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|15646011|ref|NP_208192.1| conserved hypothetical
protein [Helicobacter pylori 26695]
         (235 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|1CSJ|A  Chain A, Crystal Structure Of The Rna-Dependent ...    26  4.6
pdb|1GX6|A  Chain A, Hepatitis C Virus Rna Polymerase In Com...    26  4.6
pdb|1QUV|A  Chain A, Crystal Structure Of The Rna Directed R...    26  4.6
pdb|1GX5|A  Chain A, Hepatitis C Virus Rna Polymerase In Com...    26  4.6
pdb|1C2P|B  Chain B, Hepatitis C Virus Ns5b Rna-Dependent Rn...    26  4.6
pdb|1BG1|A  Chain A, Three-Dimensional Structure Of The Stat...    25  6.0
pdb|1HV8|A  Chain A, Crystal Structure Of A Dead Box Protein...    25  7.8
pdb|1DD9|A  Chain A, Structure Of The Dnag Catalytic Core >g...    25  7.8

>pdb|1CSJ|A Chain A, Crystal Structure Of The Rna-Dependent Rna Polymerase Of
           Hepatitis C Virus
 pdb|1CSJ|B Chain B, Crystal Structure Of The Rna-Dependent Rna Polymerase Of
           Hepatitis C Virus
          Length = 531

 Score = 25.8 bits (55), Expect = 4.6
 Identities = 11/24 (45%), Positives = 18/24 (74%)

Query: 113 VHQKTSLENRLKVLENYYRQVLRE 136
           + QK    +RL+VL+++YR VL+E
Sbjct: 47  LRQKKVTFDRLQVLDDHYRDVLKE 70



>pdb|1GX6|A Chain A, Hepatitis C Virus Rna Polymerase In Complex With Utp And
           Manganese
          Length = 531

 Score = 25.8 bits (55), Expect = 4.6
 Identities = 11/24 (45%), Positives = 18/24 (74%)

Query: 113 VHQKTSLENRLKVLENYYRQVLRE 136
           + QK    +RL+VL+++YR VL+E
Sbjct: 47  LRQKKVTFDRLQVLDDHYRDVLKE 70



>pdb|1QUV|A Chain A, Crystal Structure Of The Rna Directed Rna Polymerase Of
           Hepatitis C Virus
          Length = 578

 Score = 25.8 bits (55), Expect = 4.6
 Identities = 11/24 (45%), Positives = 18/24 (74%)

Query: 113 VHQKTSLENRLKVLENYYRQVLRE 136
           + QK    +RL+VL+++YR VL+E
Sbjct: 47  LRQKKVTFDRLQVLDDHYRDVLKE 70



>pdb|1GX5|A Chain A, Hepatitis C Virus Rna Polymerase In Complex With Gtp And
           Manganese
          Length = 536

 Score = 25.8 bits (55), Expect = 4.6
 Identities = 11/24 (45%), Positives = 18/24 (74%)

Query: 113 VHQKTSLENRLKVLENYYRQVLRE 136
           + QK    +RL+VL+++YR VL+E
Sbjct: 47  LRQKKVTFDRLQVLDDHYRDVLKE 70



>pdb|1C2P|B Chain B, Hepatitis C Virus Ns5b Rna-Dependent Rna Polymerase
 pdb|1C2P|A Chain A, Hepatitis C Virus Ns5b Rna-Dependent Rna Polymerase
          Length = 576

 Score = 25.8 bits (55), Expect = 4.6
 Identities = 11/24 (45%), Positives = 18/24 (74%)

Query: 113 VHQKTSLENRLKVLENYYRQVLRE 136
           + QK    +RL+VL+++YR VL+E
Sbjct: 53  LRQKKVTFDRLQVLDDHYRDVLKE 76



>pdb|1BG1|A Chain A, Three-Dimensional Structure Of The Stat3b Homodimer Bound
           To Dna
          Length = 722

 Score = 25.4 bits (54), Expect = 6.0
 Identities = 13/43 (30%), Positives = 23/43 (53%)

Query: 192 VVVHELLHLKTRHHNEYFRDLLSLYLPNWQRAKASLKETYLER 234
           +V H LL    + ++ + ++   LY  N +R K  L+  YLE+
Sbjct: 55  LVFHNLLGEIDQQYSRFLQESNVLYQHNLRRIKQFLQSRYLEK 97



>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The
           Hyperthermophile Methanococcus Jannaschii
 pdb|1HV8|B Chain B, Crystal Structure Of A Dead Box Protein From The
           Hyperthermophile Methanococcus Jannaschii
          Length = 367

 Score = 25.0 bits (53), Expect = 7.8
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 12/59 (20%)

Query: 150 NESIQSFKIQKMKRIWGSCNIAKRALLFNLELAKVPRKGIEYVVVHELLHLKTRHHNEY 208
           +E +    I+ +++I  +CN  KR LLF+   A  PR         E+L+L  ++  +Y
Sbjct: 157 DEXLNXGFIKDVEKILNACNKDKRILLFS---ATXPR---------EILNLAKKYXGDY 203



>pdb|1DD9|A Chain A, Structure Of The Dnag Catalytic Core
 pdb|1DDE|A Chain A, Structure Of The Dnag Catalytic Core
          Length = 338

 Score = 25.0 bits (53), Expect = 7.8
 Identities = 19/64 (29%), Positives = 32/64 (49%), Gaps = 5/64 (7%)

Query: 113 VHQKTSLENRLKVLENYYRQVLREKIQTCINRY-EK--ILNESIQSFKIQKMKRIWGSCN 169
           +HQ+ +L   +  L  +Y+Q L++ + T   +Y EK  + +E I  F I      W   N
Sbjct: 15  MHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWD--N 72

Query: 170 IAKR 173
           + KR
Sbjct: 73  VLKR 76



  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
   0.322    0.137    0.404 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,280,975
Number of Sequences: 13198
Number of extensions: 46364
Number of successful extensions: 110
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 104
Number of HSP's gapped (non-prelim): 8
length of query: 235
length of database: 2,899,336
effective HSP length: 85
effective length of query: 150
effective length of database: 1,777,506
effective search space: 266625900
effective search space used: 266625900
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: 53 (25.0 bits)