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= 023063
         (288 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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 52/218 (23%), Positives = 92/218 (42%), Gaps = 30/218 (13%)

Query: 24  MPFIFSNEVCEKLAVVGFNTNMISYLTTQLHMPLTK------AANTLTNFGGTGSLTPLI 77
           +P+I ++E CE+ +  G    +  +L T L + + +      A +   +F       PL+
Sbjct: 14  IPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLL 73

Query: 78  GAFVADAYAGRFWTITIASIIYQIGMICLTISAILPQLRPPPCEGEQVCQEANKGQVAIL 137
           G ++AD + G++ TI   S+IY +G   L I                  + + +G     
Sbjct: 74  GGWIADRFFGKYNTILWLSLIYCVGHAFLAI-----------------FEHSVQG----F 112

Query: 138 YVXXXXXXXXXXXIRPCVVAFGADQFDETDPKQATKTWKYFNWYYFVMGAAILVAVTVLV 197
           Y            I+P V +F  DQFD+++   A K    F+ +YF +      A   + 
Sbjct: 113 YTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFASLSMP 169

Query: 198 YIQDNIGWGWGLGIPTFAMFLSIIAFLIGYPLYRNLDP 235
            +  N G     GIP   MF++ + F +G   Y ++ P
Sbjct: 170 LLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPP 207


>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 = 32.7 bits (73), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 27/109 (24%), Positives = 47/109 (43%), Gaps = 10/109 (9%)

Query: 5   MEEKGSNSHVKRQKGGMITMPFIFSNEVCEKLAVVGFNTNMISYL-----TTQLHMPLTK 59
           ME+KG     K   G  + +  +F  E+ E+ +  G    ++ Y+     T  LH+    
Sbjct: 1   MEDKG-----KTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRAT 55

Query: 60  AANTLTNFGGTGSLTPLIGAFVADAYAGRFWTITIASIIYQIGMICLTI 108
           AA+ +  +     L+  IG FVAD   G    +    ++  +G I L +
Sbjct: 56  AASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLAL 104


>pdb|3CMQ|A Chain A, Crystal Structure Of Human Mitochondrial Phenylalanine
           Trna Synthetase
 pdb|3HFV|A Chain A, Crystal Structure Of Human Mitochondrial Phenylalanyl-Trna
           Synthetase Complexed With M-Tyrosine
 pdb|3TEG|A Chain A, Bacterial And Eukaryotic Phenylalanyl-Trna Synthetases
           Catalyze Misaminoacylation Of Trnaphe With
           3,4-Dihydroxy-L-Phenylalanine (L- Dopa)
 pdb|3TUP|A Chain A, Crystal Structure Of Human Mitochondrial Phers Complexed
           With Trnaphe In The Active Open State
          Length = 415

 Score = 29.6 bits (65), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 12/22 (54%), Positives = 14/22 (63%)

Query: 200 QDNIGWGWGLGIPTFAMFLSII 221
           QD IGW +GLG+   AM L  I
Sbjct: 269 QDRIGWAFGLGLERLAMILYDI 290


>pdb|3T6Q|A Chain A, Crystal Structure Of Mouse Rp105MD-1 Complex
 pdb|3T6Q|B Chain B, Crystal Structure Of Mouse Rp105MD-1 Complex
          Length = 606

 Score = 27.7 bits (60), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 18/38 (47%)

Query: 34  EKLAVVGFNTNMISYLTTQLHMPLTKAANTLTNFGGTG 71
           EKL V+ F  N I YL+ +    L +A N   N  G  
Sbjct: 153 EKLKVLDFQNNAIHYLSKEDMSSLQQATNLSLNLNGND 190


  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
   0.324    0.139    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,220,925
Number of Sequences: 62578
Number of extensions: 316028
Number of successful extensions: 714
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 707
Number of HSP's gapped (non-prelim): 6
length of query: 288
length of database: 14,973,337
effective HSP length: 98
effective length of query: 190
effective length of database: 8,840,693
effective search space: 1679731670
effective search space used: 1679731670
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: 51 (24.3 bits)