Intracellular trafficking and secretion

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Biopolymer transport protein	U	Contig56	Rpal1308	COG0811	192	2e-50
Biopolymer transport protein	U	Contig56	Rpal1309	COG0848	104	3e-24
Biopolymer transport protein	U	Contig56	Rpal1432	COG0811	137	7e-34
Biopolymer transport protein	U	Contig56	Rpal1433	COG0848	136	8e-34
Biopolymer transport protein	U	Contig56	Rpal2220	COG0811	51	1e-07
Biopolymer transport protein	U	Contig56	Rpal2418	COG0811	138	5e-34
Biopolymer transport protein	U	Contig56	Rpal2419	COG0848	136	5e-34
Biopolymer transport protein	U	Contig56	Rpal2653	COG0811	61	3e-11
Biopolymer transport protein	U	Contig56	Rpal3696	COG0848	104	2e-24
Biopolymer transport protein	U	Contig56	Rpal3697	COG0811	164	8e-42
Biopolymer transport protein	U	Contig56	Rpal3966	COG0848	117	3e-28
Biopolymer transport protein	U	Contig56	Rpal3967	COG0811	162	2e-41

FLAGELLUM STRUCTURE AND BIOGENESIS

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Flagellar biosynthesis pathway component FlhA	U	Contig56	Rpal1828	COG1298	781	0.0
Flagellar biosynthesis pathway component FlhB	U	Contig56	Rpal3620	COG1377	88	8e-20
Flagellar biosynthesis pathway component FlhB	U	Contig56	Rpal4406	COG1377	357	1.0e-100
Flagellar biosynthesis pathway component FliP	U	Contig56	Rpal4413	COG1338	271	3e-74
Flagellar biosynthesis pathway component FliQ	U	Contig56	Rpal4408	COG1987	65	8e-13
Flagellar biosynthesis pathway component FliR	U	Contig56	Rpal4407	COG1684	139	2e-34
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal0171	COG1157	246	3e-66
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal0173	COG1157	213	3e-56
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal0298	COG1157	114	1e-26
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal1050	COG1157	213	3e-56
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal1057	COG1157	236	3e-63
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal1573	COG1157	37	0.002
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal1823	COG1157	541	1.0e-155
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal2252	COG1157	39	3e-04
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal2893	COG1157	38	8e-04
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal2954	COG1157	37	0.002
Flagellar biosynthesis/type III secretory pathway ATPase	U	Contig56	Rpal3866	COG1157	34	0.009
Flagellar biosynthesis/type III secretory pathway lipoprotein	U	Contig56	Rpal1457	COG1766	375	1.0e-105
Flagellar biosynthesis/type III secretory pathway protein	U	Contig56	Rpal1459	COG1317	59	3e-10
Flagellar hook-basal body protein	U	Contig56	Rpal4409	COG1677	56	6e-10
Flagellar motor switch/type III secretory pathway protein	U	Contig56	Rpal1460	COG1886	86	7e-19
Flagellar motor switch/type III secretory pathway protein	U	Contig56	Rpal3578	COG1886	53	5e-09
Flagellar motor switch/type III secretory pathway protein	U	Contig56	Rpal4420	COG1886	38	0.002
Flagellin-specific chaperone FliS	U	Contig56	Rpal0709	COG1516	60	5e-11
Predicted ATPase involved in biogenesis of flagella	U	Contig56	Rpal0009	COG2874	60	4e-10
Predicted ATPase involved in biogenesis of flagella	U	Contig56	Rpal3499	COG2874	42	8e-05
Predicted ATPase involved in biogenesis of flagella	U	Contig56	Rpal4376	COG2874	35	0.007
