTLLTL-TASVSGLKPSCDKDACHPTGAQTAVTFVA 119
            ++AD + G++ TI   S+IYC+G   L +   SV G                    +  
Sbjct: 75  GWIADRFFGKYNTILWLSLIYCVGHAFLAIFEHSVQGF-------------------YTG 115

Query: 120 LYLIALGTGGIKPCVSSFGADQFDETDDGEREKKSSFFNWFYLSINIGALVASSVLVWIQ 179
           L+LIALG+GGIKP VSSF  DQFD+++    +K    F+ FY +IN G+  AS  +  + 
Sbjct: 116 LFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFASLSMPLLL 172

Query: 180 MNVGWGWGFGIPXXXXXXXXXXXXSGSRLYRIQKPGGSPLTRIMQVIVASFRKSNVVVPA 239
            N G    FGIP             G + Y    P   P            +  +  +P 
Sbjct: 173 KNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPP--EP------------KDPHGFLPV 218

Query: 240 DKSLLYETADEECNIQGSRKLESTSKFKF-----------------------FDKAAVET 276
            +S L    + + NI     L       +                       F  A    
Sbjct: 219 IRSALLTKVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASL 278

Query: 277 QTDRVKGSADPWRLCTVTQVEELKAIIRLLPVWASGIVFATVYSQMSTMFVLQGNTMDQH 336
           Q +R + S           V+ +++++R+L ++A    F +++ Q ++ ++LQ N M + 
Sbjct: 279 QLERARKSHPD------AAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDMVK- 331

Query: 337 MGPNFKIPSASLSLFDTLSVIFWAPIYDIVIVPFARKLTGHERGFTQLQRMGIGLLISIF 396
             P +  P A +   + L V+   P  + V+ P   ++       T L++MG G+ I+  
Sbjct: 332 --PQWFEP-AMMQALNPLLVMLLIPFNNFVLYPAIERMGVK---LTALRKMGAGIAITGL 385

Query: 397 SMVAAGILEVVRLNIVKRNNYYDIETIPMTIFWQVPQYFIVGCAEVFTFIGQLEFFYDQA 456
           S +  G ++++           D  +  ++IFWQ+  Y ++   EV      LEF Y QA
Sbjct: 386 SWIVVGTIQLMM----------DGGS-ALSIFWQILPYALLTFGEVLVSATGLEFAYSQA 434

Query: 457 PDAMRSLCSALSLTTVAVGN 476
           P AM+    +    +V VGN
Sbjct: 435 PKAMKGTIMSFWTLSVTVGN 454


>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 = 60.1 bits (144), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 48/169 (28%), Positives = 79/169 (46%), Gaps = 36/169 (21%)

Query: 12  NECCERLAYYGMSTNLVNYLQKQLNQGNV-----TASNNVTNWSGTCYITPLIGAFLADS 66
            E  ER +YYGM   L+ Y+   ++ G++     TA++ +  ++   Y++  IG F+AD 
Sbjct: 21  TEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADR 80

Query: 67  YMGR----FWTIASFSIIYCLGMTLLTLTASVSGLKPSCDKDACHPTGAQTAVTFVALYL 122
            +G     FW      ++  LG  +L L                 P GA     F ++ L
Sbjct: 81  IIGARPAVFWG----GVLIMLGHIVLAL-----------------PFGASA--LFGSIIL 117

Query: 123 IALGTGGIKPCVSSFGADQFDETDDGEREKKSSFFNWFYLSINIGALVA 171
           I +GTG +KP VS+     +DE D     ++ + F+ F   IN+GA +A
Sbjct: 118 IIIGTGFLKPNVSTLVGTLYDEHD----RRRDAGFSIFVFGINLGAFIA 162


  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
   0.324    0.138    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,991,549
Number of Sequences: 62578
Number of extensions: 577047
Number of successful extensions: 1443
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1435
Number of HSP's gapped (non-prelim): 4
length of query: 543
length of database: 14,973,337
effective HSP length: 104
effective length of query: 439
effective length of database: 8,465,225
effective search space: 3716233775
effective search space used: 3716233775
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)