#                                                                           --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name        accession  query name                       accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
#------------------- ----------             -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
Methyltransf_26	PF13659.1	gi|345133532|ref|YP_004821323.1|	-	2.7e-13	49.9	0.0	4.5e-13	49.2	0.0	1.4	1	0	0	1	1	1	1	Methyltransferase	domain
Eco57I	PF07669.6	gi|345133532|ref|YP_004821323.1|	-	7.5e-09	35.9	0.0	1.3e-08	35.0	0.0	1.3	1	0	0	1	1	1	1	Eco57I	restriction-modification	methylase
TaqI_C	PF12950.2	gi|345133532|ref|YP_004821323.1|	-	5.9e-08	32.4	0.0	9e-08	31.8	0.0	1.3	1	0	0	1	1	1	1	TaqI-like	C-terminal	specificity	domain
MTS	PF05175.9	gi|345133532|ref|YP_004821323.1|	-	0.0057	16.0	0.0	0.0089	15.4	0.0	1.2	1	0	0	1	1	1	1	Methyltransferase	small	domain
N6_Mtase	PF02384.11	gi|345133532|ref|YP_004821323.1|	-	0.0096	15.0	0.0	0.036	13.1	0.0	1.8	1	1	0	1	1	1	1	N-6	DNA	Methylase
TrmB	PF01978.14	gi|345133533|ref|YP_004821324.1|	-	0.0037	16.9	0.0	0.047	13.4	0.0	2.3	2	0	0	2	2	2	1	Sugar-specific	transcriptional	regulator	TrmB
MarR_2	PF12802.2	gi|345133533|ref|YP_004821324.1|	-	0.0045	16.6	0.3	0.032	13.8	0.1	2.1	2	0	0	2	2	2	1	MarR	family
HTH_24	PF13412.1	gi|345133533|ref|YP_004821324.1|	-	0.022	14.1	0.0	0.31	10.4	0.0	2.1	2	0	0	2	2	2	0	Winged	helix-turn-helix	DNA-binding
HTH_11	PF08279.7	gi|345133533|ref|YP_004821324.1|	-	0.024	14.2	0.1	0.043	13.4	0.0	1.3	1	0	0	1	1	1	0	HTH	domain
HTH_AsnC-type	PF13404.1	gi|345133533|ref|YP_004821324.1|	-	0.028	13.9	0.2	0.12	11.9	0.2	2.0	2	0	0	2	2	2	0	AsnC-type	helix-turn-helix	domain
HTH_20	PF12840.2	gi|345133533|ref|YP_004821324.1|	-	0.028	14.2	0.0	0.06	13.1	0.0	1.6	1	0	0	1	1	1	0	Helix-turn-helix	domain
UPF0150	PF03681.10	gi|345133538|ref|YP_004821329.1|	-	7.4e-06	25.4	0.1	1.4e-05	24.6	0.1	1.5	1	1	0	1	1	1	1	Uncharacterised	protein	family	(UPF0150)
DUF3832	PF12909.2	gi|345133538|ref|YP_004821329.1|	-	0.053	13.5	0.0	0.073	13.1	0.0	1.2	1	0	0	1	1	1	0	Protein	of	unknown	function	(DUF3832)
DUF3837	PF12939.2	gi|345133538|ref|YP_004821329.1|	-	0.091	12.7	0.0	0.14	12.1	0.0	1.3	1	0	0	1	1	1	0	Domain	of	unknown	function	(DUF3837)
YcfA	PF07927.7	gi|345133539|ref|YP_004821330.1|	-	9.6e-09	35.0	0.0	1.2e-08	34.7	0.0	1.1	1	0	0	1	1	1	1	YcfA-like	protein
Toprim_3	PF13362.1	gi|345133542|ref|YP_004821333.1|	-	0.00051	20.2	0.1	0.0029	17.8	0.0	2.5	2	0	0	2	2	2	1	Toprim	domain
Toprim_N	PF08275.6	gi|345133542|ref|YP_004821333.1|	-	0.0047	16.8	0.0	0.0083	16.0	0.0	1.5	1	0	0	1	1	1	1	DNA	primase	catalytic	core,	N-terminal	domain
