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= 040040
         (869 letters)

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

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



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

 Score = 33.9 bits (76), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 36/132 (27%), Positives = 55/132 (41%), Gaps = 30/132 (22%)

Query: 579 TTFYSGMHTLECPERANLIFQLKNPSFGSK---------SLVMLLCLIGQQVFPNLEELT 629
           T F+SGM     P R N+I    +  F  +           VM+ C +G  V P  E   
Sbjct: 69  TAFWSGMAKQYEPHRINIIDTPGHVDFTIEVERSMRVLDGAVMVYCAVGG-VQPQSE--- 124

Query: 630 LSKYIFTTWRQAQFHKLKILHFISD----GSDFFQV------GLLQNIHNLEKLVLKVEE 679
                 T WRQA  +K+  + F++     G++F +V       L  N   L+ L +  EE
Sbjct: 125 ------TVWRQANKYKVPRIAFVNKMDRMGANFLKVVNQIKTRLGANPVPLQ-LAIGAEE 177

Query: 680 HAEGIAQIKSLK 691
           H  G+  +  +K
Sbjct: 178 HFTGVVDLVKMK 189


>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 = 33.9 bits (76), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 36/132 (27%), Positives = 55/132 (41%), Gaps = 30/132 (22%)

Query: 579 TTFYSGMHTLECPERANLIFQLKNPSFGSK---------SLVMLLCLIGQQVFPNLEELT 629
           T F+SGM     P R N+I    +  F  +           VM+ C +G  V P  E   
Sbjct: 68  TAFWSGMAKQYEPHRINIIDTPGHVDFTIEVERSMRVLDGAVMVYCAVGG-VQPQSE--- 123

Query: 630 LSKYIFTTWRQAQFHKLKILHFISD----GSDFFQV------GLLQNIHNLEKLVLKVEE 679
                 T WRQA  +K+  + F++     G++F +V       L  N   L+ L +  EE
Sbjct: 124 ------TVWRQANKYKVPRIAFVNKMDRMGANFLKVVNQIKTRLGANPVPLQ-LAIGAEE 176

Query: 680 HAEGIAQIKSLK 691
           H  G+  +  +K
Sbjct: 177 HFTGVVDLVKMK 188


>pdb|4DUC|A Chain A, Cytochrome P450 Bm3h-2g9 Mri Sensor, No Ligand
 pdb|4DUC|B Chain B, Cytochrome P450 Bm3h-2g9 Mri Sensor, No Ligand
          Length = 472

 Score = 30.8 bits (68), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 268 LTLKSLPQLRSFCSVVAFPNLETLK----LSAINSE--TIWHNQLPAMSSCIQNLTRLIV 321
           +T+K +PQ ++F  +   P L T K    L  I  E   I+  + P   +C  +  RLI 
Sbjct: 1   MTIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTCYLSSQRLIK 60

Query: 322 HGCNNLKFLFSTSLVRSFVQ 341
             C+  +F  + S    FV+
Sbjct: 61  EACDESRFDKNLSQALKFVR 80


>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
 pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
 pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
 pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
          Length = 477

 Score = 30.4 bits (67), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 32/120 (26%), Positives = 57/120 (47%), Gaps = 19/120 (15%)

Query: 622 FPNLEELTLSKYIFTTWRQAQFH---KLKILHFISDGSDFFQVGLLQNIHNLEKL----- 673
           FP+LEEL L++ I +      F+    L+ L   S+      +G+   + NL KL     
Sbjct: 55  FPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDISEN 114

Query: 674 --VLKVEEHAEGIAQIKSLKL--NKLWFIKEHLWNPDSKLDSFLQNLEFLEVKECALSLI 729
             V+ ++   + +  +KSL++  N L +I    +       S L +LE L +++C L+ I
Sbjct: 115 KIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAF-------SGLNSLEQLTLEKCNLTSI 167


  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
   0.324    0.138    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,019,781
Number of Sequences: 62578
Number of extensions: 878463
Number of successful extensions: 2110
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2103
Number of HSP's gapped (non-prelim): 14
length of query: 869
length of database: 14,973,337
effective HSP length: 107
effective length of query: 762
effective length of database: 8,277,491
effective search space: 6307448142
effective search space used: 6307448142
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 56 (26.2 bits)