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|15645257|ref|NP_207427.1| quinone-reactive Ni/Fe
hydrogenase, cytochrome b subunit (hydC) [Helicobacter pylori 26695]
         (224 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|1EHK|A  Chain A, Crystal Structure Of The Aberrant Ba3-C...    27  2.5
pdb|1K9X|A  Chain A, Structure Of Pyrococcus Furiosus Carbox...    26  4.2

>pdb|1EHK|A Chain A, Crystal Structure Of The Aberrant Ba3-Cytochrome-C Oxidase
           From Thermus Thermophilus
          Length = 562

 Score = 26.6 bits (57), Expect = 2.5
 Identities = 17/46 (36%), Positives = 26/46 (55%), Gaps = 2/46 (4%)

Query: 23  VRALSIFALIATGFYIAYPFLQPNSSFYKG--VYLLQAYVRSFHVM 66
           V AL + A  AT  Y  YP L+ + +FY G  V++L  +V  + V+
Sbjct: 119 VAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWVSIYIVL 164



>pdb|1K9X|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
 pdb|1K9X|B Chain B, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
 pdb|1K9X|C Chain C, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
 pdb|1K9X|D Chain D, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
 pdb|1KA2|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Mg
 pdb|1KA4|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Nat-Pb
          Length = 499

 Score = 25.8 bits (55), Expect = 4.2
 Identities = 28/123 (22%), Positives = 46/123 (36%), Gaps = 11/123 (8%)

Query: 38  IAYPFLQPNSSFYKGVYLLQAYVRSFHVMFGFLLISALI----FRTYLFFTKESLMERKS 93
           + YP L+ N  F         Y+    V   F+   A +    F   L F  E LM  + 
Sbjct: 318 LIYPVLKENLPFMSNYTPEDVYLYFNIVRPDFIRTEADVVTYNFHILLRFKLERLMVSEE 377

Query: 94  FSQLLSPKAWIDQMKAYFLISGKPHTKGAYNPIQ----LVAYSTLIVLIVLMSLSGMVLY 149
                 P+ W D+M+    I  + +++G    I      + Y     +  L+S     LY
Sbjct: 378 IKAKDLPEMWNDEMERLLGIRPRKYSEGILQDIHWAHGSIGYFPTYTIGTLLSAQ---LY 434

Query: 150 YNV 152
           Y++
Sbjct: 435 YHI 437



  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
   0.331    0.144    0.450 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,264,487
Number of Sequences: 13198
Number of extensions: 46517
Number of successful extensions: 73
Number of sequences better than 10.0: 2
Number of HSP's better than 10.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 72
Number of HSP's gapped (non-prelim): 3
length of query: 224
length of database: 2,899,336
effective HSP length: 85
effective length of query: 139
effective length of database: 1,777,506
effective search space: 247073334
effective search space used: 247073334
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 52 (24.6 bits)