#                                                                           --- 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
#------------------- ----------             -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
VirE	PF05272.11	gi|330506034|ref|YP_004399692.1|	-	0.017	14.8	0.1	0.032	14.0	0.1	1.3	1	0	0	1	1	1	0	Virulence-associated	protein	E
DUF4872	PF16169.5	gi|330506034|ref|YP_004399692.1|	-	0.067	12.9	0.0	0.3	10.8	0.0	2.0	2	0	0	2	2	2	0	Domain	of	unknown	function	(DUF4872)
QRPTase_N	PF02749.16	gi|330506034|ref|YP_004399692.1|	-	0.1	12.6	0.0	0.29	11.2	0.0	1.7	1	0	0	1	1	1	0	Quinolinate	phosphoribosyl	transferase,	N-terminal	domain
DUF3223	PF11523.8	gi|330506035|ref|YP_004399693.1|	-	1e-15	58.3	0.3	3.2e-15	56.7	0.0	2.0	2	0	0	2	2	2	1	Protein	of	unknown	function	(DUF3223)
PG_binding_2	PF08823.11	gi|330506036|ref|YP_004399694.1|	-	0.0018	18.6	0.0	0.0028	17.9	0.0	1.3	1	0	0	1	1	1	1	Putative	peptidoglycan	binding	domain
Recombinase	PF07508.13	gi|330506036|ref|YP_004399694.1|	-	0.015	15.7	0.0	0.017	15.5	0.0	1.1	1	0	0	1	1	1	0	Recombinase
TCP	PF03634.13	gi|330506036|ref|YP_004399694.1|	-	0.055	14.0	0.0	0.06	13.9	0.0	1.1	1	0	0	1	1	1	0	TCP	family	transcription	factor
ATP-synt_DE	PF00401.20	gi|330506037|ref|YP_004399695.1|	-	0.061	13.6	4.5	0.13	12.5	4.5	1.6	1	0	0	1	1	1	0	ATP	synthase,	Delta/Epsilon	chain,	long	alpha-helix	domain
SesA	PF17107.5	gi|330506037|ref|YP_004399695.1|	-	0.13	12.4	0.5	1.2	9.3	0.5	2.1	2	0	0	2	2	2	0	N-terminal	domain	on	NACHT_NTPase	and	P-loop	NTPases
Golgin_A5	PF09787.9	gi|330506038|ref|YP_004399696.1|	-	0.00011	21.8	6.2	0.00012	21.6	6.2	1.1	1	0	0	1	1	1	1	Golgin	subfamily	A	member	5
DUF3450	PF11932.8	gi|330506038|ref|YP_004399696.1|	-	0.00066	19.1	7.7	0.00089	18.6	7.7	1.2	1	0	0	1	1	1	1	Protein	of	unknown	function	(DUF3450)
Phage_HK97_TLTM	PF06120.11	gi|330506038|ref|YP_004399696.1|	-	0.00094	18.5	3.5	0.0012	18.1	3.4	1.2	1	1	0	1	1	1	1	Tail	length	tape	measure	protein
CENP-F_leu_zip	PF10473.9	gi|330506038|ref|YP_004399696.1|	-	0.0026	17.8	9.1	0.0072	16.4	7.3	2.0	1	1	1	2	2	2	1	Leucine-rich	repeats	of	kinetochore	protein	Cenp-F/LEK1
zf-C4H2	PF10146.9	gi|330506038|ref|YP_004399696.1|	-	0.0062	16.9	3.7	0.0074	16.6	3.7	1.2	1	0	0	1	1	1	1	Zinc	finger-containing	protein
TMF_TATA_bd	PF12325.8	gi|330506038|ref|YP_004399696.1|	-	0.011	16.0	8.6	0.023	14.9	1.8	2.5	1	1	1	2	2	2	0	TATA	element	modulatory	factor	1	TATA	binding
Fez1	PF06818.15	gi|330506038|ref|YP_004399696.1|	-	0.012	16.1	6.1	0.017	15.6	6.1	1.3	1	0	0	1	1	1	0	Fez1
