-
1
-
-
0142106373
-
How well is enzyme function conserved as a function of pairwise sequence identity?
-
Tian W., Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity?. J Mol Biol 2003, 333:863-882.
-
(2003)
J Mol Biol
, vol.333
, pp. 863-882
-
-
Tian, W.1
Skolnick, J.2
-
2
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski L.B., Golding G.B. The closest BLAST hit is often not the nearest neighbor. J Mol Evol 2001, 52:540-542.
-
(2001)
J Mol Evol
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
3
-
-
74549221383
-
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
-
Schnoes A.M., Brown S.D., Dodevski I., Babbitt P.C. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 2009, 5:e1000605.
-
(2009)
PLoS Comput Biol
, vol.5
, pp. e1000605
-
-
Schnoes, A.M.1
Brown, S.D.2
Dodevski, I.3
Babbitt, P.C.4
-
4
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy S.R. Accelerated profile HMM searches. PLoS Comput Biol 2011, 7:e1002195.
-
(2011)
PLoS Comput Biol
, vol.7
, pp. e1002195
-
-
Eddy, S.R.1
-
6
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer A.A., Aravind L., Madden T.L., Shavirin S., Spouge J.L., Wolf Y.I., Koonin E.V., Altschul S.F. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001, 29:2994-3005.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
7
-
-
84855870250
-
Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification
-
Haft D.H., Payne S.H., Selengut J.D. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. J Bacteriol 2012, 194:36-48.
-
(2012)
J Bacteriol
, vol.194
, pp. 36-48
-
-
Haft, D.H.1
Payne, S.H.2
Selengut, J.D.3
-
8
-
-
0033580929
-
Evidence for covalent attachment of diphytanylglyceryl phosphate to the cell-surface glycoprotein of Halobacterium halobium
-
Kikuchi A., Sagami H., Ogura K. Evidence for covalent attachment of diphytanylglyceryl phosphate to the cell-surface glycoprotein of Halobacterium halobium. J Biol Chem 1999, 274:18011-18016.
-
(1999)
J Biol Chem
, vol.274
, pp. 18011-18016
-
-
Kikuchi, A.1
Sagami, H.2
Ogura, K.3
-
9
-
-
33748882527
-
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic
-
Haft D.H., Paulsen I.T., Ward N., Selengut J.D. Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biol 2006, 4:29.
-
(2006)
BMC Biol
, vol.4
, pp. 29
-
-
Haft, D.H.1
Paulsen, I.T.2
Ward, N.3
Selengut, J.D.4
-
10
-
-
77958526817
-
Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria
-
Selengut J.D., Haft D.H. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. J Bacteriol 2010, 192:5788-5798.
-
(2010)
J Bacteriol
, vol.192
, pp. 5788-5798
-
-
Selengut, J.D.1
Haft, D.H.2
-
11
-
-
77952511174
-
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family
-
Haft D.H., Basu M.K., Mitchell D.A. Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. BMC Biol 2010, 8:70.
-
(2010)
BMC Biol
, vol.8
, pp. 70
-
-
Haft, D.H.1
Basu, M.K.2
Mitchell, D.A.3
-
12
-
-
13844266109
-
Genome properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
-
Haft D.H., Selengut J.D., Brinkac L.M., Zafar N., White O. Genome properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 2005, 21:293-306.
-
(2005)
Bioinformatics
, vol.21
, pp. 293-306
-
-
Haft, D.H.1
Selengut, J.D.2
Brinkac, L.M.3
Zafar, N.4
White, O.5
-
13
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek R., Begley T., Butler R.M., Choudhuri J.V., Chuang H.Y., Cohoon M., de Crecy-Lagard V., Diaz N., Disz T., Edwards R., et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33:5691-5702.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
de Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
-
14
-
-
84874253819
-
Gene ontology annotations and resources
-
Blake J.A., Dolan M., Drabkin H., Hill D.P., Li N., Sitnikov D., Bridges S., Burgess S., Buza T., McCarthy F., et al. Gene ontology annotations and resources. Nucleic Acids Res 2013, 41:D530-D535.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D530-D535
-
-
Blake, J.A.1
Dolan, M.2
Drabkin, H.3
Hill, D.P.4
Li, N.5
Sitnikov, D.6
Bridges, S.7
Burgess, S.8
Buza, T.9
McCarthy, F.10
-
15
-
-
40549120596
-
The RAST Server: rapid annotations using subsystems technology
-
Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., Edwards R.A., Formsma K., Gerdes S., Glass E.M., Kubal M., et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
Formsma, K.7
Gerdes, S.8
Glass, E.M.9
Kubal, M.10
-
16
-
-
84876134492
-
TIGRFAMs and genome properties in 2013
-
Haft D.H., Selengut J.D., Richter R.A., Harkins D., Basu M.K., Beck E. TIGRFAMs and genome properties in 2013. Nucleic Acids Res 2013, 41:D387-D395.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D387-D395
-
-
Haft, D.H.1
Selengut, J.D.2
Richter, R.A.3
Harkins, D.4
Basu, M.K.5
Beck, E.6
-
18
-
-
37249090179
-
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution
-
Kensche P.R., van Noort V., Dutilh B.E., Huynen M.A. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface 2008, 5:151-170.