Predicted ATPase involved in biogenesis of flagella	U	Contig56	Rpal4814	COG2874	37	0.002

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Flp pilus assembly protein ATPase CpaE	U	Contig56	Rpal0294	COG4963	43	2e-05
Flp pilus assembly protein ATPase CpaE	U	Contig56	Rpal1623	COG4963	38	0.001
Flp pilus assembly protein ATPase CpaE	U	Contig56	Rpal2187	COG4963	48	7e-07
Flp pilus assembly protein ATPase CpaE	U	Contig56	Rpal3563	COG4963	40	2e-04
Flp pilus assembly protein ATPase CpaE	U	Contig56	Rpal3777	COG4963	50	5e-07
Flp pilus assembly protein ATPase CpaE	U	Contig56	Rpal4202	COG4963	252	5e-68
Flp pilus assembly protein ATPase CpaF	U	Contig56	Rpal4203	COG4962	481	1.0e-137
Flp pilus assembly protein CpaB	U	Contig56	Rpal4199	COG3745	86	2e-18
Flp pilus assembly protein CpaB	U	Contig56	Rpal4615	COG3745	179	2e-46
Flp pilus assembly protein pilin Flp	U	Contig56	Rpal0974	COG3847	48	1e-07
Flp pilus assembly protein pilin Flp	U	Contig56	Rpal2088	COG3847	44	3e-06
Flp pilus assembly protein pilin Flp	U	Contig56	Rpal4197	COG3847	51	1e-08
Flp pilus assembly protein protease CpaA	U	Contig56	Rpal4198	COG4960	101	3e-23
Flp pilus assembly protein secretin CpaC	U	Contig56	Rpal4200	COG4964	355	4e-99
Flp pilus assembly protein TadB	U	Contig56	Rpal4204	COG4965	244	7e-66
Flp pilus assembly protein TadB	U	Contig56	Rpal4205	COG4965	63	4e-11
Flp pilus assembly protein TadC	U	Contig56	Rpal4204	COG2064	55	5e-09
Flp pilus assembly protein TadC	U	Contig56	Rpal4205	COG2064	119	2e-28
Flp pilus assembly protein TadD contains TPR repeats	U	Contig56	Rpal1230	COG5010	48	1e-06
Flp pilus assembly protein TadD contains TPR repeats	U	Contig56	Rpal2130	COG5010	37	0.003
Flp pilus assembly protein TadD contains TPR repeats	U	Contig56	Rpal2530	COG5010	53	4e-08
Flp pilus assembly protein TadD contains TPR repeats	U	Contig56	Rpal2752	COG5010	49	9e-07
Flp pilus assembly protein TadD contains TPR repeats	U	Contig56	Rpal4206	COG5010	130	1e-31
Flp pilus assembly protein TadD contains TPR repeats	U	Contig56	Rpal4439	COG5010	56	1e-08
Flp pilus assembly protein TadD contains TPR repeats	U	Contig56	Rpal5193	COG5010	38	0.001
Flp pilus assembly protein TadG	U	Contig56	Rpal0477	COG4961	54	2e-08
Flp pilus assembly protein TadG	U	Contig56	Rpal0799	COG4961	52	1e-07
Flp pilus assembly protein TadG	U	Contig56	Rpal0800	COG4961	58	3e-10
Flp pilus assembly protein TadG	U	Contig56	Rpal0801	COG4961	53	2e-08
Flp pilus assembly protein TadG	U	Contig56	Rpal3558	COG4961	58	1e-09
Flp pilus assembly protein TadG	U	Contig56	Rpal4195	COG4961	57	8e-10
Flp pilus assembly protein TadG	U	Contig56	Rpal4196	COG4961	69	2e-13
Flp pilus assembly protein TadG	U	Contig56	Rpal4760	COG4961	50	3e-07
Hemolysin activation/secretion protein	U	Contig56	Rpal3260	COG2831	43	9e-05
Lipoprotein signal peptidase	U	Contig56	Rpal4860	COG0597	101	2e-23
Membrane protein implicated in regulation of membrane protease activity	U	Contig56	Rpal0945	COG1585	95	3e-21
Outer membrane protein	U	Contig56	Rpal0516	COG1538	35	0.010
Outer membrane protein	U	Contig56	Rpal1047	COG1538	78	2e-15
Outer membrane protein	U	Contig56	Rpal1090	COG1538	124	1e-29
Outer membrane protein	U	Contig56	Rpal2010	COG1538	36	0.006
Outer membrane protein	U	Contig56	Rpal2013	COG1538	166	2e-42
