#                                                                           --- 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
#------------------- ----------             -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
TrmB	PF01978.19	gi|284176393|ref|YP_003406668.1|	-	6.2e-05	22.8	0.0	0.00011	22.0	0.0	1.5	1	1	0	1	1	1	1	Sugar-specific	transcriptional	regulator	TrmB
HTH_20	PF12840.7	gi|284176393|ref|YP_003406668.1|	-	0.0096	16.0	0.0	0.022	14.8	0.0	1.6	1	0	0	1	1	1	1	Helix-turn-helix	domain
HTH_Crp_2	PF13545.6	gi|284176393|ref|YP_003406668.1|	-	0.021	14.8	0.0	0.067	13.2	0.0	1.8	2	0	0	2	2	2	0	Crp-like	helix-turn-helix	domain
Rrf2	PF02082.20	gi|284176393|ref|YP_003406668.1|	-	0.05	14.0	0.0	0.077	13.3	0.0	1.3	1	0	0	1	1	1	0	Transcriptional	regulator
MarR_2	PF12802.7	gi|284176393|ref|YP_003406668.1|	-	0.069	13.0	0.0	0.22	11.4	0.0	1.8	2	0	0	2	2	2	0	MarR	family
HSBP1	PF06825.12	gi|284176396|ref|YP_003406671.1|	-	0.015	15.2	0.1	0.03	14.2	0.1	1.5	1	0	0	1	1	1	0	Heat	shock	factor	binding	protein	1
IFT46_B_C	PF12317.8	gi|284176396|ref|YP_003406671.1|	-	0.017	14.9	0.2	0.021	14.6	0.2	1.2	1	0	0	1	1	1	0	Intraflagellar	transport	complex	B	protein	46	C	terminal
RHH_1	PF01402.21	gi|284176396|ref|YP_003406671.1|	-	0.044	13.7	2.6	0.044	13.7	2.6	3.0	3	0	0	3	3	3	0	Ribbon-helix-helix	protein,	copG	family
T3SS_HrpK1	PF16937.5	gi|284176396|ref|YP_003406671.1|	-	0.061	13.0	0.1	0.75	9.4	0.0	2.0	2	0	0	2	2	2	0	Type	III	secretion	system	translocator	protein,	HrpF
PhoU	PF01895.19	gi|284176396|ref|YP_003406671.1|	-	0.086	13.3	1.3	0.18	12.3	0.8	1.9	1	1	0	1	1	1	0	PhoU	domain
BLOC1_2	PF10046.9	gi|284176396|ref|YP_003406671.1|	-	0.097	13.0	0.4	0.17	12.2	0.4	1.4	1	0	0	1	1	1	0	Biogenesis	of	lysosome-related	organelles	complex-1	subunit	2
BBP1_C	PF15272.6	gi|284176396|ref|YP_003406671.1|	-	0.11	12.3	2.7	0.15	11.9	2.7	1.2	1	0	0	1	1	1	0	Spindle	pole	body	component	BBP1,	C-terminal
DUF2802	PF10975.8	gi|284176396|ref|YP_003406671.1|	-	0.23	11.6	1.4	4.9	7.4	0.1	3.1	2	1	2	4	4	4	0	Protein	of	unknown	function	(DUF2802)
PSK_trans_fac	PF07704.11	gi|284176396|ref|YP_003406671.1|	-	1	10.2	9.6	8.4	7.2	1.0	2.5	1	1	1	2	2	2	0	Rv0623-like	transcription	factor
Apolipoprotein	PF01442.18	gi|284176398|ref|YP_003406673.1|	-	1.5e-10	41.3	1.9	6e-08	32.8	0.4	2.6	1	1	1	2	2	2	2	Apolipoprotein	A1/A4/E	domain
Phasin	PF05597.11	gi|284176398|ref|YP_003406673.1|	-	1.5e-06	28.2	17.3	0.02	14.9	6.7	4.0	1	1	2	3	3	3	3	Poly(hydroxyalcanoate)	granule	associated	protein	(phasin)
DUF883	PF05957.13	gi|284176398|ref|YP_003406673.1|	-	1.1e-05	25.9	15.2	0.0027	18.3	1.7	5.3	2	1	2	4	4	4	1	Bacterial	protein	of	unknown	function	(DUF883)
YtxH	PF12732.7	gi|284176398|ref|YP_003406673.1|	-	2.5e-05	24.7	35.0	1.7	9.2	10.4	5.9	2	1	2	4	4	4	3	YtxH-like	protein
ApoLp-III	PF07464.11	gi|284176398|ref|YP_003406673.1|	-	2.5e-05	24.4	12.2	0.0056	16.8	5.3	2.9	1	1	1	2	2	2	2	Apolipophorin-III	precursor	(apoLp-III)
MT0933_antitox	PF14013.6	gi|284176398|ref|YP_003406673.1|	-	0.0025	18.1	59.7	0.23	11.8	5.8	6.0	2	2	4	6	6	6	3	MT0933-like	antitoxin	protein
