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= 008632
         (558 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 = 82.8 bits (203), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 110/495 (22%), Positives = 189/495 (38%), Gaps = 88/495 (17%)

Query: 37  RAASFIIGVEVAERFAYYGISSNLITYLTGQLGEST------ATAAAAVNVWSGTASLLP 90
           R   +II  E  ERF++YG+ + L  +L   L  S       A A    + +       P
Sbjct: 12  RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFP 71

Query: 91  LLGAFLADSFLGRFRTIVVASLIYILGXXXXXXXXXXXXXXXXDCQNNNTAKSCSPHHFQ 150
           LLG ++AD F G++ TI+  SLIY +G                     +   +   H  Q
Sbjct: 72  LLGGWIADRFFGKYNTILWLSLIYCVG---------------------HAFLAIFEHSVQ 110

Query: 151 IIVFIFSLYLVAIGQGGHKPCTQAFGADQFDAQNPQERRAKSSFFNWWYFGISFGANSTI 210
              F   L+L+A+G GG KP   +F  DQFD  N   +      F+ +YF I+FG+    
Sbjct: 111 --GFYTGLFLIALGSGGIKPLVSSFMGDQFDQSN---KSLAQKAFDMFYFTINFGSFFAS 165

Query: 211 LVVIYIQDNLNWALGFGIPCXXXXXXXXXXXXGTKTYRFSIKSKQRNPFARIGRVFVVAI 270
           L +  +  N   A+ FGIP             G K Y   +  + ++P       F+  I
Sbjct: 166 LSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRY-IHMPPEPKDPHG-----FLPVI 219

Query: 271 KTRKATLASEDEAQSSQQFKFLNK-----ALLATPDVSLEDGKLCTL------------- 312
           ++   T   E +         +       AL+  P + +  G  C +             
Sbjct: 220 RSALLT-KVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASL 278

Query: 313 -----------EDVEEAKALLRLIPIWATCLVYAIVFAQYTTFFTKQGATMDRTITRSIK 361
                        V+  +++LR++ ++A    +  +F Q  + +  Q   M +       
Sbjct: 279 QLERARKSHPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDMVKPQWFE-- 336

Query: 362 IPAASLQLXXXXXXXXXXXXYDCIFVPITRYFTQNPSGITMLQRIGAGMLLSSISMVVAA 421
            PA    L               ++  I R   +    +T L+++GAG+ ++ +S +V  
Sbjct: 337 -PAMMQALNPLLVMLLIPFNNFVLYPAIERMGVK----LTALRKMGAGIAITGLSWIVVG 391

Query: 422 LVEIKRLETAKEYGLIDKPNVTIPTSVWWLIPQYLLCGIADVFTIVGLQEFFYDQIPKEL 481
            +++          ++D  +     S++W I  Y L    +V       EF Y Q PK +
Sbjct: 392 TIQL----------MMDGGSA---LSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAM 438

Query: 482 KSFGLSIYMSVLGVG 496
           K   +S +   + VG
Sbjct: 439 KGTIMSFWTLSVTVG 453


>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 = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 44/188 (23%), Positives = 77/188 (40%), Gaps = 33/188 (17%)

Query: 46  EVAERFAYYGISSNLITYL-----TGQLGESTATAAAAVNVWSGTASLLPLLGAFLADSF 100
           E+ ERF+YYG+ + L+ Y+     TG L  + ATAA+ + +++    L   +G F+AD  
Sbjct: 22  EMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRI 81

Query: 101 LGRFRTIVVASLIYILGXXXXXXXXXXXXXXXXDCQNNNTAKSCSPHHFQIIVFIFSLYL 160
           +G    +    ++ +LG                               F       S+ L
Sbjct: 82  IGARPAVFWGGVLIMLGHIVLAL------------------------PFGASALFGSIIL 117

Query: 161 VAIGQGGHKPCTQAFGADQFDAQNPQERRAKSSFFNWWYFGISFGANSTILVVIYIQDNL 220
           + IG G  KP         +D    +  R + + F+ + FGI+ GA    L+V   Q+  
Sbjct: 118 IIIGTGFLKPNVSTLVGTLYD----EHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAA 173

Query: 221 NWALGFGI 228
            + + F +
Sbjct: 174 GYHVAFSL 181


  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    0.137    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,693,324
Number of Sequences: 62578
Number of extensions: 493050
Number of successful extensions: 953
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 940
Number of HSP's gapped (non-prelim): 10
length of query: 558
length of database: 14,973,337
effective HSP length: 104
effective length of query: 454
effective length of database: 8,465,225
effective search space: 3843212150
effective search space used: 3843212150
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)