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|15646069|ref|NP_208251.1| DNA polymerase III
alpha-subunit (dnaE) [Helicobacter pylori 26695]
         (1211 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|1HCY|    Arthropodan Hemocyanin (Deoxygenated) Refined U...    32  0.55
pdb|1FIZ|A  Chain A, Three Dimensional Structure Of Beta-Acr...    30  1.2
pdb|1PHZ|A  Chain A, Structure Of Phosphorylated Phenylalani...    30  1.6
pdb|1DXE|A  Chain A, 2-Dehydro-3-Deoxy-Galactarate Aldolase ...    30  2.1
pdb|1IW7|C  Chain C, Crystal Structure Of The Rna Polymerase...    29  3.6
pdb|1SYF|    Staphylococcal Nuclease (E.C.3.1.31.1) Mutant W...    29  3.6
pdb|1DKG|A  Chain A, Crystal Structure Of The Nucleotide Exc...    29  3.6
pdb|1A2Z|A  Chain A, Pyrrolidone Carboxyl Peptidase From The...    28  6.1
pdb|1BJ4|A  Chain A, Recombinant Serine Hydroxymethyltransfe...    28  6.1
pdb|1BCC|A  Chain A, Cytochrome Bc1 Complex From Chicken >gi...    28  6.1
pdb|1ADJ|A  Chain A, Histidyl-Trna Synthetase In Complex Wit...    28  6.1
pdb|1FFY|A  Chain A, Insights Into Editing From An Ile-Trna ...    28  6.1
pdb|1QCR|A  Chain A, Crystal Structure Of Bovine Mitochondri...    28  8.0
pdb|1BGY|A  Chain A, Cytochrome Bc1 Complex From Bovine >gi|...    28  8.0
pdb|1I6V|C  Chain C, Thermus Aquaticus Core Rna Polymerase-R...    28  8.0
pdb|1HQM|C  Chain C, Crystal Structure Of Thermus Aquaticus ...    28  8.0
pdb|1L9U|C  Chain C, Thermus Aquaticus Rna Polymerase Holoen...    28  8.0

>pdb|1HCY|   Arthropodan Hemocyanin (Deoxygenated) Refined Using Constrained 32
           Point Group Symmetry
 pdb|1HC1|   Arthropodan Hemocyanin (Deoxygenated) Subunit 1 Refined Using
           Non-Crystallographic Symmetry Restraints
 pdb|1HC2|   Arthropodan Hemocyanin (Deoxygenated) Subunit 2 Refined Using
           Non-Crystallographic Symmetry Restraints
 pdb|1HC3|   Arthropodan Hemocyanin (Deoxygenated) Subunit 3 Refined Using
           Non-Crystallographic Symmetry Restraints
 pdb|1HC4|   Arthropodan Hemocyanin (Deoxygenated) Subunit 4 Refined Using
           Non-Crystallographic Symmetry Restraints
 pdb|1HC5|   Arthropodan Hemocyanin (Deoxygenated) Subunit 5 Refined Using
           Non-Crystallographic Symmetry Restraints
 pdb|1HC6|   Arthropodan Hemocyanin (Deoxygenated) Subunit 6 Refined Using
           Non-Crystallographic Symmetry Restraints
          Length = 657

 Score = 31.6 bits (70), Expect = 0.55
 Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 11/82 (13%)

Query: 260 EMAKLFADIPEALENTQEIADKCVLEIDLKDDKKNPPTPPSFKFTKAYAQNEGLNFEDDA 319
           E+ K F  +P   E          +E   KD     P  PSF+  K  A N  +N   D 
Sbjct: 504 ELDKFFQKVPSGPET---------IERSSKDSSVTVPDMPSFQSLKEQADN-AVNGGHDL 553

Query: 320 SYFAYKAREGLKERLVLVPKEK 341
              AY+   G+ +R+ L+PK K
Sbjct: 554 DLSAYERSCGIPDRM-LLPKSK 574



>pdb|1FIZ|A Chain A, Three Dimensional Structure Of Beta-Acrosin From Boar
           Spermatozoa
          Length = 263

 Score = 30.4 bits (67), Expect = 1.2
 Identities = 15/66 (22%), Positives = 33/66 (49%)

Query: 854 FKNQKGELEKKIVFGLGAIKGVGGEPIKNIIEERAKGDYKSLEDFISRVDFSKLTKKSLE 913
           FKN+K   + +++FG   +     +P+K  ++ER   +    E ++S ++ + +    + 
Sbjct: 49  FKNKKKVTDWRLIFGANEVVWGSNKPVKPPLQERFVEEIIIHEKYVSGLEINDIALIKIT 108

