# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- LRR_3 PF07725.12 gi|386003072|ref|YP_005064092.1| - 0.067 13.1 0.0 0.1 12.5 0.0 1.2 1 0 0 1 1 1 0 Leucine Rich Repeat ZZ PF00569.17 gi|386003074|ref|YP_005064094.1| - 0.0036 17.1 0.3 0.0048 16.7 0.3 1.2 1 0 0 1 1 1 1 Zinc finger, ZZ type Prim-Pol PF09250.11 gi|386003076|ref|YP_005064096.1| - 0.00085 19.7 0.0 0.0025 18.2 0.0 1.7 1 0 0 1 1 1 1 Bifunctional DNA primase/polymerase, N-terminal RHH_1 PF01402.21 gi|386003082|ref|YP_005064102.1| - 6.9e-06 25.8 0.1 6.9e-06 25.8 0.1 2.4 3 0 0 3 3 3 1 Ribbon-helix-helix protein, copG family Arc PF03869.14 gi|386003082|ref|YP_005064102.1| - 0.00076 19.3 0.0 0.0018 18.0 0.0 1.7 1 0 0 1 1 1 1 Arc-like DNA binding domain RHH_3 PF12651.7 gi|386003082|ref|YP_005064102.1| - 0.0008 19.3 0.0 0.0014 18.5 0.0 1.4 1 0 0 1 1 1 1 Ribbon-helix-helix domain RHH_5 PF07878.11 gi|386003082|ref|YP_005064102.1| - 0.006 16.4 0.0 0.012 15.5 0.0 1.5 1 0 0 1 1 1 1 CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5 HTH_29 PF13551.6 gi|386003082|ref|YP_005064102.1| - 0.0064 16.5 0.0 0.11 12.6 0.0 2.3 2 0 0 2 2 2 1 Winged helix-turn helix HTH_38 PF13936.6 gi|386003082|ref|YP_005064102.1| - 0.018 14.8 0.1 0.15 11.9 0.1 2.3 2 0 0 2 2 2 0 Helix-turn-helix domain HTH_40 PF14493.6 gi|386003082|ref|YP_005064102.1| - 0.039 14.4 0.2 2.5 8.6 0.0 3.0 2 1 1 3 3 3 0 Helix-turn-helix domain HTH_Tnp_ISL3 PF13542.6 gi|386003082|ref|YP_005064102.1| - 0.04 13.3 0.0 0.2 11.1 0.0 2.1 2 0 0 2 2 2 0 Helix-turn-helix domain of transposase family ISL3 CopG_antitoxin PF12441.8 gi|386003082|ref|YP_005064102.1| - 0.047 14.2 1.3 0.38 11.3 0.0 2.8 3 0 0 3 3 3 0 CopG antitoxin of type II toxin-antitoxin system DUF2510 PF10708.9 gi|386003082|ref|YP_005064102.1| - 0.11 12.2 0.0 0.23 11.2 0.0 1.5 1 0 0 1 1 1 0 Protein of unknown function (DUF2510) HTH_23 PF13384.6 gi|386003082|ref|YP_005064102.1| - 0.22 11.4 3.3 0.52 10.2 0.1 3.0 3 1 0 3 3 3 0 Homeodomain-like domain RuvA_C PF07499.13 gi|386003082|ref|YP_005064102.1| - 1.9 9.0 5.7 14 6.2 0.2 3.5 4 0 0 4 4 4 0 RuvA, C-terminal domain RE_NgoBV PF09564.10 gi|386003083|ref|YP_005064103.1| - 0.17 11.3 0.0 0.21 11.0 0.0 1.1 1 0 0 1 1 1 0 NgoBV restriction endonuclease RHH_6 PF16762.5 gi|386003085|ref|YP_005064105.1| - 0.00028 21.4 0.0 0.0003 21.4 0.0 1.0 1 0 0 1 1 1 1 Ribbon-helix-helix domain SNase PF00565.17 gi|386003086|ref|YP_005064106.1| - 5.6e-10 39.7 0.0 9.4e-10 38.9 0.0 1.4 1 1 0 1 1 1 1 Staphylococcal nuclease homologue Ada_Zn_binding PF02805.16 gi|386003086|ref|YP_005064106.1| - 3.4e-06 27.0 0.1 5.8e-06 26.2 0.1 1.4 1 0 0 1 1 1 1 Metal binding domain of Ada AvrB_AvrC PF05394.11 gi|386003087|ref|YP_005064107.1| - 0.0078 15.4 0.1 0.0097 15.1 0.1 1.1 1 0 0 1 1 1 1 Avirulence protein PDDEXK_5 PF11645.8 gi|386003087|ref|YP_005064107.1| - 0.0089 16.0 0.2 0.013 15.4 0.2 1.3 1 0 0 1 1 1 1 PD-(D/E)XK endonuclease N6_N4_Mtase PF01555.18 gi|386003089|ref|YP_005064109.1| - 2.3e-38 132.2 0.0 2.8e-38 131.9 0.0 1.1 1 0 0 1 1 1 1 DNA methylase # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_harundinacea_6Ac_uid81199/NC_016637.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_harundinacea_6Ac_uid81199/NC_016637.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_harundinacea_6Ac_uid81199/NC_016637.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_harundinacea_6Ac_uid81199/NC_016637.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 15:47:19 2019 # [ok]