Immunotation of Rv2753c (dihydrodipicolinate synthase)

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(→B-Cell Epitopes)
Current revision (09:54, 5 January 2010) (edit) (undo)
(→MHC Class-I Binder)
 
(62 intermediate revisions not shown.)
Line 8: Line 8:
| PDB        = 1XXX
| PDB        = 1XXX
| DrugBank          =
| DrugBank          =
-
| chemical_formula  =  
+
| chemical_formula  = C28H37ClN4O6 [http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=18062777&loc=ec_rcs#Properties]
| molecular_weight  = 30,858 Da
| molecular_weight  = 30,858 Da
| solubility        =  
| solubility        =  
Line 18: Line 18:
L-aspartate 4-semialdehyde + pyruvate = dihydrodipicolinate + 2H<sub>2</sub>O.
L-aspartate 4-semialdehyde + pyruvate = dihydrodipicolinate + 2H<sub>2</sub>O.
-
This protein is eesential for optimal growth of M.tb and found in the cytoplasm as predicted by the [http://wolfpsort.org/aboutWoLF_PSORT.html.en WoLFPSORT] and [http://www.biohealthbase.org/brc/localizationPrograms.do?decorator=mycobacterium  Subloc] Server. HMMpfam found one domain PF00701 and has Helix Turn Helix secondary structure.
+
This protein is eesential for optimal growth of M.tb and found in the cytoplasm as predicted by the [http://www.imtech.res.in/raghava/tbpred/ TBpred]. HMMpfam found one domain PF00701 and has Helix Turn Helix secondary structure.
 +
==Protein Sequence==
 +
>Rv2753c, TB.seq  3066222:3067121 MW:30827
 +
VTTVGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVLEAVGDR
 +
ARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRA
 +
LASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKI
 +
NIAVAPLCNAMSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR
 +
 
=Human Homologue Blast Result=
=Human Homologue Blast Result=
Line 34: Line 41:
<tr><td>sp|Q7Z7B0</td><td> 27.69</td><td> 44.62</td><td> 65</td><td> 2.7</td></tr></table>
<tr><td>sp|Q7Z7B0</td><td> 27.69</td><td> 44.62</td><td> 65</td><td> 2.7</td></tr></table>
 +
 +
=Alergen Protein=
 +
Link to [http://www.imtech.res.in/raghava/algpred/ Algpred]<br>
 +
Non Allergen Predicted by AlgPred Server
 +
=Bacterial Toxin Prediction=
 +
Link to [http://www.imtech.res.in/raghava/btxpred/submission.html btxpred]<br>
 +
No Hit Fountd by btxpred server.
 +
=Subcellular Location=
 +
Link to [http://www.imtech.res.in/raghava/tbpred/ TBpred]<br>
 +
Cyoplasmic
 +
=Antigens=
=Antigens=
-
=Haptens=
+
No Hit Found in [http://www.imtech.res.in/raghava/antigendb/keyquery.html AntigenDB]<br>
-
=Epitopes=
+
No. Hit Found in [http://www.iedb.org/ IEDB]
-
===B-Cell Epitopes===
+
==B cell Epitopes==
-
Result Predicted by [http://www.imtech.res.in/raghava/bcepred/bcepred_submission.html bcelpep]  
+
====BCEpred Analysis====
 +
 
