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= 028321
         (210 letters)

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

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



>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 = 28.5 bits (62), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 23/100 (23%), Positives = 45/100 (45%), Gaps = 14/100 (14%)

Query: 66  QIFQKF---------ECRDKSDGGVICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNI 116
           +IFQK          E ++  D  ++C+VV    P ++ K +G  +++      + + N 
Sbjct: 96  KIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNN 155

Query: 117 YLQFEEVTVQNIYISEELQALIAPAILPRSFLSLQILQFI 156
           YLQ     ++ I  ++E        IL R  ++ + +Q I
Sbjct: 156 YLQ-----IRGIKKTDEGTYRCEGRILARGEINFKDIQVI 190


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

 Score = 28.5 bits (62), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 19/85 (22%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 72  ECRDKSDGGVICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNIYLQFEEVTVQNIYIS 131
           E ++  D  ++C+VV    P ++ K +G  +++      + + N YLQ     ++ I  +
Sbjct: 12  EFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQ-----IRGIKKT 66

Query: 132 EELQALIAPAILPRSFLSLQILQFI 156
           +E        IL R  ++ + +Q I
Sbjct: 67  DEGTYRCEGRILARGEINFKDIQVI 91


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

 Score = 28.1 bits (61), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 23/100 (23%), Positives = 45/100 (45%), Gaps = 14/100 (14%)

Query: 66  QIFQKF---------ECRDKSDGGVICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNI 116
           +IFQK          E ++  D  ++C+VV    P ++ K +G  +++      + + N 
Sbjct: 96  KIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNN 155

Query: 117 YLQFEEVTVQNIYISEELQALIAPAILPRSFLSLQILQFI 156
           YLQ     ++ I  ++E        IL R  ++ + +Q I
Sbjct: 156 YLQ-----IRGIKKTDEGTYRCEGRILARGEINFKDIQVI 190


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

 Score = 27.7 bits (60), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 82  ICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNIYLQFEEVTVQNI 128
           + N V +S   LLEK+      V   FD +  RN+ + F++ T ++I
Sbjct: 192 LANYVEFSSVNLLEKQYN----VPGPFDAIFCRNVMIYFDKTTQEDI 234


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

 Score = 27.7 bits (60), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 82  ICNVVRWSVPPLLEKEEGATLVVSAKFDVVSVRNIYLQFEEVTVQNI 128
           + N V +S   LLEK+      V   FD +  RN+ + F++ T ++I
Sbjct: 187 LANYVEFSSVNLLEKQYN----VPGPFDAIFCRNVMIYFDKTTQEDI 229


>pdb|1G5G|A Chain A, Fragment Of Fusion Protein From Newcastle Disease Virus
 pdb|1G5G|B Chain B, Fragment Of Fusion Protein From Newcastle Disease Virus
 pdb|1G5G|C Chain C, Fragment Of Fusion Protein From Newcastle Disease Virus
 pdb|1G5G|D Chain D, Fragment Of Fusion Protein From Newcastle Disease Virus
 pdb|1G5G|E Chain E, Fragment Of Fusion Protein From Newcastle Disease Virus
 pdb|1G5G|F Chain F, Fragment Of Fusion Protein From Newcastle Disease Virus
          Length = 481

 Score = 27.7 bits (60), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 98  EGATLVVSAKFDVVSVRNIYLQFEEVTVQ-NIYISEEL 134
           +G TL +S +FD    +NI +Q  +V V  N+ IS EL
Sbjct: 399 DGITLRLSGEFDATYQKNISIQDSQVIVTGNLDISTEL 436


  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
   0.324    0.140    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,640,892
Number of Sequences: 62578
Number of extensions: 208289
Number of successful extensions: 414
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 408
Number of HSP's gapped (non-prelim): 9
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)