Desulfovibrio vulgaris subsp. vulgaris DP4 plasmid pDVUL01, complete sequence NC_008741 GI_Number Pathogen_associated Gene_name Product Synonym Number_of_Genera COG_Number COG_Description COG_Category 120586937 Common - protein of unknown function DUF214 Dvul_3083 61 COG0577 SalY, ABC-type antimicrobial peptide transport system, permease component Defense mechanisms 120586930 Nonpathogen - hypothetical protein Dvul_3076 1 None None None 120586957 Nonpathogen - UspA domain protein Dvul_3103 5 COG0589 UspA, Universal stress protein UspA and related nucleotide-binding proteins Signal transduction mechanisms 120586866 Common - sigma54 specific transcriptional regulator, Fis family Dvul_3012 168 COG3829 RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains Transcription / Signal transduction mechanisms 120586885 Common - ABC-2 type transporter Dvul_3031 106 COG1682 TagG, ABC-type polysaccharide/polyol phosphate export systems, permease component Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane 120586950 Common - nitrogenase MoFe cofactor biosynthesis protein NifE Dvul_3096 52 COG2710 NifD, Nitrogenase molybdenum-iron protein, alpha and beta chains Energy production and conversion 120586943 Common - pyruvate carboxyltransferase Dvul_3089 169 COG0119 LeuA, Isopropylmalate/homocitrate/citramalate synthases Amino acid transport and metabolism 120586822 Common - outer membrane autotransporter barrel domain Dvul_2968 28 None None None 120586919 Common - hypothetical protein Dvul_3065 25 COG5653 COG5653, Protein involved in cellulose biosynthesis (CelD) Cell envelope biogenesis, outer membrane 120586926 Common - sugar transferase Dvul_3072 181 COG2148 WcaJ, Sugar transferases involved in lipopolysaccharide synthesis Cell envelope biogenesis, outer membrane 120586903 Nonpathogen - hypothetical protein Dvul_3049 1 COG1835 COG1835, Predicted acyltransferases Lipid metabolism 120586867 Nonpathogen - hypothetical protein Dvul_3013 1 None None None 120586844 Common - hypothetical protein Dvul_2990 2 COG3007 COG3007, Uncharacterized paraquat-inducible protein B Function unknown 120586814 Common - extracellular solute-binding protein, family 3 Dvul_2960 43 COG0834 HisJ, ABC-type amino acid transport/signal transduction systems, periplasmic component/domain Amino acid transport and metabolism / Signal transduction mechanisms 120586848 Nonpathogen - type III secretion system needle protein Dvul_2994 1 None None None 120586875 Common - hypothetical protein Dvul_3021 16 COG2984 COG2984, ABC-type uncharacterized transport system, periplasmic component General function prediction only 120586832 Common - metal dependent phosphohydrolase Dvul_2978 70 COG1203 COG1203, Predicted helicases General function prediction only 120586952 Common - Radical SAM domain protein Dvul_3098 61 COG0535 COG0535, Predicted Fe-S oxidoreductases General function prediction only 120586895 Common - hypothetical protein Dvul_3041 32 COG3274 COG3274, Uncharacterized protein conserved in bacteria Function unknown 120586855 Common - type III secretion low calcium response chaperone LcrH/SycD Dvul_3001 13 COG1729 COG1729, Uncharacterized protein conserved in bacteria Function unknown 120586915 Common - O-antigen polymerase Dvul_3061 8 COG3307 RfaL, Lipid A core - O-antigen ligase and related enzymes Cell envelope biogenesis, outer membrane 120586891 Common - glycosyl transferase, family 2 Dvul_3037 189 COG0463 WcaA, Glycosyltransferases involved in cell wall biogenesis Cell envelope biogenesis, outer membrane 120586955 Nonpathogen - hypothetical protein Dvul_3101 1 None None None 120586912 Common - glycosyl transferase, group 1 Dvul_3058 220 COG0438 RfaG, Glycosyltransferase Cell envelope biogenesis, outer membrane 120586924 Common - lipopolysaccharide biosynthesis Dvul_3070 64 COG3206 GumC, Uncharacterized protein involved in exopolysaccharide biosynthesis Cell envelope biogenesis, outer membrane 120586910 Common - transferase hexapeptide repeat containing protein Dvul_3056 27 COG0110 WbbJ, Acetyltransferase (isoleucine patch superfamily) General function prediction only 120586820 Common - transcriptional regulator, NifA, Fis Family Dvul_2966 176 COG3604 