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|15645627|ref|NP_207803.1| dihydrodipicolinate synthetase (dapA) [Helicobacter pylori 26695] (300 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|1DHP|A  Chain A, Dihydrodipicolinate Synthase >gi|194236...   194  8e-51
pdb|1FDZ|A  Chain A, N-Acetylneuraminate Lyase In Complex Wi...   108  1e-24
pdb|1NAL|1  Chain 1, Mol_id: 1; Molecule: N-Acetylneuraminat...   108  1e-24
pdb|1F6K|A  Chain A, Crystal Structure Analysis Of N-Acetyln...    80  3e-16
pdb|1M1B|A  Chain A, Crystal Structure Of Phosphoenolpyruvat...    28  1.7
pdb|3GPD|G  Chain G, Twinning In Crystals Of Human Skeletal ...    26  4.8
pdb|1B3U|A  Chain A, Crystal Structure Of Constant Regulator...    26  6.3
pdb|1NUK|A  Chain A, Crystal Structure Of The Ligand-Binding...    25  8.3
pdb|1KGY|A  Chain A, Crystal Structure Of The Ephb2-Ephrinb2...    25  8.3

>pdb|1DHP|A Chain A, Dihydrodipicolinate Synthase
 pdb|1DHP|B Chain B, Dihydrodipicolinate Synthase
          Length = 292

 Score =  194 bits (494), Expect = 8e-51
 Identities = 109/272 (40%), Positives = 162/272 (59%), Gaps = 9/272 (3%)

Query: 8   ALITPFKKDLSVDEAAYETLIKRQIFQGMDACVPVGTTGESATLTHKEHMRCIEIAIETC 67
           A++TP  +  +V  A+ + LI   +  G  A V VGTTGESATL H EH   + + ++  
Sbjct: 8   AIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLDL- 66

Query: 68  KNTKTPSNSRMKVLAGVGSNATSESLSLAKFAQKIGADAILCVSPYYNRPTQQGLFEHYK 127
                 ++ R+ V+AG G+NAT+E++SL +     G    L V+PYYNRP+Q+GL++H+K
Sbjct: 67  ------ADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQEGLYQHFK 120

Query: 128 TIAQSVEIPVMLYDVPSRTGVSIEVPTALKLFREVPNIKAIKEASGSLKRVTEL-HYYEK 186
            IA+  ++P +LY+VPSRTG  + +P  +    +V NI  IKEA+G+L RV ++      
Sbjct: 121 AIAEHTDLPQILYNVPSRTGCDL-LPETVGRLAKVKNIIGIKEATGNLTRVNQIKELVSD 179

Query: 187 DFKIFSGEDSLNHSIMFSGGCGVISVTGNLMPNLISQMVNCALKQKYQQALEIQNKLFCL 246
           DF + SG+D+     M  GG GVISVT N+    ++QM   A +  + +A  I  +L  L
Sbjct: 180 DFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPL 239

Query: 247 HQALFVETNPIPIKMAMHLAGLIENPSYRLPL 278
           H  LFVE NPIP+K A    GL+   + RLP+
Sbjct: 240 HNKLFVEPNPIPVKWACKELGLVATDTLRLPM 271

>pdb|1FDZ|A Chain A, N-Acetylneuraminate Lyase In Complex With Pyruvate Via
           Borohydride Reduction
 pdb|1FDZ|D Chain D, N-Acetylneuraminate Lyase In Complex With Pyruvate Via
           Borohydride Reduction
 pdb|1FDY|A Chain A, N-Acetylneuraminate Lyase In Complex With Hydroxypyruvate
 pdb|1FDY|B Chain B, N-Acetylneuraminate Lyase In Complex With Hydroxypyruvate
 pdb|1FDY|C Chain C, N-Acetylneuraminate Lyase In Complex With Hydroxypyruvate
 pdb|1FDY|D Chain D, N-Acetylneuraminate Lyase In Complex With Hydroxypyruvate
 pdb|1FDZ|B Chain B, N-Acetylneuraminate Lyase In Complex With Pyruvate Via
           Borohydride Reduction
 pdb|1FDZ|C Chain C, N-Acetylneuraminate Lyase In Complex With Pyruvate Via
           Borohydride Reduction
          Length = 297