 +
Link to [http://www.imtech.res.in/raghava/bcepred/bcepred_submission.html Bcepred]  
<br>
<br>
-
SGDG<br>
+
Result Predicited by [http://crdd.osdd.net/drugpedia/images/Bcepred_rv2753.pdf Bcepred]<br>
-
VDQGCDG'''LV<br>
+
-
VSGTTGESPTTTDGEKIE'''<br>
+
-
'''PYYSKPPQ'''RG<br>
+
-
'''VKDAKAD'''L<br>
+
-
Result Predicited by
+
-
[http://www.imtech.res.in/raghava/abcpred/ABC_submission.html ABCPred]
+
-
<table border='1'><tr><td>
+
-
TPEQIDALAADMRAAS
+
-
</td></tr><tr><td>
+
-
PGRSAVPIEPDTIRAL
+
-
</td></tr><tr><td>
+
-
GTTGESPTTTDGEKIE
+
-
</td></tr><tr><td>
+
-
QRGLQAHFTAVADATE
+
-
</td></tr><tr><td>
+
-
AGAGTYDTAHSIRLAK
+
-
</td></tr><tr><td>
+
-
DGLVVSGTTGESPTTT
+
-
</td></tr><tr><td>
+
-
GIDVGDPRLPQVAATP
+
-
</td></tr><tr><td>
+
-
QIMADTGLAYYSGDDA
+
-
</td></tr><tr><td>
+
-
GTLLTAMVTPFSGDGS
+
-
</td></tr><tr><td>
+
-
TPYYSKPPQRGLQAHF
+
-
</td></tr><tr><td>
+
-
SGDIATARKINIAVAP
+
-
</td></tr><tr><td>
+
-
DVAARLGTLLTAMVTP
+
-
</td></tr><tr><td>
+
-
VGVKDAKADLHSGAQI
+
-
</td></tr><tr><td>
+
-
MLLYDIPGRSAVPIEP
+
-
</td></tr><tr><td>
+
-
PWLAMGATGFISVIAH
+
-
</td></tr></table>
+
-
===MHC class I restricted T cell epitopes===
+
====ABCpred Analysis====
-
===CTL Epitopes===
+
Link to [http://www.imtech.res.in/raghava/abcpred/ABC_submission.html ABCpred]<br>
-
=MHC Binder=
+
Result Predicited by [http://crdd.osdd.net/drugpedia/images/Abcpred_rv2753c.pdf ABCPred]<br>
-
===Class-I Binder===
+
-
Result Predicted by
+
-
[http://www.imtech.res.in/raghava/nhlapred/comp.html nHLApred]
+
-
<table border='1'><tr><td>
+
-
Epitope</td><td>No of Alleles
+
-
</td></tr><tr><td>
+
-
VPIEPDTIR </td><td>      15
+
-
</td></tr><tr><td>
+
-
TPFSGDGSL </td><td>      14
+
-
</td></tr><tr><td>
+
-
TLSKAGLRL </td><td>      13
+
-
</td></tr><tr><td>
+
-
IEPDTIRAL </td><td>      13
+
-
</td></tr><tr><td>
+
-
GTYDTAHSI </td><td>      13
+
-
</td></tr><tr><td>
+
-
DDALNLPWL </td><td>      11
+
-
</td></tr><tr><td>
+
-
GFISVIAHL </td><td>    10
+
-
</td></tr><tr><td>
+
-
GATGFISVI </td><td>      10
+
-
</td></tr><tr><td>
+
-
ATPEQIDAL </td><td>      10
+
-
</td></tr><tr><td>
+
-
YDTAHSIRL </td><td>      9
+
-
</td></tr><tr><td>
+
-
GDIATARKI  </td><td>    9
+
-
</td></tr><tr><td>
+
-
AVLEAVGDR  </td><td>    9
+
-
</td></tr><tr><td>
+
-
ASHPNIVGV  </td><td>    9
+
-
</td></tr><tr><td>
+
-
QRGLQAHFT  </td><td>    7
+
-
</td></tr><tr><td>
+
-
GLQAHFTAV  </td><td>    7
+
-
</td></tr><tr><td>
+
-
AVGDRARVI  </td><td>    7
+
-
</td></tr><tr><td>
+
-
YSGDDALNL  </td><td>    6
+
-
</td></tr><tr><td>
+
-
VGFDVAARL  </td><td>    6
+
-
</td></tr><tr><td>
+
-
QLRELLSAF </td><td>      6
+
-
</td></tr><tr><td>
+
-
TAVADATEL </td><td>      5
+
-
</td></tr><tr><td>
+
-
TAARLANHL  </td><td>    5
+
-
</td></tr><tr><td>
+
-
LLRAVLEAV  </td><td>    5
+
-
</td></tr><tr><td>
+
-
GEKIELLRA  </td><td>    5
+
-
</td></tr><tr><td>
+
-
DTATAARLA  </td><td>    5
+
-
</td></tr><tr><td>
+
-
AAGQLRELL  </td><td>    5
+
-
</td></tr><tr><td>
+
-
TDGEKIELL  </td><td>    4
+
-
</td></tr><tr><td>
+
-
QAHFTAVAD  </td><td>    4
+
-
</td></tr><tr><td>
+
-
MSRLGGVTL  </td><td>    4
+
-
</td></tr><tr><td>
+
-
LDTATAARL  </td><td>    4
+
-
</td></tr><tr><td>
+
-
HPNIVGVKD  </td><td>    4
+
-
</td></tr><tr><td>
+
-
GVKDAKADL  </td><td>    4
+
-
</td></tr><tr><td>
+
-
DGEKIELLR  </td><td>    4
+
-
</td></tr><tr><td>
+
-
KIELLRAVL </td><td>      3
+
-
</td></tr><tr><td>
+
-
HSIRLAKAC  </td><td>    3
+
-
</td></tr><tr><td>
+
-
GSGDIATAR  </td><td>    3
+
-
</td></tr><tr><td>
+
-
AHLAAGQLR  </td><td>    3
+
-
</td></tr><tr><td>
+
-
PTTTDGEKI  </td><td>    2
+
-
</td></tr><tr><td>
+
-
IAHLAAGQL </td><td>      2
+
-
</td></tr><tr><td>
+
-
DLHSGAQIM  </td><td>    2
+
-
</td></tr><tr><td>
+
-
</table>
+
-
===Class-II Binder===
+
====IEDB Analysis====
-
Result predicted by [http://www.cbs.dtu.dk/services/NetMHCII/ NetMHCII]
+
Link to [http://tools.immuneepitope.org/tools/bcell/iedb_input IEDB]<br>
-
<table border='1'><tr><td>
+
Result Predicited by  [http://crdd.osdd.net/drugpedia/images/IEDB_rv2753c.pdf IEDB]<br>
-
Epitope</td><td>No of Alleles
+
 
