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Research Article
ISSN: 0974-6943
Functional Categorization
The hypothetical proteins possessing enzyme domains as per domain searching programs were categorized in percent confidence levels using following parameters:1. Four tools indicate the same enzyme functions then confidence
level set as 100 percent.
Journal of Pharmacy Research Vol.9 Issue 3.March 2015
182-189
*Corresponding author.
D G Gore
Sai Bioinfosys Institute of Bioinformatics Research,
Plot No. 271 Raghuji Nagar,
Nagpur (Maharashtra), India.440009
PFAM
CDDBLAST
Mb0021
Mb0062
Mb0065
Mb0076
Mb0083
Mb0101
Mb0103
Mb0105
Mb0107
Mb0114
Mb0120
Mb0126
Mb0132
Mb0143
Mb0146
Mb0147
Mb0150
Mb0151
Mb0168
Nitronate monooxygenase
2-Nitropropane dioxygenase
glycohydro6
glycohydro6
PIN
PIN
amidohydro1
met dependent hydro A
pyridox ox2
Pyridox ox2
FcoT
FcoT-like thioesterase domain
Phosphopantetheine
PP-binding
Cytochrome c oxidase
Cytochrome c oxidase
Cyclic nucleotide binding
glycerate dehydrogenases
Rhomboid
Rhomboid
L,D-transpeptidase
L,D-transpeptidase
Pyridox_oxidase
PPOX
Phosphotransferasr
Ble
Snoal like
SnoaL
Snoal like
Ketosteroid isomerase
NO
3-methyladenine DNA glycosylase
Leucine carboxyl methyltransferase O-Methyltransferase
Leucine carboxyl methyltransferase methyltransferase
Thioesterase
Thioesterase
Mb0169
Mb0173
Mb0174
Mb0187
Mb0191
Mb0196
Mb0197
Mb0222
Mb0227
Mb0230
Mb0234
Mb0247
Mb0269
Mb0270
Streptomyces cyclase
Permease
Permease
Pirin
NO
Major facilitator
L,D-transpeptidas
Thioesterase superfamily
O-acyltransferase,
Glyco tran
PIN
Maoc
Allophanate hydrolase
Allophanate hydrolase
DNA primase
Anhydrolase
lyoxalase
Leucine carboxyl methyltransferase
nucleoside triphosphate hydrolase
nucleoside triphosphate hydrolase
Ribbon helix protein
PIN
Phosphatidic acid phosphatase
LD transpeptidase catalytic
NO
no
Zinc permease
putative decaetylase LMBE
methyltransferase
methyltransferase
HTH Type,Tetr-N
Polyketide_cyc
Srpbcc domain
Permease
Ttg
Permease
Ttg2B
Pirin
Pirin
NO
putative metallohydrolase
Major Facilitator
Arabinose efflux permease
LD transpeptidase
L,D-transpeptidase
NO
FkbR
WES_acyltransf
acyltransf
Glyco_trans_
Glycosyltransferas
PIN
PIN Mrv
MaoC_dehydratas
Maoc dehydrates
Allophanate hydrolase
Allophanate hydrolase
Allophanate hydrolase
Allophanate hydrolase
DNA_primase
Ligd
Anhydrolas
Anhydrolase
Glyoxalase
Sphingobium chlorophenolicum
PE
PE
Leucine carboxyl methyltransferase o methyltransferase
FtsK
FtsK
Abhydrolase
Abbhydrolase6
RHH1
PHA
PIN
PIN
PAP2
PAP2
LD transpeptidase catalytic