 Score =  108 bits (269), Expect = 1e-24
 Identities = 75/290 (25%), Positives = 145/290 (49%), Gaps = 9/290 (3%)

Query: 7   SALITPFKKDLSVDEAAYETLIKRQIFQGMDACVPVGTTGESATLTHKEHMRCIEIAIET 66
           +AL+TPF +  ++D+A+   L++  I QG+D     G+TGE+   +  E  + +EI  E 
Sbjct: 10  AALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEE 69

Query: 67  CKNTKTPSNSRMKVLAGVGSNATSESLSLAKFAQKIGADAILCVSPYYNRPTQQGLFEHY 126
            K        ++K++A VG   T+ES  LA  A++ G DA+  V+P+Y   + +   +HY
Sbjct: 70  GK-------GKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHY 122

Query: 127 KTIAQSVE-IPVMLYDVPSRTGVSIEVPTALKLFREVPNIKAIKEASGSLKRVTELHYYE 185
           + I  S + +P+++Y++P+ +GV + +   +     +P + A+K+ SG L ++ ++    
Sbjct: 123 RAIIDSADGLPMVVYNIPALSGVKLTL-DQINTLVTLPGVGALKQTSGDLYQMEQIRREH 181

Query: 186 KDFKIFSGEDSLNHSIMFSGGCGVISVTGNLMPNLISQMVNCALKQKYQQALEIQNKLFC 245
            D  +++G D +  S + +G  G I  T N+M      +V    +   Q A ++Q +   
Sbjct: 182 PDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNK 241

Query: 246 LHQALFVETNPIPIKMAMHLAGLIENPSYRLPLVAPSKETIQLLEKTLQQ 295
           +   L        +K  +H   ++  P  R P     ++ +  L+   QQ
Sbjct: 242 VIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQ 291

>pdb|1NAL|1 Chain 1, Mol_id: 1; Molecule: N-Acetylneuraminate Lyase; Chain: 1,
           2, 3, 4; Ec: 4.1.3.3
 pdb|1NAL|2 Chain 2, Mol_id: 1; Molecule: N-Acetylneuraminate Lyase; Chain: 1,
           2, 3, 4; Ec: 4.1.3.3
 pdb|1NAL|3 Chain 3, Mol_id: 1; Molecule: N-Acetylneuraminate Lyase; Chain: 1,
           2, 3, 4; Ec: 4.1.3.3
 pdb|1NAL|4 Chain 4, Mol_id: 1; Molecule: N-Acetylneuraminate Lyase; Chain: 1,
           2, 3, 4; Ec: 4.1.3.3
          Length = 297

 Score =  108 bits (269), Expect = 1e-24
 Identities = 78/290 (26%), Positives = 144/290 (48%), Gaps = 10/290 (3%)

Query: 7   SALITPFKKDLSVDEAAYETLIKRQIFQGMDACVPVGTTGESATLTHKEHMRCIEIAIET 66
           +AL+TPF +  ++D+A+   L++  I QG+D     G+TGE+   +  E  + +EI  E 
Sbjct: 10  AALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEE 69

Query: 67  CKNTKTPSNSRMKVLAGVGSNATSESLSLAKFAQKIGADAILCVSPYYNRPTQQGLFEHY 126
            K        ++K++A VG   T+ES  LA  A++ G DA+  V+P+Y   + +   +HY
Sbjct: 70  GK-------GKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHY 122

Query: 127 KTIAQSVE-IPVMLYDVPSRTGVSIEVPTALKLFREVPNIKAIKEASGSLKRVTELHYYE 185
           + I  S + +P+++Y++P+ +GV + +   +     +P + A+K+ SG L ++ ++    
Sbjct: 123 RAIIDSADGLPMVVYNIPALSGVKLTL-DQINTLVTLPGVGALKQTSGDLYQMEQIRREH 181

Query: 186 KDFKIFSGEDSLNHSIMFSGGCGVISVTGNLMPNLISQMVNCALKQKYQQALEIQNKLFC 245
            D  +++G D +  S + +G  G I  T N+M      +V    +   Q A ++Q +   
Sbjct: 182 PDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNK 241

