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|15645285|ref|NP_207455.1| ribonuclease H (rnhA)
[Helicobacter pylori 26695]
         (143 letters)

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

Searching...done


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

ref|NP_223324.1|  RIBONUCLEASE HI [Helicobacter pylori J99]       285  3e-79
ref|NP_222928.1|  putative [Helicobacter pylori J99]               24  1.9
ref|NP_223295.1|  Hydrogenase expression/formation protein [...    23  3.2
ref|NP_223587.1|  putative [Helicobacter pylori J99]               23  4.1
ref|NP_224064.1|  putative Outer membrane protein [Helicobac...    22  7.1
ref|NP_223465.1|  putative [Helicobacter pylori J99]               22  7.1

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

 Score =  285 bits (730), Expect = 3e-79
 Identities = 136/143 (95%), Positives = 140/143 (97%)

Query: 1   MQEIEIFCDGSSLGNPGPGGYAAILRYKDKEKTISGGEEFTTNNRMELRALNEALKILKR 60
           MQEIEIFCDGSSLGNPGPGGYAAILRYKDKEKTISGGE FTTNNRMELRALNEALKILKR
Sbjct: 1   MQEIEIFCDGSSLGNPGPGGYAAILRYKDKEKTISGGENFTTNNRMELRALNEALKILKR 60

Query: 61  PCRITLYSDSQYVCQAINVWLANWQKKNFSKVKNVDLWKEFLEVSKGHSIVAVWIKGHNG 120
           PC ITLYSDSQYVCQAINVWL NWQKKNF+KVKNVDLWKEF++VSKGHSIVAVWIKGHNG
Sbjct: 61  PCHITLYSDSQYVCQAINVWLVNWQKKNFAKVKNVDLWKEFVKVSKGHSIVAVWIKGHNG 120

Query: 121 HAENERCDSLAKLEAQKRVKTTT 143
           HAENERC+SLAKLEAQKRVKTTT
Sbjct: 121 HAENERCNSLAKLEAQKRVKTTT 143



>ref|NP_222928.1| putative [Helicobacter pylori J99]
          Length = 326

 Score = 23.9 bits (50), Expect = 1.9
 Identities = 23/97 (23%), Positives = 43/97 (43%), Gaps = 6/97 (6%)

Query: 45  RMELRALNEALKI--LKRPCRITLYSDSQYVCQAINVWLANWQKKNFSKVKNVDLWKEFL 102
           R+ L  + E +++  LK    IT Y+ +   C++  V     +K+++  V   D+ KE  
Sbjct: 165 RVSLGTIKEVIRLNDLKSVEEITNYTKAGAFCKSC-VRPGGHEKRDYYLV---DILKEVR 220

Query: 103 EVSKGHSIVAVWIKGHNGHAENERCDSLAKLEAQKRV 139
           E  +   + A   K  NG         + K++A  +V
Sbjct: 221 EEMEAEKLKATANKSQNGELAFREMTMVQKIKAVDKV 257



>ref|NP_223295.1| Hydrogenase expression/formation protein [Helicobacter pylori
          J99]
          Length = 178

 Score = 23.1 bits (48), Expect = 3.2
 Identities = 10/23 (43%), Positives = 16/23 (69%)

Query: 75 QAINVWLANWQKKNFSKVKNVDL 97
          + I V LA++ K+NFS   +VD+
Sbjct: 18 EGIGVHLAHYLKRNFSFFPSVDI 40



>ref|NP_223587.1| putative [Helicobacter pylori J99]
          Length = 161

 Score = 22.7 bits (47), Expect = 4.1
 Identities = 9/28 (32%), Positives = 13/28 (46%)

Query: 100 EFLEVSKGHSIVAVWIKGHNGHAENERC 127
           EF E+ KG  ++ +    H    E E C
Sbjct: 52  EFFEMRKGEKLIGICGLNHINQTEAELC 79



>ref|NP_224064.1| putative Outer membrane protein [Helicobacter pylori J99]
          Length = 744

 Score = 21.9 bits (45), Expect = 7.1
 Identities = 9/32 (28%), Positives = 17/32 (53%)

Query: 2   QEIEIFCDGSSLGNPGPGGYAAILRYKDKEKT 33
           +E+++F +G  + +     Y    R+KDK  T
Sbjct: 459 KEVQVFDNGHEVRDTDGSTYDVCSRFKDKPYT 490



>ref|NP_223465.1| putative [Helicobacter pylori J99]
          Length = 108

 Score = 21.9 bits (45), Expect = 7.1
 Identities = 9/31 (29%), Positives = 17/31 (54%)

Query: 47 ELRALNEALKILKRPCRITLYSDSQYVCQAI 77
          +++    ALKI ++PC    +S  Q + Q +
Sbjct: 65 DIKNFYRALKISEKPCEEIQFSKEQKIKQLL 95



  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
   0.316    0.132    0.400 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 150,903
Number of Sequences: 1491
Number of extensions: 6220
Number of successful extensions: 13
Number of sequences better than 10.0: 6
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 8
Number of HSP's gapped (non-prelim): 6
length of query: 143
length of database: 494,079
effective HSP length: 70
effective length of query: 73
effective length of database: 389,709
effective search space: 28448757
effective search space used: 28448757
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 44 (21.6 bits)