BLASTP 2.2.1 [Apr-13-2001]


Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
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.

Query= gi|15645340|ref|NP_207512.1| conserved hypothetical
integral membrane protein [Helicobacter pylori 26695]
         (210 letters)

Database: /var/www/html/HP/blast_new/blast/db/pdbaa
           13,198 sequences; 2,899,336 total letters

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

pdb|1LXM|A  Chain A, Crystal Structure Of Streptococcus Agal...    26  3.9
pdb|1FBK|A  Chain A, Crystal Structure Of Cytoplasmically Op...    25  8.6
pdb|1GFF|1  Chain 1, Mol_id: 1; Molecule: Bacteriophage G4 C...    25  8.6

>pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
           Lyase Complexed With Hexasaccharide Unit Of Hyaluronan
 pdb|1I8Q|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
           Lyase Complexed With Enzyme Product, Unsaturated
           Disaccharide Hyaluronan
 pdb|1F1S|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
           Lyase At 2.1 Angstrom Resolution
          Length = 814

 Score = 25.8 bits (55), Expect = 3.9
 Identities = 12/35 (34%), Positives = 23/35 (65%)

Query: 165 TLSLRYGSKLLNNQKIFMGVNLFVTAIMGTLSVTL 199
           TL+ + G  +LN++ +F+G N+  T  +G +S T+
Sbjct: 588 TLTAQKGWVILNDKIVFLGSNIKNTNGIGNVSTTI 622



>pdb|1FBK|A Chain A, Crystal Structure Of Cytoplasmically Open Conformation Of
           Bacteriorhodopsin
          Length = 248

 Score = 24.6 bits (52), Expect = 8.6
 Identities = 27/112 (24%), Positives = 40/112 (35%), Gaps = 21/112 (18%)

Query: 84  AFLALKTLFQTFKKKQVQTPKKLSLKKTLLFTLGVTLLNPQVYLEMVFLIGASALSFNLA 143
           A + L TL+   K   V  P     KK    T  V  +   +YL M+   G + + F   
Sbjct: 18  ALMGLGTLYFLVKGMGVSDP---DAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGE 74

Query: 144 QKFVFLAGTLSAALSWLLLLCTLSLRYGSKLLNNQKIFMGVNLFVTAIMGTL 195
           Q  ++ A                  RY   L     + +G+ L V A  GT+
Sbjct: 75  QNPIYWA------------------RYADWLFTTPLLLLGLALLVDADQGTI 108



>pdb|1GFF|1 Chain 1, Mol_id: 1; Molecule: Bacteriophage G4 Capsid Proteins Gpf,
           Gpg, Gpj; Chain: 1, 2, 3; Mutation: Am(E)w4
          Length = 426

 Score = 24.6 bits (52), Expect = 8.6
 Identities = 15/48 (31%), Positives = 24/48 (49%), Gaps = 3/48 (6%)

Query: 93  QTFKKKQVQTPKKLSLKKTLLFTLGVTLLNPQVYLEMVFLIGASALSF 140
           QTF  K    P+    +  ++ TL VT   P   +EM +L+G   L++
Sbjct: 266 QTFNHK---VPRFYVPEHGVIMTLAVTRFPPTHEMEMHYLVGKENLTY 310



  Database: /var/www/html/HP/blast_new/blast/db/pdbaa
    Posted date:  Dec 20, 2002 11:08 AM
  Number of letters in database: 2,899,336
  Number of sequences in database:  13,198
  
Lambda     K      H
   0.334    0.145    0.419 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 951,749
Number of Sequences: 13198
Number of extensions: 30975
Number of successful extensions: 85
Number of sequences better than 10.0: 3
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 84
Number of HSP's gapped (non-prelim): 3
length of query: 210
length of database: 2,899,336
effective HSP length: 84
effective length of query: 126
effective length of database: 1,790,704
effective search space: 225628704
effective search space used: 225628704
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 52 (24.6 bits)