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|15646105|ref|NP_208287.1| general stress protein
(ctc) [Helicobacter pylori 26695]
         (178 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|1LNR|T  Chain T, Crystal Structure Of The Large Ribosoma...    49  4e-07
pdb|1FEU|D  Chain D, Crystal Structure Of Ribosomal Protein ...    47  2e-06
pdb|1LLP|    Lignin Peroxidase (Isozyme H2) Pi4.15 >gi|44309...    27  1.0
pdb|1DD5|A  Chain A, Crystal Structure Of Thermotoga Maritim...    27  1.8
pdb|1B80|A  Chain A, Rec. Lignin Peroxidase H8 Oxidatively P...    26  3.0
pdb|1B82|A  Chain A, Pristine Recomb. Lignin Peroxidase H8 >...    26  3.0
pdb|1B85|A  Chain A, Lignin Peroxidase >gi|4558110|pdb|1B85|...    26  3.0
pdb|1JHF|A  Chain A, Lexa G85d Mutant >gi|15988319|pdb|1JHF|...    24  8.7
pdb|1GL9|B  Chain B, Archaeoglobus Fulgidus Reverse Gyrase C...    24  8.7
pdb|1GKU|B  Chain B, Reverse Gyrase From Archaeoglobus Fulgidus    24  8.7
pdb|1KV4|A  Chain A, Solution Structure Of Antibacterial Pep...    24  8.7

>pdb|1LNR|T Chain T, Crystal Structure Of The Large Ribosomal Subunit From
           Deinococcus Radiodurans
          Length = 237

 Score = 48.5 bits (114), Expect = 4e-07
 Identities = 39/171 (22%), Positives = 71/171 (40%), Gaps = 3/171 (1%)

Query: 8   ESITKANAKALKKDGYLIANVYGKGIENVNGAFKLNPFIKYLKEKKHL-IFPVKL-GDKT 65
           E   K      K D  +IA V      NV+ A     F +  +++    +F + + G +T
Sbjct: 2   ELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGET 61

Query: 66  FEVVVQEYQKNPVTNELIHVDLLAVTKGVKSKFKVPIKHQGTPVGLKNKGILMLSKKRIS 125
           F  +V+  Q +      IHVD   VT G   +  VP+   G   G    G++ +    + 
Sbjct: 62  FPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQ 121

Query: 126 VEC-APEHLPDHYLVDVAPLDVNESILVRDLEKHENVKILDHDSIAVIGVI 175
           +    P  +P   +VDV  +++ + I   D++  E   +     + V+ V+
Sbjct: 122 IVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVL 172



>pdb|1FEU|D Chain D, Crystal Structure Of Ribosomal Protein Tl5, One Of The Ctc
           Family Proteins, Complexed With A Fragment Of 5s Rrna.
 pdb|1FEU|A Chain A, Crystal Structure Of Ribosomal Protein Tl5, One Of The Ctc
           Family Proteins, Complexed With A Fragment Of 5s Rrna
          Length = 206

 Score = 46.6 bits (109), Expect = 2e-06
 Identities = 36/149 (24%), Positives = 74/149 (49%), Gaps = 4/149 (2%)

Query: 17  ALKKDGYLIANVYGKGIENVNGAFKLNPFIKYLKEKK-HLIFPVKLGD-KTFEVVVQEYQ 74
           AL++ G L   +Y + + N      L  F K  ++   H +  ++L D ++   +V++  
Sbjct: 17  ALRRAGKLPGLMYNRHL-NRKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVN 75

Query: 75  KNPVTNELIHVDLLAVTKGVKSKFKVPIKHQGTPVGLKNKGILMLSKKRISVECAPEHLP 134
            +       HVD   ++      + VP++  GTP G++  G+L    + I V+ +P ++P
Sbjct: 76  LDKRRRRPEHVDFFVLSDEPVEMY-VPLRFVGTPAGVRAGGVLQEIHRDILVKVSPRNIP 134

Query: 135 DHYLVDVAPLDVNESILVRDLEKHENVKI 163
           +   VDV+ L++ +S+   DL+    V++
Sbjct: 135 EFIEVDVSGLEIGDSLHASDLKLPPGVEL 163



>pdb|1LLP|   Lignin Peroxidase (Isozyme H2) Pi4.15
 pdb|1LGA|A Chain A, Lignin Peroxidase (Lip) (E.C.1.11.1.-) (Ferric)
 pdb|1LGA|B Chain B, Lignin Peroxidase (Lip) (E.C.1.11.1.-) (Ferric)
          Length = 343

 Score = 27.3 bits (59), Expect = 1.0
 Identities = 10/23 (43%), Positives = 18/23 (77%)

Query: 156 EKHENVKILDHDSIAVIGVIKAK 178
           E HE+++++ HDSIA+   ++AK
Sbjct: 37  EAHESIRLVFHDSIAISPAMEAK 59



>pdb|1DD5|A Chain A, Crystal Structure Of Thermotoga Maritima Ribosome
           Recycling Factor, Rrf
          Length = 185

