#                                                                           --- 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_23	PF13384.6	gi|385802376|ref|YP_005838777.1|	-	0.044	13.6	0.4	3.3	7.6	0.0	2.4	2	0	0	2	2	2	0	Homeodomain-like	domain
HTH_40	PF14493.6	gi|385802376|ref|YP_005838777.1|	-	0.16	12.4	0.0	0.31	11.5	0.0	1.5	1	0	0	1	1	1	0	Helix-turn-helix	domain
HTH_15	PF12324.8	gi|385802377|ref|YP_005838778.1|	-	0.017	15.0	0.0	0.053	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|385802377|ref|YP_005838778.1|	-	0.052	13.6	0.0	0.31	11.1	0.0	2.3	2	0	0	2	2	2	0	Winged	helix-turn	helix
HTH_11	PF08279.12	gi|385802377|ref|YP_005838778.1|	-	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|385802377|ref|YP_005838778.1|	-	0.16	11.9	0.0	0.47	10.4	0.0	1.8	1	0	0	1	1	1	0	Sugar-specific	transcriptional	regulator	TrmB
AAA	PF00004.29	gi|385802379|ref|YP_005838780.1|	-	0.0032	17.9	0.0	0.0061	17.0	0.0	1.5	1	1	0	1	1	1	1	ATPase	family	associated	with	various	cellular	activities	(AAA)
HTH_31	PF13560.6	gi|385802379|ref|YP_005838780.1|	-	0.017	15.4	0.0	0.052	13.9	0.0	1.9	2	0	0	2	2	2	0	Helix-turn-helix	domain
CbiA	PF01656.23	gi|385802379|ref|YP_005838780.1|	-	0.027	14.5	0.1	0.027	14.5	0.1	1.3	1	1	0	1	1	1	0	CobQ/CobB/MinD/ParA	nucleotide	binding	domain
AAA_25	PF13481.6	gi|385802379|ref|YP_005838780.1|	-	0.032	13.8	0.2	0.15	11.6	0.2	2.0	1	1	0	1	1	1	0	AAA	domain
HTH_23	PF13384.6	gi|385802379|ref|YP_005838780.1|	-	0.056	13.3	1.1	0.072	12.9	0.0	1.7	2	0	0	2	2	2	0	Homeodomain-like	domain
ArsA_ATPase	PF02374.15	gi|385802379|ref|YP_005838780.1|	-	0.47	9.6	1.5	0.53	9.4	0.1	1.6	2	0	0	2	2	2	0	Anion-transporting	ATPase
Cytidylate_kin2	PF13189.6	gi|385802381|ref|YP_005838782.1|	-	0.079	13.1	1.2	0.1	12.7	0.6	1.5	1	1	0	1	1	1	0	Cytidylate	kinase-like	family
DUF3791	PF12668.7	gi|385802381|ref|YP_005838782.1|	-	0.087	12.9	1.1	1.1	9.3	1.1	2.2	1	1	0	1	1	1	0	Protein	of	unknown	function	(DUF3791)
Bud13	PF09736.9	gi|385802381|ref|YP_005838782.1|	-	0.82	10.1	4.3	0.91	9.9	4.3	1.0	1	0	0	1	1	1	0	Pre-mRNA-splicing	factor	of	RES	complex
RHH_1	PF01402.21	gi|385802381|ref|YP_005838782.1|	-	3.2	7.8	8.1	1.1	9.3	2.7	2.2	2	0	0	2	2	2	0	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_017458.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_017458.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloquadratum_walsbyi_C23_uid162019/NC_017458.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_017458.faa 
# Current dir:     /oak/stanford/groups/akundaje/marinovg/genomes
# Date:            Mon Mar 25 12:39:52 2019
# [ok]