#                                                                           --- 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
#------------------- ----------             -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
GerE	PF00196.19	gi|385805045|ref|YP_005841444.1|	-	0.11	12.0	0.0	0.19	11.3	0.0	1.3	1	0	0	1	1	1	0	Bacterial	regulatory	proteins,	luxR	family
HTH_15	PF12324.8	gi|385805046|ref|YP_005841445.1|	-	0.017	15.0	0.0	0.052	13.5	0.0	1.9	1	0	0	1	1	1	0	Helix-turn-helix	domain	of	alkylmercury	lyase
HTH_29	PF13551.6	gi|385805046|ref|YP_005841445.1|	-	0.11	12.6	0.0	0.31	11.1	0.0	1.8	1	0	0	1	1	1	0	Winged	helix-turn	helix
HTH_11	PF08279.12	gi|385805046|ref|YP_005841445.1|	-	0.11	12.4	0.0	0.36	10.8	0.0	1.8	2	0	0	2	2	2	0	HTH	domain
TrmB	PF01978.19	gi|385805046|ref|YP_005841445.1|	-	0.16	11.9	0.0	0.47	10.4	0.0	1.7	1	0	0	1	1	1	0	Sugar-specific	transcriptional	regulator	TrmB
AAA	PF00004.29	gi|385805048|ref|YP_005841447.1|	-	0.081	13.3	0.0	0.14	12.6	0.0	1.4	1	0	0	1	1	1	0	ATPase	family	associated	with	various	cellular	activities	(AAA)
AAA_25	PF13481.6	gi|385805048|ref|YP_005841447.1|	-	0.11	12.1	1.7	3.8	7.0	1.3	2.2	1	1	1	2	2	2	0	AAA	domain
HTH_23	PF13384.6	gi|385805048|ref|YP_005841447.1|	-	0.18	11.6	1.5	0.53	10.1	0.0	2.3	3	0	0	3	3	3	0	Homeodomain-like	domain
HTH_31	PF13560.6	gi|385805048|ref|YP_005841447.1|	-	0.2	12.0	0.7	0.6	10.5	0.1	2.1	2	0	0	2	2	2	0	Helix-turn-helix	domain
RHH_1	PF01402.21	gi|385805050|ref|YP_005841449.1|	-	0.00064	19.6	0.8	0.0012	18.7	0.8	1.5	1	0	0	1	1	1	1	Ribbon-helix-helix	protein,	copG	family
#
# Program:         hmmscan
# Version:         3.2.1 (June 2018)
# Pipeline mode:   SCAN
# Query file:      /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloquadratum_walsbyi_C23_uid162019/NC_017460.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/Haloquadratum_walsbyi_C23_uid162019/NC_017460.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloquadratum_walsbyi_C23_uid162019/NC_017460.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/Haloquadratum_walsbyi_C23_uid162019/NC_017460.faa 
# Current dir:     /oak/stanford/groups/akundaje/marinovg/genomes
# Date:            Mon Mar 25 12:41:07 2019
# [ok]