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= 008565
         (561 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 = 89.4 bits (220), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 59/170 (34%), Positives = 88/170 (51%), Gaps = 15/170 (8%)

Query: 39  FIIMVEMAQRFAYYGLAGNLIQYLTNVL-----NEPTATAAQDV-NNWVGISSIFPLLGA 92
           +II  E  +RF++YG+   L  +L   L      E     A+DV +++V     FPLLG 
Sbjct: 16  YIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGG 75

Query: 93  FVADSYLGRFNTILLSSFIYFMGMVLLSLAVSVIPLHYRKAVFFTALYILAVGEGGHKPC 152
           ++AD + G++NTIL  S IY +G   L++        +    F+T L+++A+G GG KP 
Sbjct: 76  WIADRFFGKYNTILWLSLIYCVGHAFLAI------FEHSVQGFYTGLFLIALGSGGIKPL 129

Query: 153 VQTFAADQFDERNPKDKGAKSSFFNWWYLGIVFGASAAVLVAIYLQDNVG 202
           V +F  DQFD+ N   K      F+ +Y  I FG+  A L    L  N G
Sbjct: 130 VSSFMGDQFDQSN---KSLAQKAFDMFYFTINFGSFFASLSMPLLLKNFG 176



 Score = 29.3 bits (64), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 28/116 (24%), Positives = 53/116 (45%), Gaps = 21/116 (18%)

Query: 371 PASLQSLVGLSILVAVP--------VITGHRSGITMLQRIGIGLFTSILTMIVAALVEAK 422
           PA +Q+L  L +++ +P         I      +T L+++G G+  + L+ IV   ++  
Sbjct: 337 PAMMQALNPLLVMLLIPFNNFVLYPAIERMGVKLTALRKMGAGIAITGLSWIVVGTIQL- 395

Query: 423 RVRTARENGLIDSPKAIVPISIWWLLPQYLLVSICDVFGIVGLQELFYDQMPEAMR 478
                    ++D   A+   SI+W +  Y L++  +V       E  Y Q P+AM+
Sbjct: 396 ---------MMDGGSAL---SIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMK 439


>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 = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 48/169 (28%), Positives = 77/169 (45%), Gaps = 16/169 (9%)

Query: 40  IIMVEMAQRFAYYGLAGNLIQYL-----TNVLNEPTATAAQDVNNWVGISSIFPLLGAFV 94
           + M EM +RF+YYG+   L+ Y+     T  L+   ATAA  +  +  +  +   +G FV
Sbjct: 18  LFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFV 77

Query: 95  ADSYLGRFNTILLSSFIYFMGMVLLSLAVSVIPLHYRKAVFFTALYILAVGEGGHKPCVQ 154
           AD  +G    +       F G VL+ L   V+ L +  +  F ++ ++ +G G  KP V 
Sbjct: 78  ADRIIGARPAV-------FWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVS 130

Query: 155 TFAADQFDERNPKDKGAKSSFFNWWYLGIVFGASAAVLVAIYLQDNVGW 203
           T     +DE + +     S F      GI  GA  A L+    Q+  G+
Sbjct: 131 TLVGTLYDEHDRRRDAGFSIFV----FGINLGAFIAPLIVGAAQEAAGY 175


>pdb|3DW0|A Chain A, Crystal Structure Of The Class A Carbapenemase Kpc-2 At
           1.6 Angstrom Resolution
 pdb|3DW0|B Chain B, Crystal Structure Of The Class A Carbapenemase Kpc-2 At
           1.6 Angstrom Resolution
          Length = 294

 Score = 29.6 bits (65), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 54  LAGNLIQYLTNVLNEPTATAAQDVNNWVGISSIFPLLGAFVADSYLGRFNTILLSSFIYF 113
           LAG     LTN++ EP A   QD    +G+ ++    GA V  SY       L SSF  F
Sbjct: 17  LAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATV--SYRAEERFPLCSSFKGF 74

Query: 114 MGMVLLS 120
           +   +L+
Sbjct: 75  LAAAVLA 81


  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    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,828,722
Number of Sequences: 62578
Number of extensions: 548020
Number of successful extensions: 1254
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1244
Number of HSP's gapped (non-prelim): 7
length of query: 561
length of database: 14,973,337
effective HSP length: 104
effective length of query: 457
effective length of database: 8,465,225
effective search space: 3868607825
effective search space used: 3868607825
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)