Intracellular trafficking and secretion

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Biopolymer transport protein	U	AL954747	NE0215	COG0811	180	5e-47
Biopolymer transport protein	U	AL954747	NE0216	COG0848	111	2e-26
Biopolymer transport protein	U	AL954747	NE0352	COG0848	139	9e-35
Biopolymer transport protein	U	AL954747	NE0353	COG0811	143	1e-35
Biopolymer transport protein	U	AL954747	NE0631	COG0811	52	2e-08
Biopolymer transport protein	U	AL954747	NE0756	COG0811	50	1e-07
Biopolymer transport protein	U	AL954747	NE0869	COG0848	100	9e-23
Biopolymer transport protein	U	AL954747	NE1171	COG0811	132	3e-32
Competence protein ComGC	U	AL954747	NE1253	COG4537	39	1e-04
Competence protein ComGC	U	AL954747	NE1308	COG4537	40	9e-05
Competence protein ComGC	U	AL954747	NE1602	COG4537	47	5e-07
Competence protein ComGC	U	AL954747	NE1611	COG4537	39	2e-04
Competence protein ComGC	U	AL954747	NE1746	COG4537	34	0.004
Competence protein ComGC	U	AL954747	NE1751	COG4537	36	0.002
Flagellar biosynthesis/type III secretory pathway chaperone	U	AL954747	NE2477	COG3418	35	0.002

FLAGELLUM STRUCTURE AND BIOGENESIS

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Flagellar biosynthesis chaperone	U	AL954747	NE2087	COG2882	60	7e-11
Flagellar biosynthesis pathway component FlhA	U	AL954747	NE2488	COG1298	853	0.0
Flagellar biosynthesis pathway component FlhB	U	AL954747	NE2078	COG1377	76	7e-16
Flagellar biosynthesis pathway component FlhB	U	AL954747	NE2487	COG1377	392	1.0e-110
Flagellar biosynthesis pathway component FliP	U	AL954747	NE0461	COG1338	283	1e-77
Flagellar biosynthesis pathway component FliQ	U	AL954747	NE0460	COG1987	83	4e-18
Flagellar biosynthesis pathway component FliR	U	AL954747	NE0459	COG1684	168	3e-43
Flagellar biosynthesis/type III secretory pathway ATPase	U	AL954747	NE0204	COG1157	198	6e-52
Flagellar biosynthesis/type III secretory pathway ATPase	U	AL954747	NE0206	COG1157	245	3e-66
Flagellar biosynthesis/type III secretory pathway ATPase	U	AL954747	NE0827	COG1157	34	0.008
Flagellar biosynthesis/type III secretory pathway ATPase	U	AL954747	NE0976	COG1157	35	0.009
Flagellar biosynthesis/type III secretory pathway ATPase	U	AL954747	NE1035	COG1157	115	8e-27
Flagellar biosynthesis/type III secretory pathway ATPase	U	AL954747	NE2086	COG1157	580	1.0e-167
Flagellar biosynthesis/type III secretory pathway lipoprotein	U	AL954747	NE2083	COG1766	400	1.0e-112
Flagellar biosynthesis/type III secretory pathway protein	U	AL954747	NE0492	COG1317	41	1e-04
Flagellar biosynthesis/type III secretory pathway protein	U	AL954747	NE1223	COG1317	42	6e-05
Flagellar biosynthesis/type III secretory pathway protein	U	AL954747	NE1302	COG1317	40	2e-04
Flagellar biosynthesis/type III secretory pathway protein	U	AL954747	NE2085	COG1317	102	2e-23
Flagellar hook-basal body protein	U	AL954747	NE2080	COG1677	67	3e-13
Flagellar motor switch/type III secretory pathway protein	U	AL954747	NE0463	COG1886	99	2e-22
Flagellar motor switch/type III secretory pathway protein	U	AL954747	NE0464	COG1886	35	0.007
Flagellin-specific chaperone FliS	U	AL954747	NE1596	COG1516	110	7e-26
Muramidase (flagellum-specific)	U	AL954747	NE0310	COG1705	164	1e-41
Predicted ATPase involved in biogenesis of flagella	U	AL954747	NE1808	COG2874	47	3e-06
Predicted ATPase involved in biogenesis of flagella	U	AL954747	NE1932	COG2874	36	0.004

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Flp pilus assembly protein ATPase CpaE	U	AL954747	NE0624	COG4963	36	0.003
Flp pilus assembly protein ATPase CpaE	U	AL954747	NE1495	COG4963	63	3e-11
Flp pilus assembly protein ATPase CpaE	U	AL954747	NE1803	COG4963	43	3e-05