-
</td></tr><tr><td>
+
=MHC Class-I Binder=
-
TGFISVIAHLAAGQL</td><td> 6
+
==nHLAPred Analysis==
-
</td></tr><tr><td>
+
Link to [http://www.imtech.res.in/raghava/nhlapred/comp.html nHLApred]
-
GFISVIAHLAAGQLR</td><td> 6
+
-
</td></tr><tr><td>
+
-
PDTIRALASHPNIVG </td><td>4
+
-
</td></tr><tr><td>
+
-
GATGFISVIAHLAAG </td><td>4
+
-
</td></tr><tr><td>
+
-
ATGFISVIAHLAAGQ </td><td>4
+
-
</td></tr><tr><td>
+
-
TELPMLLYDIPGRSA </td><td>3
+
-
</td></tr><tr><td>
+
-
MGATGFISVIAHLAA</td><td> 3
+
-
</td></tr><tr><td>
+
-
LVVTPYYSKPPQRGL </td><td>3
+
-
</td></tr><tr><td>
+
-
GQLRELLSAFGSGDI</td><td> 3
+
-
</td></tr><tr><td>
+
-
FISVIAHLAAGQLRE</td><td> 3
+
-
</td></tr><tr><td>
+
-
DTIRALASHPNIVGV</td><td> 3
+
-
</td></tr><tr><td>
+
-
QLRELLSAFGSGDIA</td><td> 2
+
-
</td></tr><tr><td>
+
-
PEQIDALAADMRAAS</td><td> 2
+
-
</td></tr><tr><td>
+
-
NLPWLAMGATGFISV</td><td> 2
+
-
</td></tr><tr><td>
+
-
LPWLAMGATGFISVI</td><td> 2
+
-
</td></tr><tr><td>
+
-
LNLPWLAMGATGFIS</td><td> 2
+
-
</td></tr><tr><td>
+
-
LLVVTPYYSKPPQRG</td><td> 2
+
-
</td></tr><tr><td>
+
-
LGGVTLSKAGLRLQG</td><td> 2
+
-
</td></tr><tr><td>
+
-
KAGLRLQGIDVGDPR</td><td> 2
+
-
</td></tr><tr><td>
+
-
IAGAGTYDTAHSIRL</td><td> 2
+
-
</td></tr><tr><td>
+
-
GLLVVTPYYSKPPQR</td><td>2
+
-
</td></tr><tr><td>
+
-
GGVTLSKAGLRLQGI</td><td> 2
+
-
</td></tr><tr><td>
+
-
EPDTIRALASHPNIV</td><td> 2
+
-
</td></tr><tr><td>
+
-
ELPMLLYDIPGRSAV </td><td>2
+
-
</td></tr><tr><td>
+
-
ATELPMLLYDIPGRS </td><td>2
+
-
</td></tr><tr><td>
+
-
ALNLPWLAMGATGFI</td><td> 2
+
-
</td></tr><tr><td>
+
-
AGQLRELLSAFGSGD</td><td> 2
+
-
</td></tr><tr><td>
+
-
AGLRLQGIDVGDPRL</td><td> 2
+
-
</td></tr><table>
+
<br>  
<br>  
-
Result Predicited by [http://www.imtech.res.in/raghava/propred/ Propred]
+
Result Predicited by [http://crdd.osdd.net/drugpedia/images/Nhlapred_rv2753c.pdf nHLApred]<br>
-
<table border='1'><tr><td>
+
==IEDB Analysis==
-
Epitope</td><td> No of Alleles
+
Link to [http://tools.immuneepitope.org/analyze/html/mhc_processing.html IEDB] <br>
-
</td></tr><tr><td>
+
Result Predicted by [http://crdd.osdd.net/drugpedia/images/IEDB_mhc_rv2753c.pdf IEDB]
-
IRLAKACAA  </td><td>    51
+
 