-
(2008)
J R Soc Interface
, vol.5
, pp. 151-170
-
-
Kensche, P.R.1
van Noort, V.2
Dutilh, B.E.3
Huynen, M.A.4
-
19
-
-
84871199596
-
PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species
-
Fouts D.E., Brinkac L., Beck E., Inman J., Sutton G. PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species. Nucleic Acids Res 2012, 40:e172.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. e172
-
-
Fouts, D.E.1
Brinkac, L.2
Beck, E.3
Inman, J.4
Sutton, G.5
-
20
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285:751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
21
-
-
80655139177
-
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
-
Basu M.K., Selengut J.D., Haft D.H. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC Bioinformatics 2011, 12:434.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 434
-
-
Basu, M.K.1
Selengut, J.D.2
Haft, D.H.3
-
22
-
-
84876515907
-
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
-
Franceschini A., Szklarczyk D., Frankild S., Kuhn M., Simonovic M., Roth A., Lin J., Minguez P., Bork P., von Mering C., et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 2013, 41:D808-D815.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D808-D815
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
Roth, A.6
Lin, J.7
Minguez, P.8
Bork, P.9
von Mering, C.10
-
24
-
-
77956470735
-
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus
-
Rodionov D.A., Yang C., Li X., Rodionova I.A., Wang Y., Obraztsova A.Y., Zagnitko O.P., Overbeek R., Romine M.F., Reed S., et al. Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics 2010, 11:494.
-
(2010)
BMC Genomics
, vol.11
, pp. 494
-
-
Rodionov, D.A.1
Yang, C.2
Li, X.3
Rodionova, I.A.4
Wang, Y.5
Obraztsova, A.Y.6
Zagnitko, O.P.7
Overbeek, R.8
Romine, M.F.9
Reed, S.10
-
25
-
-
84891782659
-
Pfam: the protein families database
-
Finn R.D., Bateman A., Clements J., Coggill P., Eberhardt R.Y., Eddy S.R., Heger A., Hetherington K., Holm L., Mistry J., et al. Pfam: the protein families database. Nucleic Acids Res 2013, 42:D222-D230.
-
(2013)
Nucleic Acids Res
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
Bateman, A.2
Clements, J.3
Coggill, P.4
Eberhardt, R.Y.5
Eddy, S.R.6
Heger, A.7
Hetherington, K.8
Holm, L.9
Mistry, J.10
-
26
-
-
0027442464
-
Cell wall sorting signals in surface proteins of Gram-positive bacteria
-
Schneewind O., Mihaylova-Petkov D., Model P. Cell wall sorting signals in surface proteins of Gram-positive bacteria. EMBO J 1993, 12:4803-4811.
-
(1993)
EMBO J
, vol.12
, pp. 4803-4811
-
-
Schneewind, O.1
Mihaylova-Petkov, D.2
Model, P.3
-
27
-
-
0033607265
-
Purification and characterization of sortase, the transpeptidase that cleaves surface proteins of Staphylococcus aureus at the LPXTG motif
-
Ton-That H., Liu G., Mazmanian S.K., Faull K.F., Schneewind O. Purification and characterization of sortase, the transpeptidase that cleaves surface proteins of Staphylococcus aureus at the LPXTG motif. Proc Natl Acad Sci U S A 1999, 96:12424-12429.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 12424-12429
-
-
Ton-That, H.1
Liu, G.2
Mazmanian, S.K.3
Faull, K.F.4
Schneewind, O.5
-
28
-
-
79955765269
-
Proteomic analysis of the Vibrio cholerae type II secretome reveals new proteins, including three related serine proteases
-
Sikora A.E., Zielke R.A., Lawrence D.A., Andrews P.C., Sandkvist M. Proteomic analysis of the Vibrio cholerae type II secretome reveals new proteins, including three related serine proteases. J Biol Chem 2011, 286:16555-16566.
-
(2011)
J Biol Chem
, vol.286
, pp. 16555-16566
-
-
Sikora, A.E.1
Zielke, R.A.2
Lawrence, D.A.3
Andrews, P.C.4
Sandkvist, M.5
-
29
-
-
79958173211
-
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification
-
Haft D.H., Basu M.K. Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. J Bacteriol 2011, 193:2745-2755.
-
(2011)
J Bacteriol
, vol.193
, pp. 2745-2755
-
-
Haft, D.H.1
Basu, M.K.2
-
30
-
-
78651081719
-
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
-
Haft D.H. Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. BMC Genomics 2011, 12:21.
-
(2011)
BMC Genomics
, vol.12
, pp. 21
-
-
Haft, D.H.1
-
31
-
-
2142738304
-
WebLogo: a sequence logo generator
-
Crooks G.E., Hon G., Chandonia J.M., Brenner S.E. WebLogo: a sequence logo generator. Genome Res 2004, 14:1188-1190.
-
(2004)
Genome Res
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
32
-
-
84860588660
-
Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism
-
Pathak D.T., Wei X., Bucuvalas A., Haft D.H., Gerloff D.L., Wall D. Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. PLoS Genet 2012, 8:e1002626.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002626
-
-
Pathak, D.T.1
Wei, X.2
Bucuvalas, A.3
Haft, D.H.4
Gerloff, D.L.5
Wall, D.6
-
33
-
-
84879018029
-
Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein
-
Abdul Halim M.F., Pfeiffer F., Zou J., Frisch A., Haft D., Wu S., Tolic N., Brewer H., Payne S.H., Pasa-Tolic L., et al. Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein. Mol Microbiol 2013, 88:1164-1175.
-
(2013)
Mol Microbiol
, vol.88
, pp. 1164-1175
-
-
Abdul Halim, M.F.1
Pfeiffer, F.2
Zou, J.3
Frisch, A.4
Haft, D.5
Wu, S.6
Tolic, N.7
Brewer, H.8
Payne, S.H.9
Pasa-Tolic, L.10
-
34
-
-
83355168671
-
GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease
-
Haft D.H., Varghese N. GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. PLoS ONE 2011, 6:e28886.
-
(2011)
PLoS ONE
, vol.6
, pp. e28886
-
-
Haft, D.H.1
Varghese, N.2
|