Flp pilus assembly protein ATPase CpaE	U	AL954747	NE1830	COG4963	74	1e-14
Flp pilus assembly protein ATPase CpaE	U	AL954747	NE2280	COG4963	41	4e-04
Flp pilus assembly protein ATPase CpaE	U	AL954747	NE2474	COG4963	50	1e-07
Flp pilus assembly protein ATPase CpaE	U	AL954747	NE2490	COG4963	45	6e-06
Flp pilus assembly protein ATPase CpaF	U	AL954747	NE0964	COG4962	75	9e-15
Flp pilus assembly protein ATPase CpaF	U	AL954747	NE0965	COG4962	77	3e-15
Flp pilus assembly protein ATPase CpaF	U	AL954747	NE1257	COG4962	80	6e-16
Flp pilus assembly protein ATPase CpaF	U	AL954747	NE1609	COG4962	68	2e-12
Flp pilus assembly protein ATPase CpaF	U	AL954747	NE2290	COG4962	62	2e-10
Flp pilus assembly protein protease CpaA	U	AL954747	NE0597	COG4960	39	6e-04
Flp pilus assembly protein secretin CpaC	U	AL954747	NE0705	COG4964	99	1e-21
Flp pilus assembly protein secretin CpaC	U	AL954747	NE1604	COG4964	109	8e-25
Flp pilus assembly protein secretin CpaC	U	AL954747	NE2312	COG4964	105	1e-23
Flp pilus assembly protein TadD contains TPR repeats	U	AL954747	NE0146	COG5010	40	2e-04
Flp pilus assembly protein TadD contains TPR repeats	U	AL954747	NE1298	COG5010	50	1e-06
Flp pilus assembly protein TadD contains TPR repeats	U	AL954747	NE1444	COG5010	53	1e-07
Flp pilus assembly protein TadD contains TPR repeats	U	AL954747	NE1600	COG5010	55	1e-08
Flp pilus assembly protein TadD contains TPR repeats	U	AL954747	NE2092	COG5010	39	0.002
Flp pilus assembly protein TadD contains TPR repeats	U	AL954747	NE2159	COG5010	40	1e-04
Hemolysin activation/secretion protein	U	AL954747	NE0930	COG2831	44	3e-05
Hemolysin activation/secretion protein	U	AL954747	NE1710	COG2831	70	5e-13
Lipoprotein signal peptidase	U	AL954747	NE1148	COG0597	121	2e-29
Membrane protein implicated in regulation of membrane protease activity	U	AL954747	NE2468	COG1585	61	1e-10
Negative regulator of flagellin synthesis (anti-sigma28 factor)	U	AL954747	NE2478	COG2747	46	7e-07
Outer membrane protein	U	AL954747	NE0036	COG1538	172	5e-44
Outer membrane protein	U	AL954747	NE0160	COG1538	161	8e-41
Outer membrane protein	U	AL954747	NE0170	COG1538	255	6e-69
Outer membrane protein	U	AL954747	NE0373	COG1538	115	7e-27
Outer membrane protein	U	AL954747	NE0538	COG1538	189	3e-49
Outer membrane protein	U	AL954747	NE0668	COG1538	188	5e-49
Outer membrane protein	U	AL954747	NE1080	COG1538	180	2e-46
Outer membrane protein	U	AL954747	NE1111	COG1538	252	3e-68
Outer membrane protein	U	AL954747	NE1115	COG1538	240	1e-64
Outer membrane protein	U	AL954747	NE1116	COG1538	37	0.003
Outer membrane protein	U	AL954747	NE1640	COG1538	138	1e-33
Periplasmic component of the Tol biopolymer transport system	U	AL954747	NE0218	COG0823	315	3e-87
Periplasmic component of the Tol biopolymer transport system	U	AL954747	NE0902	COG0823	89	6e-19
Periplasmic serine protease (ClpP class)	U	AL954747	NE0031	COG0616	44	1e-05
Periplasmic serine protease (ClpP class)	U	AL954747	NE1024	COG0616	212	3e-56
Periplasmic serine protease (ClpP class)	U	AL954747	NE2468	COG0616	39	9e-04
Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake	U	AL954747	NE1469	COG0758	37	0.001
Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake	U	AL954747	NE1968	COG0758	318	4e-88
Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake	U	AL954747	NE2521	COG0758	159	3e-40
Preprotein translocase subunit Sec63	U	AL954747	NE1155	COG5407	56	3e-09
Preprotein translocase subunit Sec63	U	AL954747	NE1948	COG5407	70	3e-13

PREPROTEIN TRANSLOCASE SUBUNITS

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Preprotein translocase subunit SecA (ATPase RNA helicase)	U	AL954747	NE0808	COG0653	1100	0.0
