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= 041588
         (540 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 = 80.5 bits (197), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/253 (27%), Positives = 109/253 (43%), Gaps = 44/253 (17%)

Query: 43  PFIIVNEVAERLAFFAIAVNMTAYLVREMHQSLP------TAGTHVTDWIGAAYVLTILG 96
           P+II +E  ER +F+ +   +T +L+  +  S+P       A      ++   Y   +LG
Sbjct: 15  PYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLG 74

Query: 97  AFLADAYLGQPALKHVHAIFKLQGRFRTLVVFSCIYSVGMVLLTVSGSLDSLRPPACKER 156
            ++AD + G               ++ T++  S IY VG   L +               
Sbjct: 75  GWIADRFFG---------------KYNTILWLSLIYCVGHAFLAIFEH------------ 107

Query: 157 PCVEVNGGQNGFLLCALGLIALGTRDIKPCVSSFGADQYDEADEKEAIQKYVFFNWFFFA 216
               V G   G     L LIALG+  IKP VSSF  DQ+D++++  A QK   F+ F+F 
Sbjct: 108 ---SVQGFYTG-----LFLIALGSGGIKPLVSSFMGDQFDQSNKSLA-QKA--FDMFYFT 156

Query: 217 INMGAIFGITVLVYIQEQKGWSVGFGIPTAFTICSIIIVAAGFPYYRYQKPIGSSLTRFV 276
           IN G+ F    +  + +  G +V FGIP      + +    G   Y +  P       F+
Sbjct: 157 INFGSFFASLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFL 216

Query: 277 QVIVSYVRNHLEG 289
            VI S +   +EG
Sbjct: 217 PVIRSALLTKVEG 229


>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 = 39.7 bits (91), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 169 LLCALGLIALGTRDIKPCVSSFGADQYDEADEKEAIQKYVFFNWFFFAINMGAIFGITVL 228
           L  ++ LI +GT  +KP VS+     YDE D +        F+ F F IN+GA     ++
Sbjct: 111 LFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAG----FSIFVFGINLGAFIAPLIV 166

Query: 229 VYIQEQKGWSVGFGI 243
              QE  G+ V F +
Sbjct: 167 GAAQEAAGYHVAFSL 181


>pdb|3OPY|A Chain A, Crystal Structure Of Pichia Pastoris Phosphofructokinase
           In The T- State
 pdb|3OPY|C Chain C, Crystal Structure Of Pichia Pastoris Phosphofructokinase
           In The T- State
 pdb|3OPY|E Chain E, Crystal Structure Of Pichia Pastoris Phosphofructokinase
           In The T- State
 pdb|3OPY|G Chain G, Crystal Structure Of Pichia Pastoris Phosphofructokinase
           In The T- State
          Length = 989

 Score = 28.5 bits (62), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 5/50 (10%)

Query: 132 YSVG--MVLLTVSGSLDSLRPPACKERP---CVEVNGGQNGFLLCALGLI 176
           YS+G    L T+SG  D+++  A   R     VEV GG +G+L    GLI
Sbjct: 737 YSLGSDTCLNTLSGYCDAVKQSASASRRRTFVVEVQGGYSGYLASYAGLI 786


  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    0.139    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,379,794
Number of Sequences: 62578
Number of extensions: 621901
Number of successful extensions: 1363
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: 1356
Number of HSP's gapped (non-prelim): 6
length of query: 540
length of database: 14,973,337
effective HSP length: 104
effective length of query: 436
effective length of database: 8,465,225
effective search space: 3690838100
effective search space used: 3690838100
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)