BLAST Search Results

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|15645765|ref|NP_207942.1| ribosomal protein S16 (rpS16) [Helicobacter pylori 26695] (76 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|1HNZ|P  Chain P, Structure Of The Thermus Thermophilus 3...    78  2e-16
pdb|1JGQ|S  Chain S, The Path Of Messenger Rna Through The R...    73  7e-15
pdb|1MHC|A  Chain A, Model Of Mhc Class I H2-M3 With Nonapep...    26  0.70
pdb|1B91|A  Chain A, Nmr Structure Of A Histone Acetyltranfe...    24  2.7
pdb|1JM4|B  Chain B, Nmr Structure Of PCAF BROMODOMAIN IN CO...    23  5.9
pdb|1IGY|B  Chain B, Structure Of Immunoglobulin >gi|3114314...    23  7.7
pdb|1E6O|H  Chain H, Crystal Structure Of Fab13b5 Against Hi...    23  7.7

>pdb|1HNZ|P Chain P, Structure Of The Thermus Thermophilus 30s Ribosomal
          Subunit In Complex With Hygromycin B
 pdb|1HNW|P Chain P, Structure Of The Thermus Thermophilus 30s Ribosomal
          Subunit In Complex With Tetracycline
 pdb|1HNX|P Chain P, Structure Of The Thermus Thermophilus 30s Ribosomal
          Subunit In Complex With Pactamycin
 pdb|1EMW|A Chain A, Solution Structure Of The Ribosomal Protein S16 From
          Thermus Thermophilus
 pdb|1FJG|P Chain P, Structure Of The Thermus Thermophilus 30s Ribosomal
          Subunit In Complex With The Antibiotics Streptomycin,
          Spectinomycin And Paromomycin
 pdb|1J5E|P Chain P, Structure Of The Thermus Thermophilus 30s Ribosomal
          Subunit
 pdb|1IBL|P Chain P, Structure Of The Thermus Thermophilus 30s Ribosomal
          Subunit In Complex With A Messenger Rna Fragment And
          Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
          Site And With The Antibiotic Paromomycin
 pdb|1HR0|P Chain P, Crystal Structure Of Initiation Factor If1 Bound To The
          30s Ribosomal Subunit
 pdb|1IBM|P Chain P, Structure Of The Thermus Thermophilus 30s Ribosomal
          Subunit In Complex With A Messenger Rna Fragment And
          Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
          Site
 pdb|1IBK|P Chain P, Structure Of The Thermus Thermophilus 30s Ribosomal
          Subunit In Complex With The Antibiotic Paromomycin
 pdb|1I94|P Chain P, Crystal Structures Of The Small Ribosomal Subunit With
          Tetracycline, Edeine And If3
 pdb|1I96|P Chain P, Crystal Structure Of The 30s Ribosomal Subunit From
          Thermus Thermophilus In Complex With The Translation
          Initiation Factor If3 (C-Terminal Domain)
 pdb|1I97|P Chain P, Crystal Structure Of The 30s Ribosomal Subunit From
          Thermus Thermophilus In Complex With Tetracycline
 pdb|1I95|P Chain P, Crystal Structure Of The 30s Ribosomal Subunit From
          Thermus Thermophilus In Complex With Edeine
          Length = 88

 Score = 78.2 bits (191), Expect = 2e-16
 Identities = 36/77 (46%), Positives = 50/77 (64%), Gaps = 1/77 (1%)

Query: 1  MTVIRLTRIGRKKKPFYRVVVTDSRKRRDGGWIESIGYYNPLSEPKD-IKIDKERLNYWK 59
          M  IRL R G K  P YR+VVTD+R++RDG +IE I YY+P     D +K+D ER  YW 
Sbjct: 1  MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIEYYDPRKTTPDWLKVDVERARYWL 60

Query: 60 GVGAKMSERVEKLSQKA 76
           VGA+ ++   +L ++A
Sbjct: 61 SVGAQPTDTARRLLRQA 77

>pdb|1JGQ|S Chain S, The Path Of Messenger Rna Through The Ribosome. This
          File, 1jgq, Contains The 30s Ribosome Subunit, Three
          Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
          The File 1giy
 pdb|1GIX|S Chain S, Crystal Structure Of The Ribosome At 5.5 A Resolution.
          This File, 1gix, Contains The 30s Ribosome Subunit,
          Three Trna, And Mrna Molecules. 50s Ribosome Subunit Is
          In The File 1giy
 pdb|1JGO|S Chain S, The Path Of Messenger Rna Through The Ribosome. This
          File, 1jgo, Contains The 30s Ribosome Subunit, Three
          Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
          The File 1giy
 pdb|1JGP|S Chain S, The Path Of Messenger Rna Through The Ribosome. This
          File, 1jgp, Contains The 30s Ribosome Subunit, Three
          Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
          The File 1giy
          Length = 91