DUF4618	PF15397.6	gi|330506038|ref|YP_004399696.1|	-	0.016	14.7	5.4	0.079	12.4	3.8	2.0	1	1	1	2	2	2	0	Domain	of	unknown	function	(DUF4618)
DUF4200	PF13863.6	gi|330506038|ref|YP_004399696.1|	-	0.016	15.6	12.4	0.069	13.6	9.1	2.3	1	1	1	2	2	2	0	Domain	of	unknown	function	(DUF4200)
HALZ	PF02183.18	gi|330506038|ref|YP_004399696.1|	-	0.027	14.7	2.9	0.04	14.1	1.4	2.2	2	0	0	2	2	1	0	Homeobox	associated	leucine	zipper
DUF724	PF05266.14	gi|330506038|ref|YP_004399696.1|	-	0.042	13.7	4.2	0.057	13.2	4.2	1.3	1	0	0	1	1	1	0	Protein	of	unknown	function	(DUF724)
Seryl_tRNA_N	PF02403.22	gi|330506038|ref|YP_004399696.1|	-	0.046	14.0	8.8	0.28	11.4	8.0	2.2	1	1	1	2	2	2	0	Seryl-tRNA	synthetase	N-terminal	domain
AKNA	PF12443.8	gi|330506038|ref|YP_004399696.1|	-	0.048	14.3	2.4	0.088	13.5	2.4	1.5	1	0	0	1	1	1	0	AT-hook-containing	transcription	factor
APG6_N	PF17675.1	gi|330506038|ref|YP_004399696.1|	-	0.079	13.5	13.6	0.14	12.7	13.5	1.5	1	1	0	1	1	1	0	Apg6	coiled-coil	region
RHH_1	PF01402.21	gi|330506038|ref|YP_004399696.1|	-	0.091	12.7	0.2	0.091	12.7	0.2	3.2	4	0	0	4	4	3	0	Ribbon-helix-helix	protein,	copG	family
Phage_GPO	PF05929.11	gi|330506038|ref|YP_004399696.1|	-	0.096	12.3	3.1	0.12	12.0	3.1	1.2	1	0	0	1	1	1	0	Phage	capsid	scaffolding	protein	(GPO)	serine	peptidase
HIP1_clath_bdg	PF16515.5	gi|330506038|ref|YP_004399696.1|	-	0.15	12.7	8.9	0.21	12.2	8.3	1.7	1	1	0	1	1	1	0	Clathrin-binding	domain	of	Huntingtin-interacting	protein	1
Spc7	PF08317.11	gi|330506038|ref|YP_004399696.1|	-	0.22	10.4	10.7	0.28	10.0	10.2	1.3	1	1	0	1	1	1	0	Spc7	kinetochore	protein
SurA_N_3	PF13624.6	gi|330506038|ref|YP_004399696.1|	-	0.31	10.8	3.9	0.18	11.6	0.7	1.9	1	1	1	2	2	2	0	SurA	N-terminal	domain
CorA	PF01544.18	gi|330506038|ref|YP_004399696.1|	-	0.32	10.2	10.3	0.62	9.3	10.3	1.4	1	1	0	1	1	1	0	CorA-like	Mg2+	transporter	protein
DUF1664	PF07889.12	gi|330506038|ref|YP_004399696.1|	-	0.36	10.9	3.9	4.9	7.2	0.1	2.2	1	1	1	2	2	2	0	Protein	of	unknown	function	(DUF1664)
DUF4407	PF14362.6	gi|330506038|ref|YP_004399696.1|	-	0.42	9.9	6.5	0.57	9.5	6.5	1.3	1	0	0	1	1	1	0	Domain	of	unknown	function	(DUF4407)
Fungal_TACC	PF12709.7	gi|330506038|ref|YP_004399696.1|	-	0.49	10.9	5.8	1.7	9.2	5.0	2.4	1	1	0	1	1	1	0	Fungal	Transforming	acidic	coiled-coil	(TACC)	proteins
UPF0449	PF15136.6	gi|330506038|ref|YP_004399696.1|	-	0.72	10.4	7.8	13	6.3	0.1	2.3	1	1	1	2	2	2	0	Uncharacterised	protein	family	UPF0449
YabA	PF06156.13	gi|330506038|ref|YP_004399696.1|	-	0.86	10.3	4.6	1.8	9.2	4.4	1.9	1	1	0	1	1	1	0	Initiation	control	protein	YabA
FapA	PF03961.13	gi|330506038|ref|YP_004399696.1|	-	1.1	7.8	7.1	2.5	6.6	7.1	1.6	1	1	0	1	1	1	0	Flagellar	Assembly	Protein	A
