# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- TaqI_C PF12950.7 gi|345133532|ref|YP_004821323.1| - 9.2e-08 32.2 0.0 1.4e-07 31.6 0.0 1.2 1 0 0 1 1 1 1 TaqI-like C-terminal specificity domain Eco57I PF07669.11 gi|345133532|ref|YP_004821323.1| - 7.6e-07 29.6 0.0 1.3e-06 28.9 0.0 1.3 1 0 0 1 1 1 1 Eco57I restriction-modification methylase N6_Mtase PF02384.16 gi|345133532|ref|YP_004821323.1| - 0.0017 17.7 0.0 0.0069 15.7 0.0 1.8 1 1 0 1 1 1 1 N-6 DNA Methylase MTS PF05175.14 gi|345133532|ref|YP_004821323.1| - 0.11 12.0 0.0 3.1 7.3 0.0 2.1 2 0 0 2 2 2 0 Methyltransferase small domain MarR_2 PF12802.7 gi|345133533|ref|YP_004821324.1| - 0.0012 18.7 0.3 0.011 15.6 0.1 2.2 2 0 0 2 2 2 1 MarR family TrmB PF01978.19 gi|345133533|ref|YP_004821324.1| - 0.0014 18.5 0.0 0.024 14.5 0.0 2.4 2 0 0 2 2 2 1 Sugar-specific transcriptional regulator TrmB HTH_24 PF13412.6 gi|345133533|ref|YP_004821324.1| - 0.019 14.5 0.0 0.25 10.9 0.1 2.1 2 0 0 2 2 2 0 Winged helix-turn-helix DNA-binding HTH_20 PF12840.7 gi|345133533|ref|YP_004821324.1| - 0.023 14.8 0.0 0.054 13.6 0.0 1.6 1 0 0 1 1 1 0 Helix-turn-helix domain HTH_11 PF08279.12 gi|345133533|ref|YP_004821324.1| - 0.051 13.5 0.1 0.094 12.7 0.1 1.3 1 0 0 1 1 1 0 HTH domain HTH_AsnC-type PF13404.6 gi|345133533|ref|YP_004821324.1| - 0.054 13.3 0.6 0.33 10.8 0.7 2.1 2 0 0 2 2 2 0 AsnC-type helix-turn-helix domain Sigma70_r1_1 PF03979.14 gi|345133538|ref|YP_004821329.1| - 0.056 13.5 0.1 0.08 13.0 0.1 1.2 1 0 0 1 1 1 0 Sigma-70 factor, region 1.1 HicA_toxin PF07927.12 gi|345133539|ref|YP_004821330.1| - 1.5e-12 47.3 0.0 1.8e-12 47.1 0.0 1.1 1 0 0 1 1 1 1 HicA toxin of bacterial toxin-antitoxin, CD36 PF01130.21 gi|345133542|ref|YP_004821333.1| - 0.18 10.3 0.0 0.28 9.7 0.0 1.1 1 0 0 1 1 1 0 CD36 family DUF3324 PF11797.8 gi|345133543|ref|YP_004821334.1| - 0.13 12.3 0.0 0.18 11.8 0.0 1.2 1 0 0 1 1 1 0 Protein of unknown function C-terminal (DUF3324) DUF3659 PF12396.8 gi|345133543|ref|YP_004821334.1| - 0.13 12.2 0.8 0.38 10.7 0.1 2.1 2 1 0 2 2 2 0 Protein of unknown function (DUF3659) zf-LSD1 PF06943.12 gi|345133544|ref|YP_004821335.1| - 0.1 12.5 0.8 0.16 11.8 0.8 1.3 1 0 0 1 1 1 0 LSD1 zinc finger Crp PF00325.20 gi|345133545|ref|YP_004821336.1| - 0.00074 19.1 0.1 0.0017 18.0 0.1 1.6 1 0 0 1 1 1 1 Bacterial regulatory proteins, crp family HTH_Crp_2 PF13545.6 gi|345133545|ref|YP_004821336.1| - 0.002 18.1 0.0 0.0043 17.0 0.0 1.5 1 0 0 1 1 1 1 Crp-like helix-turn-helix domain HTH_11 PF08279.12 gi|345133545|ref|YP_004821336.1| - 0.0039 17.1 0.1 0.02 14.8 0.0 2.0 1 1 1 2 2 2 1 HTH domain FaeA PF04703.12 gi|345133545|ref|YP_004821336.1| - 0.0052 17.1 0.0 0.013 15.8 0.0 1.7 2 0 0 2 2 2 1 FaeA-like protein HTH_DeoR PF08220.12 gi|345133545|ref|YP_004821336.1| - 