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= 017981
         (363 letters)

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

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



>pdb|1F9U|A Chain A, Crystal Structures Of Mutants Reveal A Signalling Pathway
           For Activation Of The Kinesin Motor Atpase
          Length = 347

 Score = 29.6 bits (65), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 253 LYVVHELHSLTK-AVVDYGIECILDYDSPE--DVAQAVVDMLRDIKNI-KSLSLSSGTMF 308
           ++++H   S  K     YG   ++D    E  +V+Q V D LR+ +NI KSLS     + 
Sbjct: 220 IFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINVSQVVGDRLRETQNIKKSLSCLGDVIH 279

Query: 309 ALDRLDYANDHSFPTFPFLN 328
           AL + D    H     PF N
Sbjct: 280 ALGQPDSTKRH----IPFRN 295


>pdb|2RDO|7 Chain 7, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
          Length = 704

 Score = 29.3 bits (64), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 11/84 (13%)

Query: 217 LRLELEAPEEDY------ITKYKVIIRAPNLEQLYIRDHGP-----GLYVVHELHSLTKA 265
           +++E+E PEE+       +++ + +++    E   ++ H             +L SLTK 
Sbjct: 617 MKVEVETPEENTGDVIGDLSRRRGMLKGQESEVTGVKIHAEVPLSEMFGYATQLRSLTKG 676

Query: 266 VVDYGIECILDYDSPEDVAQAVVD 289
              Y +E +   ++P +VAQAV++
Sbjct: 677 RASYTMEFLKYDEAPSNVAQAVIE 700


>pdb|3J0E|H Chain H, Models For The T. Thermophilus Ribosome Recycling Factor
           And The E. Coli Elongation Factor G Bound To The E. Coli
           Post-Termination Complex
          Length = 702

 Score = 29.3 bits (64), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 11/84 (13%)

Query: 217 LRLELEAPEEDY------ITKYKVIIRAPNLEQLYIRDHGP-----GLYVVHELHSLTKA 265
           +++E+E PEE+       +++ + +++    E   ++ H             +L SLTK 
Sbjct: 616 MKVEVETPEENTGDVIGDLSRRRGMLKGQESEVTGVKIHAEVPLSEMFGYATQLRSLTKG 675

Query: 266 VVDYGIECILDYDSPEDVAQAVVD 289
              Y +E +   ++P +VAQAV++
Sbjct: 676 RASYTMEFLKYDEAPSNVAQAVIE 699


>pdb|1VKD|A Chain A, Crystal Structure Of A Predicted Glycosidase (tm1225) From
           Thermotoga Maritima Msb8 At 2.10 A Resolution
 pdb|1VKD|B Chain B, Crystal Structure Of A Predicted Glycosidase (tm1225) From
           Thermotoga Maritima Msb8 At 2.10 A Resolution
 pdb|1VKD|C Chain C, Crystal Structure Of A Predicted Glycosidase (tm1225) From
           Thermotoga Maritima Msb8 At 2.10 A Resolution
 pdb|1VKD|D Chain D, Crystal Structure Of A Predicted Glycosidase (tm1225) From
           Thermotoga Maritima Msb8 At 2.10 A Resolution
 pdb|1VKD|E Chain E, Crystal Structure Of A Predicted Glycosidase (tm1225) From
           Thermotoga Maritima Msb8 At 2.10 A Resolution
 pdb|1VKD|F Chain F, Crystal Structure Of A Predicted Glycosidase (tm1225) From
           Thermotoga Maritima Msb8 At 2.10 A Resolution
          Length = 338

 Score = 27.7 bits (60), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 2/40 (5%)

Query: 193 LSIKGYIY--GTDSVTLNIPSLTLKRLRLELEAPEEDYIT 230
           L+  GY+Y  G   + L+ PS  L R R  L  PEE+Y T
Sbjct: 247 LTCNGYVYSFGAALLDLDDPSKVLYRSRYYLLTPEEEYET 286


  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
   0.323    0.138    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,327,897
Number of Sequences: 62578
Number of extensions: 406455
Number of successful extensions: 845
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 843
Number of HSP's gapped (non-prelim): 4
length of query: 363
length of database: 14,973,337
effective HSP length: 100
effective length of query: 263
effective length of database: 8,715,537
effective search space: 2292186231
effective search space used: 2292186231
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)