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= 039905
         (168 letters)

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

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



>pdb|2XI9|A Chain A, Pilus-Presented Adhesin, Spy0125 (Cpa), P1 Form
 pdb|2XI9|B Chain B, Pilus-Presented Adhesin, Spy0125 (Cpa), P1 Form
 pdb|2XIC|A Chain A, Pilus-Presented Adhesin, Spy0125 (Cpa), P212121 Form (Esrf
           Data)
 pdb|2XIC|B Chain B, Pilus-Presented Adhesin, Spy0125 (Cpa), P212121 Form (Esrf
           Data)
          Length = 457

 Score = 30.8 bits (68), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 13/73 (17%)

Query: 19  RAKSYHEF-------VVLLKMIIA---SSNPLQSTAVTFLMPNDEKLSEVVAT---PEHL 65
           + K YH F       + + K+++     SNP Q T + F +PN+ K   ++ T   PE L
Sbjct: 262 KLKDYHGFGDXNDSTLAVAKILVEYAQDSNPPQLTDLDFFIPNNNKYQSLIGTQWHPEDL 321

Query: 66  HDFILSHSIPTVL 78
            D I       V+
Sbjct: 322 VDIIRXEDKKEVI 334


>pdb|2XID|A Chain A, Pilus-Presented Adhesin, Spy0125 (Cpa), P212121 Form (Dls)
 pdb|2XID|B Chain B, Pilus-Presented Adhesin, Spy0125 (Cpa), P212121 Form (Dls)
          Length = 457

 Score = 30.4 bits (67), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 13/64 (20%)

Query: 19  RAKSYHEF-------VVLLKMIIA---SSNPLQSTAVTFLMPNDEKLSEVVAT---PEHL 65
           + K YH F       + + K+++     SNP Q T + F +PN+ K   ++ T   PE L
Sbjct: 262 KLKDYHGFGDMNDSTLAVAKILVEYAQDSNPPQLTDLDFFIPNNNKYQSLIGTQWHPEDL 321

Query: 66  HDFI 69
            D I
Sbjct: 322 VDII 325


>pdb|3T3K|A Chain A, 1.24 A Structure Of Friedreich's Ataxia Frataxin Variant
           Q148r
          Length = 129

 Score = 28.1 bits (61), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 100 MLSMTNSGKLGTYVNNARLVNFNVWMNS 127
           +L++   G LGTYV N R  N  +W++S
Sbjct: 50  VLTVKLGGDLGTYVINKRTPNKQIWLSS 77


>pdb|3T3X|A Chain A, 1.57 A Structure Of Friedreich's Ataxia Frataxin Variant
           R165c
 pdb|3T3X|B Chain B, 1.57 A Structure Of Friedreich's Ataxia Frataxin Variant
           R165c
          Length = 129

 Score = 26.2 bits (56), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 100 MLSMTNSGKLGTYVNNARLVNFNVWMNS 127
           +L++   G LGTYV N +  N  +W++S
Sbjct: 50  VLTVKLGGDLGTYVINKQTPNKQIWLSS 77


>pdb|3S4M|A Chain A, Crystal Structure Of Wild-Type Human Frataxin
          Length = 129

 Score = 26.2 bits (56), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 100 MLSMTNSGKLGTYVNNARLVNFNVWMNS 127
           +L++   G LGTYV N +  N  +W++S
Sbjct: 50  VLTVKLGGDLGTYVINKQTPNKQIWLSS 77


>pdb|1LY7|A Chain A, The Solution Structure Of The The C-Terminal Domain Of
           Frataxin, The Protein Responsible For Friedreich Ataxia
          Length = 121

 Score = 26.2 bits (56), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 100 MLSMTNSGKLGTYVNNARLVNFNVWMNS 127
           +L++   G LGTYV N +  N  +W++S
Sbjct: 42  VLTVKLGGDLGTYVINKQTPNKQIWLSS 69


>pdb|3BGH|A Chain A, Crystal Structure Of Putative Neuraminyllactose-Binding
           Hemagglutinin Homolog From Helicobacter Pylori
 pdb|3BGH|B Chain B, Crystal Structure Of Putative Neuraminyllactose-Binding
           Hemagglutinin Homolog From Helicobacter Pylori
          Length = 236

 Score = 26.2 bits (56), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 9/27 (33%), Positives = 19/27 (70%)

Query: 2   FIHQINQTDLETAVAETRAKSYHEFVV 28
           F+H+I +TD + A+ +   ++YH+ +V
Sbjct: 177 FVHRIKETDHDQAIRKIMNQAYHKVMV 203


  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
   0.319    0.132    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,171,226
Number of Sequences: 62578
Number of extensions: 141293
Number of successful extensions: 657
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 647
Number of HSP's gapped (non-prelim): 10
length of query: 168
length of database: 14,973,337
effective HSP length: 92
effective length of query: 76
effective length of database: 9,216,161
effective search space: 700428236
effective search space used: 700428236
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)