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= 026582
         (236 letters)

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

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



>pdb|1VJF|A Chain A, Crystal Structure Of A Putative Dna-Binding Protein
           (Cc_0111) From Caulobacter Crescentus Cb15 At 1.62 A
           Resolution
          Length = 180

 Score = 57.0 bits (136), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 41/71 (57%)

Query: 13  GSVTPFALVNESARDVALLLDKGFKAQERCFFHPLSNDMSISLNTNDLDKFLKSIGRDPA 72
           GSVT F L+N++ + V  +LDK     +   FHPL ND + +++   L +FL ++G +P 
Sbjct: 110 GSVTAFGLINDTEKRVRFVLDKALADSDPVNFHPLKNDATTAVSQAGLRRFLAALGVEPX 169

Query: 73  YVDLEANPAVG 83
            VD  A   VG
Sbjct: 170 IVDFAAXEVVG 180


>pdb|1VKI|A Chain A, Crystal Structure Of A Putative Oligo-Nucleotide Binding
           Protein (Atu3699, Agr_l_2275) From Agrobacterium
           Tumefaciens Str. C58 At 1.60 A Resolution
 pdb|1VKI|B Chain B, Crystal Structure Of A Putative Oligo-Nucleotide Binding
           Protein (Atu3699, Agr_l_2275) From Agrobacterium
           Tumefaciens Str. C58 At 1.60 A Resolution
          Length = 181

 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 35/59 (59%)

Query: 13  GSVTPFALVNESARDVALLLDKGFKAQERCFFHPLSNDMSISLNTNDLDKFLKSIGRDP 71
           GSVT F  +N++AR V  +LD      E    HPLSND + ++ + DL +FL++ G  P
Sbjct: 116 GSVTVFGAINDTARQVTFVLDSDLLENELVNGHPLSNDQTTTIASKDLIRFLEATGHAP 174


>pdb|3IKW|A Chain A, Structure Of Heparinase I From Bacteroides
           Thetaiotaomicron
          Length = 374

 Score = 27.3 bits (59), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 63  FLKSIGRDP-AYVDLEANPAVGKDQPPDLAAFVPSGSTVLPDLPDPASAVQSAGGSHVNA 121
           F K++G +  A +D + NP   K+  P   A  P+G  V      P +   S G  ++ A
Sbjct: 181 FKKNVGHEKVARLDKQGNPVKDKNGKPVYKAGKPNGWLVEQGGYPPLAFGFSGGLFYIKA 240

Query: 122 NNNCKAATEK 131
           N++ K  T+K
Sbjct: 241 NSDRKWLTDK 250


>pdb|3ILR|A Chain A, Structure Of Heparinase I From Bacteroides
           Thetaiotaomicron In Complex With Tetrasaccharide Product
          Length = 370

 Score = 27.3 bits (59), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 63  FLKSIGRDP-AYVDLEANPAVGKDQPPDLAAFVPSGSTVLPDLPDPASAVQSAGGSHVNA 121
           F K++G +  A +D + NP   K+  P   A  P+G  V      P +   S G  ++ A
Sbjct: 177 FKKNVGHEKVARLDKQGNPVKDKNGKPVYKAGKPNGWLVEQGGYPPLAFGFSGGLFYIKA 236

Query: 122 NNNCKAATEK 131
           N++ K  T+K
Sbjct: 237 NSDRKWLTDK 246


  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
   0.314    0.130    0.374 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,849,456
Number of Sequences: 62578
Number of extensions: 271023
Number of successful extensions: 508
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: 506
Number of HSP's gapped (non-prelim): 7
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)