FhlA, Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains Transcription / Signal transduction mechanisms 120586836 Common - putative anti-sigma regulatory factor, serine/threonine protein kinase Dvul_2982 28 COG2172 RsbW, Anti-sigma regulatory factor (Ser/Thr protein kinase) Signal transduction mechanisms 120586888 Nonpathogen - sulfotransferase family protein Dvul_3034 6 None None None 120586818 Nonpathogen - Tir chaperone family protein Dvul_2964 1 None None None 120586829 Common - CRISPR-associated protein, Csd2 family Dvul_2975 55 COG3649 COG3649, Uncharacterized protein predicted to be involved in DNA repair DNA replication, recombination, and repair 120586816 Common - major facilitator superfamily MFS_1 Dvul_2962 7 COG2814 AraJ, Arabinose efflux permease Carbohydrate transport and metabolism 120586846 Nonpathogen - hypothetical protein Dvul_2992 1 None None None 120586905 Common - glycosyl hydrolase, BNR repeat-containing protein Dvul_3051 44 None None None 120586917 Common - glycosyl transferase, family 2 Dvul_3063 116 COG1215 COG1215, Glycosyltransferases, probably involved in cell wall biogenesis Cell envelope biogenesis, outer membrane 120586841 Nonpathogen - type III secretion YscO fmaily protein Dvul_2987 1 None None None 120586941 Nonpathogen - hypothetical protein Dvul_3087 3 None None None 120586873 Common - protein of unknown function DUF554 Dvul_3019 37 COG1811 COG1811, Uncharacterized membrane protein, possible Na+ channel or pump General function prediction only 120586830 Common - CRISPR-associated protein, Csd1 family Dvul_2976 31 None None None 120586869 Common - Glycerol-1-phosphate dehydrogenase (NAD(P)(+)) Dvul_3015 87 COG0371 GldA, Glycerol dehydrogenase and related enzymes Energy production and conversion 120586898 Common - hypothetical protein Dvul_3044 64 COG1541 PaaK, Coenzyme F390 synthetase Coenzyme metabolism 120586839 Common - type III secretion system apparatus protein YscQ/HrcQ Dvul_2985 14 COG1886 FliN, Flagellar motor switch/type III secretory pathway protein Cell motility and secretion / Intracellular trafficking and secretion 120586860 Common - NA protein Dvul_3006 2 None None None 120586826 Common - CRISPR-associated protein Cas2 Dvul_2972 45 COG1343 COG1343, Uncharacterized protein predicted to be involved in DNA repair DNA replication, recombination, and repair 120586838 Common - type III secretion system protein Dvul_2984 128 COG4790 EscR, Type III secretory pathway, component EscR Intracellular trafficking and secretion 120586880 Nonpathogen - hypothetical protein Dvul_3026 1 None None None 120586913 Common - glycosyl transferase, group 1 Dvul_3059 42 COG0438 RfaG, Glycosyltransferase Cell envelope biogenesis, outer membrane 120586931 Nonpathogen - hypothetical protein Dvul_3077 1 None None None 120586942 Nonpathogen - hypothetical protein Dvul_3088 1 None None None 120586949 Common - ferredoxin, 2fe-2s Dvul_3095 43 COG3411 COG3411, Ferredoxin Energy production and conversion 120586953 Common - hypothetical protein Dvul_3099 11 None None None 120586862 Common - type III secretion protein, HrcV family Dvul_3008 127 COG4789 EscV, Type III secretory pathway, component EscV Intracellular trafficking and secretion 120586889 Common - asparagine synthase (glutamine-hydrolyzing) Dvul_3035 166 COG0367 AsnB, Asparagine synthase (glutamine-hydrolyzing) Amino acid transport and metabolism 120586833 Nonpathogen - hypothetical protein Dvul_2979 1 None None None 120586817 Common - hypothetical protein Dvul_2963 8 COG2984 COG2984, ABC-type uncharacterized transport system, periplasmic component General function prediction only 120586871 Nonpathogen - hypothetical protein Dvul_3017 1 None None None 120586852 Nonpathogen - Tir chaperone family protein Dvul_2998 1 None None None 120586863 Common - type III secretion protein, HrpO family Dvul_3009 115 COG4794 EscS, Type III secretory pathway, component EscS Intracellular trafficking and secretion 120586810 Common - Cobyrinic acid a,c-diamide synthase Dvul_2956 220 COG1192 Soj, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 120586882 Common - glycosyl transferase, family 2 Dvul_3028 209 COG0438 RfaG, Glycosyltransferase Cell envelope