REF	PF05755.12	gi|284176398|ref|YP_003406673.1|	-	0.021	14.6	14.1	0.23	11.2	6.9	2.6	1	1	1	2	2	2	0	Rubber	elongation	factor	protein	(REF)
DUF445	PF04286.12	gi|284176398|ref|YP_003406673.1|	-	0.042	13.7	1.2	0.073	12.9	1.2	1.3	1	0	0	1	1	1	0	Protein	of	unknown	function	(DUF445)
DUF1451	PF07295.11	gi|284176398|ref|YP_003406673.1|	-	0.057	13.5	1.7	0.096	12.7	0.2	2.0	1	1	1	2	2	2	0	Zinc-ribbon	containing	domain
DUF2884	PF11101.8	gi|284176398|ref|YP_003406673.1|	-	0.059	12.9	8.3	0.18	11.3	7.2	1.9	1	1	0	1	1	1	0	Protein	of	unknown	function	(DUF2884)
Baculo_PEP_C	PF04513.12	gi|284176398|ref|YP_003406673.1|	-	0.083	12.9	2.0	1.5	8.9	0.5	2.3	1	1	1	2	2	2	0	Baculovirus	polyhedron	envelope	protein,	PEP,	C	terminus
Prominin	PF05478.11	gi|284176398|ref|YP_003406673.1|	-	0.16	9.9	1.8	0.23	9.4	1.8	1.2	1	0	0	1	1	1	0	Prominin
ApoO	PF09769.9	gi|284176398|ref|YP_003406673.1|	-	0.22	11.5	0.1	15	5.5	0.4	3.0	1	1	1	2	2	2	0	Apolipoprotein	O
DUF948	PF06103.11	gi|284176398|ref|YP_003406673.1|	-	0.35	11.2	26.9	1.8e+04	-9.5	26.9	4.1	1	1	0	1	1	0	0	Bacterial	protein	of	unknown	function	(DUF948)
Mitofilin	PF09731.9	gi|284176398|ref|YP_003406673.1|	-	0.42	9.4	9.2	0.94	8.2	9.2	1.6	1	0	0	1	1	1	0	Mitochondrial	inner	membrane	protein
ISG65-75	PF11727.8	gi|284176398|ref|YP_003406673.1|	-	1.1	8.4	15.1	3	7.0	9.1	2.3	1	1	0	2	2	2	0	Invariant	surface	glycoprotein
MttA_Hcf106	PF02416.16	gi|284176399|ref|YP_003406674.1|	-	3.9e-08	32.5	1.4	3.9e-08	32.5	1.4	1.1	1	0	0	1	1	1	1	mttA/Hcf106	family
Sortilin-Vps10	PF15902.5	gi|284176400|ref|YP_003406675.1|	-	0.00022	20.2	0.0	0.00031	19.6	0.0	1.2	1	0	0	1	1	1	1	Sortilin,	neurotensin	receptor	3,
BNR	PF02012.20	gi|284176400|ref|YP_003406675.1|	-	0.046	13.7	0.5	0.046	13.7	0.5	3.9	3	0	0	3	3	3	0	BNR/Asp-box	repeat
BNR_2	PF13088.6	gi|284176400|ref|YP_003406675.1|	-	0.052	12.9	0.0	0.082	12.2	0.0	1.3	1	0	0	1	1	1	0	BNR	repeat-like	domain
UCR_Fe-S_N	PF10399.9	gi|284176400|ref|YP_003406675.1|	-	0.18	11.2	1.6	0.31	10.4	1.6	1.4	1	0	0	1	1	1	0	Ubiquitinol-cytochrome	C	reductase	Fe-S	subunit	TAT	signal
D5_N	PF08706.11	gi|284176401|ref|YP_003406676.1|	-	1.4e-14	54.6	1.0	1.6e-13	51.2	0.0	2.7	2	0	0	2	2	2	1	D5	N	terminal	like
Pox_D5	PF03288.16	gi|284176401|ref|YP_003406676.1|	-	4.1e-06	27.2	0.3	1.3e-05	25.6	0.2	1.9	2	0	0	2	2	2	1	Poxvirus	D5	protein-like
RFX_DNA_binding	PF02257.15	gi|284176401|ref|YP_003406676.1|	-	0.0012	19.5	0.1	0.0024	18.4	0.1	1.5	1	0	0	1	1	1	1	RFX	DNA-binding	domain
Cdc6_C	PF09079.11	gi|284176401|ref|YP_003406676.1|	-	0.47	10.5	3.8	0.33	10.9	0.2	2.5	2	0	0	2	2	2	0	CDC6,	C	terminal	winged	helix	domain
Fe_dep_repress	PF01325.19	gi|284176403|ref|YP_003406678.1|	-	0.00065	19.8	0.0	0.00092	19.4	0.0	1.2	1	0	0	1	1	1	1	Iron	dependent	repressor,	N-terminal	DNA	binding	domain
DsrD	PF08679.11	gi|284176403|ref|YP_003406678.1|	-	0.06	13.6	0.0	0.063	13.5	0.0	1.1	1	0	0	1	1	1	0	Dissimilatory	sulfite	reductase	D	(DsrD)
HrcA_DNA-bdg	PF03444.15	gi|284176403|ref|YP_003406678.1|	-	0.092	12.4	0.0	0.13	12.0	0.0	1.2	1	0	0	1	1	1	0	Winged	helix-turn-helix	transcription	repressor,	HrcA	DNA-binding
