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= 025125
         (257 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|1U7L|A Chain A, Crystal Structure Of Subunit C (Vma5p) Of The Yeast
           V-Atpase
          Length = 392

 Score =  126 bits (317), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 114/208 (54%), Gaps = 1/208 (0%)

Query: 39  FNIPNLRVGTXXXXXXXXXXXVKSNSFVESVSHKIRRQIEELERVSGIESSSLSVDGVPV 98
           F IP  ++G+            K ++ + +   KI   ++ L   S     +L ++ +PV
Sbjct: 48  FKIPEFKIGSLDTLIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPV 107

Query: 99  DTYLTRFVWDEAKYPTMSPLREIVDGIHTLVAKIEDDLKVRVAEYNNVRSQLNAINRKQS 158
             YL  F W   K+     +++++  I    ++++ D++   A YN+ ++ L A  RK++
Sbjct: 108 PEYLENFQWQTRKFKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKT 167

Query: 159 GSLAVRDLSNLVKPED-IITSEHLVTLLAVVPKYSQKDWLASYETLTSYVVPRSSKLLYE 217
           G L+VR L ++VKPED ++ SEHL T+L  VPK  + D+  SYETL+  VVP S+ ++ E
Sbjct: 168 GDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAE 227

Query: 218 DNEYALYTVTLFGRVADNFRIAAREKGF 245
           D EY L+ V LF +    F  AAREK F
Sbjct: 228 DAEYVLFNVHLFKKNVQEFTTAAREKKF 255


>pdb|4DL0|I Chain I, Crystal Structure Of The Heterotrimeric Egchead Peripheral
           Stalk Complex Of The Yeast Vacuolar Atpase
 pdb|4DL0|C Chain C, Crystal Structure Of The Heterotrimeric Egchead Peripheral
           Stalk Complex Of The Yeast Vacuolar Atpase
 pdb|4EFA|C Chain C, Crystal Structure Of The Heterotrimeric Egchead Peripheral
           Stalk Complex Of The Yeast Vacuolar Atpase - Second
           Conformation
          Length = 130

 Score = 94.0 bits (232), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 48/97 (49%), Positives = 64/97 (65%), Gaps = 1/97 (1%)

Query: 150 LNAINRKQSGSLAVRDLSNLVKPED-IITSEHLVTLLAVVPKYSQKDWLASYETLTSYVV 208
           L A  RK++G L+VR L ++VKPED ++ SEHL T+L  VPK  + D+  SYETL+  VV
Sbjct: 12  LAAAERKKTGDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVV 71

Query: 209 PRSSKLLYEDNEYALYTVTLFGRVADNFRIAAREKGF 245
           P S+ ++ ED EY L+ V LF +    F  AAREK F
Sbjct: 72  PASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKF 108


>pdb|4A01|A Chain A, Crystal Structure Of The H-Translocating Pyrophosphatase
 pdb|4A01|B Chain B, Crystal Structure Of The H-Translocating Pyrophosphatase
          Length = 766

 Score = 34.7 bits (78), Expect = 0.058,   Method: Compositional matrix adjust.
 Identities = 27/114 (23%), Positives = 50/114 (43%), Gaps = 8/114 (7%)

Query: 115 MSPLREIVDGIHTLVAKIEDDLKVRVAEYNNVRSQLNAINRKQSGSLAVRDLSNLVKPED 174
            S +  ++ G+ +LV+     L +++A Y N R+ L A  RK  G   +    +      
Sbjct: 141 FSTVSFLLGGVTSLVSGF---LGMKIATYANARTTLEA--RKGVGKAFITAFRSGAVMGF 195

Query: 175 IITSEHLVTL---LAVVPKYSQKDWLASYETLTSYVVPRSSKLLYEDNEYALYT 225
           ++ +  L+ L   + +   Y   DW   +E +T Y +  SS  L+      +YT
Sbjct: 196 LLAANGLLVLYIAINLFKIYYGDDWGGLFEAITGYGLGGSSMALFGRVGGGIYT 249


>pdb|2PMS|C Chain C, Crystal Structure Of The Complex Of Human Lactoferrin
           N-Lobe And Lactoferrin-Binding Domain Of Pneumococcal
           Surface Protein A
 pdb|2PMS|D Chain D, Crystal Structure Of The Complex Of Human Lactoferrin
           N-Lobe And Lactoferrin-Binding Domain Of Pneumococcal
           Surface Protein A
          Length = 125

 Score = 32.0 bits (71), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 12/84 (14%)

Query: 69  VSHKIRRQIEELERVSGIESSSLSVDG--VPVDTYLTRFVWDEAKYPTMSPLREIVDGIH 126
           + +++ R  +EL+ +   ES   + +G   P+ + L      +AK   +S L E+ D I 
Sbjct: 18  LENQVHRLEQELKEIDESESEDYAKEGFRAPLQSKL------DAKKAKLSKLEELSDKID 71

Query: 127 TL---VAKIEDDLKVRVAEYNNVR 147
            L   +AK+ED LK    E NNV 
Sbjct: 72  ELDAEIAKLEDQLKA-AEENNNVE 94


  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
   0.317    0.132    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,720,314
Number of Sequences: 62578
Number of extensions: 243364
Number of successful extensions: 665
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 661
Number of HSP's gapped (non-prelim): 6
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)