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= 007637
         (595 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 = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 52/239 (21%), Positives = 99/239 (41%), Gaps = 33/239 (13%)

Query: 32  RTMPFIIVNESFEKVASYGLLPNMIFYLMNGYHV---EAANGASMLSIWSSIS---NFLA 85
           R +P+II +E+ E+ + YG+   +  +LM    +   E   GA    ++ S      F  
Sbjct: 12  RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFP 71

Query: 86  IVGAFLADSYMGRFWVIXXXXXXXXXXXXXXXXXAMIPQLKPAPCNQLVSSNCSSATPAQ 145
           ++G ++AD + G++                      I  L    C   V     +     
Sbjct: 72  LLGGWIADRFFGKY--------------------NTILWLSLIYC---VGHAFLAIFEHS 108

Query: 146 FAILLSSFALISIGAGCVRPCSIAFGADQLDNKDNPKNKRVLETFFNWYYASTSVSGMLA 205
                +   LI++G+G ++P   +F  DQ D      NK + +  F+ +Y + +     A
Sbjct: 109 VQGFYTGLFLIALGSGGIKPLVSSFMGDQFDQS----NKSLAQKAFDMFYFTINFGSFFA 164

Query: 206 FTIIVYIQDHLGWKIGFGVRAILMVLSTLMFLFGSHLYIKVQPDKSLFTSFIQVIVASL 264
              +  +  + G  + FG+  +LM ++T+ F  G   YI + P+      F+ VI ++L
Sbjct: 165 SLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSAL 223



 Score = 38.9 bits (89), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 447 LVDEPQKVMD----MSAMWLIPQFSLIGLAEAFNAIGQIEFYYSQLPKSMSSMAMAIFTL 502
           +V   Q +MD    +S  W I  ++L+   E   +   +EF YSQ PK+M    M+ +TL
Sbjct: 389 VVGTIQLMMDGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTL 448

Query: 503 GMAVANL 509
            + V NL
Sbjct: 449 SVTVGNL 455


>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 = 40.8 bits (94), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 42/211 (19%), Positives = 84/211 (39%), Gaps = 40/211 (18%)

Query: 37  IIVNESFEKVASYGLLPNMIFYL-----MNGYHVEAANGASMLSIWSSISNFLAIVGAFL 91
           + + E +E+ + YG+   +++Y+         H+  A  AS+++I++S+      +G F+
Sbjct: 18  LFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFV 77

Query: 92  ADSYMGRFWVIXXXXXXXXXXXXXXXXXAMIPQLKPA---PCNQLVSSNCSSATPAQFAI 148
           AD  +G                            +PA       ++  +   A P   + 
Sbjct: 78  ADRIIGA---------------------------RPAVFWGGVLIMLGHIVLALPFGASA 110

Query: 149 LLSSFALISIGAGCVRPCSIAFGADQLDNKDNPKNKRVLETFFNWYYASTSVSGMLAFTI 208
           L  S  LI IG G ++P          D  D  ++       F+ +    ++   +A  I
Sbjct: 111 LFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAG-----FSIFVFGINLGAFIAPLI 165

Query: 209 IVYIQDHLGWKIGFGVRAILMVLSTLMFLFG 239
           +   Q+  G+ + F + AI M +  L++ FG
Sbjct: 166 VGAAQEAAGYHVAFSLAAIGMFIGLLVYYFG 196


>pdb|3NUR|A Chain A, Crystal Structure Of A Putative Amidohydrolase From
           Staphylococcus Aureus
          Length = 357

 Score = 28.9 bits (63), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 25/113 (22%), Positives = 43/113 (38%), Gaps = 13/113 (11%)

Query: 181 PKNKRVLETFFNWYYASTSVSGMLAFTIIVYIQDHLGWKIGFGVRAILMVLSTLMFLFGS 240
           P N  + ++++   Y   + +    F          GW I  G+ AI +VLS +      
Sbjct: 195 PVNSDIYQSYYKGNYPEVTAATFACFG--------YGWHIDVGIHAIHLVLSGIF----- 241

Query: 241 HLYIKVQPDKSLFTSFIQVIVASLRKISLYPSSNTVNYYHAKDSNYVTPTDNL 293
             Y K+      +  FI   +    +       N    Y+ K+S Y+TP+  L
Sbjct: 242 DRYPKLNXIIGHWGEFIPFFLERXDEALFAEHLNHSVSYYFKNSFYITPSGXL 294


  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
   0.323    0.136    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,167,191
Number of Sequences: 62578
Number of extensions: 613081
Number of successful extensions: 1075
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: 1071
Number of HSP's gapped (non-prelim): 5
length of query: 595
length of database: 14,973,337
effective HSP length: 104
effective length of query: 491
effective length of database: 8,465,225
effective search space: 4156425475
effective search space used: 4156425475
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)