NO
Snoal like
snoal like
NO
NO
NO
NO
PIGL-L
PIG
methyltransferase
AT4G
methyltransferase
Adomet-Mtases
Mb0278
Mb0280
Mb0285
Mb0289
Mb0292
Mb0301
Mb0308
Mb0309
Mb0315
Mb0316
Mb0318
Mb0322
Mb0328
Mb0331
Mb0333
Mb0336
CATH
NO
75
NO
75
smg6
100
no
75
NO
75
NO
75
NO
75
NO
75
Adenosylhomocysteinase
100
Rhomboid
100
Erfk Family like
75
FMN binding protein
100
NO
50
Steroid Delta-isomerase
100
NO
75
N-glycosylase/DNA lyase
75
Putative S-adenosyl-L-methionine100
Putative S-adenosyl-L-methionine
100
1,4-dihydroxy-2-naphthoyl100
CoA hydrolase
NO
75
NO
50
NO
50
Quercetin 2,3-dioxygenase
100
NO
25
Sugar efflux transporter B
25
ErfK
100
ribosomal
75
NO
75
NO
75
NO
75
Nodulation like
100
NO
75
NO
75
NO
50
Anhydrolase
100
4 hydroxyphenylpyruvate dioxygenase 100
NO
25
Putative S-adenosyl-L-methionine
100
FtsK
25
NO
50
NO
25
SMG6 PROTEIN
75
Lipid phosphatidic phosphatase
50
NO
25
Bile acid 7 alpha dehydratase
75
NO
25
NO
25
1D Myo-inositol
50
AT4G
50
NO
75
182-189
PFAM
CDDBLAST
MDMPIC
DinB2
Snoal like
snoal like
NO
NO
MobA-like NTP transferase domain Glycosyltransferase family
NO
NO
NO
NO
Peptidase family
Peptidase
NO
Glyco_tranf_GTA_
Glycosyl hydrolase
Predicted glycosyl hydrolase
Zeta toxin
AAA domain
VWA
vWFA
NTP transferase
glycosyltransferase
XdhC and CoxI
XdhC Rossmann
XdhC and CoxI
XdhC and CoxI
NO
Proline-rich
oxidoreductase
reductase
Rhodanese
Rhodanese Homolog
NO
HNH endonuclease
NO
NO
Mycobacterium membrane
Mycobacterium membrane protein
Alpha/beta hydrolase
Alpha/beta hydrolase
NO
NO
NO
NO
Lon protease
Lon protease
NO
NO
Rska
rskA
Rhodanese Homolog
Rhodanese Homolog
Abhydrolase_
Abhydrolase_
GDSL-like Lipase/
SGNH_hydrolase
RDD
RDD
NO
SIS
thioredoxin
thioredoxin
diphosphate synthase
undecaprenyl diphosphate synthase
PemK
MazF
Carboxylesterase
Carboxylesterase
Carboxylesterase
Esterases and lipases
NO
YbjN
PIN
PIN
Adenylate& Guanylate
Adenylate & Guanylate
cyclase catalyti
cyclase
NO
acyltransferase
Isoprenylcysteine
methyltransferase
carboxyl methyltransfe
S-adenosylmethionine
SAM methyltransferase
-dependent methyltransferase
HNH nucleases;
HNH nucleases;
Pyridoxamine 5'-phosphate oxidase PPOX
HhH-GPD
HhH-GPD
NO
alpha/beta subunit
Helicase superfamily
Helicase
c-terminal domain
Alpha/beta hydrolase
Alpha/beta hydrolase
hydrolase
Putative lysophospholipase;
Abhydrolase
Abhydrolase
AAA16
AAA16
Lysine_decarbox
TIGR
CATH
NO
50
NO
50
NO
25
NO
50
NO
25
NO
25
NO
50
NO
50
NO
75
putativ
50
collagen aipha3
25
NO
75
NO
75
NO
50
NO
25
reductase
100
Calcium sensing receptor,
75
NO
25
NO
25
NO
50
embryogenic ass.