0.014 15.2 0.1 0.038 13.7 0.1 1.7 1 0 0 1 1 1 0 DeoR-like helix-turn-helix domain TrmB PF01978.19 gi|345133545|ref|YP_004821336.1| - 0.024 14.5 0.1 0.22 11.4 0.0 2.3 2 0 0 2 2 2 0 Sugar-specific transcriptional regulator TrmB HTH_17 PF12728.7 gi|345133545|ref|YP_004821336.1| - 0.047 13.9 0.1 0.094 12.9 0.1 1.5 1 0 0 1 1 1 0 Helix-turn-helix domain HTH_20 PF12840.7 gi|345133545|ref|YP_004821336.1| - 0.049 13.7 0.3 0.29 11.2 0.3 2.4 2 1 0 2 2 2 0 Helix-turn-helix domain HTH_23 PF13384.6 gi|345133545|ref|YP_004821336.1| - 0.082 12.7 3.0 0.12 12.2 0.3 2.5 2 1 0 2 2 2 0 Homeodomain-like domain HTH_AsnC-type PF13404.6 gi|345133545|ref|YP_004821336.1| - 0.084 12.7 0.1 0.21 11.5 0.1 1.7 1 0 0 1 1 1 0 AsnC-type helix-turn-helix domain HTH_30 PF13556.6 gi|345133545|ref|YP_004821336.1| - 0.1 12.4 0.1 0.18 11.6 0.1 1.4 1 0 0 1 1 1 0 PucR C-terminal helix-turn-helix domain PaaX PF07848.12 gi|345133545|ref|YP_004821336.1| - 0.12 12.6 0.4 0.26 11.5 0.4 1.5 1 0 0 1 1 1 0 PaaX-like protein MarR_2 PF12802.7 gi|345133545|ref|YP_004821336.1| - 0.15 12.0 1.2 4 7.4 0.4 3.1 4 0 0 4 4 4 0 MarR family DDE_Tnp_1 PF01609.21 gi|345133548|ref|YP_004821339.1| - 1e-06 28.6 0.1 2e-06 27.6 0.1 1.5 1 0 0 1 1 1 1 Transposase DDE domain HTH_23 PF13384.6 gi|345133550|ref|YP_004821341.1| - 0.00052 19.7 0.0 0.0013 18.4 0.0 1.7 1 0 0 1 1 1 1 Homeodomain-like domain Sigma70_r4_2 PF08281.12 gi|345133550|ref|YP_004821341.1| - 0.0032 17.1 0.0 0.028 14.1 0.0 2.4 2 0 0 2 2 2 1 Sigma-70, region 4 CENP-B_N PF04218.13 gi|345133550|ref|YP_004821341.1| - 0.06 13.0 1.7 0.11 12.2 0.0 2.0 2 0 0 2 2 2 0 CENP-B N-terminal DNA-binding domain Glyco_hyd_101C PF17451.2 gi|345133553|ref|YP_004821344.1| - 0.032 14.5 0.2 0.05 13.9 0.2 1.3 1 0 0 1 1 1 0 Glycosyl hydrolase 101 beta sandwich domain LIM_bind PF01803.16 gi|345133553|ref|YP_004821344.1| - 0.17 11.4 0.0 0.22 11.0 0.0 1.1 1 0 0 1 1 1 0 LIM-domain binding protein DDE_Tnp_1 PF01609.21 gi|345133555|ref|YP_004821346.1| - 0.031 13.9 0.1 0.085 12.5 0.1 1.7 1 1 0 1 1 1 0 Transposase DDE domain CagE_TrbE_VirB PF03135.14 gi|345133556|ref|YP_004821347.1| - 5.5e-06 26.6 0.0 1e-05 25.8 0.0 1.3 1 0 0 1 1 1 1 CagE, TrbE, VirB family, component of type IV transporter system HypA PF01155.19 gi|345133557|ref|YP_004821348.1| - 2e-05 24.6 7.1 0.0044 17.0 0.3 2.1 1 1 1 2 2 2 2 Hydrogenase/urease nickel incorporation, metallochaperone, hypA DZR PF12773.7 gi|345133557|ref|YP_004821348.1| - 0.00064 19.7 9.8 0.0012 18.9 9.8 1.4 1 1 0 1 1 1 1 Double zinc ribbon zinc_ribbon_2 PF13240.6 gi|345133557|ref|YP_004821348.1| - 0.0014 18.3 19.9 0.015 15.0 4.6 2.2 2 0 0 2 2 2 2 zinc-ribbon domain Zn_Tnp_IS1595 PF12760.7 gi|345133557|ref|YP_004821348.1| - 0.0044 17.0 4.7 0.075 13.0 0.2 3.1 2 1 