Outer membrane protein	U	Contig56	Rpal2170	COG1538	36	0.004
Outer membrane protein	U	Contig56	Rpal2171	COG1538	35	0.010
Outer membrane protein	U	Contig56	Rpal2298	COG1538	116	3e-27
Outer membrane protein	U	Contig56	Rpal2344	COG1538	103	3e-23
Outer membrane protein	U	Contig56	Rpal2616	COG1538	242	5e-65
Outer membrane protein	U	Contig56	Rpal2841	COG1538	222	5e-59
Outer membrane protein	U	Contig56	Rpal2851	COG1538	167	1e-42
Outer membrane protein	U	Contig56	Rpal4983	COG1538	41	6e-04
Periplasmic component of the Tol biopolymer transport system	U	Contig56	Rpal1311	COG0823	374	1.0e-105
Periplasmic serine protease (ClpP class)	U	Contig56	Rpal0068	COG0616	195	4e-51
Periplasmic serine protease (ClpP class)	U	Contig56	Rpal0720	COG0616	39	3e-04
Periplasmic serine protease (ClpP class)	U	Contig56	Rpal1235	COG0616	198	5e-52
Periplasmic serine protease (ClpP class)	U	Contig56	Rpal1962	COG0616	37	0.001
Periplasmic serine protease (ClpP class)	U	Contig56	Rpal3309	COG0616	47	1e-06
Phosphatidylinositol kinase and protein kinase of the PI-3 kinase family	U	Contig56	Rpal3635	COG5032	38	0.002
Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake	U	Contig56	Rpal3531	COG0758	294	8e-81
Preprotein translocase subunit Sec63	U	Contig56	Rpal0337	COG5407	55	6e-09
Preprotein translocase subunit Sec63	U	Contig56	Rpal1391	COG5407	54	2e-08
Preprotein translocase subunit Sec63	U	Contig56	Rpal3560	COG5407	39	4e-04

PREPROTEIN TRANSLOCASE SUBUNITS

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Preprotein translocase subunit SecA (ATPase RNA helicase)	U	Contig56	Rpal0511	COG0653	1028	0.0
Preprotein translocase subunit SecA (ATPase RNA helicase)	U	Contig56	Rpal2456	COG0653	41	7e-05
Preprotein translocase subunit SecA (ATPase RNA helicase)	U	Contig56	Rpal2936	COG0653	37	0.004
Preprotein translocase subunit SecB	U	Contig56	Rpal0304	COG1952	158	1e-40
Preprotein translocase subunit SecD	U	Contig56	Rpal0100	COG0342	49	2e-06
Preprotein translocase subunit SecD	U	Contig56	Rpal1045	COG0342	38	0.003
Preprotein translocase subunit SecD	U	Contig56	Rpal1213	COG0342	38	0.004
Preprotein translocase subunit SecD	U	Contig56	Rpal1529	COG0342	70	7e-13
Preprotein translocase subunit SecD	U	Contig56	Rpal1685	COG0342	57	9e-09
Preprotein translocase subunit SecD	U	Contig56	Rpal1954	COG0342	42	2e-04
Preprotein translocase subunit SecD	U	Contig56	Rpal2172	COG0342	46	1e-05
Preprotein translocase subunit SecD	U	Contig56	Rpal2300	COG0342	38	0.005
Preprotein translocase subunit SecD	U	Contig56	Rpal2843	COG0342	61	4e-10
Preprotein translocase subunit SecD	U	Contig56	Rpal2844	COG0342	43	1e-04
Preprotein translocase subunit SecD	U	Contig56	Rpal3171	COG0342	79	6e-16
Preprotein translocase subunit SecD	U	Contig56	Rpal3172	COG0342	493	1.0e-140
Preprotein translocase subunit SecD	U	Contig56	Rpal3305	COG0342	56	1e-08
Preprotein translocase subunit SecD	U	Contig56	Rpal3428	COG0342	75	3e-14
Preprotein translocase subunit SecD	U	Contig56	Rpal3972	COG0342	65	2e-11
Preprotein translocase subunit SecD	U	Contig56	Rpal4254	COG0342	37	0.006
Preprotein translocase subunit SecD	U	Contig56	Rpal4296	COG0342	64	5e-11
Preprotein translocase subunit SecD	U	Contig56	Rpal4426	COG0342	58	3e-09
Preprotein translocase subunit SecD	U	Contig56	Rpal4901	COG0342	40	0.001
