Transcription

BASAL TRANSCRIPTION FACTORS

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Transcription antiterminator	K	Contig119	72	COG0250	122	1e-29
Transcription elongation factor	K	Contig188	512	COG0782	131	2e-32
Transcription elongation factor	K	Contig88	777	COG0195	151	7e-38
Transcription termination factor	K	Contig113	41	COG1158	61	2e-11
Transcription termination factor	K	Contig157	258	COG0781	65	2e-12
Transcription termination factor	K	Contig188	513	COG1158	41	2e-04
Transcription termination factor	K	Contig91	784	COG1158	631	0.0

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Cold shock protein	K	Contig174	366	COG1278	71	1e-14
DNA-binding winged-HTH domains	K	Contig193	567	COG3710	47	1e-06

DNA-DEPENDENT RNA POLYMERASE SUBUNITS

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
DNA-directed RNA polymerase alpha subunit/40 kD subunit	K	Contig145	187	COG0202	279	2e-76
DNA-directed RNA polymerase beta subunit/140 kD subunit	K	Contig158	262	COG0085	666	0.0
DNA-directed RNA polymerase beta subunit/140 kD subunit	K	Contig158	263	COG0085	268	2e-73
DNA-directed RNA polymerase beta' subunit/160 kD subunit	K	Contig158	264	COG0086	790	0.0
DNA-directed RNA polymerase delta subunit	K	Contig166	299	COG3343	40	0.001
DNA-directed RNA polymerase delta subunit	K	Contig192	555	COG3343	41	2e-04
DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)	K	Contig197	639	COG0568	316	3e-87
DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)	K	Contig89	778	COG0568	112	2e-26
DNA-directed RNA polymerase specialized sigma subunit	K	Contig197	639	COG1191	121	1e-28
DNA-directed RNA polymerase specialized sigma subunit	K	Contig89	778	COG1191	35	0.005
DNA-directed RNA polymerase subunit E'	K	Contig177	392	COG1095	48	2e-06
DNA-directed RNA polymerase subunit K/omega	K	Contig144	182	COG1758	60	7e-11

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
DNA helicase TIP49 TBP-interacting protein	K	Contig186	486	COG1224	49	6e-07
DNA helicase TIP49 TBP-interacting protein	K	Contig189	523	COG1224	45	1e-05
DNA or RNA helicase of superfamily II	K	Contig143	179	COG1061	47	2e-06
DNA or RNA helicase of superfamily II	K	Contig167	306	COG1061	79	1e-15
DNA or RNA helicase of superfamily II	K	Contig196	612	COG1061	58	4e-09
dsRNA-specific ribonuclease	K	Contig108	26	COG0571	217	6e-58
Exoribonuclease R	K	Contig129	114	COG0557	39	8e-04
Exoribonuclease R	K	Contig177	392	COG0557	37	0.003
Histone chaperone involved in gene silencing	K	Contig166	299	COG5137	41	4e-04
Histone chaperone involved in gene silencing	K	Contig192	555	COG5137	40	4e-04
Nucleosome binding factor SPN SPT16 subunit	K	Contig166	299	COG5406	39	0.001
Nucleosome binding factor SPN SPT16 subunit	K	Contig192	555	COG5406	42	2e-04
Predicted transcriptional regulator BolA superfamily protein	K	Contig118	69	COG5007	51	2e-08
Predicted transcriptional regulator protein containing CBS domains	K	Contig166	300	COG4109	36	0.005
RecG-like helicase	K	Contig143	179	COG1200	51	2e-07
RecG-like helicase	K	Contig167	306	COG1200	574	1.0e-165
RecG-like helicase	K	Contig196	612	COG1200	311	2e-85
Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain	K	Contig134	131	COG4567	43	4e-05
Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain	K	Contig193	567	COG4567	44	9e-06
Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain	K	Contig197	636	COG4567	50	5e-07
Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain	K	Contig200	681	COG4567	65	2e-11
Response regulator containing a CheY-like receiver domain and an HD-GYP domain	K	Contig134	131	COG3437	108	7e-25
Response regulator containing a CheY-like receiver domain and an HD-GYP domain	K	Contig193	567	COG3437	57	2e-09
Response regulator containing a CheY-like receiver domain and an HD-GYP domain	K	Contig197	636	COG3437	65	2e-11
Response regulator containing a CheY-like receiver domain and an HD-GYP domain	K	Contig200	681	COG3437	80	4e-16
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain	K	Contig134	131	COG2197	75	1e-14
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain	K	Contig193	567	COG2197	64	1e-11
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain	K	Contig197	636	COG2197	56	1e-08
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain	K	Contig200	681	COG2197	68	1e-12
Response regulator of citrate/malate metabolism	K	Contig134	131	COG4565	57	3e-09
Response regulator of citrate/malate metabolism	K	Contig193	567	COG4565	56	2e-09
Response regulator of citrate/malate metabolism	K	Contig197	636	COG4565	47	7e-06
Response regulator of citrate/malate metabolism	K	Contig200	681	COG4565	70	3e-13
Response regulator of the LytR/AlgR family	K	Contig134	131	COG3279	51	2e-07
Response regulator of the LytR/AlgR family	K	Contig193	567	COG3279	36	0.002
Response regulator of the LytR/AlgR family	K	Contig197	636	COG3279	47	9e-06
Response regulator of the LytR/AlgR family	K	Contig200	681	COG3279	50	3e-07
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain	K	Contig134	131	COG0745	103	2e-23
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain	K	Contig193	567	COG0745	187	5e-49
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain	K	Contig197	636	COG0745	62	1e-10
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain	K	Contig200	681	COG0745	88	1e-18
Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain	K	Contig200	681	COG4650	84	3e-17
SOS-response transcriptional repressors (RecA-mediated autopeptidase)	K	Contig193	568	COG1974	38	4e-04
Superfamily II DNA and RNA helicase	K	Contig167	306	COG0513	70	5e-13
Superfamily II DNA and RNA helicase	K	Contig196	612	COG0513	74	6e-14
Transcriptional accessory protein	K	Contig129	114	COG2183	63	5e-11
Transcriptional accessory protein	K	Contig177	392	COG2183	55	1e-08
Transcriptional activator of acetoin/glycerol metabolism	K	Contig200	681	COG3284	202	6e-53