biogenesis, outer membrane 120586945 Common - nitrogen regulatory protein P-II Dvul_3091 183 COG0347 GlnK, Nitrogen regulatory protein PII Amino acid transport and metabolism 120586824 Common - two component transcriptional regulator, LuxR family Dvul_2970 169 COG2197 CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain Signal transduction mechanisms / Transcription 120586894 Nonpathogen - hypothetical protein Dvul_3040 1 COG1807 ArnT, 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family Cell envelope biogenesis, outer membrane 120586935 Nonpathogen - hypothetical protein Dvul_3081 1 None None None 120586947 Common - nitrogenase molybdenum-iron protein alpha chain Dvul_3093 62 COG2710 NifD, Nitrogenase molybdenum-iron protein, alpha and beta chains Energy production and conversion 120586840 Nonpathogen - type III secretion system needle length determinant Dvul_2986 1 None None None 120586940 Nonpathogen - Abortive infection protein Dvul_3086 11 COG1266 COG1266, Predicted metal-dependent membrane protease General function prediction only 120586928 Nonpathogen - hypothetical protein Dvul_3074 1 None None None 120586951 Common - Nitrogenase Dvul_3097 50 COG2710 NifD, Nitrogenase molybdenum-iron protein, alpha and beta chains Energy production and conversion 120586883 Common - glycosyl transferase, family 2 Dvul_3029 161 COG0463 WcaA, Glycosyltransferases involved in cell wall biogenesis Cell envelope biogenesis, outer membrane 120586933 Nonpathogen - hypothetical protein Dvul_3079 1 None None None 120586853 Common - type III secretion system protein, IpaC family, putative Dvul_2999 2 None None None 120586827 Common - CRISPR-associated protein Cas1 Dvul_2973 98 COG1518 COG1518, Uncharacterized protein predicted to be involved in DNA repair DNA replication, recombination, and repair 120586907 Nonpathogen - hypothetical protein Dvul_3053 9 None None None 120586878 Common - response regulator receiver modulated metal dependent phosphohydrolase Dvul_3024 208 COG3437 COG3437, Response regulator containing a CheY-like receiver domain and an HD-GYP domain Transcription / Signal transduction mechanisms 120586858 Common - type III secretion regulator YopN/LcrE/InvE/MxiC Dvul_3004 10 None None None 120586812 Common - HipA domain protein Dvul_2958 50 COG3550 HipA, Uncharacterized protein related to capsule biosynthesis enzymes General function prediction only 120586900 Common - Orn/DAP/Arg decarboxylase 2 Dvul_3046 215 COG0019 LysA, Diaminopimelate decarboxylase Amino acid transport and metabolism 120586842 Common - type III secretion system ATPase Dvul_2988 247 COG1157 FliI, Flagellar biosynthesis/type III secretory pathway ATPase Cell motility and secretion / Intracellular trafficking and secretion 120586819 Nonpathogen - hypothetical protein Dvul_2965 1 None None None 120586865 Common - type III secretion protein, YscU/HrpY family Dvul_3011 130 COG1377 FlhB, Flagellar biosynthesis pathway, component FlhB Cell motility and secretion / Intracellular trafficking and secretion 120586821 Nonpathogen - hypothetical protein Dvul_2967 1 None None None 120586856 Common - hypothetical protein Dvul_3002 2 None None None 120586904 Common - hypothetical protein Dvul_3050 16 COG3919 COG3919, Predicted ATP-grasp enzyme General function prediction only 120586847 Common - hypothetical protein Dvul_2993 2 None None None 120586843 Common - type III secretion system protein Dvul_2989 36 COG1317 FliH, Flagellar biosynthesis/type III secretory pathway protein Cell motility and secretion / Intracellular trafficking and secretion 120586899 Common - Methicillin resistance protein Dvul_3045 38 COG2348 COG2348, Uncharacterized protein involved in methicillin resistance Defense mechanisms 120586896 Common - Patatin Dvul_3042 22 COG1752 RssA, Predicted esterase of the alpha-beta hydrolase superfamily General function prediction only 120586877 Common - response regulator receiver protein Dvul_3023 193 COG2204 AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains Signal transduction mechanisms 120586916 Nonpathogen - hypothetical protein Dvul_3062 5 None None None 120586876 Common - multi-sensor signal transduction histidine kinase Dvul_3022 