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|15645632|ref|NP_207808.1| hypothetical protein
[Helicobacter pylori 26695]
         (48 letters)

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

Searching...done


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

ref|NP_223124.1|  PROTEASE DO [Helicobacter pylori J99]            73  1e-15
ref|NP_224176.1|  TRANSCRIPTION-REPAIR COUPLING FACTOR [Heli...    25  0.42
ref|NP_223966.1|  CATION EFFLUX SYSTEM PROTEIN [Helicobacter...    23  1.2
ref|NP_222729.1|  putative Outer membrane protein [Helicobac...    22  2.7
ref|NP_223829.1|  CARBONIC ANHYDRASE [Helicobacter pylori J99]     22  3.6
ref|NP_223952.1|  50S RIBOSOMAL PROTEIN L22 [Helicobacter py...    21  4.7
ref|NP_223566.1|  Outer membrane protein/porin [Helicobacter...    21  6.1

>ref|NP_223124.1| PROTEASE DO [Helicobacter pylori J99]
          Length = 476

 Score = 73.2 bits (178), Expect = 1e-15
 Identities = 35/40 (87%), Positives = 39/40 (97%)

Query: 1  MKKTLFISLALALSLNAGNIQIQSMPKVKERVSVPSKDDT 40
          MKKT F+SLALALSLNAGNIQIQ+MPKVKER+SVPSK+DT
Sbjct: 2  MKKTFFVSLALALSLNAGNIQIQNMPKVKERISVPSKEDT 41



>ref|NP_224176.1| TRANSCRIPTION-REPAIR COUPLING FACTOR [Helicobacter pylori J99]
          Length = 1001

 Score = 24.6 bits (52), Expect = 0.42
 Identities = 13/32 (40%), Positives = 17/32 (52%)

Query: 11  LALSLNAGNIQIQSMPKVKERVSVPSKDDTDL 42
           L LS    NI +    + KE +  PSKDD D+
Sbjct: 953 LKLSNFNQNITLTYSDEKKESLKAPSKDDNDI 984



>ref|NP_223966.1| CATION EFFLUX SYSTEM PROTEIN [Helicobacter pylori J99]
          Length = 341

 Score = 23.1 bits (48), Expect = 1.2
 Identities = 15/37 (40%), Positives = 19/37 (50%), Gaps = 4/37 (10%)

Query: 1  MKKTLFISLALALSLNAGNIQ----IQSMPKVKERVS 33
          MK+ L ++LAL  SL+  N Q     Q   K KE  S
Sbjct: 1  MKRLLLLALALFFSLSCTNAQEIKETQETKKTKETKS 37



>ref|NP_222729.1| putative Outer membrane protein [Helicobacter pylori J99]
          Length = 668

 Score = 21.9 bits (45), Expect = 2.7
 Identities = 10/17 (58%), Positives = 13/17 (75%)

Query: 1  MKKTLFISLALALSLNA 17
          MKKTL +SL+ +  LNA
Sbjct: 1  MKKTLLLSLSASSLLNA 17



>ref|NP_223829.1| CARBONIC ANHYDRASE [Helicobacter pylori J99]
          Length = 247

 Score = 21.6 bits (44), Expect = 3.6
 Identities = 10/15 (66%), Positives = 11/15 (72%)

Query: 1  MKKTLFISLALALSL 15
          MKKT  I+LAL  SL
Sbjct: 1  MKKTFLIALALTASL 15



>ref|NP_223952.1| 50S RIBOSOMAL PROTEIN L22 [Helicobacter pylori J99]
          Length = 122

 Score = 21.2 bits (43), Expect = 4.7
 Identities = 9/37 (24%), Positives = 22/37 (59%)

Query: 8   SLALALSLNAGNIQIQSMPKVKERVSVPSKDDTDLFL 44
           +L ++  ++AG +  +S+P+ K R +   K  + +F+
Sbjct: 64  ALIVSCRVDAGPVLRRSIPRAKGRATAIRKPTSHVFV 100



>ref|NP_223566.1| Outer membrane protein/porin [Helicobacter pylori J99]
          Length = 520

 Score = 20.8 bits (42), Expect = 6.1
 Identities = 9/26 (34%), Positives = 14/26 (53%)

Query: 15  LNAGNIQIQSMPKVKERVSVPSKDDT 40
           LNAGN+   +M K  E+    + + T
Sbjct: 174 LNAGNVFFNAMNKALEKNGTATANST 199



 Score = 20.4 bits (41), Expect = 7.9
 Identities = 8/14 (57%), Positives = 12/14 (85%)

Query: 3  KTLFISLALALSLN 16
          +TLF+SLAL  S++
Sbjct: 6  RTLFLSLALCASIS 19



  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
   0.321    0.136    0.368 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 43,225
Number of Sequences: 1491
Number of extensions: 1079
Number of successful extensions: 8
Number of sequences better than 10.0: 7
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 8
length of query: 48
length of database: 494,079
effective HSP length: 24
effective length of query: 24
effective length of database: 458,295
effective search space: 10999080
effective search space used: 10999080
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 41 (20.4 bits)