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= 017229
         (375 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 =  189 bits (479), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 108/308 (35%), Positives = 170/308 (55%), Gaps = 5/308 (1%)

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 DNEYALYTVTLFGRVADNFRIAAREKGFQIRDFEYSSEAQESRNQELEKLVHDQESLRSS 277
           D EY L+ V LF +    F  AAREK F  R+F YS E  +   +E +     ++SLR  
Sbjct: 228 DAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQ 287

Query: 278 LLQWCYTSYGEVFSSWMHFCAVRVFAESILRYGLPPSFLACVLAPSVKGEKKVRSILEE- 336
           L++   T+Y +VF +W H  A+RV+ ES+LRYGLPP F   ++A   K   K +S L + 
Sbjct: 288 LVRLAKTAYVDVFINWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDA 347

Query: 337 ---LCGNA 341
              L GNA
Sbjct: 348 FGFLGGNA 355


>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 =  102 bits (254), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 53/107 (49%), Positives = 70/107 (65%), Gaps = 1/107 (0%)

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 PRSSKLLYEDNEYALYTVTLFGRVADNFRIAAREKGFQIRDFEYSSE 255
           P S+ ++ ED EY L+ V LF +    F  AAREK F  R+F YS E
Sbjct: 72  PASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYSEE 118


>pdb|2F3O|A Chain A, Crystal Structure Of A Glycyl Radical Enzyme From
           Archaeoglobus Fulgidus
 pdb|2F3O|B Chain B, Crystal Structure Of A Glycyl Radical Enzyme From
           Archaeoglobus Fulgidus
          Length = 776

 Score = 32.0 bits (71), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 38/155 (24%), Positives = 66/155 (42%), Gaps = 29/155 (18%)

Query: 199 SYETLTSYVVPRSSKLLYEDNEYALYTVTLFGRVADNFRIAAREKGFQIRDFEYSSEAQE 258
           + E     ++P   ++LY  + + L  +     VA N+    R      R F +  E  E
Sbjct: 123 TIEAFAFPLMPDIMQILYTGSVFVLTEIAGISHVAVNYPYLLR------RGFRWFLEESE 176

Query: 259 SRNQELEKLVHDQESLRSSLLQWCYTSYGEVFSSWMHFCAVRVFAESILRYGLPPSFLAC 318
            R + LE+         S + +      GE +S +    A ++ +E+++ YGL  S LA 
Sbjct: 177 RRIRALEE---------SGVYE------GEKYSFYQ---AAKIVSEAVINYGLRYSKLAE 218

Query: 319 VLAPSVKGEK-----KVRSILEELCGNANSTFWKS 348
            LA S  GE+     K+  I  ++      TFW++
Sbjct: 219 ELAESEDGERREELLKIAEICRKVPAEKPETFWEA 253


>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 = 0.62,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 12/85 (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---VAKIEDDLKVRVAEYNNVRS 148
            L   +AK+ED LK    E NNV  
Sbjct: 72  ELDAEIAKLEDQLKA-AEENNNVED 95


  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    0.131    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,713,489
Number of Sequences: 62578
Number of extensions: 356386
Number of successful extensions: 1008
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1002
Number of HSP's gapped (non-prelim): 7
length of query: 375
length of database: 14,973,337
effective HSP length: 100
effective length of query: 275
effective length of database: 8,715,537
effective search space: 2396772675
effective search space used: 2396772675
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: 52 (24.6 bits)