Query: 914 PLVKSG 919
           P V  G
Sbjct: 109 PPVPCG 114



>pdb|1PHZ|A Chain A, Structure Of Phosphorylated Phenylalanine Hydroxylase
 pdb|2PHM|A Chain A, Structure Of Phenylalanine Hydroxylase Dephosphorylated
          Length = 429

 Score = 30.0 bits (66), Expect = 1.6
 Identities = 15/59 (25%), Positives = 32/59 (53%)

Query: 27 ILAKRVKELGMKSVSVTDHGNMFGAIDFYTSMKKEGIKPIIGMEAYIHNDDNLSSKETK 85
          +L++++ + G ++  + D+ N  GAI    S+K+E       +  +  ND NL+  E++
Sbjct: 10 VLSRKLSDFGQETSYIEDNSNQNGAISLIFSLKEEVGALAKVLRLFEENDINLTHIESR 68



>pdb|1DXE|A Chain A, 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia
           Coli
 pdb|1DXE|B Chain B, 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia
           Coli
          Length = 256

 Score = 29.6 bits (65), Expect = 2.1
 Identities = 15/62 (24%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 24  KIKILAKRVKELGMKSVSVTDHGNMFGAIDFYTSMKKEGIKPIIGMEAY--IHNDDNLSS 81
           ++ + + R    G++ VSV+   NMFG +  Y +   + I  ++ +E+   + N D +++
Sbjct: 107 ELAVASTRYPPEGIRGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAA 166

Query: 82  KE 83
            E
Sbjct: 167 TE 168



>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
          Length = 1119

 Score = 28.9 bits (63), Expect = 3.6
 Identities = 25/97 (25%), Positives = 44/97 (44%), Gaps = 1/97 (1%)

Query: 510 ELEPKIKELVESNELAKQVWEYSLNLENLNRNAGVHAAALVVDSQKELWHKTPLFASEKT 569
           EL+P ++E+V      K+  +    L N + N GV A  L V+    L   TP+      
Sbjct: 814 ELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNP 873

Query: 570 GGIVTQYSMKYLEPVDL-IKFDFLGLKTLTVIDDALK 605
            G+ ++ ++  +    L +   FLG + ++ I D  K
Sbjct: 874 LGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAK 910



>pdb|1SYF|   Staphylococcal Nuclease (E.C.3.1.31.1) Mutant With Pro 117
           Replaced By Thr (P117t) Complexed With
           2'-Deoxy-3'-5'-Diphosphothymidine And Calcium
 pdb|1SYE|   Staphylococcal Nuclease (E.C.3.1.31.1) Mutant With Pro 117
           Replaced By Thr (P117t)
          Length = 149

 Score = 28.9 bits (63), Expect = 3.6
 Identities = 17/68 (25%), Positives = 32/68 (47%)

Query: 161 KGYDEAKKIACEYQEIFEDDFYLEIMRHGILDQRFIDEQVIKMSLETGLKIIATNDTHYT 220
           K  + AKKI  E+ +    D Y   + +   D + ++E +++  L     +  TN+TH  
Sbjct: 64  KMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKTNNTHEQ 123

Query: 221 MPNDAKAQ 228
               ++AQ
Sbjct: 124 HLRKSEAQ 131



>pdb|1DKG|A Chain A, Crystal Structure Of The Nucleotide Exchange Factor Grpe
           Bound To The Atpase Domain Of The Molecular Chaperone
           Dnak
 pdb|1DKG|B Chain B, Crystal Structure Of The Nucleotide Exchange Factor Grpe
           Bound To The Atpase Domain Of The Molecular Chaperone
           Dnak
          Length = 197

 Score = 28.9 bits (63), Expect = 3.6
 Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 8/78 (10%)

Query: 439 IEYMIEKYGKYNVAQVITFNKMLAKGVIRDVARVLDMPYKEADDFAKLIPNRLGITLKGY 498
           ++ M++   K+ V  +   N  L   V + +A V      E+DD A    N LGI  KGY
Sbjct: 127 LKSMLDVVRKFGVEVIAETNVPLDPNVHQAIAMV------ESDDVAP--GNVLGIMQKGY 178

Query: 499 EKNGEFIEGAWELEPKIK 516
             NG  I  A     K K
Sbjct: 179 TLNGRTIRAAMVTVAKAK 196



>pdb|1A2Z|A Chain A, Pyrrolidone Carboxyl Peptidase From Thermococcus Litoralis
 pdb|1A2Z|B Chain B, Pyrrolidone Carboxyl Peptidase From Thermococcus Litoralis
 pdb|1A2Z|C Chain C, Pyrrolidone Carboxyl Peptidase From Thermococcus Litoralis
 pdb|1A2Z|D Chain D, Pyrrolidone Carboxyl Peptidase From Thermococcus Litoralis
          Length = 220

