Rhizobium etli CFN 42 plasmid p42a, complete sequence NC_007762 GI_Number Pathogen_associated Gene_name Product Synonym Number_of_Genera COG_Number COG_Description COG_Category 86359728 Common - putative hydrolase protein RHE_PA00023 25 COG0561 Cof, Predicted hydrolases of the HAD superfamily General function prediction only 86359707 Common intA site-specific integrase protein RHE_PA00002 47 COG4973 XerC, Site-specific recombinase XerC DNA replication, recombination, and repair 86359831 Common - hypothetical protein RHE_PA00132 9 None None None 86359716 Common - putative peptidase protein (caspase-1 like protein) RHE_PA00011 15 COG4249 COG4249, Uncharacterized protein containing caspase domain General function prediction only 86359759 Common virC2 virulence VirC2 protein RHE_PA00054 2 None None None 86359780 Nonpathogen - hypothetical protein RHE_PA00080 6 None None None 86359828 Common - hypothetical protein RHE_PA00129 55 COG1262 COG1262, Uncharacterized conserved protein Function unknown 86359811 Nonpathogen - hypothetical protein RHE_PA00111 1 None None None 86359775 Common - putative insertion sequence transposase protein, IS3 family RHE_PA00074 20 None None None 86359712 Nonpathogen - hypothetical protein RHE_PA00007 3 COG4796 HofQ, Type II secretory pathway, component HofQ Intracellular trafficking and secretion 86359850 Common - hypothetical protein RHE_PA00152 4 None None None 86359762 Nonpathogen - putative insertion sequence transposase protein RHE_PA00058 1 None None None 86359864 Nonpathogen traM conjugal transfer transcriptional regulator (repressor) protein RHE_PA00166 2 None None None 86359754 Common virB8a transport secretion system IV, VirB8 protein RHE_PA00049 19 COG3736 VirB8, Type IV secretory pathway, component VirB8 Intracellular trafficking and secretion 86359771 Common virD4 transport secretion system IV, VirD4 protein RHE_PA00070 72 COG3505 VirD4, Type IV secretory pathway, VirD4 components Intracellular trafficking and secretion 86359747 Common virA two-component sensor histidine kinase VirA protein RHE_PA00042 214 COG4191 COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system Signal transduction mechanisms 86359839 Common - probable DNA methylase RHE_PA00141 44 COG4646 COG4646, DNA methylase Transcription / DNA replication, recombination, and repair 86359821 Nonpathogen - putative insertion sequence transposase protein, IS5 family RHE_PA00122 4 None None None 86359790 Common - probable insertion sequence transposase protein, IS3/IS911 family RHE_PA00090 62 None None None 86359798 Common - probable insertion sequence transposase protein, IS66 family RHE_PA00098 67 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359867 Common trbI conjugal transfer protein I RHE_PA00169 58 COG2948 VirB10, Type IV secretory pathway, VirB10 components Intracellular trafficking and secretion 86359710 Nonpathogen - hypothetical protein RHE_PA00005 1 None None None 86359833 Common - putative insertion sequence transposase protein RHE_PA00135 40 COG3328 COG3328, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359726 Common - putative transcriptional regulator protein, AsnC/GntR family RHE_PA00021 70 COG2390 DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain Transcription 86359737 Nonpathogen - hypothetical protein RHE_PA00032 2 COG3916 LasI, N-acyl-L-homoserine lactone synthetase Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism 86359781 Common - probable insertion sequence ATP-binding protein, IS21 family RHE_PA00081 92 COG1484 DnaC, DNA replication protein DNA replication, recombination, and repair 86359714 Common - probable insertion sequence transposase protein, IS21/IS408/IS1162 family RHE_PA00009 72 COG4584 COG4584, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359852 Common - hypothetical protein RHE_PA00154 14 COG3831 COG3831, Uncharacterized conserved protein Function unknown 86359769 Common virD1 T-DNA border endonuclease, VirD1 protein RHE_PA00067 3 None None None 86359778 Common - putative insertion sequence ATP-binding protein, IS21 family RHE_PA00078 105 COG1484 DnaC, DNA replication protein DNA replication, recombination, and repair 86359875 Common trbC conjugal transfer protein C RHE_PA00177 11 COG3838 VirB2, Type IV secretory pathway, VirB2 components (pilins) Intracellular trafficking and secretion 86359735 Nonpathogen - hypothetical protein RHE_PA00030 3 COG5160 ULP1, Protease, Ulp1 family Posttranslational modification, protein turnover, chaperones 86359858 Common traF