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|15644645|ref|NP_206814.1| DNA primase (dnaG) [Helicobacter pylori 26695] (559 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|1DD9|A  Chain A, Structure Of The Dnag Catalytic Core >g...   145  2e-35
pdb|1EQN|A  Chain A, E.Coli Primase Catalytic Core >gi|92569...   137  3e-33
pdb|1D0Q|A  Chain A, Structure Of The Zinc-Binding Domain Of...    90  8e-19
pdb|1HLE|A  Chain A, Horse Leukocyte Elastase Inhibitor (Hlei)     31  0.32
pdb|1GPJ|A  Chain A, Glutamyl-Trna Reductase From Methanopyr...    27  4.6
pdb|1G0W|A  Chain A, Crystal Structure Of Bovine Retinal Cre...    27  7.8
pdb|1F0X|A  Chain A, Crystal Structure Of D-Lactate Dehydrog...    27  7.8

>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 =  145 bits (365), Expect = 2e-35
 Identities = 89/282 (31%), Positives = 147/282 (51%), Gaps = 9/282 (3%)

Query: 96  YDKGVYYDHKEDYHLLEMVSSLYQEELFN--APFFLNYLQKRGLSLESIKAFKLGLCTNR 153
           +  G  +  +  Y L++ +++ YQ+ L    A     YL+KRGLS E I  F +G     
Sbjct: 10  HGSGSMHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPG 69

Query: 154 IDYGIENKG---LNKDKLIELGVLGKSDNDQKTYLRFLDRIMFPIYSPSAQVVGFGGRTL 210
            D  ++  G    N+  LI+ G+L  +D   ++Y RF +R+MFPI     +V+GFGGR L
Sbjct: 70  WDNVLKRFGGNPENRQSLIDAGMLVTNDQG-RSYDRFRERVMFPIRDKRGRVIGFGGRVL 128

Query: 211 KEKAAKYINSPQSKLFDKSSLLYGYHLAKEHIYKQKQVIVTEGYLDVILLHQAGFKNAIA 270
                KY+NSP++ +F K   LYG + A++   +  +++V EGY+DV+ L Q G   A+A
Sbjct: 129 GNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVA 188

Query: 271 TLGTALTPSHLPLLKKGDPEILLSYDGDKAGRNAAYKA---SLMLAKEQRRGGVILFENN 327
           +LGT+ T  H+ LL +    ++  YDGD+AGR+AA++A   +L    + R+   +   + 
Sbjct: 189 SLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDG 248

Query: 328 LDPADMIANGQIETLKNWLSHPMAFIEFVLRRMADSYLLDDP 369
            DP  ++     E  +  +   M    F+   +     L  P
Sbjct: 249 EDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTP 290

>pdb|1EQN|A Chain A, E.Coli Primase Catalytic Core
 pdb|1EQN|C Chain C, E.Coli Primase Catalytic Core
 pdb|1EQN|B Chain B, E.Coli Primase Catalytic Core
 pdb|1EQN|D Chain D, E.Coli Primase Catalytic Core
 pdb|1EQN|E Chain E, E.Coli Primase Catalytic Core
          Length = 321

 Score =  137 bits (345), Expect = 3e-33
 Identities = 78/206 (37%), Positives = 119/206 (56%), Gaps = 6/206 (2%)

Query: 108 YHLLEMVSSLYQEELFN--APFFLNYLQKRGLSLESIKAFKLGLCTNRIDYGIENKG--- 162
           Y L + +++ YQ+ L    A     YL+KRGLS E I  F +G      D  ++  G   
Sbjct: 9   YQLXDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNP 68

Query: 163 LNKDKLIELGVLGKSDNDQKTYLRFLDRIMFPIYSPSAQVVGFGGRTLKEKAAKYINSPQ 222
            N+  LI+ G L  +D   ++Y RF +R+ FPI     +V+GFGGR L     KY+NSP+
Sbjct: 69  ENRQSLIDAGXLVTNDQG-RSYDRFRERVXFPIRDKRGRVIGFGGRVLGNDTPKYLNSPE 127

Query: 223 SKLFDKSSLLYGYHLAKEHIYKQKQVIVTEGYLDVILLHQAGFKNAIATLGTALTPSHLP 282
           + +F K   LYG + A++   +  +++V EGY DV+ L Q G   A+A+LGT+ T  H+ 
Sbjct: 128 TDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYXDVVALAQYGINYAVASLGTSTTADHIQ 187

Query: 283 LLKKGDPEILLSYDGDKAGRNAAYKA 308
           LL +    ++  YDGD+AGR+AA++A
Sbjct: 188 LLFRATNNVICCYDGDRAGRDAAWRA 213

>pdb|1D0Q|A Chain A, Structure Of The Zinc-Binding Domain Of Bacillus
          Stearothermophilus Dna Primase
 pdb|1D0Q|B Chain B, Structure Of The Zinc-Binding Domain Of Bacillus
          Stearothermophilus Dna Primase
          Length = 103

