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= 010145
         (517 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 = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 66/361 (18%), Positives = 142/361 (39%), Gaps = 46/361 (12%)

Query: 89  FAGLYIVALGVGGIKGSLAPHGAEQYDETTQ-LGRKQRSAFFNYYVFCLSCGALIAVTFV 147
           + GL+++ALG GGIK  ++    +Q+D++ + L +K     F+ + F ++ G+  A   +
Sbjct: 113 YTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA----FDMFYFTINFGSFFASLSM 168

Query: 148 VWIEDNKGWQWGFGISTATILLSIPIFLLGSPFYRNKIPTGSPLTTIFKVLTAAIFNTCK 207
             +  N G    FGI    + ++   F LG   Y +  P          V+ +A+    +
Sbjct: 169 PLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKVE 228

Query: 208 SKNSSNAVTEVHSSPTCSNESRD-------EGNSNVKEKVPSQKPTEDIKFLNRALRNNP 260
            K +   V  +    + +    +        G       V           L RA +++P
Sbjct: 229 GKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERARKSHP 288

Query: 261 AYPIVQCTXXXXXXXXXXXXXFPIFMSTIMLNCCLAQLSTFSVQQAATMNTKLGSLKVP- 319
              +                     +  ++L   +    +   Q+A+T   +   +  P 
Sbjct: 289 DAAVDGVRSV---------------LRILVLFALVTPFWSLFDQKASTWILQANDMVKPQ 333

Query: 320 ---PASLPVFPVIFILILAPVYNHVIIPFARKVTKTEMGITHLQRIGTGLILSIVAMAVA 376
              PA +     + +++L P  N V+ P    + +  + +T L+++G G+ ++ ++  V 
Sbjct: 334 WFEPAMMQALNPLLVMLLIPFNNFVLYP---AIERMGVKLTALRKMGAGIAITGLSWIVV 390

Query: 377 ALVEIKRKRVAVNSGLVNSSEPLPITFLWVALQYLFLGSADLFTLAGMMEFFFTDAPLSM 436
             +++          +++    L I   W  L Y  L   ++   A  +EF ++ AP +M
Sbjct: 391 GTIQL----------MMDGGSALSI--FWQILPYALLTFGEVLVSATGLEFAYSQAPKAM 438

Query: 437 R 437
           +
Sbjct: 439 K 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 = 33.5 bits (75), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 21/90 (23%), Positives = 45/90 (50%), Gaps = 4/90 (4%)

Query: 88  LFAGLYIVALGVGGIKGSLAPHGAEQYDETTQLGRKQRSAFFNYYVFCLSCGALIAVTFV 147
           LF  + ++ +G G +K +++      YDE      ++R A F+ +VF ++ GA IA   V
Sbjct: 111 LFGSIILIIIGTGFLKPNVSTLVGTLYDEH----DRRRDAGFSIFVFGINLGAFIAPLIV 166

Query: 148 VWIEDNKGWQWGFGISTATILLSIPIFLLG 177
              ++  G+   F ++   + + + ++  G
Sbjct: 167 GAAQEAAGYHVAFSLAAIGMFIGLLVYYFG 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
   0.325    0.137    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,100,572
Number of Sequences: 62578
Number of extensions: 483932
Number of successful extensions: 1145
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: 1143
Number of HSP's gapped (non-prelim): 4
length of query: 517
length of database: 14,973,337
effective HSP length: 103
effective length of query: 414
effective length of database: 8,527,803
effective search space: 3530510442
effective search space used: 3530510442
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)