Preprotein translocase subunit SecD	U	Contig56	Rpal5161	COG0342	60	9e-10
Preprotein translocase subunit SecE	U	Contig56	Rpal3694	COG0690	47	2e-07
Preprotein translocase subunit SecF	U	Contig56	Rpal0100	COG0341	43	1e-04
Preprotein translocase subunit SecF	U	Contig56	Rpal1213	COG0341	41	6e-04
Preprotein translocase subunit SecF	U	Contig56	Rpal1529	COG0341	38	0.003
Preprotein translocase subunit SecF	U	Contig56	Rpal1685	COG0341	42	2e-04
Preprotein translocase subunit SecF	U	Contig56	Rpal2172	COG0341	40	8e-04
Preprotein translocase subunit SecF	U	Contig56	Rpal2843	COG0341	39	0.002
Preprotein translocase subunit SecF	U	Contig56	Rpal2844	COG0341	46	2e-05
Preprotein translocase subunit SecF	U	Contig56	Rpal3171	COG0341	307	6e-85
Preprotein translocase subunit SecF	U	Contig56	Rpal3172	COG0341	87	4e-18
Preprotein translocase subunit SecF	U	Contig56	Rpal3305	COG0341	42	2e-04
Preprotein translocase subunit SecF	U	Contig56	Rpal3428	COG0341	56	2e-08
Preprotein translocase subunit SecF	U	Contig56	Rpal3972	COG0341	37	0.006
Preprotein translocase subunit SecF	U	Contig56	Rpal4296	COG0341	37	0.009
Preprotein translocase subunit SecF	U	Contig56	Rpal4426	COG0341	44	6e-05
Preprotein translocase subunit SecF	U	Contig56	Rpal5161	COG0341	38	0.004
Preprotein translocase subunit SecG	U	Contig56	Rpal3232	COG1314	73	8e-15
Preprotein translocase subunit SecY	U	Contig56	Rpal3647	COG0201	446	1.0e-126
Preprotein translocase subunit YajC	U	Contig56	Rpal3173	COG1862	98	2e-22
Preprotein translocase subunit YidC	U	Contig56	Rpal0636	COG0706	255	7e-69

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Protease subunit of ATP-dependent Clp protease	U	Contig56	Rpal0068	COG0740	36	0.004
Protease subunit of ATP-dependent Clp protease	U	Contig56	Rpal1235	COG0740	34	0.009
Protease subunit of ATP-dependent Clp protease	U	Contig56	Rpal3309	COG0740	292	2e-80
Sec-independent protein secretion pathway components	U	Contig56	Rpal3188	COG1826	46	1e-06
Sec-independent protein secretion pathway components	U	Contig56	Rpal3189	COG1826	60	4e-11
Sec-independent protein secretion pathway component TatC	U	Contig56	Rpal3187	COG0805	213	1e-56
Signal peptidase I	U	Contig56	Rpal0892	COG0681	63	2e-11
Signal peptidase I	U	Contig56	Rpal2971	COG0681	77	2e-15
Signal recognition particle GTPase	U	Contig56	Rpal0207	COG0552	350	8e-98
Signal recognition particle GTPase	U	Contig56	Rpal0207	COG0541	227	1e-60
Signal recognition particle GTPase	U	Contig56	Rpal0246	COG0552	206	4e-54
Signal recognition particle GTPase	U	Contig56	Rpal0246	COG0541	570	1.0e-163
Signal recognition particle GTPase	U	Contig56	Rpal0824	COG0552	37	0.005
Signal recognition particle GTPase	U	Contig56	Rpal0824	COG0541	36	0.010
Signal recognition particle GTPase	U	Contig56	Rpal1710	COG0552	42	6e-05
Signal recognition particle GTPase	U	Contig56	Rpal2033	COG0552	42	5e-05
Signal recognition particle GTPase	U	Contig56	Rpal2033	COG0541	36	0.005
Signal recognition particle GTPase	U	Contig56	Rpal2187	COG0541	37	0.002
Signal recognition particle GTPase	U	Contig56	Rpal3777	COG0541	40	8e-04
Tfp pilus assembly protein ATPase PilU	U	Contig56	Rpal4203	COG5008	63	3e-11
Tfp pilus assembly protein FimV	U	Contig56	Rpal0183	COG3170	35	0.007
Tfp pilus assembly protein FimV	U	Contig56	Rpal0492	COG3170	37	0.006
