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 3 ORFs in majority-annotated mixed COGs that do not appear to 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
Existing annotation of pseudogene				Frameshift 3' fragment^c
876	EcoK12	1488620-1487985	gap	1036	Bbur	21098-20445	queA
2340	Sent	4738725-4740071	dhaS/aldA	1750	Bhal	984866-983856	celB
2433	Sent	4745051-4743573	hsdB	1188	Bhal	1359362-1360555	recD
1895	Sent	3243737-3244861	fadH	2257	Bhal	3182850-3181696	ilvI/poxB/alsS
1399	Sent	461578-461874		88	Bsub	3671944-3672555	gtaB
653	Sent	2505700-2506824	ptsP	641	Hinf	1525427-1524561	thiI
1058	Sent	3413535-3416306	acrD/mdtC/mdtB	2031	Hinf	1719924-1718821	tldD
3088	Sent	4084807-4083605		2473	Mgal	431452-431778	fldA
815	Sent	1360931-1362226	rhlE	2309	Mgen	416785-416336	acpD
3104	Sent	4009730-4009993		975	Mmyc	57011-56760	recR
569	Sent	1969437-1970648	penA	686	Mmyc	690895-690356	rpsB
				1319	Nmen	107757-109406	msbA
Annotated in GenomeReviews but with different stop				842	Nmen	1995043-1994876
928	Bsub	2500726-2499347	bfmBC	556	VchoI	553588-552383	dnaG
157	Cper	2751593-2751051	rplD	745	VchoI	555313-556182	gcp
999	EcoO157	3613249-3610595	alaS	106	VchoI	1087924-1089819	uvrB
107	Hinf	655042-654365	metI	2435	VchoI	2612949-2611972
589	Mpne	329463-331229	lepA	2807	VchoII	1060889-1060107	qseC
210	Mpul	150772-151668	grpE
743	Sent	2492196-2490763	gltX	Frameshift 5' fragment^c
534	Tpal	478406-478777		697	Bhal	3580443-3579682	csd
166	Upar	279005-279949	rplV	2029	Bsub	2304436-2305248	metA
				2049	Bsub	3032201-3032512
Fragments around stop codons (nonsense)^c				2	Cpne	383405-384037	recF
928	Bsub	2500726-2499347	bfmBC	462	Cpne	1088259-1088711	ispE
157	Cper	2751593-2751051	rplD	2769	EcoK12	3814680-3813886	rph
999	EcoO157	3613249-3610595	alaS	2257	EcoK12	3948538-3949566	ilvI/poxB/alsS
107	Hinf	655042-654365	metI	2433	Hinf	232074-232991
589	Mpne	329463-331229	lepA	3066	Hinf	1377365-1378063	dgt
210	Mpul	150772-151668	grpE	1075	Hinf	1477189-1476557	pstB
743	Sent	2492196-2490763		641	Hinf	1526028-1525285	thiI
				2571	Nmen	292645-294051
				220	Tpal	220772-221749	dnaJ
				556	VchoI	554244-553561	dnaG
				1826	VchoI	637551-638246	amt
				42	VchoI	851189-849954	oadA
				1082	VchoII	690599-690273	glpF

^aThe identifers 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 categories represent probable pseudogenes or sequencing errors.

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ISSN: 1471-2105

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