conjugal transfer protein F RHE_PA00160 34 COG4959 TraF, Type IV secretory pathway, protease TraF Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion 86359880 Common repCa1 plasmid replication protein RepCa1 RHE_PA00182 18 None None None 86359756 Common virB10a transport secretion system IV, VirB10 protein RHE_PA00051 59 COG2948 VirB10, Type IV secretory pathway, VirB10 components Intracellular trafficking and secretion 86359804 Common kupa potassium transporter protein RHE_PA00104 88 COG3158 Kup, K+ transporter Inorganic ion transport and metabolism 86359768 Common - putative insertion sequence ATP-binding protein, IS21/IS1162 family RHE_PA00066 99 COG1484 DnaC, DNA replication protein DNA replication, recombination, and repair 86359792 Common - probable insertion sequence transposase protein, IS4 family RHE_PA00092 56 COG3293 COG3293, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359745 Nonpathogen virF1 virulence VirF1 protein RHE_PA00040 1 None None None 86359818 Nonpathogen - hypothetical protein RHE_PA00119 1 None None None 86359740 Common repCa2 plasmid replication protein RepCa2 RHE_PA00035 17 None None None 86359869 Common trbG conjugal transfer protein G RHE_PA00171 44 COG3504 VirB9, Type IV secretory pathway, VirB9 components Intracellular trafficking and secretion 86359823 Common - putative insertion sequence ATP-binding protein RHE_PA00124 41 COG1961 PinR, Site-specific recombinases, DNA invertase Pin homologs DNA replication, recombination, and repair 86359824 Common - putative insertion sequence transposase protein RHE_PA00125 86 COG3547 COG3547, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359846 Common - hypothetical protein RHE_PA00148 8 None None None 86359878 Common repAa1 plasmid partitioning protein RepAa1 RHE_PA00180 213 COG1192 Soj, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 86359785 Common - hypothetical protein RHE_PA00085 5 None None None 86359767 Nonpathogen - hypothetical protein RHE_PA00064 3 None None None 86359719 Nonpathogen - hypothetical protein RHE_PA00014 2 COG0476 ThiF, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 Coenzyme metabolism 86359724 Nonpathogen - putative nucleotidyltransferase protein RHE_PA00019 3 None None None 86359755 Common virB9a transport secretion system IV, VirB9 protein RHE_PA00050 41 COG3504 VirB9, Type IV secretory pathway, VirB9 components Intracellular trafficking and secretion 86359873 Common trbE conjugal transfer protein E RHE_PA00175 59 COG3451 VirB4, Type IV secretory pathway, VirB4 components Intracellular trafficking and secretion 86359782 Common - probable insertion sequence transposase protein RHE_PA00082 24 COG2963 COG2963, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359834 Common - hypothetical protein RHE_PA00136 3 None None None 86359842 Common - hypothetical protein RHE_PA00144 8 None None None 86359856 Common traCa conjugal transfer protein C RHE_PA00158 6 None None None 86359816 Common - putative insertion sequence transposase protein, IS4 family RHE_PA00117 39 None None None 86359764 Common virE1 virulence VirE1 protein RHE_PA00060 2 None None None 86359794 Common - putative insertion sequence transposase protein RHE_PA00094 24 None None None 86359757 Common virB11a transport secretion system IV, VirB11 protein RHE_PA00052 214 COG0630 VirB11, Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis Cell motility and secretion / Intracellular trafficking and secretion 86359750 Common virB4a transport secretion system IV, VirB4 protein RHE_PA00045 56 COG3451 VirB4, Type IV secretory pathway, VirB4 components Intracellular trafficking and secretion 86359801 Common - putative insertion sequence transposase protein, IS66 family RHE_PA00101 61 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359802 Common - putative insertion sequence transposase protein RHE_PA00102 36 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359787 Common otsAa trehalose-6-phosphate synthase protein RHE_PA00087 96 COG0380 OtsA, Trehalose-6-phosphate synthase Carbohydrate transport and metabolism 86359765 Common virE2 virulence VirE2 protein RHE_PA00061 2 None None None 86359876 Common trbB conjugal transfer protein B RHE_PA00178 174 COG4962 CpaF, Flp pilus assembly protein, ATPase CpaF Intracellular trafficking and secretion 86359838 Common - hypothetical protein RHE_PA00140 8 None None None 86359871 Common trbL conjugal transfer protein L RHE_PA00173 36 COG3846 TrbL, Type IV secretory pathway, TrbL components Intracellular