Atg14	PF10186.9	gi|330506038|ref|YP_004399696.1|	-	1.2	8.1	11.5	2.1	7.3	11.5	1.5	1	1	0	1	1	1	0	Vacuolar	sorting	38	and	autophagy-related	subunit	14
Cep57_CLD_2	PF14197.6	gi|330506038|ref|YP_004399696.1|	-	2	8.6	13.6	0.45	10.6	4.9	2.8	1	1	1	2	2	2	0	Centrosome	localisation	domain	of	PPC89
DivIC	PF04977.15	gi|330506038|ref|YP_004399696.1|	-	4.1	7.2	9.3	1.6	8.6	4.5	2.7	1	1	1	3	3	3	0	Septum	formation	initiator
DUF4140	PF13600.6	gi|330506038|ref|YP_004399696.1|	-	5.3	7.5	9.7	14	6.2	7.3	2.5	1	1	1	2	2	2	0	N-terminal	domain	of	unknown	function	(DUF4140)
Mei5	PF10376.9	gi|330506039|ref|YP_004399697.1|	-	8.3e-05	22.5	1.3	0.00012	22.0	1.3	1.2	1	0	0	1	1	1	1	Double-strand	recombination	repair	protein
RNase_H	PF00075.24	gi|330506039|ref|YP_004399697.1|	-	0.015	15.5	0.0	0.02	15.1	0.0	1.2	1	0	0	1	1	1	0	RNase	H
Bap31_Bap29_C	PF18035.1	gi|330506039|ref|YP_004399697.1|	-	0.018	15.1	4.2	0.027	14.5	3.7	1.6	1	1	0	1	1	1	0	Bap31/Bap29	cytoplasmic	coiled-coil	domain
COMP	PF11598.8	gi|330506039|ref|YP_004399697.1|	-	0.021	15.3	2.6	0.039	14.4	0.2	2.1	2	0	0	2	2	2	0	Cartilage	oligomeric	matrix	protein
TMF_TATA_bd	PF12325.8	gi|330506039|ref|YP_004399697.1|	-	0.022	15.0	2.9	0.032	14.5	2.9	1.2	1	0	0	1	1	1	0	TATA	element	modulatory	factor	1	TATA	binding
CENP-H	PF05837.12	gi|330506039|ref|YP_004399697.1|	-	0.06	13.8	2.5	0.08	13.3	2.5	1.2	1	0	0	1	1	1	0	Centromere	protein	H	(CENP-H)
DUF4140	PF13600.6	gi|330506039|ref|YP_004399697.1|	-	0.061	13.8	0.6	0.13	12.7	0.6	1.5	1	0	0	1	1	1	0	N-terminal	domain	of	unknown	function	(DUF4140)
ADIP	PF11559.8	gi|330506039|ref|YP_004399697.1|	-	0.066	13.3	5.8	0.099	12.7	5.8	1.2	1	0	0	1	1	1	0	Afadin-	and	alpha	-actinin-Binding
DivIC	PF04977.15	gi|330506039|ref|YP_004399697.1|	-	0.11	12.3	1.9	0.21	11.4	1.9	1.5	1	0	0	1	1	1	0	Septum	formation	initiator
YabA	PF06156.13	gi|330506039|ref|YP_004399697.1|	-	0.32	11.7	1.7	0.47	11.1	1.7	1.2	1	0	0	1	1	1	0	Initiation	control	protein	YabA
DUF4337	PF14235.6	gi|330506039|ref|YP_004399697.1|	-	0.82	9.8	3.3	2.6	8.2	3.3	1.8	1	1	0	1	1	1	0	Domain	of	unknown	function	(DUF4337)
HTH_24	PF13412.6	gi|330506040|ref|YP_004399698.1|	-	7.5e-08	31.8	0.0	1.2e-07	31.2	0.0	1.4	1	0	0	1	1	1	1	Winged	helix-turn-helix	DNA-binding
TrmB	PF01978.19	gi|330506040|ref|YP_004399698.1|	-	9.6e-07	28.6	0.1	1.3e-06	28.2	0.1	1.2	1	0	0	1	1	1	1	Sugar-specific	transcriptional	regulator	TrmB
MarR	PF01047.22	gi|330506040|ref|YP_004399698.1|	-	2.9e-06	27.1	0.0	4e-06	26.7	0.0	1.2	1	0	0	1	1	1	1	MarR	family