 Score = 28.1 bits (61), Expect = 6.1
 Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 588 KFDFLGLKTLTVIDDA-LKIIKTQHKISVDFLSLDMDDPKV 627
           KF  LG  T ++  +A +K I+   K+S+D+L  D DD K+
Sbjct: 178 KFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKI 218



>pdb|1BJ4|A Chain A, Recombinant Serine Hydroxymethyltransferase (Human)
          Length = 470

 Score = 28.1 bits (61), Expect = 6.1
 Identities = 14/62 (22%), Positives = 28/62 (44%), Gaps = 2/62 (3%)

Query: 52  IDFYTSMKKEGIKPIIGMEAYIHNDDNLSSKETKQRFHLCLFAKNQEGYENLMFLSSMAY 111
           ++ Y  +KKE  +  +G+E      +N +S+   +    CL  K  EGY    +     +
Sbjct: 21  VEVYNIIKKESNRQRVGLELIA--SENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEF 78

Query: 112 LE 113
           ++
Sbjct: 79  ID 80



>pdb|1BCC|A Chain A, Cytochrome Bc1 Complex From Chicken
 pdb|2BCC|A Chain A, Stigmatellin-Bound Cytochrome Bc1 Complex From Chicken
 pdb|3BCC|A Chain A, Stigmatellin And Antimycin Bound Cytochrome Bc1 Complex
           From Chicken
          Length = 446

 Score = 28.1 bits (61), Expect = 6.1
 Identities = 21/64 (32%), Positives = 32/64 (49%), Gaps = 11/64 (17%)

Query: 222 PNDAKAQEVAMCVAMGKTLNDKGRLKHSVHEFYIKSPEEMAKLFADIPEALENTQEIADK 281
           P +A  +EV    +MG  LN     +H+   +YIK+      L  D+P+A+E   +I   
Sbjct: 71  PQNALEKEVE---SMGAHLNAYSSREHTA--YYIKA------LSKDVPKAVELLADIVQN 119

Query: 282 CVLE 285
           C LE
Sbjct: 120 CSLE 123



>pdb|1ADJ|A Chain A, Histidyl-Trna Synthetase In Complex With Histidine
 pdb|1ADJ|B Chain B, Histidyl-Trna Synthetase In Complex With Histidine
 pdb|1ADJ|C Chain C, Histidyl-Trna Synthetase In Complex With Histidine
 pdb|1ADJ|D Chain D, Histidyl-Trna Synthetase In Complex With Histidine
 pdb|1ADY|A Chain A, Histidyl-Trna Synthetase In Complex With
           Histidyl-Adenylate
 pdb|1ADY|B Chain B, Histidyl-Trna Synthetase In Complex With
           Histidyl-Adenylate
 pdb|1ADY|C Chain C, Histidyl-Trna Synthetase In Complex With
           Histidyl-Adenylate
 pdb|1ADY|D Chain D, Histidyl-Trna Synthetase In Complex With
           Histidyl-Adenylate
 pdb|1H4V|B Chain B, Histidyl-Trna Synthetase From Thermus Thermophilus (Ligand
           Free)
          Length = 421

 Score = 28.1 bits (61), Expect = 6.1
 Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 8/99 (8%)

Query: 821 ESVARYIDEVRALEIEVMPPHINSSMQDFSVAEFKNQKGELEKKIVFGLGAIKGVGGEPI 880
           E  ARY   +R    EV+ PH  +  +D      +N    L+ K       +K +G  P+
Sbjct: 170 EDRARYNAYLR----EVLSPHREALSEDSKERLEENPMRILDSKSERDQALLKELGVRPM 225

Query: 881 KNIIEERAKGDYKSLEDFISRVDFSKLTKKSLEPLVKSG 919
            + + E A+   K +E  + R+         LEP +  G
Sbjct: 226 LDFLGEEARAHLKEVERHLERLS----VPYELEPALVRG 260



>pdb|1FFY|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
           Structure With Trna(Ile) And Mupirocin
 pdb|1QU2|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
           Structure With Trna(Ile) And Mupirocin
 pdb|1QU3|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
           Structure With Trna(Ile) And Mupirocin
          Length = 917

 Score = 28.1 bits (61), Expect = 6.1
 Identities = 29/117 (24%), Positives = 52/117 (43%), Gaps = 7/117 (5%)

Query: 177 FEDDFYLEIMRHGILDQRFIDEQVIKMSLETGLKIIATNDTHYTMPNDAKAQEVAMCVAM 236
           +E+  YL I +     Q FI+ ++    L+ G  I+        +    +     + V M
Sbjct: 696 YENFDYLNIYQEV---QNFINVELSNFYLDYGKDILYIEQRDSHIRRSMQTVLYQILVDM 752