trafficking and secretion 86359844 Common - hypothetical protein RHE_PA00146 4 None None None 86359722 Nonpathogen - hypothetical protein RHE_PA00017 2 None None None 86359729 Common - hypothetical protein RHE_PA00024 4 COG0395 UgpE, ABC-type sugar transport system, permease component Carbohydrate transport and metabolism 86359733 Common - putative glycerol-3-phosphate dehydrogenase (NAD(P)+) protein RHE_PA00028 134 COG0240 GpsA, Glycerol-3-phosphate dehydrogenase Energy production and conversion 86359717 Nonpathogen - hypothetical protein RHE_PA00012 6 None None None 86359727 Common - putative glycerol 1-phosphate dehydrogenase protein (L-arabinose utilization protein) protein RHE_PA00022 54 COG0371 GldA, Glycerol dehydrogenase and related enzymes Energy production and conversion 86359840 Nonpathogen - hypothetical protein RHE_PA00142 1 None None None 86359814 Common - putative insertion sequence transposase protein, IS1111A/IS1328/IS1533 family RHE_PA00115 45 COG3547 COG3547, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359749 Common virB3a transport secretion system IV, VirB3 protein RHE_PA00044 12 COG3702 VirB3, Type IV secretory pathway, VirB3 components Intracellular trafficking and secretion 86359808 Common - putative insertion sequence transposase protein RHE_PA00108 44 COG3293 COG3293, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359796 Nonpathogen - hypothetical protein RHE_PA00096 1 None None None 86359836 Common - putative insertion sequence transposase protein RHE_PA00138 53 COG3547 COG3547, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359744 Common - putative insertion sequence transposase protein RHE_PA00039 19 None None None 86359862 Nonpathogen - hypothetical protein RHE_PA00164 5 COG2442 COG2442, Uncharacterized conserved protein Function unknown 86359826 Common - putative insertion sequence transposase protein RHE_PA00127 31 COG4584 COG4584, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359731 Common - probable sugar ABC transporter, ATP-binding protein RHE_PA00026 249 COG3839 MalK, ABC-type sugar transport systems, ATPase components Carbohydrate transport and metabolism 86359784 Common - putative insertion sequence transposase protein, IS66 family RHE_PA00084 67 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359752 Common virB6a transport secretion system IV, VirB6 protein RHE_PA00047 10 COG3704 VirB6, Type IV secretory pathway, VirB6 components Intracellular trafficking and secretion 86359720 Common - hypothetical protein RHE_PA00015 5 None None None 86359813 Nonpathogen - hypothetical protein RHE_PA00113 2 None None None 86359854 Common traGa conjugal transfer protein G RHE_PA00156 69 COG3505 VirD4, Type IV secretory pathway, VirD4 components Intracellular trafficking and secretion 86359805 Nonpathogen - hypothetical protein RHE_PA00105 5 None None None 86359736 Common - hypothetical protein RHE_PA00031 21 COG0630 VirB11, Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis Cell motility and secretion / Intracellular trafficking and secretion 86359806 Common - putative insertion sequence transposase protein, IS3/IS4 family RHE_PA00106 42 None None None 86359776 Nonpathogen - hypothetical protein RHE_PA00076 1 None None None 86359843 Common - hypothetical protein RHE_PA00145 8 None None None 86359770 Common virD2 T-DNA border endonuclease, VirD2 protein RHE_PA00068 13 COG3843 VirD2, Type IV secretory pathway, VirD2 components (relaxase) Intracellular trafficking and secretion 86359812 Common - hypothetical protein RHE_PA00112 26 COG5489 COG5489, Uncharacterized conserved protein Function unknown 86359748 Common virB1a transport secretion system IV, VirB1 protein RHE_PA00043 19 None None None 86359866 Common cinRa autoinducer transcriptional regulator protein RHE_PA00168 49 COG2771 CsgD, DNA-binding HTH domain-containing proteins Transcription 86359797 Common - hypothetical protein RHE_PA00097 5 None None None 86359820 Common - putative insertion sequence transposase protein RHE_PA00121 26 None None None 86359708 Common - hypothetical protein RHE_PA00003 42 COG0641 AslB, Arylsulfatase regulator (Fe-S oxidoreductase) General function prediction only 86359788 Common ocs D-lysopine dehydrogenase/D-octopine dehydrogenase protein RHE_PA00088 25 COG0240 GpsA, Glycerol-3-phosphate dehydrogenase Energy production and conversion 86359715 Nonpathogen - hypothetical protein RHE_PA00010 2 None None None 86359709 Common - hypothetical protein RHE_PA00004 12 COG0535 COG0535, Predicted Fe-S