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= 013295
         (446 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 = 29.3 bits (64), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 40/86 (46%), Gaps = 10/86 (11%)

Query: 247 RDHGPGLYVVHELHSLTK-AVVDYGIECILDYDSPE--DVAQAVVDMLRDIKNI-KSLSL 302
           R H   ++++H   S  K     YG   ++D    E  +V+Q V D LR+ +NI KSLS 
Sbjct: 216 RSHS--IFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINVSQVVGDRLRETQNIKKSLSC 273

Query: 303 SSGTMFALDRLDYANDHSFPTFPFLN 328
               + AL + D    H     PF N
Sbjct: 274 LGDVIHALGQPDSTKRH----IPFRN 295


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

 Score = 29.3 bits (64), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 22/91 (24%), Positives = 44/91 (48%), Gaps = 11/91 (12%)

Query: 210 PSLTLKRLRLELEAPEEDY------ITKYKVIIRAPNLEQLYIRDHGP-----GLYVVHE 258
           P L    +++E+E PEE+       +++ + +++    E   ++ H             +
Sbjct: 610 PVLLEPIMKVEVETPEENTGDVIGDLSRRRGMLKGQESEVTGVKIHAEVPLSEMFGYATQ 669

Query: 259 LHSLTKAVVDYGIECILDYDSPEDVAQAVVD 289
           L SLTK    Y +E +   ++P +VAQAV++
Sbjct: 670 LRSLTKGRASYTMEFLKYDEAPSNVAQAVIE 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 = 28.9 bits (63), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 22/91 (24%), Positives = 44/91 (48%), Gaps = 11/91 (12%)

Query: 210 PSLTLKRLRLELEAPEEDY------ITKYKVIIRAPNLEQLYIRDHGP-----GLYVVHE 258
           P L    +++E+E PEE+       +++ + +++    E   ++ H             +
Sbjct: 609 PVLLEPIMKVEVETPEENTGDVIGDLSRRRGMLKGQESEVTGVKIHAEVPLSEMFGYATQ 668

Query: 259 LHSLTKAVVDYGIECILDYDSPEDVAQAVVD 289
           L SLTK    Y +E +   ++P +VAQAV++
Sbjct: 669 LRSLTKGRASYTMEFLKYDEAPSNVAQAVIE 699


>pdb|1M6D|A Chain A, Crystal Structure Of Human Cathepsin F
 pdb|1M6D|B Chain B, Crystal Structure Of Human Cathepsin F
          Length = 214

 Score = 28.5 bits (62), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 21/43 (48%)

Query: 380 VKIIVIGEFEGEENEMKLIKYLLKNGEVLNAMIIGGEQFQRRG 422
            K+ +    E  +NE KL  +L K G +  A+   G QF R G
Sbjct: 103 AKVYIQDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHG 145


  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    0.139    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,941,007
Number of Sequences: 62578
Number of extensions: 531871
Number of successful extensions: 1179
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1178
Number of HSP's gapped (non-prelim): 5
length of query: 446
length of database: 14,973,337
effective HSP length: 102
effective length of query: 344
effective length of database: 8,590,381
effective search space: 2955091064
effective search space used: 2955091064
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)