MarR_2	PF12802.7	gi|330506040|ref|YP_004399698.1|	-	5.6e-06	26.2	0.0	7.9e-06	25.7	0.0	1.2	1	0	0	1	1	1	1	MarR	family
PaaX	PF07848.12	gi|330506040|ref|YP_004399698.1|	-	0.0055	16.9	0.0	0.0087	16.3	0.0	1.3	1	0	0	1	1	1	1	PaaX-like	protein
PadR	PF03551.14	gi|330506040|ref|YP_004399698.1|	-	0.01	15.8	0.0	0.017	15.1	0.0	1.5	1	1	0	1	1	1	0	Transcriptional	regulator	PadR-like	family
HTH_11	PF08279.12	gi|330506040|ref|YP_004399698.1|	-	0.018	15.0	0.0	0.032	14.2	0.0	1.4	1	0	0	1	1	1	0	HTH	domain
HTH_34	PF13601.6	gi|330506040|ref|YP_004399698.1|	-	0.025	14.8	0.0	0.03	14.5	0.0	1.2	1	0	0	1	1	1	0	Winged	helix	DNA-binding	domain
HTH_AsnC-type	PF13404.6	gi|330506040|ref|YP_004399698.1|	-	0.035	13.9	0.0	0.064	13.1	0.0	1.5	1	0	0	1	1	1	0	AsnC-type	helix-turn-helix	domain
HTH_IclR	PF09339.10	gi|330506040|ref|YP_004399698.1|	-	0.043	13.6	0.0	0.066	13.0	0.0	1.2	1	0	0	1	1	1	0	IclR	helix-turn-helix	domain
FAF	PF11250.8	gi|330506040|ref|YP_004399698.1|	-	0.071	13.4	0.0	0.13	12.6	0.0	1.3	1	0	0	1	1	1	0	Fantastic	Four	meristem	regulator
IF2_N	PF04760.15	gi|330506040|ref|YP_004399698.1|	-	0.084	12.7	0.0	0.15	11.9	0.0	1.4	1	0	0	1	1	1	0	Translation	initiation	factor	IF-2,	N-terminal	region
SMC_ScpB	PF04079.16	gi|330506040|ref|YP_004399698.1|	-	0.12	11.9	0.0	0.18	11.4	0.0	1.2	1	0	0	1	1	1	0	Segregation	and	condensation	complex	subunit	ScpB
MarR	PF01047.22	gi|330506042|ref|YP_004399700.1|	-	0.00061	19.7	0.2	0.11	12.4	0.0	2.8	3	0	0	3	3	3	1	MarR	family
HTH_38	PF13936.6	gi|330506042|ref|YP_004399700.1|	-	0.0011	18.7	0.3	0.0072	16.1	0.3	2.3	1	1	0	1	1	1	1	Helix-turn-helix	domain
HTH_24	PF13412.6	gi|330506042|ref|YP_004399700.1|	-	0.0033	17.0	0.0	0.014	15.0	0.0	2.0	2	0	0	2	2	2	1	Winged	helix-turn-helix	DNA-binding
MarR_2	PF12802.7	gi|330506042|ref|YP_004399700.1|	-	0.02	14.8	0.0	0.041	13.8	0.0	1.6	1	0	0	1	1	1	0	MarR	family
TrmB	PF01978.19	gi|330506042|ref|YP_004399700.1|	-	0.13	12.1	0.0	0.3	11.0	0.0	1.6	1	0	0	1	1	1	0	Sugar-specific	transcriptional	regulator	TrmB
DUF892	PF05974.12	gi|330506043|ref|YP_004399701.1|	-	0.014	15.4	0.4	0.19	11.7	0.0	2.5	3	0	0	3	3	3	0	Domain	of	unknown	function	(DUF892)
Snapin_Pallidin	PF14712.6	gi|330506043|ref|YP_004399701.1|	-	0.082	13.3	0.7	0.33	11.4	0.3	2.1	2	0	0	2	2	2	0	Snapin/Pallidin
ABC_tran_CTD	PF16326.5	gi|330506043|ref|YP_004399701.1|	-	0.17	12.1	6.0	0.73	10.1	1.0	3.5	3	1	1	4	4	4	0	ABC	transporter	C-terminal	domain
DUF2205	PF10224.9	gi|330506043|ref|YP_004399701.1|	-	0.25	11.3	1.8	0.44	10.6	0.5	2.1	2	1	0	2	2	2	0	Short	coiled-coil	protein
BLOC1_2	PF10046.9	gi|330506043|ref|YP_004399701.1|	-	0.31	11.4	2.0	2.7	8.4	0.4	2.5	3	0	0	3	3	3	0	Biogenesis	of	lysosome-related	organelles	complex-1	subunit	2
