#                                                                           --- 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
#------------------- ----------             -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
HTH_28	PF13518.1	gi|304315533|ref|YP_003850679.1|	-	2.8e-05	24.0	0.1	7.4e-05	22.6	0.0	1.7	1	0	0	1	1	1	1	Helix-turn-helix	domain
HTH_17	PF12728.2	gi|304315533|ref|YP_003850679.1|	-	0.00039	20.6	0.1	0.0011	19.1	0.0	1.8	1	0	0	1	1	1	1	Helix-turn-helix	domain
HTH_3	PF01381.17	gi|304315533|ref|YP_003850679.1|	-	0.00058	19.6	0.0	0.0014	18.3	0.0	1.7	1	0	0	1	1	1	1	Helix-turn-helix
HTH_23	PF13384.1	gi|304315533|ref|YP_003850679.1|	-	0.00081	18.9	0.2	0.0044	16.6	0.0	2.2	2	0	0	2	2	2	1	Homeodomain-like	domain
HTH_19	PF12844.2	gi|304315533|ref|YP_003850679.1|	-	0.019	15.0	0.0	0.06	13.3	0.0	1.9	1	0	0	1	1	1	0	Helix-turn-helix	domain
DEAD	PF00270.24	gi|304315533|ref|YP_003850679.1|	-	0.034	13.6	0.0	0.31	10.5	0.0	2.3	1	1	0	1	1	1	0	DEAD/DEAH	box	helicase
DUF4349	PF14257.1	gi|304315533|ref|YP_003850679.1|	-	0.038	13.2	0.2	0.53	9.4	0.1	2.2	1	1	0	1	1	1	0	Domain	of	unknown	function	(DUF4349)
HTH_Tnp_1	PF01527.15	gi|304315533|ref|YP_003850679.1|	-	0.046	13.6	0.0	0.12	12.3	0.0	1.6	1	0	0	1	1	1	0	Transposase
HTH_38	PF13936.1	gi|304315533|ref|YP_003850679.1|	-	0.046	13.2	0.0	0.18	11.3	0.0	2.0	1	0	0	1	1	1	0	Helix-turn-helix	domain
HTH_31	PF13560.1	gi|304315533|ref|YP_003850679.1|	-	0.051	13.7	0.0	0.11	12.6	0.0	1.5	1	0	0	1	1	1	0	Helix-turn-helix	domain
HTH_26	PF13443.1	gi|304315533|ref|YP_003850679.1|	-	0.054	13.7	0.2	0.2	11.8	0.0	2.0	2	0	0	2	2	1	0	Cro/C1-type	HTH	DNA-binding	domain
HTH_29	PF13551.1	gi|304315533|ref|YP_003850679.1|	-	0.056	13.5	0.0	0.12	12.4	0.0	1.5	1	0	0	1	1	1	0	Winged	helix-turn	helix
DUF1323	PF07037.6	gi|304315533|ref|YP_003850679.1|	-	0.073	13.2	0.2	0.74	9.9	0.0	2.5	2	0	0	2	2	2	0	Putative	transcription	regulator	(DUF1323)
HTH_36	PF13730.1	gi|304315533|ref|YP_003850679.1|	-	0.074	13.1	0.0	0.3	11.2	0.0	2.1	2	0	0	2	2	1	0	Helix-turn-helix	domain
HTH_Tnp_4	PF13613.1	gi|304315533|ref|YP_003850679.1|	-	0.12	11.9	0.0	0.23	11.0	0.0	1.5	1	0	0	1	1	1	0	Helix-turn-helix	of	DDE	superfamily	endonuclease
Phage_AlpA	PF05930.7	gi|304315533|ref|YP_003850679.1|	-	0.14	11.9	0.0	0.37	10.5	0.0	1.7	1	0	0	1	1	1	0	Prophage	CP4-57	regulatory	protein	(AlpA)
HTH_IclR	PF09339.5	gi|304315533|ref|YP_003850679.1|	-	0.15	11.6	0.0	0.3	10.7	0.0	1.4	1	0	0	1	1	1	0	IclR	helix-turn-helix	domain
RAP1	PF07218.6	gi|304315535|ref|YP_003850681.1|	-	0.058	11.4	3.3	0.056	11.5	2.3	1.0	1	0	0	1	1	1	0	Rhoptry-associated	protein	1	(RAP-1)
Flp_N	PF03930.9	gi|304315536|ref|YP_003850682.1|	-	0.15	11.8	0.0	0.22	11.2	0.0	1.2	1	0	0	1	1	1	0	Recombinase	Flp	protein	N-terminus