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= 007288
         (609 letters)

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

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



>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Ca
          Length = 501

 Score = 34.3 bits (77), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 29/110 (26%), Positives = 48/110 (43%), Gaps = 13/110 (11%)

Query: 398 EAIELFDEMVKSGVRPDRIVFMAVLTACSHAGLVDE---------GLKYFKSMNDYNVNP 448
           EA+ L+DE  ++GV+  +  +  +L  CS A    E         G   FK M    V P
Sbjct: 44  EALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVP 103

Query: 449 NKEIYGCVVDLLGRAGRVKEAYELIKSMP---FKPDESVWGP-LLGACKE 494
           N+  +     L       + A++++K M     +P    +GP L G C++
Sbjct: 104 NEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRK 153


>pdb|2XHY|A Chain A, Crystal Structure Of E.Coli Bgla
 pdb|2XHY|B Chain B, Crystal Structure Of E.Coli Bgla
 pdb|2XHY|C Chain C, Crystal Structure Of E.Coli Bgla
 pdb|2XHY|D Chain D, Crystal Structure Of E.Coli Bgla
          Length = 479

 Score = 32.0 bits (71), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 5/60 (8%)

Query: 393 HGHGKEAIELFDEMVKSGVRPDRIVFMAVLTACSHAGLVDEGLKYFKSMND----YNVNP 448
           +GH KE I+LF EM     R   I +  +      A   +EGLK++  M D    YN+ P
Sbjct: 70  YGHYKEDIKLFAEMGFKCFRTS-IAWTRIFPKGDEAQPNEEGLKFYDDMFDELLKYNIEP 128


>pdb|2ZKQ|LL Chain l, Structure Of A Mammalian Ribosomal 40s Subunit Within An
           80s Complex Obtained By Docking Homology Models Of The
           Rna And Proteins Into An 8.7 A Cryo-Em Map
          Length = 143

 Score = 30.4 bits (67), Expect = 3.3,   Method: Composition-based stats.
 Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 173 DMKWKNDVSWTTLITGYAHSGNGYGGLGVFKEMLLEGVEMNPYSFSIAVRACASTGWVSF 232
           D KW +D  +     G A   N +GG    K ++LE V +     + A+R C     +  
Sbjct: 19  DQKW-HDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKN 77

Query: 233 GKLIHAAVIKHG 244
           GK I A V   G
Sbjct: 78  GKKITAFVPNDG 89


>pdb|2HYP|A Chain A, Crystal Structure Of Rv0805 D66a Mutant
          Length = 280

 Score = 29.6 bits (65), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 371 IFSEMSDRDLVTWTSMMIGYGAHGHGKEAIELFDEMVKSGVRPDRIVFMAVLTA 424
           +   +SD  L+     +  YGA        EL +++ +SG+RPD IVF   L A
Sbjct: 17  VLLHISDTHLIGGDRRL--YGAVDADDRLGELLEQLNQSGLRPDAIVFTGDLAA 68


>pdb|2AJA|A Chain A, X-Ray Structure Of An Ankyrin Repeat Family Protein Q5zsv0
           From Legionella Pneumophila. Northeast Structural
           Genomics Consortium Target Lgr21.
 pdb|2AJA|B Chain B, X-Ray Structure Of An Ankyrin Repeat Family Protein Q5zsv0
           From Legionella Pneumophila. Northeast Structural
           Genomics Consortium Target Lgr21
          Length = 376

 Score = 28.9 bits (63), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 385 SMMIGYGAHGHGKEAIELFDEMVKSGVRPDRIVFMAVLTACSHA 428
            ++  Y AH + + A +L+ +  K G++ + I F+A +T CS A
Sbjct: 65  QLLCLYYAH-YNRNAKQLWSDAHKKGIKSEVICFVAAITGCSSA 107


  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
   0.321    0.135    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,344,969
Number of Sequences: 62578
Number of extensions: 762756
Number of successful extensions: 1637
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1635
Number of HSP's gapped (non-prelim): 9
length of query: 609
length of database: 14,973,337
effective HSP length: 105
effective length of query: 504
effective length of database: 8,402,647
effective search space: 4234934088
effective search space used: 4234934088
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: 54 (25.4 bits)