Query: 237 GKTLNDKGRLKHSVHEFYIKSP--EEMAKLFADIPEALENTQEIADKCVLEIDLKDD 291
            K L     L H+  E +  +P  +E +   AD+P+ +E  Q + DK    ++L+DD
Sbjct: 753 TKLLAPI--LVHTAEEVWSHTPHVKEESVHLADMPKVVEVDQALLDKWRTFMNLRDD 807



>pdb|1QCR|A Chain A, Crystal Structure Of Bovine Mitochondrial Cytochrome Bc1
           Complex, Alpha Carbon Atoms Only
          Length = 446

 Score = 27.7 bits (60), Expect = 8.0
 Identities = 21/64 (32%), Positives = 32/64 (49%), Gaps = 11/64 (17%)

Query: 222 PNDAKAQEVAMCVAMGKTLNDKGRLKHSVHEFYIKSPEEMAKLFADIPEALENTQEIADK 281
           P +A  +EV    +MG  LN     +H+   +YIK+      L  D+P+A+E   +I   
Sbjct: 71  PGNALEKEVE---SMGAHLNAYSTREHTA--YYIKA------LSKDLPKAVELLADIVQN 119

Query: 282 CVLE 285
           C LE
Sbjct: 120 CSLE 123



>pdb|1BGY|A Chain A, Cytochrome Bc1 Complex From Bovine
 pdb|1BGY|M Chain M, Cytochrome Bc1 Complex From Bovine
 pdb|1BE3|A Chain A, Cytochrome Bc1 Complex From Bovine
          Length = 446

 Score = 27.7 bits (60), Expect = 8.0
 Identities = 21/64 (32%), Positives = 32/64 (49%), Gaps = 11/64 (17%)

Query: 222 PNDAKAQEVAMCVAMGKTLNDKGRLKHSVHEFYIKSPEEMAKLFADIPEALENTQEIADK 281
           P +A  +EV    +MG  LN     +H+   +YIK+      L  D+P+A+E   +I   
Sbjct: 71  PGNALEKEVE---SMGAHLNAYSTREHTA--YYIKA------LSKDLPKAVELLADIVQN 119

Query: 282 CVLE 285
           C LE
Sbjct: 120 CSLE 123



>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
          Length = 1118

 Score = 27.7 bits (60), Expect = 8.0
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 17/100 (17%)

Query: 436 KEIIEYMIEKYGKYNVAQVITFNKMLAKGVIRDVARVLDMPYKEADDFAKLIPNRLGIT- 494
           +E++   + +  K  V   +  N+   KGV+  +  V DMP+        +I N LG+  
Sbjct: 819 REVVRVFVAQKRKLQVGDKLA-NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPS 877

Query: 495 -------------LKGYEKNGEFIEGAWE--LEPKIKELV 519
                        L GY     +I   ++   EP+IKEL+
Sbjct: 878 RMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELL 917



>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna
           Polymerase- Includes Complete Structure With Side-Chains
           (Except For Disordered Regions)-Further Refined From
           Original Deposition-Contains Additional Sequence
           Information
          Length = 1119

 Score = 27.7 bits (60), Expect = 8.0
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 17/100 (17%)

Query: 436 KEIIEYMIEKYGKYNVAQVITFNKMLAKGVIRDVARVLDMPYKEADDFAKLIPNRLGIT- 494
           +E++   + +  K  V   +  N+   KGV+  +  V DMP+        +I N LG+  
Sbjct: 820 REVVRVFVAQKRKLQVGDKLA-NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPS 878

Query: 495 -------------LKGYEKNGEFIEGAWE--LEPKIKELV 519
                        L GY     +I   ++   EP+IKEL+
Sbjct: 879 RMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELL 918



>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
          Length = 1118

 Score = 27.7 bits (60), Expect = 8.0
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 17/100 (17%)

Query: 436 KEIIEYMIEKYGKYNVAQVITFNKMLAKGVIRDVARVLDMPYKEADDFAKLIPNRLGIT- 494
           +E++   + +  K  V   +  N+   KGV+  +  V DMP+        +I N LG+  
Sbjct: 819 REVVRVFVAQKRKLQVGDKLA-NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPS 877

Query: 495 -------------LKGYEKNGEFIEGAWE--LEPKIKELV 519
                        L GY     +I   ++   EP+IKEL+
Sbjct: 878 RMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELL 917



  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
   0.318    0.137    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: 7,055,326
Number of Sequences: 13198
Number of extensions: 310008
Number of successful extensions: 761
Number of sequences better than 10.0: 17
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 754
Number of HSP's gapped (non-prelim): 24
length of query: 1211
length of database: 2,899,336
effective HSP length: 99
effective length of query: 1112
effective length of database: 1,592,734
effective search space: 1771120208
effective search space used: 1771120208
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (27.7 bits)