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= 027059
         (229 letters)

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

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



>pdb|1JOS|A Chain A, Ribosome Binding Factor A(Rbfa)
          Length = 128

 Score = 67.0 bits (162), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 41/117 (35%), Positives = 68/117 (58%), Gaps = 16/117 (13%)

Query: 68  RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKV 127
           +R   VA++IQ+E++ +L  +       + +  +G       + T+SDVEVS+DL   K+
Sbjct: 6   KRSDRVAQEIQKEIAVILQRE-------VKDPRIG-------MVTVSDVEVSSDLSYAKI 51

Query: 128 YVSVF--GDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRV 182
           +V+     D+   E  + GL+  + Y+RS LG+ M+LR+ PEIRFI D+S   G R+
Sbjct: 52  FVTFLFDHDEMAIEQGMKGLEKASPYIRSLLGKAMRLRIVPEIRFIYDQSLVEGMRM 108


>pdb|1KKG|A Chain A, Nmr Structure Of Ribosome-Binding Factor A (Rbfa)
          Length = 108

 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 41/123 (33%), Positives = 69/123 (56%), Gaps = 20/123 (16%)

Query: 62  KCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSAD 121
           K    P+RV   A+++Q+E++ ++L  ++             D  L  +TT+S VE+S D
Sbjct: 3   KEFGRPQRV---AQEMQKEIA-LILQREI------------KDPRLGMMTTVSGVEMSRD 46

Query: 122 LQVVKVYVSVFGDDRGKEVAIAGLKS---KAKYVRSQLGRRMKLRLTPEIRFIEDESFER 178
           L   KVYV+ F +D+ ++   AG+K+    + ++RS LG+ M+LR+ PE+ F  D S   
Sbjct: 47  LAYAKVYVT-FLNDKDEDAVKAGIKALQEASGFIRSLLGKAMRLRIVPELTFFYDNSLVE 105

Query: 179 GSR 181
           G R
Sbjct: 106 GMR 108


>pdb|2KZF|A Chain A, Solution Nmr Structure Of The Thermotoga Maritima Protein
           Tm0855 A Putative Ribosome Binding Factor A
          Length = 106

 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 35/68 (51%)

Query: 110 LTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIR 169
             T S VE+S D +   VYVS  G    ++  +  L     + R+ + + ++L + PEIR
Sbjct: 35  FVTFSRVELSKDKRYADVYVSFLGTPEERKETVEILNRAKGFFRTFIAKNLRLYVAPEIR 94

Query: 170 FIEDESFE 177
           F ED+  E
Sbjct: 95  FYEDKGIE 102


  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
   0.319    0.133    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,594,467
Number of Sequences: 62578
Number of extensions: 171979
Number of successful extensions: 300
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 283
Number of HSP's gapped (non-prelim): 15
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)