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|15645939|ref|NP_208118.1| hypothetical protein
[Helicobacter pylori 26695]
         (125 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|1TMY|    Chey From Thermotoga Maritima (Apo-I) >gi|27811...    30  0.082
pdb|1G7K|A  Chain A, Crystal Structure Of Dsred, A Red Fluor...    25  2.0
pdb|1GGX|A  Chain A, Red Fluorescent Protein (Fp583 Or Dsred...    25  2.6
pdb|1JID|A  Chain A, Human Srp19 In Complex With Helix 6 Of ...    24  4.5
pdb|1MFQ|B  Chain B, Crystal Structure Analysis Of A Ternary...    24  4.5

>pdb|1TMY|   Chey From Thermotoga Maritima (Apo-I)
 pdb|3TMY|A Chain A, Chey From Thermotoga Maritima (Mn-Iii)
 pdb|3TMY|B Chain B, Chey From Thermotoga Maritima (Mn-Iii)
 pdb|2TMY|   Chey From Thermotoga Maritima (Apo-Ii)
 pdb|4TMY|A Chain A, Chey From Thermotoga Maritima (Mg-Iv)
 pdb|4TMY|B Chain B, Chey From Thermotoga Maritima (Mg-Iv)
          Length = 120

 Score = 30.0 bits (66), Expect = 0.082
 Identities = 17/51 (33%), Positives = 26/51 (50%)

Query: 34 IKSVGNPIKGDNTFILSPTLKGKALEKAIVRVQFMMPEMPGMPAMKEMAQV 84
          I   G  + G+ T       K K L+  IV +   MPEM G+ A+KE+ ++
Sbjct: 22 ITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKI 72



>pdb|1G7K|A Chain A, Crystal Structure Of Dsred, A Red Fluorescent Protein From
           Discosoma Sp. Red
 pdb|1G7K|B Chain B, Crystal Structure Of Dsred, A Red Fluorescent Protein From
           Discosoma Sp. Red
 pdb|1G7K|C Chain C, Crystal Structure Of Dsred, A Red Fluorescent Protein From
           Discosoma Sp. Red
 pdb|1G7K|D Chain D, Crystal Structure Of Dsred, A Red Fluorescent Protein From
           Discosoma Sp. Red
          Length = 234

 Score = 25.4 bits (54), Expect = 2.0
 Identities = 29/104 (27%), Positives = 46/104 (43%), Gaps = 6/104 (5%)

Query: 22  EQTLKANDLEVKIKSVGNPIKGDNTFILSPTLKGKALEKA--IVRVQFMMPEMPGMPA-M 78
           E T+  ++ E++ +  G P +G NT  L  T KG  L  A  I+  QF        PA +
Sbjct: 30  EGTVNGHEFEIEGEGEGRPYEGHNTVKLKVT-KGGPLPFAWDILSPQFXSKVYVKHPADI 88

Query: 79  KEMAQVSEKNGL-YEAKTNLSMNGTWQVRVDIKSKEG-QVYRAK 120
            +  ++S   G  +E   N    G   V  D   ++G  +Y+ K
Sbjct: 89  PDYKKLSFPEGFKWERVXNFEDGGVVTVTQDSSLQDGCFIYKVK 132



>pdb|1GGX|A Chain A, Red Fluorescent Protein (Fp583 Or Dsred(Clontech)) From
           Discosoma Sp.
 pdb|1GGX|B Chain B, Red Fluorescent Protein (Fp583 Or Dsred(Clontech)) From
           Discosoma Sp.
 pdb|1GGX|C Chain C, Red Fluorescent Protein (Fp583 Or Dsred(Clontech)) From
           Discosoma Sp.
 pdb|1GGX|D Chain D, Red Fluorescent Protein (Fp583 Or Dsred(Clontech)) From
           Discosoma Sp
          Length = 223

 Score = 25.0 bits (53), Expect = 2.6
 Identities = 29/104 (27%), Positives = 46/104 (43%), Gaps = 6/104 (5%)

Query: 22  EQTLKANDLEVKIKSVGNPIKGDNTFILSPTLKGKALEKA--IVRVQFMMPEMPGMPA-M 78
           E T+  ++ E++ +  G P +G NT  L  T KG  L  A  I+  QF        PA +
Sbjct: 19  EGTVNGHEFEIEGEGEGRPYEGHNTVKLKVT-KGGPLPFAWDILSPQFXSKVYVKHPADI 77

Query: 79  KEMAQVSEKNGL-YEAKTNLSMNGTWQVRVDIKSKEG-QVYRAK 120
            +  ++S   G  +E   N    G   V  D   ++G  +Y+ K
Sbjct: 78  PDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVK 121



>pdb|1JID|A Chain A, Human Srp19 In Complex With Helix 6 Of Human Srp Rna
          Length = 128

 Score = 24.3 bits (51), Expect = 4.5
 Identities = 10/31 (32%), Positives = 18/31 (57%)

Query: 86  EKNGLYEAKTNLSMNGTWQVRVDIKSKEGQV 116
           EKN +Y  + N  +    +VRV +K ++G +
Sbjct: 63  EKNKMYSREWNRDVQYRGRVRVQLKQEDGSL 93



>pdb|1MFQ|B Chain B, Crystal Structure Analysis Of A Ternary S-Domain Complex
           Of Human Signal Recognition Particle
          Length = 108

 Score = 24.3 bits (51), Expect = 4.5
 Identities = 10/31 (32%), Positives = 18/31 (57%)

Query: 86  EKNGLYEAKTNLSMNGTWQVRVDIKSKEGQV 116
           EKN +Y  + N  +    +VRV +K ++G +
Sbjct: 51  EKNKMYSREWNRDVQYRGRVRVQLKQEDGSL 81



  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
   0.315    0.131    0.361 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 682,457
Number of Sequences: 13198
Number of extensions: 24647
Number of successful extensions: 61
Number of sequences better than 10.0: 5
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 56
Number of HSP's gapped (non-prelim): 5
length of query: 125
length of database: 2,899,336
effective HSP length: 77
effective length of query: 48
effective length of database: 1,883,090
effective search space: 90388320
effective search space used: 90388320
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: 49 (23.5 bits)