oxidoreductases General function prediction only 86359751 Common virB5a transport secretion system IV, VirB5 protein RHE_PA00046 3 None None None 86359845 Common - hypothetical protein RHE_PA00147 2 None None None 86359742 Nonpathogen - hypothetical protein RHE_PA00037 3 None None None 86359810 Common - putative antirestriction protein RHE_PA00110 44 COG4227 COG4227, Antirestriction protein DNA replication, recombination, and repair 86359819 Nonpathogen - hypothetical protein RHE_PA00120 1 None None None 86359725 Common xylBa xylulokinase protein RHE_PA00020 180 COG1070 XylB, Sugar (pentulose and hexulose) kinases Carbohydrate transport and metabolism 86359711 Nonpathogen - hypothetical protein RHE_PA00006 10 COG3904 COG3904, Predicted periplasmic protein Function unknown 86359774 Common - probable insertion sequence ATP-binding protein, IS21 family RHE_PA00073 105 COG1484 DnaC, DNA replication protein DNA replication, recombination, and repair 86359830 Nonpathogen - hypothetical protein RHE_PA00131 7 None None None 86359874 Common trbD conjugal transfer protein D RHE_PA00176 15 COG5268 TrbD, Type IV secretory pathway, TrbD component Cell motility and secretion / Intracellular trafficking and secretion 86359851 Nonpathogen - hypothetical protein RHE_PA00153 1 None None None 86359761 Common - probable insertion sequence transposase protein, IS4 family RHE_PA00056 49 COG3293 COG3293, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359718 Nonpathogen - hypothetical protein RHE_PA00013 7 None None None 86359803 Common - putative insertion sequence transposase protein RHE_PA00103 10 COG2963 COG2963, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359859 Common traB conjugal transfer protein B RHE_PA00161 6 COG0815 Lnt, Apolipoprotein N-acyltransferase Cell envelope biogenesis, outer membrane 86359753 Common virB7a transport secretion system IV, VirB7 protein RHE_PA00048 3 None None None 86359723 Nonpathogen - hypothetical protein RHE_PA00018 4 COG2159 COG2159, Predicted metal-dependent hydrolase of the TIM-barrel fold General function prediction only 86359799 Common - putative insertion sequence transposase protein RHE_PA00099 52 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359868 Common trbH conjugal transfer protein H RHE_PA00170 4 None None None 86359760 Common virC1 virulence VirC1 protein RHE_PA00055 27 COG1192 Soj, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 86359791 Common - probable insertion sequence transposase protein RHE_PA00091 130 COG2801 Tra5, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359746 Nonpathogen - hypothetical protein RHE_PA00041 1 None None None 86359848 Nonpathogen - hypothetical protein RHE_PA00150 1 None None None 86359822 Nonpathogen - hypothetical protein RHE_PA00123 1 None None None 86359861 Nonpathogen - hypothetical protein RHE_PA00163 6 COG4634 COG4634, Uncharacterized protein conserved in bacteria Function unknown 86359772 Common - probable insertion sequence transposase protein, IS4 family RHE_PA00071 22 COG3385 COG3385, FOG: Transposase and inactivated derivatives DNA replication, recombination, and repair 86359872 Common trbJ conjugal transfer protein J RHE_PA00174 38 COG5314 COG5314, Conjugal transfer/entry exclusion protein Intracellular trafficking and secretion 86359789 Nonpathogen - hypothetical protein RHE_PA00089 1 None None None 86359738 Common repAa2 plasmid partitioning protein RepAa2 RHE_PA00033 204 COG1192 Soj, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 86359713 Common - probable insertion sequence ATP-binding protein, IS21 family RHE_PA00008 99 COG1484 DnaC, DNA replication protein DNA replication, recombination, and repair 86359777 Nonpathogen - hypothetical protein RHE_PA00077 10 None None None 86359853 Common - putative nuclease protein RHE_PA00155 11 COG1525 COG1525, Micrococcal nuclease (thermonuclease) homologs DNA replication, recombination, and repair 86359860 Common traH conjugal transfer protein H RHE_PA00162 3 None None None 86359743 Common - probable insertion sequence transposase protein RHE_PA00038 37 COG1961 PinR, Site-specific recombinases, DNA invertase Pin homologs DNA replication, recombination, and repair 86359835 Common - putative insertion sequence transposase protein RHE_PA00137 22 None None None 86359793 Common - probable insertion sequence transposase protein, mutator family RHE_PA00093 84 COG3328 COG3328, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359817 Common - putative insertion sequence transposase