Query: 246 LHQALFVETNPIPIKMAMHLAGLIENPSYRLPLVAPSKETIQLLEKTLQQ 295
           +   L        +K  +H   ++  P  R P   P  E  Q   K L Q
Sbjct: 242 VIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPF-GPVDEKYQPELKALAQ 290

>pdb|1F6K|A Chain A, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Ii
 pdb|1F74|A Chain A, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Ii Complexed
           With 4-Deoxy-Sialic Acid
 pdb|1F74|C Chain C, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Ii Complexed
           With 4-Deoxy-Sialic Acid
 pdb|1F7B|A Chain A, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Ii In Complex
           With 4-Oxo-Sialic Acid
 pdb|1F5Z|A Chain A, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form I
 pdb|1F5Z|B Chain B, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form I
 pdb|1F5Z|C Chain C, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form I
 pdb|1F5Z|D Chain D, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form I
 pdb|1F6P|A Chain A, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Iii
 pdb|1F6P|B Chain B, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Iii
 pdb|1F6P|C Chain C, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Iii
 pdb|1F6P|D Chain D, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Iii
 pdb|1F73|A Chain A, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Iii In Complex
           With Sialic Acid Alditol
 pdb|1F73|B Chain B, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Iii In Complex
           With Sialic Acid Alditol
 pdb|1F73|C Chain C, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Iii In Complex
           With Sialic Acid Alditol
 pdb|1F73|D Chain D, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Iii In Complex
           With Sialic Acid Alditol
 pdb|1F7B|C Chain C, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Ii In Complex
           With 4-Oxo-Sialic Acid
 pdb|1F6K|C Chain C, Crystal Structure Analysis Of N-Acetylneuraminate Lyase
           From Haemophilus Influenzae: Crystal Form Ii
          Length = 293

 Score = 80.1 bits (196), Expect = 3e-16
 Identities = 64/263 (24%), Positives = 123/263 (46%), Gaps = 9/263 (3%)

Query: 7   SALITPFKKDLSVDEAAYETLIKRQIFQ-GMDACVPVGTTGESATLTHKEHMRCIEIAIE 65
           SAL+  F +D +++E     +I+  I +  +D     G+TGE+  L+ +E      IA +
Sbjct: 9   SALLVSFNEDGTINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKD 68

Query: 66  TCKNTKTPSNSRMKVLAGVGSNATSESLSLAKFAQKIGADAILCVSPYYNRPTQQGLFEH 125
             K+       ++ ++A VGS    E++ L K+A ++G D +  V+P+Y + +   +  +
Sbjct: 69  EAKD-------QIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSFPEIKHY 121

Query: 126 YKTIAQSVEIPVMLYDVPSRTGVSIEVPTALKLFREVPNIKAIKEASGSLKRVTELHYYE 185
           Y TI       +++Y +P  TGV++ +    +L++  P +  +K  +G    +  L    
Sbjct: 122 YDTIIAETGSNMIVYSIPFLTGVNMGIEQFGELYKN-PKVLGVKFTAGDFYLLERLKKAY 180

Query: 186 KDFKIFSGEDSLNHSIMFSGGCGVISVTGNLMPNLISQMVNCALKQKYQQALEIQNKLFC 245
            +  I++G D +       G  G I  T N+      Q+       K ++ALEIQ+    
Sbjct: 181 PNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTKAGKLKEALEIQHVTND 240

Query: 246 LHQALFVETNPIPIKMAMHLAGL 268
           L + +      + IK  + L G+
Sbjct: 241 LIEGILANGLYLTIKELLKLEGV 263

>pdb|1M1B|A Chain A, Crystal Structure Of Phosphoenolpyruvate Mutase Complexed
           With Sulfopyruvate
 pdb|1M1B|B Chain B, Crystal Structure Of Phosphoenolpyruvate Mutase Complexed
           With Sulfopyruvate
          Length = 295

 Score = 27.7 bits (60), Expect = 1.7
 Identities = 29/150 (19%), Positives = 62/150 (41%), Gaps = 16/150 (10%)