0 3 3 3 1 Transposase zinc-ribbon domain zf-RRN7 PF11781.8 gi|345133557|ref|YP_004821348.1| - 0.019 14.7 16.8 1.7 8.4 0.3 4.1 3 1 1 4 4 4 0 Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 NMD3 PF04981.13 gi|345133557|ref|YP_004821348.1| - 0.026 14.0 1.9 0.026 14.0 1.9 1.4 1 1 0 1 1 1 0 NMD3 family DUF1451 PF07295.11 gi|345133557|ref|YP_004821348.1| - 0.048 13.7 7.6 1.5 8.8 1.0 2.2 2 0 0 2 2 2 0 Zinc-ribbon containing domain DUF4379 PF14311.6 gi|345133557|ref|YP_004821348.1| - 0.055 13.8 9.7 0.092 13.1 0.7 2.8 1 1 0 2 2 2 0 Probable Zinc-ribbon domain zf-RING_10 PF16685.5 gi|345133557|ref|YP_004821348.1| - 0.1 12.7 7.1 0.66 10.2 1.0 2.1 1 1 1 2 2 2 0 zinc RING finger of MSL2 Cytochrom_c3_2 PF14537.6 gi|345133557|ref|YP_004821348.1| - 0.16 12.5 10.9 0.23 11.9 1.2 2.2 1 1 1 2 2 2 0 Cytochrome c3 TackOD1 PF18551.1 gi|345133557|ref|YP_004821348.1| - 0.19 11.4 6.0 0.22 11.2 0.1 2.1 1 1 1 2 2 2 0 Thaumarchaeal output domain 1 Zn-ribbon_8 PF09723.10 gi|345133557|ref|YP_004821348.1| - 0.28 11.3 13.8 1.4 9.1 2.2 2.8 2 1 0 2 2 2 0 Zinc ribbon domain zinc_ribbon_15 PF17032.5 gi|345133557|ref|YP_004821348.1| - 0.37 11.6 7.9 1.9 9.3 0.5 2.2 2 0 0 2 2 2 0 zinc-ribbon family DUF2072 PF09845.9 gi|345133557|ref|YP_004821348.1| - 0.78 10.0 7.8 0.68 10.2 0.5 2.2 1 1 1 2 2 2 0 Zn-ribbon containing protein zf-UBP PF02148.19 gi|345133557|ref|YP_004821348.1| - 0.86 10.0 5.9 5.1 7.5 1.4 2.4 2 1 0 2 2 2 0 Zn-finger in ubiquitin-hydrolases and other protein ADK_lid PF05191.14 gi|345133557|ref|YP_004821348.1| - 1.2 9.1 15.4 0.18 11.8 1.9 2.9 2 1 0 2 2 2 0 Adenylate kinase, active site lid Nudix_N_2 PF14803.6 gi|345133557|ref|YP_004821348.1| - 5.5 7.0 12.1 7.5 6.6 0.4 3.9 4 0 0 4 4 4 0 Nudix N-terminal HTH_24 PF13412.6 gi|345133559|ref|YP_004821350.1| - 0.034 13.7 0.0 0.1 12.2 0.0 1.8 2 0 0 2 2 2 0 Winged helix-turn-helix DNA-binding HTH_20 PF12840.7 gi|345133559|ref|YP_004821350.1| - 0.038 14.0 0.0 0.069 13.2 0.0 1.4 1 0 0 1 1 1 0 Helix-turn-helix domain Hemerythrin PF01814.23 gi|345133561|ref|YP_004821352.1| - 0.073 13.7 0.0 0.087 13.4 0.0 1.1 1 0 0 1 1 1 0 Hemerythrin HHE cation binding domain XhoI PF04555.13 gi|345133562|ref|YP_004821353.1| - 7.3e-90 300.0 0.0 8.6e-90 299.8 0.0 1.0 1 0 0 1 1 1 1 Restriction endonuclease XhoI # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/halophilic_archaeon_DL31_uid72619/NC_015959.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/halophilic_archaeon_DL31_uid72619/NC_015959.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/halophilic_archaeon_DL31_uid72619/NC_015959.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/halophilic_archaeon_DL31_uid72619/NC_015959.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 12:32:21 2019 # [ok]