Tfp pilus assembly protein FimV	U	Contig56	Rpal1976	COG3170	36	0.006
Tfp pilus assembly protein FimV	U	Contig56	Rpal3555	COG3170	37	0.004
Tfp pilus assembly protein PilF	U	Contig56	Rpal0872	COG3063	40	2e-04
Tfp pilus assembly protein PilF	U	Contig56	Rpal1230	COG3063	45	2e-05
Tfp pilus assembly protein PilF	U	Contig56	Rpal2528	COG3063	42	2e-04
Tfp pilus assembly protein PilF	U	Contig56	Rpal2530	COG3063	61	3e-10
Tfp pilus assembly protein PilF	U	Contig56	Rpal2752	COG3063	68	1e-12
Tfp pilus assembly protein PilF	U	Contig56	Rpal4206	COG3063	41	1e-04
Tfp pilus assembly protein PilF	U	Contig56	Rpal4439	COG3063	67	5e-12
Tfp pilus assembly protein PilF	U	Contig56	Rpal4676	COG3063	41	1e-04
Tfp pilus assembly protein PilF	U	Contig56	Rpal4997	COG3063	37	0.001
Tfp pilus assembly protein PilF	U	Contig56	Rpal5158	COG3063	41	2e-04
Tfp pilus assembly protein PilF	U	Contig56	Rpal5193	COG3063	49	7e-07
Tfp pilus assembly protein pilus retraction ATPase PilT	U	Contig56	Rpal4203	COG2805	72	1e-13
Type III secretory pathway component EscR	U	Contig56	Rpal4413	COG4790	174	5e-45
Type III secretory pathway component EscS	U	Contig56	Rpal4408	COG4794	51	2e-08
Type III secretory pathway component EscT	U	Contig56	Rpal4407	COG4791	77	1e-15
Type III secretory pathway component EscU	U	Contig56	Rpal3620	COG4792	56	4e-10
Type III secretory pathway component EscU	U	Contig56	Rpal4406	COG4792	214	7e-57
Type III secretory pathway component EscV	U	Contig56	Rpal1828	COG4789	495	1.0e-141
Type III secretory pathway lipoprotein EscJ	U	Contig56	Rpal1457	COG4669	66	6e-12
Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB	U	Contig56	Rpal0282	COG2804	36	0.008
Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB	U	Contig56	Rpal4203	COG2804	88	2e-18
Type II secretory pathway component HofQ	U	Contig56	Rpal4200	COG4796	96	4e-21
Type II secretory pathway component PulD	U	Contig56	Rpal4200	COG1450	129	4e-31
Type II secretory pathway component PulF	U	Contig56	Rpal4204	COG1459	35	0.007
Type IV secretory pathway protease TraF	U	Contig56	Rpal2971	COG4959	38	0.001
Type IV secretory pathway TrbL protein	U	Contig56	Rpal0237	COG3846	36	6e-04
Type IV secretory pathway TrbL protein	U	Contig56	Rpal1324	COG3846	38	0.001
Type IV secretory pathway TrbL protein	U	Contig56	Rpal1881	COG3846	39	0.004
Type IV secretory pathway TrbL protein	U	Contig56	Rpal3646	COG3846	38	0.001
Type IV secretory pathway VirB10 protein	U	Contig56	Rpal0948	COG2948	37	0.005
Type IV secretory pathway VirB10 protein	U	Contig56	Rpal3555	COG2948	40	7e-04
Type IV secretory pathway VirB10 protein	U	Contig56	Rpal3684	COG2948	38	0.002
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	Contig56	Rpal3684	COG0630	41	4e-04
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	Contig56	Rpal4203	COG0630	219	4e-58
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	Contig56	Rpal4210	COG0630	37	0.003
Type IV secretory pathway VirB4 protein	U	Contig56	Rpal1425	COG3451	35	0.006
Type IV secretory pathway VirB4 protein	U	Contig56	Rpal2238	COG3451	42	1e-04
Type IV secretory pathway VirB4 protein	U	Contig56	Rpal5263	COG3451	35	0.007
Type IV secretory pathway VirJ protein	U	Contig56	Rpal4365	COG3946	36	0.008

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