 Score = 26.6 bits (57), Expect = 1.8
 Identities = 28/92 (30%), Positives = 40/92 (43%), Gaps = 18/92 (19%)

Query: 42  LNPFIKYLKEKKHLIFPVKLGDKTFEVVVQEYQK------NPVTNELIHVDLLAVTKGVK 95
           +NPFIK  KEK           +T E +  E +K      +P   E I VD   V   V 
Sbjct: 2   VNPFIKEAKEKM---------KRTLEKIEDELRKMRTGKPSPAILEEIKVDYYGVPTPVN 52

Query: 96  SKFKVPIKHQGTPVGLK--NKGILMLSKKRIS 125
               + I  + T V +K  +K +L L +K I+
Sbjct: 53  QLATISISEERTLV-IKPWDKSVLSLIEKAIN 83



>pdb|1B80|A Chain A, Rec. Lignin Peroxidase H8 Oxidatively Processed
 pdb|1B80|B Chain B, Rec. Lignin Peroxidase H8 Oxidatively Processed
          Length = 351

 Score = 25.8 bits (55), Expect = 3.0
 Identities = 9/23 (39%), Positives = 18/23 (78%)

Query: 156 EKHENVKILDHDSIAVIGVIKAK 178
           E HE+++++ HDSIA+   ++A+
Sbjct: 44  EAHESIRLVFHDSIAISPAMEAQ 66



>pdb|1B82|A Chain A, Pristine Recomb. Lignin Peroxidase H8
 pdb|1B82|B Chain B, Pristine Recomb. Lignin Peroxidase H8
          Length = 351

 Score = 25.8 bits (55), Expect = 3.0
 Identities = 9/23 (39%), Positives = 18/23 (78%)

Query: 156 EKHENVKILDHDSIAVIGVIKAK 178
           E HE+++++ HDSIA+   ++A+
Sbjct: 44  EAHESIRLVFHDSIAISPAMEAQ 66



>pdb|1B85|A Chain A, Lignin Peroxidase
 pdb|1B85|B Chain B, Lignin Peroxidase
          Length = 351

 Score = 25.8 bits (55), Expect = 3.0
 Identities = 9/23 (39%), Positives = 18/23 (78%)

Query: 156 EKHENVKILDHDSIAVIGVIKAK 178
           E HE+++++ HDSIA+   ++A+
Sbjct: 44  EAHESIRLVFHDSIAISPAMEAQ 66



>pdb|1JHF|A Chain A, Lexa G85d Mutant
 pdb|1JHF|B Chain B, Lexa G85d Mutant
          Length = 202

 Score = 24.3 bits (51), Expect = 8.7
 Identities = 14/44 (31%), Positives = 23/44 (51%), Gaps = 1/44 (2%)

Query: 129 APEHLPDHYLVDVAPLDVNESILVR-DLEKHENVKILDHDSIAV 171
           A +H+  HY VD +    N   L+R      +++ I+D D +AV
Sbjct: 90  AQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAV 133



>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
 pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
          Length = 1054

 Score = 24.3 bits (51), Expect = 8.7
 Identities = 11/28 (39%), Positives = 15/28 (53%)

Query: 48   YLKEKKHLIFPVKLGDKTFEVVVQEYQK 75
            Y+ EK   + P KLG   F  +V+ Y K
Sbjct: 988  YVVEKYGRMIPTKLGIDVFRFLVRRYAK 1015



>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
          Length = 1054

 Score = 24.3 bits (51), Expect = 8.7
 Identities = 11/28 (39%), Positives = 15/28 (53%)

Query: 48   YLKEKKHLIFPVKLGDKTFEVVVQEYQK 75
            Y+ EK   + P KLG   F  +V+ Y K
Sbjct: 988  YVVEKYGRMIPTKLGIDVFRFLVRRYAK 1015



>pdb|1KV4|A Chain A, Solution Structure Of Antibacterial Peptide (Moricin)
          Length = 42

 Score = 24.3 bits (51), Expect = 8.7
 Identities = 15/42 (35%), Positives = 20/42 (46%), Gaps = 4/42 (9%)

Query: 12 KANAKALKKDGYLIANVYGKGIENVNGAFKLNPFIKYLKEKK 53
          K   KA+K  G  +    GKG+  +N A   N    +LK KK
Sbjct: 2  KIPIKAIKTVGKAV----GKGLRAINIASTANDVFNFLKPKK 39



  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    0.139    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,018,354
Number of Sequences: 13198
Number of extensions: 42420
Number of successful extensions: 114
Number of sequences better than 10.0: 11
Number of HSP's better than 10.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 106
Number of HSP's gapped (non-prelim): 11
length of query: 178
length of database: 2,899,336
effective HSP length: 82
effective length of query: 96
effective length of database: 1,817,100
effective search space: 174441600
effective search space used: 174441600
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: 51 (24.3 bits)