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= 032501
         (139 letters)

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

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



>pdb|4DL0|J Chain J, Crystal Structure Of The Heterotrimeric Egchead Peripheral
           Stalk Complex Of The Yeast Vacuolar Atpase
 pdb|4DL0|E Chain E, Crystal Structure Of The Heterotrimeric Egchead Peripheral
           Stalk Complex Of The Yeast Vacuolar Atpase
 pdb|4EFA|E Chain E, Crystal Structure Of The Heterotrimeric Egchead Peripheral
           Stalk Complex Of The Yeast Vacuolar Atpase - Second
           Conformation
          Length = 233

 Score = 65.9 bits (159), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 41/124 (33%), Positives = 75/124 (60%), Gaps = 1/124 (0%)

Query: 6   VSKQIQQMVRFIRQEAEEKANEISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQVEIR 65
           V+ ++ +M  FIR+EAEEKA EI + A++E+ IEK  +V  E   I   ++ K K+  + 
Sbjct: 13  VNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLS 72

Query: 66  KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASKEVLNVSRDHNSYKKLLKGLIVQVSGIK 125
           ++I  S   N  R+KVL A++  +  + E   +++  ++ + + YK +L+ LIV+ + +K
Sbjct: 73  QQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVE-ALLK 131

Query: 126 LVFP 129
           L+ P
Sbjct: 132 LLEP 135


>pdb|2KZ9|A Chain A, Structure Of E1-69 Of Yeast V-Atpase
          Length = 69

 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 36/57 (63%)

Query: 6  VSKQIQQMVRFIRQEAEEKANEISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQV 62
          V+ ++ +M  FIR+EAEEKA EI + A++E+ IEK  +V  E   I   ++ K K+ 
Sbjct: 13 VNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKA 69


>pdb|3QKT|A Chain A, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
           Complex With Amp- Pnp
 pdb|3QKT|B Chain B, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
           Complex With Amp- Pnp
 pdb|3QKT|C Chain C, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
           Complex With Amp- Pnp
 pdb|3QKT|D Chain D, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
           Complex With Amp- Pnp
          Length = 339

 Score = 28.5 bits (62), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 7/56 (12%)

Query: 66  KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASK---EVLNVSRDHNSYKKL--LKG 116
           K I Y++ LNA  I + Q Q D +    EA  K   EVLN+ +   +YKKL  LKG
Sbjct: 125 KLIPYNIFLNA--IYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKLSELKG 178


>pdb|3QKU|A Chain A, Mre11 Rad50 Binding Domain In Complex With Rad50 And
           Amp-Pnp
 pdb|3QKU|B Chain B, Mre11 Rad50 Binding Domain In Complex With Rad50 And
           Amp-Pnp
          Length = 359

 Score = 27.3 bits (59), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 66  KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASK---EVLNVSRDHNSYKKL 113
           K I Y++ LNA  I + Q Q D +    EA  K   EVLN+ +   +YKKL
Sbjct: 125 KLIPYNIFLNA--IYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKL 173


>pdb|3QKR|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
 pdb|3QKS|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
          Length = 203

 Score = 26.9 bits (58), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 66  KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASK---EVLNVSRDHNSYKKL 113
           K I Y++ LNA  I + Q Q D +    EA  K   EVLN+ +   +YKKL
Sbjct: 125 KLIPYNIFLNA--IYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKL 173


>pdb|1II8|A Chain A, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
          Length = 195

 Score = 26.9 bits (58), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 66  KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASK---EVLNVSRDHNSYKKL 113
           K I Y++ LNA  I + Q Q D +    EA  K   EVLN+ +   +YKKL
Sbjct: 125 KLIPYNIFLNA--IYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKL 173


  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
   0.314    0.128    0.323 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,956,752
Number of Sequences: 62578
Number of extensions: 89676
Number of successful extensions: 387
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 357
Number of HSP's gapped (non-prelim): 58
length of query: 139
length of database: 14,973,337
effective HSP length: 89
effective length of query: 50
effective length of database: 9,403,895
effective search space: 470194750
effective search space used: 470194750
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 46 (22.3 bits)