Smr	PF01713.16	gi|345133542|ref|YP_004821333.1|	-	0.0077	16.3	0.0	0.037	14.2	0.0	2.3	2	0	0	2	2	2	1	Smr	domain
Toprim_4	PF13662.1	gi|345133542|ref|YP_004821333.1|	-	0.046	13.7	0.0	0.12	12.3	0.0	1.8	1	0	0	1	1	1	0	Toprim	domain
DUF3324	PF11797.3	gi|345133543|ref|YP_004821334.1|	-	0.11	12.1	0.0	0.17	11.6	0.0	1.2	1	0	0	1	1	1	0	Protein	of	unknown	function	C-terminal	(DUF3324)
DUF3659	PF12396.3	gi|345133543|ref|YP_004821334.1|	-	0.13	11.9	0.8	0.35	10.5	0.1	2.1	2	1	0	2	2	2	0	Protein	of	unknown	function	(DUF3659)
zf-LSD1	PF06943.7	gi|345133544|ref|YP_004821335.1|	-	0.079	12.5	1.1	0.14	11.7	0.8	1.4	1	0	0	1	1	1	0	LSD1	zinc	finger
Crp	PF00325.15	gi|345133545|ref|YP_004821336.1|	-	0.00081	18.8	0.1	0.0017	17.7	0.0	1.5	1	0	0	1	1	1	1	Bacterial	regulatory	proteins,	crp	family
TrmB	PF01978.14	gi|345133545|ref|YP_004821336.1|	-	0.0024	17.5	0.1	0.024	14.3	0.0	2.2	2	0	0	2	2	2	1	Sugar-specific	transcriptional	regulator	TrmB
HTH_11	PF08279.7	gi|345133545|ref|YP_004821336.1|	-	0.0038	16.8	0.1	0.02	14.5	0.0	2.0	1	1	1	2	2	2	1	HTH	domain
FaeA	PF04703.7	gi|345133545|ref|YP_004821336.1|	-	0.0043	17.1	0.0	0.011	15.8	0.0	1.7	2	0	0	2	2	2	1	FaeA-like	protein
HTH_Crp_2	PF13545.1	gi|345133545|ref|YP_004821336.1|	-	0.005	16.6	0.0	0.0096	15.6	0.0	1.4	1	0	0	1	1	1	1	Crp-like	helix-turn-helix	domain
HTH_DeoR	PF08220.7	gi|345133545|ref|YP_004821336.1|	-	0.011	15.1	0.1	0.032	13.7	0.1	1.7	1	0	0	1	1	1	0	DeoR-like	helix-turn-helix	domain
MarR_2	PF12802.2	gi|345133545|ref|YP_004821336.1|	-	0.024	14.3	1.0	0.47	10.1	0.3	2.9	4	0	0	4	4	4	0	MarR	family
HTH_17	PF12728.2	gi|345133545|ref|YP_004821336.1|	-	0.077	13.2	0.2	0.18	12.1	0.1	1.6	1	0	0	1	1	1	0	Helix-turn-helix	domain
PaaX	PF07848.7	gi|345133545|ref|YP_004821336.1|	-	0.084	12.8	0.4	0.18	11.8	0.3	1.5	1	0	0	1	1	1	0	PaaX-like	protein
HTH_20	PF12840.2	gi|345133545|ref|YP_004821336.1|	-	0.09	12.5	0.1	0.62	9.9	0.1	2.3	2	1	1	3	3	3	0	Helix-turn-helix	domain
HTH_23	PF13384.1	gi|345133545|ref|YP_004821336.1|	-	0.1	12.2	3.7	0.18	11.5	0.4	2.7	2	1	0	2	2	2	0	Homeodomain-like	domain
SHOCT	PF09851.4	gi|345133545|ref|YP_004821336.1|	-	0.12	11.8	0.6	0.29	10.6	0.4	1.6	1	0	0	1	1	1	0	Short	C-terminal	domain
SpaB_C	PF14028.1	gi|345133545|ref|YP_004821336.1|	-	0.49	9.8	7.4	36	3.7	5.1	2.0	1	1	0	1	1	1	0	SpaB	C-terminal	domain
DDE_Tnp_1	PF01609.16	gi|345133548|ref|YP_004821339.1|	-	5.6e-07	29.3	0.1	1e-06	28.4	0.1	1.4	1	0	0	1	1	1	1	Transposase	DDE	domain
DNA_ligase_IV	PF11411.3	gi|345133549|ref|YP_004821340.1|	-	0.06	13.0	0.0	0.18	11.5	0.0	1.8	2	0	0	2	2	2	0	DNA	ligase	IV
HTH_23	PF13384.1	gi|345133550|ref|YP_004821341.1|	-	0.00025	20.5	0.0	0.00065	19.2	0.0	1.7	1	0	0	1	1	1	1	Homeodomain-like	domain