75
NO
25
NO
25
NO
50
NO
25
NO
25
tRNA sulfurtransferase
100
NO
75
Conserved exported
75
RDD
100
NO
25
Spermatogenesis
75
Undecaprenyl pyrophosphate synthase 100
25
NO
75
NO
75
NO
25
PIN
100
Adenylate cyclas
100
NO
NO
MPBQ/MSBQ methyltransferas
100
NO
FMN-binding protein
N-glycosylase/DNA lyase
NO
ATP-dependent DNA
helicase uvsW
Haloalkane dehalogenase
NO
Put ative uncharacterized protein
ATP-dependent protease
Cytokinin riboside
5'-monophosphate
75
100
100
25
100
Lysine_decarbox
TIGR
Cytokinin riboside
5'-monophosphate
Xaa-Pro dipeptidyl-peptidas
Phospholipid methyltransferase
NO
Transglycosylase
PIN
Uracil-DNA glycosylase
FAD binding domain
NO
Peptidase_
Calcineurin-like phosphoesterase
AAA domain
Carbonic anhydrase
LysM domain
Xaa-Pro dipeptidyl-peptidas
methyltransferase
PRK
Transglycosylase
PIN
Uracil-DNA glycosylase
hydroxylase
NO
Peptidase_
DNA repair exonuclease
AAA domain
Carbonic anhydrases (CA
hydrolase
Xaa-Pro dipeptidyl-peptidas
NO
NO
Transglycosylase
PIN
Uracil-DNA glycosylase
NO
NO
NO
NO
NO
NO
NO
25
75
100
75
75
50
75
75
100
75
25
100
100
100
75
25
75
75
75
75
50
182-189
PFAM
CDDBLAST
Modification methylase
Methyltransferase domain
SAM methyltransferases
HemK (IPR004556)
NO
Telomere recombination
tRNA threonylcarbamoyl adenosine
ATP synthase protein I (IPR005598)
ATP synthase I chain
NO
Transposase
Transposase
Transposase
Transposase
Helix-turn-helix domain of
transposase
transposase family ISL3
ATP:cob(I)alamin adenosyltransferase
Cobalamin adenosyltransferase
cob(I)alamin adenosyltransferase
Mb1355
Mb1357
NO
Glyoxalase/
Bleomycin resistance protein
Mb1369
NO
Prokaryotic homologs
of the JAB domain
isopeptidase activity
Mb1372
Rhomboid family
Rhomboid family
Mb1374
Beta-lactamase-like
Mb1382
Acyl-CoA N-acyltransferase
Mb1392
Diguanylate phosphodiesterase
EAL domain
EAL domain
Mb1399
Protein phosphatase
2C (PP2C)-like domain
PAS fold
Sulphate Transporter
and Anti-Sigma factor
Mb1401
RelA/SpoT
Region found in
RelA / SpoT proteins
NT_Rel-Spo_like[cd05399],
Nucleotidyltransferase (NT)
domain of RelA- and SpoT-like pp
Gpp synthetases and hydrolases
Mb1402
Beta-lactamase/transpeptidase-like
Beta-lactamase
Beta-lactamase
Mb1405
Mb1406
Mb1413
Mb1432
HNH nucleases
VapC family
NO
PIN domain
HNH nucleases
PIN domain of ribonucleases
Mb1433
Ribbon-helix-helix
Mb1448
Alanine racemase,
N-terminal domain
Mb1449
Mb1456
Mb1457
NO
MethylmalonylCoA epimerase
Beta-lactamase superfamily
Metal-dependent
domain
hydrolase
Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain
Ribbon-helix-helix
protein, copG family
Alanine racemase,
N-terminal domain
Ribbon-helix
-helix protein
Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes,
Low Specificity D-Threonine
Aldolase-like
Putative serine dehydratase domain Predicted amino acid aldolase or racemase
P-loop ATPase protein family
P-loop ATPase protein family
CATH
NO
75
NO
NO
NO
NO
50
50
75
75
cob(I)alamin
adenosyltransferase
NO
4-hydroxyphenylpyruvate
dioxygenase -like
domain 1/2
COP9 signalosome
complex subunit 5
-like domain
Rhomboid protein 2
-like domain
Hydroxyacylglutathione
hydrolases-like domain
Mycothiol
acetyltransferase -like
domain 1/2/3
Signaling protein
ykoW -like domain
Phosphoserine
phosphatase rsbP
-like domain
GTP pyrophosphokinase
-like domain
100
Glutaminase
-like domain
NO
Chalcone synthase
-like domain 1
NO
SMG6 protein
-like domain
Nickel-responsive
regulator -like domain
Alanine racemase
-like domain
100
Uncharacterised protein
family UPF0052
proteins similar to
B.subtilis YvcK
Mb1460
Acyltransferase, WS/DGAT/MGAT
Mb1463
Phospholipid/glycerol acyltransferase
Mb1468