Query: 62  IAIETCKNTKTPSNSRM--KVLAGVGSNATSESLSLAKFAQKIGADAILCVSPYYNRPTQ 119
           + I+ CK+++T  +  +  +V A +      E+L  A+  +  GADAIL  S   +    
Sbjct: 140 LKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDI 199

Query: 120 QGLFEHYKTIAQSVEIPVMLYDVPS----RTGVSI----------EVPTALKLFREVPNI 165
           +   + +      V +P   Y  P+      GVS+           V    +  +++ + 
Sbjct: 200 EAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDD 259

Query: 166 KAIKEASGSLKRVTELHYYEKDFKIFSGED 195
           +++      +  V E+   ++D ++   ED
Sbjct: 260 QSLVNVEDKIVSVKEIFRLQRDDELVQAED 289

>pdb|3GPD|G Chain G, Twinning In Crystals Of Human Skeletal Muscle D-
           Glyceraldehyde-3-Phosphate Dehydrogenase
 pdb|3GPD|R Chain R, Twinning In Crystals Of Human Skeletal Muscle D-
           Glyceraldehyde-3-Phosphate Dehydrogenase
          Length = 334

 Score = 26.2 bits (56), Expect = 4.8
 Identities = 24/76 (31%), Positives = 36/76 (46%), Gaps = 15/76 (19%)

Query: 146 TGVSIEVPTA----------LKLFREVPNIK-AIKEAS-GSLKRVTELHYYEKDFKIFSG 193
           TG++  VPTA          L+   +  +IK  +KEAS G LK +     Y +D  +   
Sbjct: 228 TGMAFRVPTANVSVLDLTCRLEKPAKYDDIKKVVKEASEGPLKGILG---YTEDEVVSDD 284

Query: 194 EDSLNHSIMFSGGCGV 209
            +  NHS +F  G G+
Sbjct: 285 FNGSNHSSIFDAGAGI 300

>pdb|1B3U|A Chain A, Crystal Structure Of Constant Regulatory Domain Of Human
           Pp2a, Pr65alpha
 pdb|1B3U|B Chain B, Crystal Structure Of Constant Regulatory Domain Of Human
           Pp2a, Pr65alpha
          Length = 588

 Score = 25.8 bits (55), Expect = 6.3
 Identities = 16/59 (27%), Positives = 24/59 (40%)

Query: 45  TGESATLTHKEHMRCIEIAIETCKNTKTPSNSRMKVLAGVGSNATSESLSLAKFAQKIG 103
           +G+   L     + CI +  E C    T  +    VL   G    +   ++AK  QKIG
Sbjct: 489 SGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQKIG 547

>pdb|1NUK|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The
           Ephb2 Receptor Tyrosine Kinase
          Length = 183

 Score = 25.4 bits (54), Expect = 8.3
 Identities = 11/29 (37%), Positives = 15/29 (50%)

Query: 162 VPNIKAIKEASGSLKRVTELHYYEKDFKI 190
           V +  +I    GS K    L+YYE DF +
Sbjct: 75  VRDCSSIPSVPGSCKETFNLYYYEADFDL 103

>pdb|1KGY|A Chain A, Crystal Structure Of The Ephb2-Ephrinb2 Complex
 pdb|1KGY|B Chain B, Crystal Structure Of The Ephb2-Ephrinb2 Complex
 pdb|1KGY|C Chain C, Crystal Structure Of The Ephb2-Ephrinb2 Complex
 pdb|1KGY|D Chain D, Crystal Structure Of The Ephb2-Ephrinb2 Complex
          Length = 181

 Score = 25.4 bits (54), Expect = 8.3
 Identities = 11/29 (37%), Positives = 15/29 (50%)

Query: 162 VPNIKAIKEASGSLKRVTELHYYEKDFKI 190
           V +  +I    GS K    L+YYE DF +
Sbjct: 76  VRDCSSIPSVPGSCKETFNLYYYEADFDL 104

  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    0.133    0.374 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,575,027
Number of Sequences: 13198
Number of extensions: 59788
Number of successful extensions: 178
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 164
Number of HSP's gapped (non-prelim): 9
length of query: 300
length of database: 2,899,336
effective HSP length: 88
effective length of query: 212
effective length of database: 1,737,912
effective search space: 368437344
effective search space used: 368437344
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: 54 (25.4 bits)