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|15646058|ref|NP_208240.1| conserved hypothetical
protein [Helicobacter pylori 26695]
         (117 letters)

Database: NC_000921.faa
           1491 sequences; 494,079 total letters

Searching...done


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

ref|NP_224060.1|  putative [Helicobacter pylori J99]              229  2e-62
ref|NP_223986.1|  putative [Helicobacter pylori J99]               25  0.75
ref|NP_223624.1|  GLYCYL-TRNA SYNTHETASE BETA CHAIN [Helicob...    24  0.99
ref|NP_223324.1|  RIBONUCLEASE HI [Helicobacter pylori J99]        22  3.7

>ref|NP_224060.1| putative [Helicobacter pylori J99]
          Length = 118

 Score =  229 bits (584), Expect = 2e-62
 Identities = 112/118 (94%), Positives = 113/118 (94%), Gaps = 1/118 (0%)

Query: 1   MRNNKTPFLSAIFTASIRGYQRFFSAFTPSSCRFYPTCSNYALWLLCFESPLSAMGKIAI 60
           MRNNKTPFLSAIFTASIRGYQRFFSAFT SSCRFYPTCSNYALWLLCFESPL AMGKIAI
Sbjct: 1   MRNNKTPFLSAIFTASIRGYQRFFSAFTFSSCRFYPTCSNYALWLLCFESPLVAMGKIAI 60

Query: 61  RILSCNPFCSGGIAYPTTRLKRPSLIQSHKDSNRNFKTITFWLVP-TKSHATYYIIKV 117
           RILSCNPFCSGGIAYPTTRLKRPSL+QSHKD NRNFKTITFWLVP TKS ATYYIIKV
Sbjct: 61  RILSCNPFCSGGIAYPTTRLKRPSLLQSHKDFNRNFKTITFWLVPTTKSRATYYIIKV 118



>ref|NP_223986.1| putative [Helicobacter pylori J99]
          Length = 387

 Score = 24.6 bits (52), Expect = 0.75
 Identities = 9/16 (56%), Positives = 13/16 (81%)

Query: 92  SNRNFKTITFWLVPTK 107
           SNR FKT++F  +PT+
Sbjct: 251 SNRQFKTLSFSAIPTQ 266



>ref|NP_223624.1| GLYCYL-TRNA SYNTHETASE BETA CHAIN [Helicobacter pylori J99]
          Length = 701

 Score = 24.3 bits (51), Expect = 0.99
 Identities = 12/31 (38%), Positives = 16/31 (50%)

Query: 10  SAIFTASIRGYQRFFSAFTPSSCRFYPTCSN 40
           S I T S++  QR+F+ F   S    PT  N
Sbjct: 280 SEIITTSMKENQRYFAIFNQKSQEESPTLHN 310



>ref|NP_223324.1| RIBONUCLEASE HI [Helicobacter pylori J99]
          Length = 143

 Score = 22.3 bits (46), Expect = 3.7
 Identities = 11/25 (44%), Positives = 13/25 (52%)

Query: 80  LKRPSLIQSHKDSNRNFKTITFWLV 104
           LKRP  I  + DS    + I  WLV
Sbjct: 58  LKRPCHITLYSDSQYVCQAINVWLV 82



  Database: NC_000921.faa
    Posted date:  Dec 10, 2001  4:36 PM
  Number of letters in database: 494,079
  Number of sequences in database:  1491
  
Lambda     K      H
   0.327    0.137    0.444 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 120,625
Number of Sequences: 1491
Number of extensions: 4204
Number of successful extensions: 10
Number of sequences better than 10.0: 4
Number of HSP's better than 10.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 5
Number of HSP's gapped (non-prelim): 4
length of query: 117
length of database: 494,079
effective HSP length: 67
effective length of query: 50
effective length of database: 394,182
effective search space: 19709100
effective search space used: 19709100
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 43 (21.2 bits)