Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

Powell, Bradford C; Hutchison, Clyde A

doi:10.1186/1471-2105-7-31

Table 2 ORFs in Majority-annotated mixed COGs of stringency 6 that may represent missed genes

ORF COG id^a	Organism	Genomic coordinates^b	Annotated gene(s) present in COG^c	ORF COG id^a	Organism	Genomic coordinates^b	Annotated gene(s) present in COG^c
Potential genes missed in current annotations				Potential genes missed in current annotations (continued)
678	Bbur	117772-116825	cdsA	397	Nmen	340008-339358	coaE
314	Bhal	1503738-1503905	rpmG	871	Nmen	554238-552676	mucD/deg
314	Bsub	2477091-2476963	rpmG	723	Nmen	666433-665363	potA/cysA/malK
2346	Bsub	4202360-4202148		119	Nmen	690163-687386	trkH
1717	Cace	243535-242696	alx	1382	Nmen	1056138-1057340	hflX
1908	Cace	1395172-1395522	minE	464	Nmen	1147918-1149261	tilS
2064	Cace	2284461-2283778		464	Nmen	1179954-1181297	tilS
148	Cace	3287735-3286509	tufA	2743	Nmen	1400226-1401977
1840	Cace	3650828-3649308		978	Nmen	1484110-1486353	dnaX
659	Cace	3842459-3840768	plpB	635	Nmen	1527781-1528521
1551	EcoK12	311756-311598	rpmJ	1248	Nmen	1629570-1628017	pepA
148	EcoK12	3469408-3468167	tufA	2793	Nmen	1749455-1752016	gcvP
1551	EcoO157	344941-344783	rpmJ	618	Nmen	2119341-2120882	hrpB
2748	EcoO157	4240898-4240665		618	Nmen	2124720-2128169	hrpB
2531	Hinf	131970-132959	mltA	788	Nmen	2199859-2200686	folD
2319	Hinf	170676-169396	dcuB	2519	Paer	224101-225219	ald
2432	Hinf	235913-238519		1385	Paer	434829-433933
2947	Hinf	370735-372912		38	Paer	4143744-4142569	prfA
1098	Hpyl	315887-316504	dppC	2748	Sent	4247574-4247864
309	Lmon	640139-639558	bioY	192	Tpal	213049-213270	rpmD
2023	Mgen	180733-181020		653	Tpal	624206-625738	ptsP
994	Mmob	102995-102588	nusB	890	Tpal	946250-944889	comM
3131	Mmob	201807-201646	rpmG	946	Tpal	1032059-1031772
3175	Mmob	317659-317411	secG	39	Upar	3002-3886	hemK
3186	Mmob	449811-451241		142	Upar	3861-4427
3000	Mmyc	441031-441783		3131	Upar	725869-726024	rpmG
542	Mmyc	441031-441783		38	VchoI	709524-710558	prfA
199	Mmyc	830915-830742	rpmI	2932	VchoI	1045279-1044317
73	Mmyc	831148-830924	infA	2947	VchoI	1627856-1625871
182	Mmyc	836915-836712	rpsN	1246	VchoI	2869620-2871836	pulA/glgX
3175	Mmyc	973088-973423	secG	2793	VchoII	295059-292882	gcvP
3131	Mmyc	1089962-1090141	rpmG	2621	VchoII	299032-300000	gcvT
314	Mmyc	1089962-1090141	rpmG	2699	VchoII	406033-405167	sbp
1670	Mpen	2755-3009		2573	VchoII	987698-986424	aroF/aroG/aroH
3131	Mpen	1191375-1191163	rpmG	2340	VchoII	1026697-1023563	dhaS/aldA
879	Mpen	1226934-1226722	rpmI
199	Mpen	1317088-1316960	rpmI	Gene annotated in different frame^d
166	Mpen	1327926-1326898	rplV	1769	Bhal	251734-251429	nrdG
2023	Mpne	207436-207717		3183	Mpul	130854-130480
2090	Nmen	70930-70358		3175	Mpul	412829-413074	secG
148	Nmen	149590-150777	tufA	946	Rpro	433751-433479
2564	Nmen	238562-237666		363	Tpal	262583-262897	rpsT
2572	Nmen	299359-298070	phr

^aThe identifiers for COGs are local to this study. They do not correspond to numbers in the NCBI COG database.
^bCoordinates in which the first number is greater than the second indicate that the ORF is on the minus strand.
^cA named annotated putative ortholog in another organism or paralog within the organism to the ORF listed.
^dThese COGs may indicate both that the ORF listed is a missed gene and that the annotated

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ISSN: 1471-2105

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