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= 003249
         (836 letters)

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

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



>pdb|2Q7F|A Chain A, Crystal Structure Of Yrrb: A Tpr Protein With An Unusual
           Peptide- Binding Site
 pdb|2Q7F|B Chain B, Crystal Structure Of Yrrb: A Tpr Protein With An Unusual
           Peptide- Binding Site
          Length = 243

 Score = 30.8 bits (68), Expect = 3.0,   Method: Composition-based stats.
 Identities = 24/92 (26%), Positives = 46/92 (50%), Gaps = 10/92 (10%)

Query: 322 ERVVEIFSHANRQHRSIMVGLASFSLYCLLSEVAMNLDPRSDKTVCFLERLLESAETDRQ 381
           E+  E F+ A  +++   +   +F+   LLS V        ++ + F ++ LE    D  
Sbjct: 40  EKAAEAFTKAIEENKEDAIPYINFA--NLLSSVN-----ELERALAFYDKALE---LDSS 89

Query: 382 RLLAFHQLGCVRLLRKEYDEAEHLFEAAVNAG 413
              A++  G V ++++ Y EA+ +FE A+ AG
Sbjct: 90  AATAYYGAGNVYVVKEMYKEAKDMFEKALRAG 121


>pdb|2FO1|E Chain E, Crystal Structure Of The Csl-Notch-Mastermind Ternary
           Complex Bound To Dna
          Length = 373

 Score = 30.8 bits (68), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 28/54 (51%)

Query: 275 DRKLASLVASREDAVELMGYAIEENSPVLAVSCLQVFLRELPDCLNDERVVEIF 328
           D K    +A++E  +E++ Y I++ + V AV       R+L    N   +V+IF
Sbjct: 312 DGKTPIXLAAQEGRIEVVXYLIQQGASVEAVDATDHTARQLAQANNHHNIVDIF 365


>pdb|3H75|A Chain A, Crystal Structure Of A Periplasmic Sugar-Binding Protein
           From The Pseudomonas Fluorescens
          Length = 350

 Score = 29.6 bits (65), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 76  ELCPLQERSSLYLLQFQVFKGLGEAKLMRRSLRKAWQKASTVH-EKLVFGAW 126
           +L P+     + LL F   K    A+L  R LR+A  +   VH  +LV+G W
Sbjct: 136 KLGPVPAGHGIELLAFSGLKVTPAAQLRERGLRRALAEHPQVHLRQLVYGEW 187


  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
   0.322    0.135    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,716,563
Number of Sequences: 62578
Number of extensions: 807309
Number of successful extensions: 1765
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1757
Number of HSP's gapped (non-prelim): 14
length of query: 836
length of database: 14,973,337
effective HSP length: 107
effective length of query: 729
effective length of database: 8,277,491
effective search space: 6034290939
effective search space used: 6034290939
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: 56 (26.2 bits)