L,D-transpeptidase
catalytic domain
L,D-transpeptidase
catalytic domain
Mb1474
SnoaL-like domain
Mb1478
Polyketide cyclase/dehydrase
Polyketide cyclase /
dehydrase and lipid
Mb1517
Mb1523
NO
75
100
100
100
25
100
100
75
100
50
50
25
100
NO
UPF0042 nucleotidebinding protein CMS1991
-like domain
2-phospho-L
-lactate transferase
-like domain
NO
LPPG:FO 2-phospho
-L-lactate transferase
CofD/UPF0052
Mb1458 Sporulation regulator WhiA
NfeD-like C-terminal,
partner-binding
25
100
Nodulation efficiency
protein D family protein
-like domain
75
75
50
75
75
75
100
75
75
100
75
182-189
Mb1558
Mb1560
Mb1567
Mb1573
Mb1584
Mb1587
Mb1592
Mb1598
Mb1613
Mb1618
Mb1619
Mb1623
Mb1624
Mb1645
Mb1658
Mb1663
Mb1666
Mb1674
Mb1700
Mb1703
Mb1707
Mb1719
Mb1723
Mb1726
Mb1728
Mb1744
Mb1745
Mb1746
Mb1749
PFAM
CDDBLAST
CATH
75
100
100
75
100
100
75
75
75
75
75
25
100
75
50
50
75
75
75
50
25
50
100
100
100
75
100
50
50
100
100
50
100
100
25
100
182-189
PFAM
Mb1754
HxlR-like helixturn-helix
HxlR-like helix-turn-helix
Mb1756
Conserved hypothetical
protein CHP03083,
actinobacterial-type
Leucine carboxyl
methyltransferase
Mycothiol maleylpyruvate
isomerase N-ter
Mb1758
Mb1761
Thioredoxin-like fold
Mb1763
Mb1770
Mb1780
Mb1781
Chloramphenicol acetyltransferase
-like domain
PIN domain-like
Aromatic-ring hydroxylase-like
NO
Mb1785
Mb1791
Mb1794
Mb1796
AhpD-like
Mb1798
PLP-binding barrel
Mb1799
Mb1812
Mb1822
Mb1823
Mb1826
CbxX/CfqX
FtsK/SpoIIIE family
EspG family
WXG100 protein secretion
system (Wss), p
ATPase
Mb1838
Mb1845
PPE family
Trypsin-like cysteine/
serine peptidase domain
Succinate dehydrogenase/fumarate
reductase flavoprotein,
catalytic domain
Thiamine pyrophosphate enzyme,
N-terminal TPP-binding domain
Mb1848
Mb1851
AhpC/TSA family
2-oxoacid dehydrogenases
acyltransferase
NO
FAD binding domain
NO
Carboxymuconolactone
decarboxylase
Alanine racemase, N-terminal
domain
CDDBLAST
O-Methyltransferase involved in
polyketide biosynthesis [Secondary
metabolites biosynthesis, ...
Peroxiredoxin (PRX)-like 1 family
NO
25
Putative S-adenosyl-L-methionine
-dependent -like domain
100
Glutathione peroxidase
-like domain
Dihydrolipoyllysine-residue
succinyltransferase -like domain
NO
NO
Inositol 2-dehydrogenase -like domain
2-oxoacid dehydrogenases
acyltransferase (catalytic domain)
PIN (PilT N terminus) domain
NAD(P)-binding Rossmann-like domain
Predicted dehydrogenases and related
proteins [General function prediction only]
Glycosyltransferase
NO
acyltransferase domain
NO
HNH endonuclease
NO
gamma-carboxymuconolactone
decarboxylase
Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes Similar
to D-Serine Dehydratase and
Zinc peptidases M18, M20,
M28, and M42
FtsK/SpoIIIE family
EspG family
type VII secretion integral membrane
protein EccD
The AAA+ (ATPases
100
100
50
75
50
75
75
75
NO
50
100
100
75
75
75
100
100
1-deoxy-D-xylulose-5-phosphate
synthase -like domain 1/2/3
100
NO
Xaa-Pro dipeptidyl-peptidase
-like domain
Mediator of RNA polymerase II
transcription -like domain
75
100
100
100
100
1,4-dihydroxy-2-naphthoyl-CoA
hydrolase -like domain
NO
Putative uncharacterized
protein -like domain 2
NO
NO
NO
FMN-binding protein -like domain
100
Thiamine pyrophosphate
enzyme, N-termina
Mb1867
Mb1872
CBS domain
CBS domain
Mb1873
Mb1876
CBS domain
Peptidase family M48
CBS domain
Peptidase family M48
Mb1878
Thioesterase-like superfamily
Thioesterase-like superfamily
Mb1894
Mb1897
Bifunctional nuclease
X-Pro dipeptidyl-peptidase
(S15 family)
Bacterial extracellular
solute-binding p
Mb1921
Mb1922
Mb1927
Mb1931
Mb1915
100
PPE family
NO
Bifunctional nuclease
CocE/NonD hydrolase
Mb1911