-
</td></tr><tr><td>
+
=MHC Class-II Binder=
-
INIAVAPLC  </td><td>    51
+
==Propred Analysis==
-
</td></tr><tr><td>
+
Link to [http://www.imtech.res.in/raghava/propred/ Propred]<br>
-
VVSGTTGES  </td><td>    48
+
Result Predicted by [http://crdd.osdd.net/drugpedia/images/Propred_rv2753c.pdf Propred]
-
</td></tr><tr><td>
+
 
-
LLVVTPYYS </td><td>      48
+
 
-
</td></tr><tr><td>
+
==NetMHC-II Analysis==
-
IRALASHPN </td><td>      46
+
Link to [http://www.cbs.dtu.dk/services/NetMHCII/ NetMHC-II]<br>
-
</td></tr><tr><td>
+
Result Predicted by [http://crdd.osdd.net/drugpedia/images/NetMHC-II_rv2753c.pdf NetMHC-II]
-
LTAMVTPFS  </td><td>    44
+
-
</td></tr><tr><td>
+
-
LQAHFTAVA  </td><td>    43
+
-
</td></tr><tr><td>
+
-
LGTLLTAMV  </td><td>    43
+
-
</td></tr><tr><td>
+
-
LLTAMVTPF  </td><td>    42
+
-
</td></tr><tr><td>
+
-
VAPLCNAMS  </td><td>    41
+
-
</td></tr><tr><td>
+
-
IATARKINI </td><td>      40
+
-
</td></tr><tr><td>
+
-
LRELLSAFG </td><td>      38
+
-
</td></tr><tr><td>
+
-
LLYDIPGRS  </td><td>    38
+
-
</td></tr><tr><td>
+
-
LVVSGTTGE  </td><td>    37
+
-
</td></tr><tr><td>
+
-
VIAHLAAGQ  </td><td>    36
+
-
</td></tr><tr><td>
+
-
MLLYDIPGR  </td><td>    36
+
-
</td></tr><tr><td>
+
-
LRLQGIDVG  </td><td>    35
+
-
</td></tr><tr><td>
+
-
ISVIAHLAA  </td><td>    34
+
-
</td></tr><tr><td>
+
-
LQGIDVGDP  </td><td>    33
+
-
</td></tr><tr><td>
+
-
FISVIAHLA </td><td>      33
+
-
</td></tr><tr><td>
+
-
WLAMGATGF  </td><td>    32
+
-
</td></tr><tr><td>
+
-
LLRAVLEAV  </td><td>    30
+
-
</td></tr><tr><td>
+
-
IELLRAVLE  </td><td>    30
+
-
</td></tr><tr><td>
+
-
YYSKPPQRG  </td><td>    25
+
-
</td></tr><tr><td>
+
-
IAVAPLCNA </td><td>      24
+
-
</td></tr><tr><td>
+
-
LAADMRAAS </td><td>      22
+
-
</td></tr><tr><td>
+
-
IVGVKDAKA </td><td>      22
+
-
</td></tr><tr><td>
+
-
LCNAMSRLG </td><td>      21
+
-
</td></tr><tr><td>
+
-
LANHLVDQG  </td><td>    21
+
-
</td></tr><tr><td>
+
-
LAMGATGFI  </td><td>    21
+
-
</td></tr><tr><td>
+
-
FGSGDIATA  </td><td>    20
+
-
</td></tr><tr><td>
+
-
YSGDDALNL </td><td>      19
+
-
</td></tr><tr><td>
+
-
VGFDVAARL </td><td>      18