protein RHE_PA00118 56 COG3328 COG3328, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359739 Common repBa2 plasmid partitioning protein RepBa2 RHE_PA00034 73 COG1475 Spo0J, Predicted transcriptional regulators Transcription 86359783 Common - probable insertion sequence transposase protein RHE_PA00083 52 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359863 Common - putative transcriptional regulator protein RHE_PA00165 43 COG1476 COG1476, Predicted transcriptional regulators Transcription 86359758 Common virG two-component response regulator VirG protein RHE_PA00053 207 COG0745 OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain Signal transduction mechanisms / Transcription 86359857 Common traAa conjugal transfer protein A RHE_PA00159 101 COG0507 RecD, ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member DNA replication, recombination, and repair 86359832 Common - hypothetical protein RHE_PA00133 4 None None None 86359732 Common - short chain dehydrogenase RHE_PA00027 232 COG3347 COG3347, Uncharacterized conserved protein Function unknown 86359809 Common virF2 virulence VirF2 protein RHE_PA00109 2 None None None 86359800 Common - putative insertion sequence transposase protein RHE_PA00100 24 COG2963 COG2963, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359827 Common virB2a transport secretion system IV, VirB2 protein RHE_PA00128 9 COG3838 VirB2, Type IV secretory pathway, VirB2 components (pilins) Intracellular trafficking and secretion 86359779 Common - putative insertion sequence transposase protein RHE_PA00079 83 COG4584 COG4584, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359870 Common trbF conjugal transfer protein F RHE_PA00172 33 COG3701 TrbF, Type IV secretory pathway, TrbF components Intracellular trafficking and secretion 86359879 Common repBa1 plasmid partitioning protein RepBa1 RHE_PA00181 89 COG1475 Spo0J, Predicted transcriptional regulators Transcription 86359730 Common - probable oxidoreductase protein, short-chain dehydrogenase-reductase family RHE_PA00025 236 COG4221 COG4221, Short-chain alcohol dehydrogenase of unknown specificity General function prediction only 86359766 Common virE3 virulence VirE3 protein RHE_PA00062 2 None None None 86359849 Common - hypothetical protein RHE_PA00151 26 COG5489 COG5489, Uncharacterized conserved protein Function unknown 86359825 Common - putative insertion sequence transposase protein RHE_PA00126 61 None None None 86359721 Nonpathogen - hypothetical protein RHE_PA00016 3 None None None 86359807 Common - putative insertion sequence transposase protein RHE_PA00107 34 COG3328 COG3328, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359795 Common - putative insertion sequence transposase protein RHE_PA00095 22 None None None 86359865 Common traR conjugal transfer transcriptional regulator protein, LuxR family RHE_PA00167 44 COG2771 CsgD, DNA-binding HTH domain-containing proteins Transcription 86359763 Common - probable insertion sequence transposase protein RHE_PA00059 17 COG3415 COG3415, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359773 Common - probable insertion sequence ATP-binding protein RHE_PA00072 83 COG4584 COG4584, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359815 Common - hypothetical protein RHE_PA00116 5 None None None 86359837 Common - hypothetical protein RHE_PA00139 10 None None None 86359829 Nonpathogen - hypothetical protein RHE_PA00130 1 None None None 86359741 Nonpathogen - hypothetical protein RHE_PA00036 1 None None None 86359855 Common traDa conjugal transfer protein D RHE_PA00157 10 None None None 86359841 Common - probable chromosome partitioning protein RHE_PA00143 162 COG1475 Spo0J, Predicted transcriptional regulators Transcription 86359786 Common - probable insertion sequence transposase protein, IS4 family RHE_PA00086 55 COG3293 COG3293, Transposase and inactivated derivatives DNA replication, recombination, and repair 86359877 Common traIa autoinducer synthesis protein I RHE_PA00179 28 COG3916 LasI, N-acyl-L-homoserine lactone synthetase Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism 86359706 Common - hypothetical protein RHE_PA00001 3 None None None 86359847 Common ardCa conjugal transfer antirestriction protein RHE_PA00149 48 COG4227 COG4227, Antirestriction protein DNA replication, recombination, and repair 86359734 Common - putative glycerol-3-phosphate dehydrogenase protein RHE_PA00029 93 COG0578 GlpA, Glycerol-3-phosphate dehydrogenase Energy production and conversion