#                                                                           --- 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	PF13518.6	gi|304315533|ref|YP_003850679.1|	-	0.00057	19.9	0.0	0.0015	18.6	0.0	1.7	1	0	0	1	1	1	1	Helix-turn-helix	domain
HTH_36	PF13730.6	gi|304315533|ref|YP_003850679.1|	-	0.00066	19.6	0.0	0.0036	17.2	0.0	2.3	3	0	0	3	3	3	1	Helix-turn-helix	domain
HTH_3	PF01381.22	gi|304315533|ref|YP_003850679.1|	-	0.0007	19.6	0.0	0.0018	18.3	0.0	1.7	1	0	0	1	1	1	1	Helix-turn-helix
HTH_17	PF12728.7	gi|304315533|ref|YP_003850679.1|	-	0.0014	18.8	0.1	0.0038	17.4	0.1	1.7	1	0	0	1	1	1	1	Helix-turn-helix	domain
HTH_23	PF13384.6	gi|304315533|ref|YP_003850679.1|	-	0.0033	17.2	0.2	0.01	15.6	0.0	2.0	2	0	0	2	2	2	1	Homeodomain-like	domain
HTH_29	PF13551.6	gi|304315533|ref|YP_003850679.1|	-	0.006	16.6	0.0	0.014	15.4	0.0	1.5	1	0	0	1	1	1	1	Winged	helix-turn	helix
HTH_31	PF13560.6	gi|304315533|ref|YP_003850679.1|	-	0.036	14.4	0.0	0.074	13.4	0.0	1.5	1	0	0	1	1	1	0	Helix-turn-helix	domain
HTH_26	PF13443.6	gi|304315533|ref|YP_003850679.1|	-	0.046	14.2	0.0	0.16	12.4	0.0	1.9	1	0	0	1	1	1	0	Cro/C1-type	HTH	DNA-binding	domain
YdaS_antitoxin	PF15943.5	gi|304315533|ref|YP_003850679.1|	-	0.048	13.5	0.0	0.15	12.0	0.0	1.8	1	0	0	1	1	1	0	Putative	antitoxin	of	bacterial	toxin-antitoxin	system,	YdaS/YdaT
DUF4349	PF14257.6	gi|304315533|ref|YP_003850679.1|	-	0.14	11.5	0.2	0.95	8.9	0.2	2.2	1	1	0	1	1	1	0	Domain	of	unknown	function	(DUF4349)
HTH_IclR	PF09339.10	gi|304315533|ref|YP_003850679.1|	-	0.16	11.8	0.0	0.31	10.9	0.0	1.5	1	0	0	1	1	1	0	IclR	helix-turn-helix	domain
Phage_AlpA	PF05930.12	gi|304315533|ref|YP_003850679.1|	-	0.17	11.7	0.0	0.48	10.3	0.0	1.7	1	0	0	1	1	1	0	Prophage	CP4-57	regulatory	protein	(AlpA)
DUF1323	PF07037.11	gi|304315533|ref|YP_003850679.1|	-	0.18	12.2	0.2	1.7	9.1	0.0	2.5	2	0	0	2	2	2	0	Putative	transcription	regulator	(DUF1323)
RAP1	PF07218.11	gi|304315535|ref|YP_003850681.1|	-	0.057	11.7	3.3	0.058	11.7	3.3	1.0	1	0	0	1	1	1	0	Rhoptry-associated	protein	1	(RAP-1)
Flp_N	PF03930.14	gi|304315536|ref|YP_003850682.1|	-	0.18	11.8	0.0	0.27	11.2	0.0	1.2	1	0	0	1	1	1	0	Recombinase	Flp	protein	N-terminus
#
# Program:         hmmscan
# Version:         3.2.1 (June 2018)
# Pipeline mode:   SCAN
# Query file:      /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanothermobacter_marburgensis_Marburg_uid51637/NC_014409.faa
# Target file:     /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# Option settings: /oak/stanford/groups/akundaje/marinovg/programs/hmmer-3.2.1/bin/hmmscan -o /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanothermobacter_marburgensis_Marburg_uid51637/NC_014409.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanothermobacter_marburgensis_Marburg_uid51637/NC_014409.PFam32-A.tblout --cpu 20 /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanothermobacter_marburgensis_Marburg_uid51637/NC_014409.faa 
# Current dir:     /oak/stanford/groups/akundaje/marinovg/genomes
# Date:            Mon Mar 25 15:51:56 2019
# [ok]