TRANSCRIPTIONAL REGULATORS

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Predicted transcriptional regulator protein consists of a Zn-ribbon and ATP-cone domains	K	Contig178	398	COG1327	185	1e-48
Predicted transcriptional regulator protein	K	Contig130	120	COG1396	42	3e-05
Predicted transcriptional regulator protein	K	Contig130	120	COG1476	36	0.002
Predicted transcriptional regulator protein	K	Contig138	151	COG1959	110	3e-25
Predicted transcriptional regulator protein	K	Contig180	416	COG1475	141	5e-35
Predicted transcriptional regulator protein	K	Contig193	568	COG1396	47	8e-07
Predicted transcriptional regulator protein	K	Contig193	568	COG2932	66	2e-12
Predicted transcriptional regulator protein	K	Contig195	602	COG0789	47	3e-07
Putative transcriptional regulator protein	K	Contig140	160	COG1521	153	1e-38
Transcriptional regulator containing GAF AAA-type ATPase and DNA binding domains	K	Contig124	89	COG3604	40	6e-04
Transcriptional regulator containing GAF AAA-type ATPase and DNA binding domains	K	Contig200	681	COG3604	244	9e-66
Transcriptional regulator containing PAS AAA-type ATPase and DNA-binding domains	K	Contig124	89	COG3829	47	2e-06
Transcriptional regulator containing PAS AAA-type ATPase and DNA-binding domains	K	Contig189	523	COG3829	37	0.004
Transcriptional regulator containing PAS AAA-type ATPase and DNA-binding domains	K	Contig200	681	COG3829	261	7e-71
Transcriptional regulator of aromatic amino acids metabolism	K	Contig200	681	COG3283	178	7e-46
Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs	K	Contig109	30	COG1167	42	1e-04
Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs	K	Contig138	152	COG1167	40	3e-04
Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs	K	Contig146	188	COG1167	123	2e-29
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain	K	Contig124	89	COG1221	52	1e-07
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain	K	Contig154	238	COG1221	39	6e-04
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain	K	Contig169	323	COG1221	42	2e-04
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain	K	Contig200	681	COG1221	202	3e-53

COG Name	Group	Contig	Gene	COG ID	Score	Evalue
Transcription-repair coupling factor (superfamily II helicase)	K	Contig143	179	COG1197	43	4e-05
Transcription-repair coupling factor (superfamily II helicase)	K	Contig167	306	COG1197	314	1e-86
Transcription-repair coupling factor (superfamily II helicase)	K	Contig196	612	COG1197	959	0.0

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