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= 023858
         (276 letters)

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

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



>pdb|3GTD|A Chain A, 2.4 Angstrom Crystal Structure Of Fumarate Hydratase From
           Rickettsia Prowazekii
 pdb|3GTD|B Chain B, 2.4 Angstrom Crystal Structure Of Fumarate Hydratase From
           Rickettsia Prowazekii
          Length = 482

 Score = 28.9 bits (63), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 31  QMKVSGSATVAVDRTQVSEFELENKKHDLLSTIQGTQRGQNTNADQRSIIEEALVGLEG 89
           + K++ S   A+DR    EFE +N    +  T  GTQ   N N    SI  E L G +G
Sbjct: 87  EYKIATSIDKAIDRILAGEFE-DNFPLVVWQTGSGTQTNMNMNEVIASIANEELTGKKG 144


>pdb|1QZ1|A Chain A, Crystal Structure Of The Ig 1-2-3 Fragment Of Ncam
          Length = 291

 Score = 28.9 bits (63), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 23/100 (23%), Positives = 45/100 (45%), Gaps = 14/100 (14%)

Query: 132 QIFQKF---------ECRDKSDGGVICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNI 182
           +IFQK          E ++  D  ++C+VV    P ++ K +G  +++      + + N 
Sbjct: 96  KIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNN 155

Query: 183 YLQFEEVTVQNIYISEELQALIAPAILPRSFLSLQILQFI 222
           YLQ     ++ I  ++E        IL R  ++ + +Q I
Sbjct: 156 YLQ-----IRGIKKTDEGTYRCEGRILARGEINFKDIQVI 190


>pdb|1EPF|A Chain A, Crystal Structure Of The Two N-Terminal Immunoglobulin
           Domains Of The Neural Cell Adhesion Molecule (Ncam)
 pdb|1EPF|B Chain B, Crystal Structure Of The Two N-Terminal Immunoglobulin
           Domains Of The Neural Cell Adhesion Molecule (Ncam)
 pdb|1EPF|C Chain C, Crystal Structure Of The Two N-Terminal Immunoglobulin
           Domains Of The Neural Cell Adhesion Molecule (Ncam)
 pdb|1EPF|D Chain D, Crystal Structure Of The Two N-Terminal Immunoglobulin
           Domains Of The Neural Cell Adhesion Molecule (Ncam)
          Length = 191

 Score = 28.9 bits (63), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 23/100 (23%), Positives = 45/100 (45%), Gaps = 14/100 (14%)

Query: 132 QIFQKF---------ECRDKSDGGVICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNI 182
           +IFQK          E ++  D  ++C+VV    P ++ K +G  +++      + + N 
Sbjct: 96  KIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNN 155

Query: 183 YLQFEEVTVQNIYISEELQALIAPAILPRSFLSLQILQFI 222
           YLQ     ++ I  ++E        IL R  ++ + +Q I
Sbjct: 156 YLQ-----IRGIKKTDEGTYRCEGRILARGEINFKDIQVI 190


>pdb|1BC5|A Chain A, Chemotaxis Receptor Recognition By Protein
           Methyltransferase Cher
          Length = 269

 Score = 28.1 bits (61), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 148 ICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNIYLQFEEVTVQNI 194
           + N V +S   LLEK+      V   FD +  RN+ + F++ T ++I
Sbjct: 187 LANYVEFSSVNLLEKQYN----VPGPFDAIFCRNVMIYFDKTTQEDI 229


>pdb|1AF7|A Chain A, Cher From Salmonella Typhimurium
          Length = 274

 Score = 28.1 bits (61), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 148 ICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNIYLQFEEVTVQNI 194
           + N V +S   LLEK+      V   FD +  RN+ + F++ T ++I
Sbjct: 192 LANYVEFSSVNLLEKQYN----VPGPFDAIFCRNVMIYFDKTTQEDI 234


>pdb|3NCM|A Chain A, Neural Cell Adhesion Molecule, Module 2, Nmr, 20
           Structures
          Length = 92

 Score = 27.7 bits (60), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 19/85 (22%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 138 ECRDKSDGGVICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNIYLQFEEVTVQNIYIS 197
           E ++  D  ++C+VV    P ++ K +G  +++      + + N YLQ     ++ I  +
Sbjct: 12  EFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQ-----IRGIKKT 66

Query: 198 EELQALIAPAILPRSFLSLQILQFI 222
           +E        IL R  ++ + +Q I
Sbjct: 67  DEGTYRCEGRILARGEINFKDIQVI 91


  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    0.134    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,959,622
Number of Sequences: 62578
Number of extensions: 262055
Number of successful extensions: 481
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 478
Number of HSP's gapped (non-prelim): 7
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
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: 51 (24.3 bits)