 Score = 72.8 bits (177), Expect = 7e-15
 Identities = 37/80 (46%), Positives = 51/80 (63%), Gaps = 4/80 (5%)

Query: 1  MTVIRLTRIGRKKKPFY---RVVVTDSRKRRDGGWIESIGYYNPLSEPKD-IKIDKERLN 56
          M  IRL R G K  P Y   R+VVTD+R++RDG +IE IGYY+P     D +K+D ER  
Sbjct: 1  MVKIRLARFGSKHNPHYPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERAR 60

Query: 57 YWKGVGAKMSERVEKLSQKA 76
          YW  VGA+ ++   +L ++A
Sbjct: 61 YWLSVGAQPTDTARRLLRQA 80

>pdb|1MHC|A Chain A, Model Of Mhc Class I H2-M3 With Nonapeptide From Rat Nd1
          Refined At 2.3 Angstroms Resolution
 pdb|1MHC|D Chain D, Model Of Mhc Class I H2-M3 With Nonapeptide From Rat Nd1
          Refined At 2.3 Angstroms Resolution
          Length = 282

 Score = 26.2 bits (56), Expect = 0.70
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 8/71 (11%)

Query: 6  LTRIGRKKKPFYRVVVTDSRKRRDGGWIESIGYYNPLSEPKDIKIDKERLNYWKGVGAKM 65
          ++R GR +  +  V   D  + +    IE I    P  EP+   ++KER  YWK    ++
Sbjct: 12 VSRPGRGEPQYISVGYVDDVQFQRCDSIEEI----PRMEPRAPWMEKERPEYWK----EL 63

Query: 66 SERVEKLSQKA 76
            +V+ ++Q A
Sbjct: 64 KLKVKNIAQSA 74

>pdb|1B91|A Chain A, Nmr Structure Of A Histone Acetyltranferase Bromodomain
          Length = 118

 Score = 24.3 bits (51), Expect = 2.7
 Identities = 10/22 (45%), Positives = 13/22 (58%)

Query: 34 ESIGYYNPLSEPKDIKIDKERL 55
          E+ GYY  +  P D+K   ERL
Sbjct: 42 EAPGYYEVIRSPMDLKTMSERL 63

>pdb|1JM4|B Chain B, Nmr Structure Of PCAF BROMODOMAIN IN COMPLEX WITH HIV-1
          Tat Peptide
          Length = 118

 Score = 23.1 bits (48), Expect = 5.9
 Identities = 10/22 (45%), Positives = 13/22 (58%)

Query: 34 ESIGYYNPLSEPKDIKIDKERL 55
          E+ GYY  +  P D+K   ERL
Sbjct: 42 EAPGYYEVIRFPMDLKTMSERL 63

>pdb|1IGY|B Chain B, Structure Of Immunoglobulin
 pdb|1IGY|D Chain D, Structure Of Immunoglobulin
          Length = 434

 Score = 22.7 bits (47), Expect = 7.7
 Identities = 10/18 (55%), Positives = 12/18 (66%)

Query: 26 KRRDGGWIESIGYYNPLS 43
          K+R G  +E IGY NP S
Sbjct: 37 KQRPGQGLEWIGYINPSS 54

>pdb|1E6O|H Chain H, Crystal Structure Of Fab13b5 Against Hiv-1 Capsid
          Protein P24
 pdb|1E6J|H Chain H, Crystal Structure Of Hiv-1 Capsid Protein (P24) In
          Complex With Fab13b5
          Length = 219

 Score = 22.7 bits (47), Expect = 7.7
 Identities = 10/18 (55%), Positives = 12/18 (66%)

Query: 26 KRRDGGWIESIGYYNPLS 43
          K+R G  +E IGY NP S
Sbjct: 38 KQRPGQGLEWIGYINPSS 55

  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
   0.317    0.137    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 449,587
Number of Sequences: 13198
Number of extensions: 15637
Number of successful extensions: 58
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: 48
Number of HSP's gapped (non-prelim): 7
length of query: 76
length of database: 2,899,336
effective HSP length: 52
effective length of query: 24
effective length of database: 2,213,040
effective search space: 53112960
effective search space used: 53112960
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: 47 (22.7 bits)