209 COG4191 COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system Signal transduction mechanisms 120586859 Common - type III secretion chaperone SycN Dvul_3005 3 None None None 120586925 Common - polysaccharide export protein Dvul_3071 108 COG1596 Wza, Periplasmic protein involved in polysaccharide export Cell envelope biogenesis, outer membrane 120586944 Common nifH nitrogenase reductase Dvul_3090 73 COG1348 NifH, Nitrogenase subunit NifH (ATPase) Inorganic ion transport and metabolism 120586938 Common - ABC transporter related Dvul_3084 249 COG1136 SalX, ABC-type antimicrobial peptide transport system, ATPase component Defense mechanisms 120586813 Common - DNA-binding protein, putative Dvul_2959 10 None None None 120586902 Common - hypothetical protein Dvul_3048 23 COG3503 COG3503, Predicted membrane protein Function unknown 120586884 Common - Adenylyl-sulfate kinase Dvul_3030 144 COG0529 CysC, Adenylylsulfate kinase and related kinases Inorganic ion transport and metabolism 120586849 Nonpathogen - hypothetical protein Dvul_2995 1 None None None 120586815 Nonpathogen - hypothetical protein Dvul_2961 3 COG3170 FimV, Tfp pilus assembly protein FimV Cell motility and secretion / Intracellular trafficking and secretion 120586845 Common - type III secretion apparatus lipoprotein, YscJ/HrcJ family Dvul_2991 38 COG4669 EscJ, Type III secretory pathway, lipoprotein EscJ Intracellular trafficking and secretion 120586909 Common - glycosyl transferase, group 1 Dvul_3055 221 COG0438 RfaG, Glycosyltransferase Cell envelope biogenesis, outer membrane 120586906 Common - two component, sigma54 specific, transcriptional regulator, Fis family Dvul_3052 192 COG2204 AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains Signal transduction mechanisms 120586868 Common - Stage II sporulation E family protein Dvul_3014 120 COG2208 RsbU, Serine phosphatase RsbU, regulator of sigma subunit Signal transduction mechanisms / Transcription 120586918 Common - DegT/DnrJ/EryC1/StrS aminotransferase Dvul_3064 50 COG0399 WecE, Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis Cell envelope biogenesis, outer membrane 120586897 Common - integral membrane sensor signal transduction histidine kinase Dvul_3043 204 COG0642 BaeS, Signal transduction histidine kinase Signal transduction mechanisms 120586890 Common - glycosyl transferase, group 1 Dvul_3036 165 COG0438 RfaG, Glycosyltransferase Cell envelope biogenesis, outer membrane 120586874 Nonpathogen - hypothetical protein Dvul_3020 2 None None None 120586921 Nonpathogen - lipoprotein, putative Dvul_3067 4 None None None 120586923 Common - polysaccharide biosynthesis protein, putative Dvul_3069 146 COG0489 Mrp, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 120586958 Common - histone family protein DNA-binding protein Dvul_3104 3 COG0776 HimA, Bacterial nucleoid DNA-binding protein DNA replication, recombination, and repair 120586886 Common - ABC transporter related Dvul_3032 249 COG1134 TagH, ABC-type polysaccharide/polyol phosphate transport system, ATPase component Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane 120586850 Common - type III secretion apparatus protein, YscD/HrpQ family Dvul_2996 2 None None None 120586911 Common - Acetyltransferase (isoleucine patch superfamily)-like protein Dvul_3057 87 COG0110 WbbJ, Acetyltransferase (isoleucine patch superfamily) General function prediction only 120586887 Common - Radical SAM domain protein Dvul_3033 24 COG0535 COG0535, Predicted Fe-S oxidoreductases General function prediction only 120586835 Common - Lytic transglycosylase, catalytic Dvul_2981 179 COG0741 MltE, Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) Cell envelope biogenesis, outer membrane 120586834 Nonpathogen - Tir chaperone family protein Dvul_2980 1 None None None 120586872 Common - Catalase Dvul_3018 126 COG0753 KatE, Catalase Inorganic ion transport and metabolism 120586861 Common - Tetratricopeptide TPR_4 Dvul_3007 2 None None None 120586837 Common - anti-sigma-factor antagonist Dvul_2983 36 COG1366 SpoIIAA, Anti-anti-sigma regulatory factor (antagonist of anti-sigma factor) Signal transduction mechanisms 120586825 Common - zinc transporter