HTH-type transcriptional
regulator yodB -like domain
PPE family
NO
Mb1860
Mb1866
Mb1899
Mb1901
Mb1902
Mb1906
CATH
75
50
25
75
100
75
50
25
100
NO
75
NO
75
Putative S-adenosyl-L
-methionine-dependent -like domain
Putative S-adenosyl-Lmethionine-dependent -like domain
NO
Putative S-adenosyl-L-
100
100
75
100
182-189
PFAM
Mb1948
Beta-lactamase-like
Mb1954
Polyketide cyclase/dehydrase
Mb1955
Mb1965
Mb1980
Mb1988
HNH nucleases
PIN domain-like
HNH nucleases
NO
Mb1997
Mb2000
VapC family
S-adenosyl-L-methioninedependent methyltransferase-like
VapC family
PIN domain
Methyltransferase domain
Mb2021
Pyruvate/Phosphoenolpyruvate
kinase-like domain
Phosphoenolpyruvate
phosphomutase
Mb2022
Mb2024
Mb2004
Mb2026
Mb2027
Mb2031
Mb2033
Mb2038
Mb2043
Mb2049
Mb2055
Metallo-beta-lactamase
superfamily
Polyketide cyclase / dehydrase
and lipid
PIN domain
Acyl-ACP thioesterase
[Lipid metabolism]
Methyltransferase domain
AAA domain
AAA domain
PIN domain
HNH nucleases
NO
Restriction endonuclease
Erythromycin esterase
CDDBLAST
CATH
Zn-dependent hydrolases,
including glyoxylases
Pyrabactin resistance 1 (PYR1), PYR1like (PYL), regulatory component
of abscisic acid ...
Lysophospholipid Acyltransferases (LPLATs)
of Glycerophospholipid Biosynthesis
Type 1 glutamine amidotransferase
(GATase1)-like domain
HNH nucleases
Predicted nucleic acid-binding protein,
contains PIN domain
PIN (PilT N terminus) domain
S-adenosyl-L-methionine-dependent
methyltransferase-like
PIN domain of the VapC-like UPF0110
protein Mb0640 and homologs
Members of the ICL/PEPM enzyme family.
catalyze either P-C or C-C
bond formation/cleavage.
Amino acid transporters
Acyl-ACP thioesterase
[Lipid metabolism]
S-adenosylmethionine-dependent
methyltransferases
Predicted kinase
Predicted ATPase (AAA+ superfamily)
PIN domain of the Rv0301 toxin
HNH nucleases
Predicted helicase
DEAD-like helicases superfamily
Erythromycin esterase
CONCLUSION
The Bioinformatics based study of protein data available for the M.
bovis has given the opportunity to elucidate enzyme functions in the
hypothetical proteins for linking them to particular metabolic pathway. Study aimed at enzyme function linking in the 468 hypothetical
proteins screened of M. bovis out of those, 347 hypothetical proteins
computationally predicted to harbor enzymatic domains. In those,
254 proteins having confidence limit not less than 50% which represented some better existence probability of them. The functionality
finding in all available hypothetical proteins of M. bovis will remain
the first priority in the future due to its pathogenicity.6 Similar studies
with different bacteria successfully reported the probability of enzyme coding ability of hypothetical proteins in Shigella flexneri,
Bacillus anthracis, H. influenzae and Helicobacter pylori.14 -17 Study
concluded that, available domain search tools linked with rich protein
databases information, proved to be beneficial and filtered out some
of the important enzyme coding proteins out of hypothetical pool of
M. bovis and in future it may assist in relational linking of todays
hypothetical protein in tomorrows functional proteins probably by
involving gene cloning, microarray and marker based experiments.
REFERENCES
1. Lagrange PH, Hurtrel B, and Stach JL, Vaccines against
2.
3.
4.
5.
6.
7.
8.
%
100
100
100
75
75
50
NO
High-molecular-weight
protein 2 -like domain
NO
75
100
100
NO
Ribosomal RNA-processing
protein 8 -like domain
NO
Origin recognition complex
protein 5 -like domain
SMG6 protein -like domain
NO
NO
NO
NO
75
50
75
100
75
100
100
75
25
75
75
182-189
10.
11.
12.
13.
14.
15.
16.
17.
182-189