Sigma70_r4_2	PF08281.7	gi|345133550|ref|YP_004821341.1|	-	0.0026	17.1	0.0	0.023	14.1	0.0	2.4	2	0	0	2	2	2	1	Sigma-70,	region	4
CENP-B_N	PF04218.8	gi|345133550|ref|YP_004821341.1|	-	0.051	13.0	1.9	0.068	12.5	0.0	2.0	2	0	0	2	2	2	0	CENP-B	N-terminal	DNA-binding	domain
DUF2209	PF09974.4	gi|345133550|ref|YP_004821341.1|	-	0.12	12.5	0.0	0.23	11.5	0.0	1.6	1	0	0	1	1	1	0	Uncharacterized	protein	conserved	in	archaea	(DUF2209)
HTH_IclR	PF09339.5	gi|345133550|ref|YP_004821341.1|	-	0.12	11.9	0.0	0.21	11.1	0.0	1.4	1	0	0	1	1	1	0	IclR	helix-turn-helix	domain
HTH_28	PF13518.1	gi|345133550|ref|YP_004821341.1|	-	0.17	11.9	2.3	0.29	11.1	0.0	2.5	3	0	0	3	3	3	0	Helix-turn-helix	domain
DUF1839	PF08893.5	gi|345133551|ref|YP_004821342.1|	-	0.1	11.5	0.0	0.11	11.5	0.0	1.1	1	0	0	1	1	1	0	Domain	of	unknown	function	(DUF1839)
LIM_bind	PF01803.11	gi|345133553|ref|YP_004821344.1|	-	0.15	11.1	0.0	0.18	10.8	0.0	1.2	1	0	0	1	1	1	0	LIM-domain	binding	protein
DUF3110	PF11360.3	gi|345133554|ref|YP_004821345.1|	-	0.044	13.5	0.0	0.06	13.1	0.0	1.3	1	0	0	1	1	1	0	Protein	of	unknown	function	(DUF3110)
DDE_Tnp_1	PF01609.16	gi|345133555|ref|YP_004821346.1|	-	0.01	15.4	0.1	0.044	13.3	0.1	2.0	1	1	0	1	1	1	0	Transposase	DDE	domain
AAA_10	PF12846.2	gi|345133556|ref|YP_004821347.1|	-	3.1e-10	39.9	0.8	8.1e-10	38.6	0.0	1.9	2	1	0	2	2	2	1	AAA-like	domain
CagE_TrbE_VirB	PF03135.9	gi|345133556|ref|YP_004821347.1|	-	4.3e-07	29.8	0.1	8.9e-07	28.8	0.0	1.4	1	1	0	1	1	1	1	CagE,	TrbE,	VirB	family,	component	of	type	IV	transporter	system
DUF4355	PF14265.1	gi|345133556|ref|YP_004821347.1|	-	0.13	12.2	2.2	0.29	11.0	1.5	1.5	1	0	0	1	1	1	0	Domain	of	unknown	function	(DUF4355)
Zn_Tnp_IS1595	PF12760.2	gi|345133557|ref|YP_004821348.1|	-	0.00014	21.5	3.3	0.012	15.4	0.0	3.1	2	1	1	3	3	3	1	Transposase	zinc-ribbon	domain
DZR	PF12773.2	gi|345133557|ref|YP_004821348.1|	-	0.00016	21.3	10.9	0.00035	20.3	7.6	1.5	1	1	0	1	1	1	1	Double	zinc	ribbon
DnaJ_CXXCXGXG	PF00684.14	gi|345133557|ref|YP_004821348.1|	-	0.00081	19.3	8.2	0.0015	18.5	5.7	1.4	1	0	0	1	1	1	1	DnaJ	central	domain
HypA	PF01155.14	gi|345133557|ref|YP_004821348.1|	-	0.0043	16.7	6.9	0.054	13.1	0.2	2.1	1	1	1	2	2	2	2	Hydrogenase	expression/synthesis	hypA	family
NMD3	PF04981.8	gi|345133557|ref|YP_004821348.1|	-	0.049	12.7	0.5	0.049	12.7	0.4	1.4	1	1	0	1	1	1	0	NMD3	family
PyrI_C	PF02748.10	gi|345133557|ref|YP_004821348.1|	-	0.056	12.8	0.1	0.42	10.0	0.0	2.0	2	0	0	2	2	2	0	Aspartate	carbamoyltransferase	regulatory	chain,	metal	binding	domain
DUF4379	PF14311.1	gi|345133557|ref|YP_004821348.1|	-	0.08	12.7	8.8	0.37	10.6	0.5	3.2	2	1	2	4	4	4	0	Domain	of	unknown	function	(DUF4379)