 Score = 89.7 bits (221), Expect = 8e-19
 Identities = 40/93 (43%), Positives = 62/93 (66%)

Query: 2  ILKSSIDRLLQTIDIVEVISSYVNLRKSGSSYMACCPFHEERSASFSVNQIKGFYHCFGC 61
          I + +I+ + + +DIV+VI  YV L++ G +Y   CPFH E++ SFSV+  K  +HCFGC
Sbjct: 5  IPEETIEAIRRGVDIVDVIGEYVQLKRQGRNYFGLCPFHGEKTPSFSVSPEKQIFHCFGC 64

Query: 62 GASGDSIKFVMAFEKLSFVEALEKLAHRFNIVL 94
          GA G++  F+M  E + FVEA ++LA +  + L
Sbjct: 65 GAGGNAFTFLMDIEGIPFVEAAKRLAAKAGVDL 97

>pdb|1HLE|A Chain A, Horse Leukocyte Elastase Inhibitor (Hlei)
          Length = 345

 Score = 31.2 bits (69), Expect = 0.32
 Identities = 34/128 (26%), Positives = 52/128 (40%), Gaps = 20/128 (15%)

Query: 77  LSFVEALEKLAHRFNIVLEYDKGVYYDHKEDYH-----------------LLEMVSSLYQ 119
           +S   A+  L  R N   +  K +Y+D  ED H                 +L++ + LY 
Sbjct: 36  ISSALAMIFLGTRGNTAAQVSKALYFDTVEDIHSRFQSLNADINKPGAPYILKLANRLYG 95

Query: 120 EELFN--APFFLNYLQKRGLSLESIKAFKLGLCTNRIDYGIENKGLNKDKLIELGVLGKS 177
           E+ +N  A F  +  +  G  L S+  F+      R +     KG  + K+ EL V G  
Sbjct: 96  EKTYNFLADFLASTQKMYGAELASVD-FQQAPEDARKEINEWVKGQTEGKIPELLVKGMV 154

Query: 178 DNDQKTYL 185
           DN  K  L
Sbjct: 155 DNMTKLVL 162

>pdb|1GPJ|A Chain A, Glutamyl-Trna Reductase From Methanopyrus Kandleri
          Length = 404

 Score = 27.3 bits (59), Expect = 4.6
 Identities = 17/48 (35%), Positives = 25/48 (51%), Gaps = 3/48 (6%)

Query: 511 ELRLLILRYFERQLKEIPKSSLPFSEKMICLKKARQAIMKLKQGELVA 558
           +LR++     ER+ KEIPK      E+   L    + + KLK+  LVA
Sbjct: 288 DLRVIARENLERRRKEIPKVEKLIEEE---LSTVEEELEKLKERRLVA 332

>pdb|1G0W|A Chain A, Crystal Structure Of Bovine Retinal Creatine Kinase
          Length = 380

 Score = 26.6 bits (57), Expect = 7.8
 Identities = 17/48 (35%), Positives = 25/48 (51%), Gaps = 1/48 (2%)

Query: 290 EILLSYDGDKAGRNAAYKASLMLAKEQRRGGVILFENNLDPADMIANG 337
           E L S DGD AGR  A K+     ++Q      LF+  + P  ++A+G
Sbjct: 159 EALSSLDGDLAGRYYALKSMTEAEQQQLIDDHFLFDKPVSPL-LLASG 205

>pdb|1F0X|A Chain A, Crystal Structure Of D-Lactate Dehydrogenase, A Peripheral
           Membrane Respiratory Enzyme.
 pdb|1F0X|B Chain B, Crystal Structure Of D-Lactate Dehydrogenase, A Peripheral
           Membrane Respiratory Enzyme
          Length = 571

 Score = 26.6 bits (57), Expect = 7.8
 Identities = 25/101 (24%), Positives = 45/101 (43%), Gaps = 8/101 (7%)

Query: 53  KGFYHCFGCGASGDSIKFVMAFEKLSFVEALEKLAHRFNIVLEYDKGVYYDHKEDYHLLE 112
           K F H F   A+G +I++    + +   E  + LA   +I L  +   +Y+H       +
Sbjct: 429 KAFLHRFA--AAGAAIRY----QAVHSDEVEDILA--LDIALRRNDTEWYEHLPPEIDSQ 480

Query: 113 MVSSLYQEELFNAPFFLNYLQKRGLSLESIKAFKLGLCTNR 153
           +V  LY        F  +Y+ K+G+ + ++K   L L   R
Sbjct: 481 LVHKLYYGHFMCYVFHQDYIVKKGVDVHALKEQMLELLQQR 521

  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    0.140    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,141,440
Number of Sequences: 13198
Number of extensions: 135124
Number of successful extensions: 377
Number of sequences better than 10.0: 7
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 370
Number of HSP's gapped (non-prelim): 9
length of query: 559
length of database: 2,899,336
effective HSP length: 93
effective length of query: 466
effective length of database: 1,671,922
effective search space: 779115652
effective search space used: 779115652
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: 57 (26.6 bits)