Preprotein translocase subunit SecB	U	AL954747	NE2210	COG1952	161	2e-41
Preprotein translocase subunit SecD	U	AL954747	NE0157	COG0342	65	4e-11
Preprotein translocase subunit SecD	U	AL954747	NE0168	COG0342	70	1e-12
Preprotein translocase subunit SecD	U	AL954747	NE0345	COG0342	49	1e-06
Preprotein translocase subunit SecD	U	AL954747	NE0375	COG0342	40	0.001
Preprotein translocase subunit SecD	U	AL954747	NE0669	COG0342	44	5e-05
Preprotein translocase subunit SecD	U	AL954747	NE1112	COG0342	57	7e-09
Preprotein translocase subunit SecD	U	AL954747	NE1143	COG0342	439	1.0e-124
Preprotein translocase subunit SecD	U	AL954747	NE1144	COG0342	83	2e-17
Preprotein translocase subunit SecD	U	AL954747	NE1638	COG0342	42	2e-04
Preprotein translocase subunit SecD	U	AL954747	NE1759	COG0342	43	1e-04
Preprotein translocase subunit SecD	U	AL954747	NE2036	COG0342	51	4e-07
Preprotein translocase subunit SecF	U	AL954747	NE0157	COG0341	40	8e-04
Preprotein translocase subunit SecF	U	AL954747	NE0168	COG0341	45	2e-05
Preprotein translocase subunit SecF	U	AL954747	NE0345	COG0341	37	0.010
Preprotein translocase subunit SecF	U	AL954747	NE0540	COG0341	42	2e-04
Preprotein translocase subunit SecF	U	AL954747	NE1143	COG0341	84	2e-17
Preprotein translocase subunit SecF	U	AL954747	NE1144	COG0341	300	1e-82
Preprotein translocase subunit SecF	U	AL954747	NE1759	COG0341	38	0.003
Preprotein translocase subunit SecF	U	AL954747	NE2036	COG0341	47	7e-06
Preprotein translocase subunit SecG	U	AL954747	NE1778	COG1314	67	4e-13
Preprotein translocase subunit SecY	U	AL954747	NE0421	COG0201	451	1.0e-128
Preprotein translocase subunit YajC	U	AL954747	NE1142	COG1862	98	2e-22
Preprotein translocase subunit YidC	U	AL954747	NE0387	COG0706	253	4e-68

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Protease subunit of ATP-dependent Clp protease	U	AL954747	NE0031	COG0740	304	2e-84
Sec-independent protein secretion pathway components	U	AL954747	NE0638	COG1826	62	1e-11
Sec-independent protein secretion pathway components	U	AL954747	NE0639	COG1826	68	2e-13
Sec-independent protein secretion pathway component TatC	U	AL954747	NE0637	COG0805	197	6e-52
Signal peptidase I	U	AL954747	NE2326	COG0681	62	4e-11
Signal recognition particle GTPase	U	AL954747	NE1415	COG0552	368	1.0e-103
Signal recognition particle GTPase	U	AL954747	NE1415	COG0541	226	2e-60
Signal recognition particle GTPase	U	AL954747	NE1460	COG0552	223	2e-59
Signal recognition particle GTPase	U	AL954747	NE1460	COG0541	595	1.0e-171
Signal recognition particle GTPase	U	AL954747	NE2489	COG0552	82	6e-17
Signal recognition particle GTPase	U	AL954747	NE2489	COG0541	74	2e-14
Tfp pilus assembly protein ATPase PilM	U	AL954747	NE0996	COG4972	68	2e-12
Tfp pilus assembly protein ATPase PilM	U	AL954747	NE2070	COG4972	36	0.004
Tfp pilus assembly protein ATPase PilM	U	AL954747	NE2316	COG4972	312	2e-86
Tfp pilus assembly protein ATPase PilU	U	AL954747	NE0964	COG5008	562	1.0e-161
Tfp pilus assembly protein ATPase PilU	U	AL954747	NE0965	COG5008	346	1e-96
Tfp pilus assembly protein ATPase PilU	U	AL954747	NE1257	COG5008	123	3e-29
Tfp pilus assembly protein ATPase PilU	U	AL954747	NE1609	COG5008	105	1e-23
Tfp pilus assembly protein ATPase PilU	U	AL954747	NE2290	COG5008	108	1e-24
Tfp pilus assembly protein FimT	U	AL954747	NE1308	COG4970	47	7e-07
Tfp pilus assembly protein FimT	U	AL954747	NE1602	COG4970	45	2e-06
Tfp pilus assembly protein FimT	U	AL954747	NE1603	COG4970	50	6e-08
Tfp pilus assembly protein FimT	U	AL954747	NE1611	COG4970	44	6e-06
Tfp pilus assembly protein FimT	U	AL954747	NE1746	COG4970	45	3e-06
Tfp pilus assembly protein FimT	U	AL954747	NE1751	COG4970	106	9e-25