zf-MYND	PF01753.13	gi|345133557|ref|YP_004821348.1|	-	0.09	12.6	6.5	2.4	8.1	0.1	2.2	2	0	0	2	2	2	0	MYND	finger
Cytochrome_C7	PF14522.1	gi|345133557|ref|YP_004821348.1|	-	0.15	11.7	7.5	0.51	10.0	5.3	1.9	1	1	0	1	1	1	0	Cytochrome	c7
Spt4	PF06093.8	gi|345133557|ref|YP_004821348.1|	-	0.26	11.1	2.4	0.48	10.3	0.1	2.1	2	0	0	2	2	2	0	Spt4/RpoE2	zinc	finger
DUF1451	PF07295.6	gi|345133557|ref|YP_004821348.1|	-	0.33	10.7	6.3	4.3	7.0	0.3	2.2	2	0	0	2	2	2	0	Protein	of	unknown	function	(DUF1451)
zf-C4pol	PF14260.1	gi|345133557|ref|YP_004821348.1|	-	0.82	9.7	5.8	11	6.0	4.0	2.2	1	1	0	1	1	1	0	C4-type	zinc-finger	of	DNA	polymerase	delta
zf-C3HC4_3	PF13920.1	gi|345133557|ref|YP_004821348.1|	-	0.9	9.2	7.9	6	6.6	1.1	2.2	2	0	0	2	2	2	0	Zinc	finger,	C3HC4	type	(RING	finger)
Terminase_GpA	PF05876.7	gi|345133557|ref|YP_004821348.1|	-	0.95	7.7	4.1	10	4.3	2.3	2.2	1	1	1	2	2	2	0	Phage	terminase	large	subunit	(GpA)
Copper-fist	PF00649.13	gi|345133557|ref|YP_004821348.1|	-	1.1	8.5	4.6	0.24	10.6	0.3	2.0	2	0	0	2	2	2	0	Copper	fist	DNA	binding	domain
DUF2072	PF09845.4	gi|345133557|ref|YP_004821348.1|	-	1.6	8.6	7.0	1.6	8.6	0.3	2.2	1	1	1	2	2	2	0	Zn-ribbon	containing	protein	(DUF2072)
zf-UBP	PF02148.14	gi|345133557|ref|YP_004821348.1|	-	1.7	8.8	6.0	7.1	6.8	1.0	2.4	2	1	0	2	2	2	0	Zn-finger	in	ubiquitin-hydrolases	and	other	protein
Cytochrom_c3_2	PF14537.1	gi|345133557|ref|YP_004821348.1|	-	2.1	8.7	8.8	6.8	7.1	6.1	1.8	1	1	0	1	1	1	0	Cytochrome	c3
Nudix_N_2	PF14803.1	gi|345133557|ref|YP_004821348.1|	-	2.2	8.0	11.8	5.7	6.7	0.3	4.0	4	0	0	4	4	4	0	Nudix	N-terminal
Ribosomal_L37e	PF01907.14	gi|345133557|ref|YP_004821348.1|	-	2.3	8.0	7.5	4.4	7.1	0.2	2.6	2	1	0	2	2	2	0	Ribosomal	protein	L37e
NCD3G	PF07562.9	gi|345133557|ref|YP_004821348.1|	-	2.6	7.8	9.0	4.4	7.0	0.9	2.3	2	0	0	2	2	2	0	Nine	Cysteines	Domain	of	family	3	GPCR
zf-ribbon_3	PF13248.1	gi|345133557|ref|YP_004821348.1|	-	3.5	6.9	14.3	0.32	10.2	1.6	2.5	2	1	0	2	2	2	0	zinc-ribbon	domain
zinc_ribbon_2	PF13240.1	gi|345133557|ref|YP_004821348.1|	-	8.7	5.9	17.6	2.1	7.9	2.6	2.3	2	0	0	2	2	2	0	zinc-ribbon	domain
HTH_24	PF13412.1	gi|345133559|ref|YP_004821350.1|	-	0.064	12.6	0.0	0.21	10.9	0.0	1.8	2	0	0	2	2	2	0	Winged	helix-turn-helix	DNA-binding
HTH_IclR	PF09339.5	gi|345133559|ref|YP_004821350.1|	-	0.15	11.6	0.0	0.23	11.0	0.0	1.3	1	0	0	1	1	1	0	IclR	helix-turn-helix	domain
UPF0150	PF03681.10	gi|345133561|ref|YP_004821352.1|	-	1.5e-05	24.5	0.1	2.5e-05	23.8	0.0	1.4	1	0	0	1	1	1	1	Uncharacterised	protein	family	(UPF0150)
XhoI	PF04555.8	gi|345133562|ref|YP_004821353.1|	-	2.2e-64	216.5	0.0	2.6e-64	216.2	0.0	1.0	1	0	0	1	1	1	1	Restriction	endonuclease	XhoI