+
-
</td></tr><tr><td>
+
-
LRAVLEAVG </td><td>      17
+
-
</td></tr><tr><td>
+
-
LGGVTLSKA </td><td>      17
+
-
</td></tr><tr><td>
+
-
IEPDTIRAL </td><td>      17
+
-
</td></tr><tr><td>
+
-
LVVTPYYSK </td><td>      16
+
-
</td></tr><tr><td>
+
-
LSKAGLRLQ  </td><td>    16
+
-
</td></tr><tr><td>
+
-
LHSGAQIMA </td><td>      16
+
-
</td></tr><tr><td>
+
-
IMADTGLAY </td><td>      16
+
-
</td></tr><tr><td>
+
-
IAHLAAGQL  </td><td>    16
+
-
</td></tr><tr><td>
+
-
VGVKDAKAD </td><td>      15
+
-
</td></tr><tr><td>
+
-
MVTPFSGDG  </td><td>    15
+
-
</td></tr><tr><td>
+
-
LASHPNIVG </td><td>      15
+
-
</td></tr><tr><td>
+
-
FSGDGSLDT  </td><td>    14
+
-
</td></tr><tr><td>
+
-
LNLPWLAMG </td><td>      13
+
-
</td></tr><tr><td>
+
-
VGDRARVIA </td><td>      12
+
-
</td></tr><tr><td>
+
-
IAGAGTYDT </td><td>      11
+
-
</td></tr><tr><td>
+
-
FDVAARLGT </td><td>      11
+
-
</td></tr><tr><td>
+
-
IPGRSAVPI </td><td>      10
+
-
</td></tr><tr><td>
+
-
VTPYYSKPP  </td><td>    9
+
-
</td></tr><tr><td>
+
-
MSRLGGVTL </td><td>      9
+
-
</td></tr><tr><td>
+
-
LSAFGSGDI  </td><td>    9
+
-
</td></tr><tr><td>
+
-
YDTAHSIRL </td><td>      8
+
-
</td></tr><tr><td>
+
-
VTLSKAGLR </td><td>      6
+
-
</td></tr><tr><td>
+
-
MGATGFISV  </td><td>    5
+
-
</td></tr><tr><td>
+
-
LYDIPGRSA  </td><td>    5
+
-
</td></tr><tr><td>
+
-
LVDQGCDGL </td><td>      5
+
-
</td></tr><tr><td>
+
-
LAYYSGDDA </td><td>      5
+
-
</td></tr><tr><td>
+
-
VAARLGTLL </td><td>      4
+
-
</td></tr><tr><td>
+
-
LDTATAARL </td><td>      4
+
-
</td></tr><tr><td>
+
-
VTPFSGDGS  </td><td>    3
+
-
</td></tr><tr><td>
+
-
VPIEPDTIR  </td><td>    3
+
-
</td></tr><tr><td>
+
-
LLSAFGSGD  </td><td>    3
+
-
</td></tr><tr><td>
+
-
LAKACAAEG  </td><td>    3
+
-
</td></tr><tr><td>
+
-
YSKPPQRGL </td><td>      2
+
-
</td></tr><tr><td>
+
-
YDIPGRSAV </td><td>      2
+
-
</td></tr><tr><td>
+
-
VVTPYYSKP  </td><td>    2
+
-
</td></tr><tr><td>
+
-
LPQVAATPE </td><td>      2
+
-
</td></tr><tr><td>
+
-
LEAVGDRAR  </td><td>    2
+
-
</td></tr><tr><td>
+
-
LAAGQLREL  </td><td>    2
+
-
</td></tr><table>
+
-
=Alergen Protein=
 
