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= 022890
         (290 letters)

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

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



>pdb|3BBN|E Chain E, Homology Model For The Spinach Chloroplast 30s Subunit
           Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
          Length = 308

 Score = 32.7 bits (73), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 33/115 (28%), Positives = 57/115 (49%), Gaps = 10/115 (8%)

Query: 78  YRIVRANADDAFYELQNPKEQIQAYVFDVVRALVPRMTLDE-LFEQKGEVAKAVLEELEK 136
           Y I + + D  F+E  NP E+I     +     +P   +DE  FE + E+A A     E+
Sbjct: 55  YCIKKDDIDITFFEQDNPDEEITFDPPEKPEGYIPPRAVDEPPFESEEEIALA----YEE 110

Query: 137 VMGAYGYSIEHILMVDIIP-DPAVRKAMNEINAAQRLQLASVYKGEAEKILQVKR 190
           + GA  YS E +L  D+   D  ++KA    + +++ ++     G  E ++QV+R
Sbjct: 111 LYGA-AYSGESLLGNDVYAMDSKIKKATGFGSKSKKEKIRD---GFEENVVQVRR 161


>pdb|3BK6|A Chain A, Crystal Structure Of A Core Domain Of Stomatin From
           Pyrococcus Horikoshii
 pdb|3BK6|B Chain B, Crystal Structure Of A Core Domain Of Stomatin From
           Pyrococcus Horikoshii
 pdb|3BK6|C Chain C, Crystal Structure Of A Core Domain Of Stomatin From
           Pyrococcus Horikoshii
          Length = 188

 Score = 32.0 bits (71), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 34/140 (24%), Positives = 69/140 (49%), Gaps = 3/140 (2%)

Query: 46  AGILSTRINSLDVRI-ETKTKDNVFVQLLCSIQYRIVRANADDAFYELQNPKEQIQAYVF 104
           A I+  R   LDV + ET TKDNV V++   + +R+V  +   A  +++N          
Sbjct: 6   AVIVDLRTQVLDVPVQETITKDNVPVRVNAVVYFRVV--DPVKAVTQVKNYIMATSQISQ 63

Query: 105 DVVRALVPRMTLDELFEQKGEVAKAVLEELEKVMGAYGYSIEHILMVDIIPDPAVRKAMN 164
             +R+++ +  LDEL  ++ ++   +   +++    +G  +  + + D+     ++KAM 
Sbjct: 64  TTLRSVIGQAHLDELLSERDKLNMQLQRIIDEATDPWGIKVTAVEIKDVELPAGMQKAMA 123

Query: 165 EINAAQRLQLASVYKGEAEK 184
               A+R + A +   EAE+
Sbjct: 124 RQAEAERERRARITLAEAER 143


>pdb|2CVF|A Chain A, Crystal Structure Of The Radb Recombinase
 pdb|2CVF|B Chain B, Crystal Structure Of The Radb Recombinase
 pdb|2CVH|A Chain A, Crystal Structure Of The Radb Recombinase
 pdb|2CVH|B Chain B, Crystal Structure Of The Radb Recombinase
          Length = 220

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 7/69 (10%)

Query: 98  QIQAYVFDVVRALVPRMTLDEL-FEQKGEVAKAVLEELEKVMGAYGYSIEHILMVDIIPD 156
           Q+Q  ++   +  +P + ++++ F+ + E+ K V E+        GY  + IL +D +P 
Sbjct: 134 QLQVLLWIARKHNIPVIVINQVHFDSRTEMTKPVAEQ------TLGYRCKDILRLDKLPK 187

Query: 157 PAVRKAMNE 165
           P +R A+ E
Sbjct: 188 PGLRVAVLE 196


  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
   0.320    0.136    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,005,048
Number of Sequences: 62578
Number of extensions: 307540
Number of successful extensions: 1063
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1058
Number of HSP's gapped (non-prelim): 9
length of query: 290
length of database: 14,973,337
effective HSP length: 98
effective length of query: 192
effective length of database: 8,840,693
effective search space: 1697413056
effective search space used: 1697413056
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: 51 (24.3 bits)