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= 008177
         (575 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 = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 71/346 (20%), Positives = 131/346 (37%), Gaps = 42/346 (12%)

Query: 133 GSGCLKPNIISHGADQFKKQESKKLSTYFNVAYFAFCMGQLIALTLLVWVQTHSGMDIGF 192
           GSG +KP + S   DQF +         F++ YF    G   A   +  +  + G  + F
Sbjct: 122 GSGGIKPLVSSFMGDQFDQSNKSLAQKAFDMFYFTINFGSFFASLSMPLLLKNFGAAVAF 181

Query: 193 GVSAAAMAVGLISLIFGIFVY-----RNKSPRGSIFTPIAQVFVAAITKRKQICPSNTYI 247
           G+    M V  +    G   Y       K P G  F P+ +   A +TK           
Sbjct: 182 GIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHG--FLPVIRS--ALLTK----------- 226

Query: 248 LHGSQNNIATNRVLAISPNNRNLLHTEKFRFLDKACIK-------VQDGAN---ESPWKL 297
           + G  N      ++        L++      +   C         V  GA+   E   K 
Sbjct: 227 VEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERARKS 286

Query: 298 CTVTQVEQVKIIMSVVPIFACTIIFNTILAQLQTFSVQQGSAMDNKITNRFQIPPASLQA 357
                V+ V+ ++ ++ +FA    F ++  Q  +  + Q     N +       PA +QA
Sbjct: 287 HPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQA----NDMVKPQWFEPAMMQA 342

Query: 358 IPYILLIFVVPLYEIVFVPVASKFTKKDSGISPLQRVGVGLFVATFSMVAAALIEKKRRT 417
           +  +L++ ++P    V  P   +   K   ++ L+++G G+ +   S +    I+     
Sbjct: 343 LNPLLVMLLIPFNNFVLYPAIERMGVK---LTALRKMGAGIAITGLSWIVVGTIQLM--- 396

Query: 418 AALNSNQILSIFWIAPQFLIFGLSEMFTAVGLIEFFYKQSLEGMQS 463
             ++    LSIFW    + +    E+  +   +EF Y Q+ + M+ 
Sbjct: 397 --MDGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKG 440


>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 = 36.2 bits (82), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 133 GSGCLKPNIISHGADQFKKQESKKLSTYFNVAYFAFCMGQLIALTLLVWVQTHSGMDIGF 192
           G+G LKPN+ +     + + + ++    F++  F   +G  IA  ++   Q  +G  + F
Sbjct: 121 GTGFLKPNVSTLVGTLYDEHDRRR-DAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAF 179

Query: 193 GVSAAAMAVGLISLIFG 209
            ++A  M +GL+   FG
Sbjct: 180 SLAAIGMFIGLLVYYFG 196


>pdb|4F35|D Chain D, Crystal Structure Of A Bacterial DicarboxylateSODIUM
           SYMPORTER
 pdb|4F35|B Chain B, Crystal Structure Of A Bacterial DicarboxylateSODIUM
           SYMPORTER
 pdb|4F35|A Chain A, Crystal Structure Of A Bacterial DicarboxylateSODIUM
           SYMPORTER
 pdb|4F35|C Chain C, Crystal Structure Of A Bacterial DicarboxylateSODIUM
           SYMPORTER
          Length = 449

 Score = 31.2 bits (69), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 4/43 (9%)

Query: 139 PNIISHGADQFKKQESKKLSTYFNVAYFAFCMGQLIALTLLVW 181
           PN I   +   K+ E  ++  Y N+A    C+G L A+  L W
Sbjct: 410 PNAIVFASGHIKQSEXXRVGLYLNIA----CIGLLTAIAXLFW 448


  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    0.136    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,667,054
Number of Sequences: 62578
Number of extensions: 479353
Number of successful extensions: 1091
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: 1087
Number of HSP's gapped (non-prelim): 4
length of query: 575
length of database: 14,973,337
effective HSP length: 104
effective length of query: 471
effective length of database: 8,465,225
effective search space: 3987120975
effective search space used: 3987120975
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: 54 (25.4 bits)