-
Non Allergen Predicted by AlgPred Server
 
-
=Antibacterial=
 
-
=Bacterial Toxin=
 
=External Links=
=External Links=
 +
* [http://www.biohealthbase.org/mycobacterium Database] of ''Mycobacterium tuberculosis'' genome sequences and related information.
[[Category:C2D]]
[[Category:C2D]]
[[Category:Mtb Immunotation]]
[[Category:Mtb Immunotation]]

Current revision

Immunotation of Rv2753c (dihydrodipicolinate synthase)
Name
Dihydrodipicolinate Synthase
Identifiers
Swiss Prot P63945
Genbank 888289
PDB 1XXX
Chemical data
Formula C28H37ClN4O6 [1]
Mol. wt. 30,858 Da
Pharmacokinetic data
Bioavailability  ?
Solubility  ?
Isoelectric-Point 5.57

Contents

[edit] General

dapA catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate.

L-aspartate 4-semialdehyde + pyruvate = dihydrodipicolinate + 2H2O.

This protein is eesential for optimal growth of M.tb and found in the cytoplasm as predicted by the TBpred. HMMpfam found one domain PF00701 and has Helix Turn Helix secondary structure.

[edit] Protein Sequence

>Rv2753c, TB.seq 3066222:3067121 MW:30827 VTTVGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVLEAVGDR ARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRA LASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKI NIAVAPLCNAMSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR

[edit] Human Homologue Blast Result

subject ids% identity% positivesalignment length evalue
sp|Q9BXD5 28 46.33 300 3.00E-023
sp|Q86XE5 26.57 46.15 286 4.00E-022
sp|Q9UG63 26.49 37.75 151 0.45
sp|O14556 22.09 50 86 2
sp|Q7Z7B0 27.69 44.62 65 2.7

[edit] Alergen Protein

Link to Algpred
Non Allergen Predicted by AlgPred Server

[edit] Bacterial Toxin Prediction

Link to btxpred
No Hit Fountd by btxpred server.

[edit] Subcellular Location

Link to TBpred
Cyoplasmic

[edit] Antigens

No Hit Found in AntigenDB
No. Hit Found in IEDB

[edit] B cell Epitopes

[edit] BCEpred Analysis

Link to Bcepred  
Result Predicited by Bcepred

[edit] ABCpred Analysis

Link to ABCpred
Result Predicited by ABCPred

[edit] IEDB Analysis

Link to IEDB
Result Predicited by IEDB

[edit] MHC Class-I Binder

[edit] nHLAPred Analysis

Link to nHLApred
Result Predicited by nHLApred

[edit] IEDB Analysis

Link to IEDB
Result Predicted by IEDB

[edit] MHC Class-II Binder

[edit] Propred Analysis

Link to Propred
Result Predicted by Propred


[edit] NetMHC-II Analysis

Link to NetMHC-II
Result Predicted by NetMHC-II

[edit] External Links

  • Database of Mycobacterium tuberculosis genome sequences and related information.
Retrieved from "http://277988.efsst.group/drugpedia/index.php/Immunotation_of_Rv2753c_%28dihydrodipicolinate_synthase%29"