DUF2460	PF09343.10	gi|284176404|ref|YP_003406679.1|	-	0.031	13.8	0.0	0.042	13.3	0.0	1.2	1	0	0	1	1	1	0	Conserved	hypothetical	protein	2217	(DUF2460)
DUF5040	PF16443.5	gi|284176404|ref|YP_003406679.1|	-	0.11	11.8	0.0	0.12	11.8	0.0	1.1	1	0	0	1	1	1	0	Domain	of	unknown	function	(DUF5040)
UBA_6	PF18039.1	gi|284176406|ref|YP_003406681.1|	-	0.097	12.6	0.0	0.12	12.3	0.0	1.2	1	0	0	1	1	1	0	UBA-like	domain
LapA_dom	PF06305.11	gi|284176407|ref|YP_003406682.1|	-	0.61	9.9	3.4	0.75	9.7	0.0	2.0	2	0	0	2	2	2	0	Lipopolysaccharide	assembly	protein	A	domain
DZR	PF12773.7	gi|284176408|ref|YP_003406683.1|	-	0.00089	19.2	0.4	0.0016	18.4	0.4	1.3	1	0	0	1	1	1	1	Double	zinc	ribbon
Zn-ribbon_8	PF09723.10	gi|284176408|ref|YP_003406683.1|	-	0.006	16.7	1.0	0.014	15.5	1.0	1.6	1	0	0	1	1	1	1	Zinc	ribbon	domain
TF_Zn_Ribbon	PF08271.12	gi|284176408|ref|YP_003406683.1|	-	0.0097	15.4	0.4	2.4	7.7	0.1	2.3	2	0	0	2	2	2	2	TFIIB	zinc-binding
zf-HIT	PF04438.16	gi|284176408|ref|YP_003406683.1|	-	0.016	15.1	2.0	0.047	13.6	0.3	2.1	2	0	0	2	2	2	0	HIT	zinc	finger
HypA	PF01155.19	gi|284176408|ref|YP_003406683.1|	-	0.038	14.0	0.8	0.063	13.3	0.1	1.6	1	1	1	2	2	2	0	Hydrogenase/urease	nickel	incorporation,	metallochaperone,	hypA
zf-ribbon_3	PF13248.6	gi|284176408|ref|YP_003406683.1|	-	0.26	10.8	2.6	14	5.3	0.7	2.3	2	0	0	2	2	2	0	zinc-ribbon	domain
Zn_ribbon_SprT	PF17283.2	gi|284176408|ref|YP_003406683.1|	-	0.26	11.2	0.3	0.26	11.2	0.3	2.5	3	0	0	3	3	3	0	SprT-like	zinc	ribbon	domain
RinB	PF06116.12	gi|284176409|ref|YP_003406684.1|	-	0.065	13.3	0.1	0.11	12.6	0.1	1.4	1	0	0	1	1	1	0	Transcriptional	activator	RinB
DpaA_N	PF16924.5	gi|284176409|ref|YP_003406684.1|	-	0.16	12.0	0.0	0.24	11.5	0.0	1.3	1	1	0	1	1	1	0	Dipicolinate	synthase	subunit	A	N-terminal	domain
Mating_N	PF12731.7	gi|284176411|ref|YP_003406686.1|	-	0.016	15.3	0.9	0.13	12.3	0.1	2.1	2	0	0	2	2	2	0	Mating-type	protein	beta	1
Phage_gp53	PF11246.8	gi|284176411|ref|YP_003406686.1|	-	0.032	13.9	0.0	0.04	13.6	0.0	1.2	1	0	0	1	1	1	0	Base	plate	wedge	protein	53
SMBP	PF16785.5	gi|284176411|ref|YP_003406686.1|	-	0.043	14.0	1.7	1.4	9.1	0.2	2.2	2	0	0	2	2	2	0	Small	metal-binding	protein
Phage_integrase	PF00589.22	gi|284176412|ref|YP_003406687.1|	-	1.2e-25	90.3	0.1	1.5e-25	90.0	0.1	1.0	1	0	0	1	1	1	1	Phage	integrase	family
#
# Program:         hmmscan
# Version:         3.2.1 (June 2018)
# Pipeline mode:   SCAN
# Query file:      /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloterrigena_turkmenica_DSM_5511_uid43501/NC_013749.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/Haloterrigena_turkmenica_DSM_5511_uid43501/NC_013749.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloterrigena_turkmenica_DSM_5511_uid43501/NC_013749.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/Haloterrigena_turkmenica_DSM_5511_uid43501/NC_013749.faa 
# Current dir:     /oak/stanford/groups/akundaje/marinovg/genomes
# Date:            Mon Mar 25 15:32:15 2019
# [ok]