ZupT Dvul_2971 100 COG0428 COG0428, Predicted divalent heavy-metal cations transporter Inorganic ion transport and metabolism 120586892 Common - Methyltransferase type 11 Dvul_3038 16 COG4627 COG4627, Uncharacterized protein conserved in bacteria Function unknown 120586956 Common - CBS domain containing protein Dvul_3102 155 COG2239 MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain) Inorganic ion transport and metabolism 120586851 Common - type III secretion outer membrane pore, YscC/HrcC family Dvul_2997 128 COG1450 PulD, Type II secretory pathway, component PulD Cell motility and secretion / Intracellular trafficking and secretion 120586908 Common - eight transmembrane protein EpsH Dvul_3054 33 None None None 120586929 Common - hypothetical protein Dvul_3075 153 COG0476 ThiF, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 Coenzyme metabolism 120586932 Nonpathogen - hypothetical protein Dvul_3078 1 None None None 120586922 Common - AAA ATPase Dvul_3068 68 COG3267 ExeA, Type II secretory pathway, component ExeA (predicted ATPase) Intracellular trafficking and secretion 120586939 Common - secretion protein HlyD family protein Dvul_3085 112 COG1566 EmrA, Multidrug resistance efflux pump Defense mechanisms 120586954 Nonpathogen - hypothetical protein Dvul_3100 1 None None None 120586854 Common - type III secretion system target, YopB family Dvul_3000 4 COG5613 COG5613, Uncharacterized conserved protein Function unknown 120586857 Common - hypothetical protein Dvul_3003 2 None None None 120586948 Common - nitrogenase molybdenum-iron protein beta chain Dvul_3094 55 COG2710 NifD, Nitrogenase molybdenum-iron protein, alpha and beta chains Energy production and conversion 120586828 Common - CRISPR-associated protein Cas4 Dvul_2974 53 COG1468 COG1468, RecB family exonuclease DNA replication, recombination, and repair 120586879 Common - hypothetical protein Dvul_3025 62 COG1112 COG1112, Superfamily I DNA and RNA helicases and helicase subunits DNA replication, recombination, and repair 120586811 Nonpathogen - hypothetical protein Dvul_2957 1 None None None 120586870 Common - Radical SAM domain protein Dvul_3016 42 COG0535 COG0535, Predicted Fe-S oxidoreductases General function prediction only 120586901 Common - protein of unknown function DUF201 Dvul_3047 15 COG0458 CarB, Carbamoylphosphate synthase large subunit (split gene in MJ) Amino acid transport and metabolism / Nucleotide transport and metabolism 120586881 Common - phage integrase family protein Dvul_3027 182 COG4974 XerD, Site-specific recombinase XerD DNA replication, recombination, and repair 120586823 Common - integral membrane sensor signal transduction histidine kinase Dvul_2969 110 COG4585 COG4585, Signal transduction histidine kinase Signal transduction mechanisms 120586864 Common - type III secretion protein SpaR/YscT/HrcT Dvul_3010 85 COG4791 EscT, Type III secretory pathway, component EscT Intracellular trafficking and secretion 120586809 Common - hypothetical protein Dvul_2955 9 None None None 120586893 Common - Methyltransferase type 12 Dvul_3039 81 COG2246 COG2246, Predicted membrane protein Function unknown 120586936 Common - putative two component, sigma54 specific, transcriptional regulator, Fis family Dvul_3082 168 COG2204 AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains Signal transduction mechanisms 120586946 Common - nitrogen regulatory protein P-II Dvul_3092 186 COG0347 GlnK, Nitrogen regulatory protein PII Amino acid transport and metabolism 120586831 Common - CRISPR-associated protein Cas5 family Dvul_2977 38 None None None 120586914 Common - polysaccharide biosynthesis protein Dvul_3060 22 COG2244 RfbX, Membrane protein involved in the export of O-antigen and teichoic acid General function prediction only 120586927 Common - Tetratricopeptide TPR_2 repeat protein Dvul_3073 100 COG3063 PilF, Tfp pilus assembly protein PilF Cell motility and secretion / Intracellular trafficking and secretion 120586920 Common - polysaccharide deacetylase Dvul_3066 124 COG0726 CDA1, Predicted xylanase/chitin deacetylase Carbohydrate transport and metabolism 120586934 Nonpathogen - type IV pilus assembly PilZ Dvul_3080 1 None None None