Tfp pilus assembly protein FimV	U	AL954747	NE0690	COG3170	140	4e-34
Tfp pilus assembly protein FimV	U	AL954747	NE0791	COG3170	38	0.002
Tfp pilus assembly protein major pilin PilA	U	AL954747	NE1308	COG4969	75	1e-15
Tfp pilus assembly protein major pilin PilA	U	AL954747	NE1602	COG4969	45	2e-06
Tfp pilus assembly protein major pilin PilA	U	AL954747	NE1603	COG4969	47	6e-07
Tfp pilus assembly protein major pilin PilA	U	AL954747	NE1611	COG4969	49	2e-07
Tfp pilus assembly protein major pilin PilA	U	AL954747	NE1746	COG4969	53	9e-09
Tfp pilus assembly protein major pilin PilA	U	AL954747	NE1751	COG4969	46	2e-06
Tfp pilus assembly protein PilE	U	AL954747	NE1253	COG4968	40	5e-05
Tfp pilus assembly protein PilE	U	AL954747	NE1308	COG4968	62	2e-11
Tfp pilus assembly protein PilE	U	AL954747	NE1602	COG4968	59	1e-10
Tfp pilus assembly protein PilE	U	AL954747	NE1603	COG4968	54	4e-09
Tfp pilus assembly protein PilE	U	AL954747	NE1611	COG4968	54	5e-09
Tfp pilus assembly protein PilE	U	AL954747	NE1746	COG4968	108	1e-25
Tfp pilus assembly protein PilE	U	AL954747	NE1751	COG4968	50	8e-08
Tfp pilus assembly protein PilF	U	AL954747	NE0146	COG3063	155	2e-39
Tfp pilus assembly protein PilF	U	AL954747	NE1298	COG3063	59	2e-09
Tfp pilus assembly protein PilF	U	AL954747	NE1444	COG3063	59	1e-09
Tfp pilus assembly protein PilF	U	AL954747	NE1600	COG3063	41	2e-04
Tfp pilus assembly protein PilF	U	AL954747	NE2159	COG3063	43	1e-05
Tfp pilus assembly protein PilN	U	AL954747	NE1607	COG3166	38	5e-04
Tfp pilus assembly protein PilN	U	AL954747	NE2315	COG3166	118	3e-28
Tfp pilus assembly protein PilO	U	AL954747	NE2314	COG3167	177	6e-46
Tfp pilus assembly protein PilP	U	AL954747	NE2313	COG3168	124	3e-30
Tfp pilus assembly protein pilus retraction ATPase PilT	U	AL954747	NE0964	COG2805	380	1.0e-107
Tfp pilus assembly protein pilus retraction ATPase PilT	U	AL954747	NE0965	COG2805	538	1.0e-154
Tfp pilus assembly protein pilus retraction ATPase PilT	U	AL954747	NE1257	COG2805	185	8e-48
Tfp pilus assembly protein pilus retraction ATPase PilT	U	AL954747	NE1609	COG2805	157	2e-39
Tfp pilus assembly protein pilus retraction ATPase PilT	U	AL954747	NE2290	COG2805	156	5e-39
Tfp pilus assembly protein PilV	U	AL954747	NE1750	COG4967	65	3e-12
Tfp pilus assembly protein PilW	U	AL954747	NE1602	COG4966	39	2e-04
Tfp pilus assembly protein PilW	U	AL954747	NE1749	COG4966	84	2e-17
Tfp pilus assembly protein PilX	U	AL954747	NE1308	COG4726	33	0.005
Tfp pilus assembly protein PilX	U	AL954747	NE1602	COG4726	34	0.004
Tfp pilus assembly protein PilX	U	AL954747	NE1748	COG4726	101	9e-23
Tfp pilus assembly protein tip-associated adhesin PilY1	U	AL954747	NE1747	COG3419	404	1.0e-113
Type III secretory pathway component EscR	U	AL954747	NE0461	COG4790	163	2e-41
Type III secretory pathway component EscS	U	AL954747	NE0460	COG4794	51	2e-08
Type III secretory pathway component EscT	U	AL954747	NE0459	COG4791	97	1e-21
Type III secretory pathway component EscU	U	AL954747	NE2078	COG4792	49	8e-08
Type III secretory pathway component EscU	U	AL954747	NE2487	COG4792	219	2e-58
Type III secretory pathway component EscV	U	AL954747	NE2488	COG4789	491	1.0e-140
Type III secretory pathway lipoprotein EscJ	U	AL954747	NE2083	COG4669	58	1e-09
Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB	U	AL954747	NE0964	COG2804	156	3e-39
Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB	U	AL954747	NE0965	COG2804	178	6e-46
Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB	U	AL954747	NE1257	COG2804	479	1.0e-136
Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB	U	AL954747	NE1609	COG2804	486	1.0e-138
Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB	U	AL954747	NE2290	COG2804	426	1.0e-120
Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB	U	AL954747	NE2402	COG2804	37	0.004
Type II secretory pathway component ExeA (predicted ATPase)	U	AL954747	NE1801	COG3267	133	1e-32
Type II secretory pathway component ExeA (predicted ATPase)	U	AL954747	NE2452	COG3267	36	0.010
Type II secretory pathway component HofQ	U	AL954747	NE0705	COG4796	118	1e-27
Type II secretory pathway component HofQ	U	AL954747	NE1604	COG4796	163	4e-41
Type II secretory pathway component HofQ	U	AL954747	NE2312	COG4796	358	1.0e-99
Type II secretory pathway component PulC	U	AL954747	NE1508	COG3031	42	6e-05
Type II secretory pathway component PulD	U	AL954747	NE0558	COG1450	35	0.006
Type II secretory pathway component PulD	U	AL954747	NE0705	COG1450	253	5e-68
Type II secretory pathway component PulD	U	AL954747	NE1088	COG1450	36	0.009
Type II secretory pathway component PulD	U	AL954747	NE1604	COG1450	138	1e-33
Type II secretory pathway component PulD	U	AL954747	NE2312	COG1450	153	3e-38
Type II secretory pathway component PulF	U	AL954747	NE0596	COG1459	384	1.0e-108
Type II secretory pathway component PulF	U	AL954747	NE1256	COG1459	236	3e-63
Type II secretory pathway component PulF	U	AL954747	NE1610	COG1459	287	7e-79
Type II secretory pathway component PulJ	U	AL954747	NE1252	COG4795	44	1e-05
Type II secretory pathway component PulJ	U	AL954747	NE1308	COG4795	35	0.002
Type II secretory pathway component PulJ	U	AL954747	NE1602	COG4795	33	0.008
Type II secretory pathway component PulJ	U	AL954747	NE1611	COG4795	33	0.009
Type II secretory pathway component PulJ	U	AL954747	NE1746	COG4795	36	0.001
Type II secretory pathway component PulJ	U	AL954747	NE1749	COG4795	56	5e-09
Type II secretory pathway component PulJ	U	AL954747	NE1751	COG4795	46	1e-06
Type II secretory pathway prepilin signal peptidase PulO and related peptidase	U	AL954747	NE0597	COG1989	142	3e-35
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1252	COG2165	44	1e-05
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1253	COG2165	45	2e-06
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1255	COG2165	72	1e-14
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1308	COG2165	50	7e-08
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1601	COG2165	50	1e-07
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1602	COG2165	65	2e-12
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1603	COG2165	72	2e-14
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1611	COG2165	96	1e-21
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1746	COG2165	54	5e-09
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1749	COG2165	37	0.002
Type II secretory pathway pseudopilin PulG	U	AL954747	NE1751	COG2165	47	8e-07
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	AL954747	NE0720	COG0630	37	0.004
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	AL954747	NE0964	COG0630	78	1e-15
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	AL954747	NE0965	COG0630	76	3e-15
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	AL954747	NE1257	COG0630	88	2e-18
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	AL954747	NE1609	COG0630	91	2e-19
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	AL954747	NE2290	COG0630	75	2e-14
Type IV secretory pathway VirB11 protein involved in flagella biosynthesis	U	AL954747	NE2528	COG0630	37	0.007
Type IV secretory pathway VirB4 protein	U	AL954747	NE2489	COG3451	37	0.002
Type IV secretory pathway VirD4 protein	U	AL954747	NE0246	COG3505	175	9e-45

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