VirE	PF05272.11	gi|330506047|ref|YP_004399705.1|	-	0.0062	16.3	0.1	0.0094	15.7	0.1	1.2	1	0	0	1	1	1	1	Virulence-associated	protein	E
tRNA-synt_1g	PF09334.11	gi|330506049|ref|YP_004399707.1|	-	2.1e-39	135.4	0.0	2.3e-39	135.3	0.0	1.0	1	0	0	1	1	1	1	tRNA	synthetases	class	I	(M)
DZR	PF12773.7	gi|330506049|ref|YP_004399707.1|	-	0.035	14.1	9.0	0.19	11.8	3.5	2.3	1	1	2	3	3	3	0	Double	zinc	ribbon
TackOD1	PF18551.1	gi|330506049|ref|YP_004399707.1|	-	0.49	10.0	3.4	0.19	11.3	1.0	1.6	2	0	0	2	2	2	0	Thaumarchaeal	output	domain	1
CpXC	PF14353.6	gi|330506049|ref|YP_004399707.1|	-	0.59	10.2	4.3	23	5.0	0.0	3.0	2	1	1	3	3	3	0	CpXC	protein
zinc_ribbon_2	PF13240.6	gi|330506049|ref|YP_004399707.1|	-	0.63	9.8	12.0	1.1	9.1	6.7	3.0	2	2	0	2	2	2	0	zinc-ribbon	domain
A2L_zn_ribbon	PF08792.10	gi|330506049|ref|YP_004399707.1|	-	0.64	9.8	4.2	9.2	6.1	0.1	3.2	3	0	0	3	3	3	0	A2L	zinc	ribbon	domain
NMD3	PF04981.13	gi|330506049|ref|YP_004399707.1|	-	0.65	9.4	0.0	0.65	9.4	0.0	2.2	1	1	1	2	2	2	0	NMD3	family
TerY_C	PF15616.6	gi|330506049|ref|YP_004399707.1|	-	1.4	9.0	6.7	2.4	8.3	3.6	2.1	1	1	1	2	2	2	0	TerY-C	metal	binding	domain
zinc-ribbons_6	PF07191.12	gi|330506049|ref|YP_004399707.1|	-	2.1	8.4	6.8	4.4	7.4	3.1	2.2	1	1	1	2	2	2	0	zinc-ribbons
zf-RING_7	PF02591.15	gi|330506049|ref|YP_004399707.1|	-	2.4	8.4	6.6	5.2	7.3	0.1	3.3	3	0	0	3	3	3	0	C4-type	zinc	ribbon	domain
zf-C3HC4_3	PF13920.6	gi|330506049|ref|YP_004399707.1|	-	5.6	6.9	7.9	0.69	9.8	0.4	2.5	3	0	0	3	3	3	0	Zinc	finger,	C3HC4	type	(RING	finger)
zf-ribbon_3	PF13248.6	gi|330506049|ref|YP_004399707.1|	-	5.9	6.4	17.5	0.28	10.7	1.7	4.0	4	1	0	4	4	4	0	zinc-ribbon	domain
HypA	PF01155.19	gi|330506049|ref|YP_004399707.1|	-	7	6.7	6.5	5.3	7.1	1.4	2.2	1	1	1	2	2	2	0	Hydrogenase/urease	nickel	incorporation,	metallochaperone,	hypA
zf_C2H2_10	PF18414.1	gi|330506049|ref|YP_004399707.1|	-	7.8	6.1	8.1	0.25	10.9	0.6	2.2	2	0	0	2	2	2	0	C2H2	type	zinc-finger
#
# Program:         hmmscan
# Version:         3.2.1 (June 2018)
# Pipeline mode:   SCAN
# Query file:      /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_concilii_GP6_uid66207/NC_015430.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/Methanosaeta_concilii_GP6_uid66207/NC_015430.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_concilii_GP6_uid66207/NC_015430.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/Methanosaeta_concilii_GP6_uid66207/NC_015430.faa 
# Current dir:     /oak/stanford/groups/akundaje/marinovg/genomes
# Date:            Mon Mar 25 15:47:20 2019
# [ok]