# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- Phage_integrase PF00589.22 gi|109644368|ref|YP_659398.1| - 4.2e-21 75.5 2.0 2.5e-20 73.0 2.0 1.8 1 1 0 1 1 1 1 Phage integrase family DUF3435 PF11917.8 gi|109644368|ref|YP_659398.1| - 0.04 12.9 0.6 0.053 12.5 0.6 1.2 1 0 0 1 1 1 0 Protein of unknown function (DUF3435) HTH_8 PF02954.19 gi|109644368|ref|YP_659398.1| - 0.09 12.6 0.6 9.4 6.1 0.1 3.2 4 0 0 4 4 4 0 Bacterial regulatory protein, Fis family RST PF12174.8 gi|109644368|ref|YP_659398.1| - 0.2 11.6 0.9 0.33 10.9 0.1 1.8 2 0 0 2 2 2 0 RCD1-SRO-TAF4 (RST) plant domain Yip1 PF04893.17 gi|109644371|ref|YP_659401.1| - 3.4 7.4 24.1 3 7.5 17.3 3.0 1 1 1 2 2 2 0 Yip1 domain bPH_2 PF03703.14 gi|109644372|ref|YP_659402.1| - 0.0042 17.2 0.6 0.024 14.8 0.0 2.0 2 0 0 2 2 2 1 Bacterial PH domain MG2 PF01835.19 gi|109644373|ref|YP_659403.1| - 0.00043 20.7 0.0 0.0012 19.2 0.0 1.8 1 0 0 1 1 1 1 MG2 domain Caskin-tail PF16632.5 gi|109644375|ref|YP_659405.1| - 0.022 15.2 0.2 0.037 14.4 0.2 1.3 1 0 0 1 1 1 0 C-terminal region of Caskin Arc PF03869.14 gi|109644376|ref|YP_659406.1| - 0.052 13.4 0.0 0.092 12.6 0.0 1.5 1 0 0 1 1 1 0 Arc-like DNA binding domain RHH_8 PF17723.1 gi|109644376|ref|YP_659406.1| - 0.19 11.9 0.0 0.33 11.1 0.0 1.4 2 0 0 2 2 2 0 Ribbon-Helix-Helix transcriptional regulator family Astro_capsid_p PF12226.8 gi|109644378|ref|YP_659408.1| - 0.084 12.0 4.8 0.097 11.8 4.8 1.1 1 0 0 1 1 1 0 Turkey astrovirus capsid protein Motilin_assoc PF04643.12 gi|109644378|ref|YP_659408.1| - 0.91 9.4 4.8 22 5.0 0.3 3.0 1 1 1 2 2 2 0 Motilin/ghrelin-associated peptide N6_Mtase PF02384.16 gi|109644379|ref|YP_659409.1| - 4.8e-07 29.4 0.2 0.03 13.6 0.0 3.5 3 0 0 3 3 3 2 N-6 DNA Methylase Eco57I PF07669.11 gi|109644379|ref|YP_659409.1| - 0.00041 20.8 0.1 1.5 9.4 0.0 2.8 2 0 0 2 2 2 2 Eco57I restriction-modification methylase PLDc_2 PF13091.6 gi|109644380|ref|YP_659410.1| - 2.3e-25 89.0 0.4 1.9e-24 86.1 0.0 2.8 3 0 0 3 3 3 1 PLD-like domain Helicase_C PF00271.31 gi|109644380|ref|YP_659410.1| - 5.2e-19 68.6 0.5 2e-17 63.5 0.0 3.0 2 0 0 2 2 2 1 Helicase conserved C-terminal domain ResIII PF04851.15 gi|109644380|ref|YP_659410.1| - 3.3e-10 40.2 0.2 2.6e-09 37.3 0.0 2.7 2 1 0 3 3 3 1 Type III restriction enzyme, res subunit SNF2_N PF00176.23 gi|109644380|ref|YP_659410.1| - 3.7e-10 39.0 0.3 1e-08 34.3 0.3 2.2 1 1 0 1 1 1 1 SNF2 family N-terminal domain DUF2075 PF09848.9 gi|109644380|ref|YP_659410.1| - 0.00015 21.1 0.7 0.00063 19.1 0.0 2.3 3 0 0 3 3 3 1 Uncharacterized conserved protein (DUF2075) SWI2_SNF2 PF18766.1 gi|109644380|ref|YP_659410.1| - 0.00034 20.4 0.2 0.0013 18.4 0.0 2.3 2 0 0 2 2 2 1 SWI2/SNF2 ATPase AAA_22 PF13401.6 gi|109644380|ref|YP_659410.1| - 0.058 13.7 0.0 0.27 11.5 0.0 2.2 1 0 0 1 1 1 0 AAA domain Latarcin PF10279.9 gi|109644380|ref|YP_659410.1| - 0.23 11.9 6.3 80 3.7 5.5 4.8 4 3 0 4 4 4 0 Latarcin precursor LPD26 PF18842.1 gi|109644382|ref|YP_659412.1| - 0.0016 18.4 0.0 0.0026 17.7 0.0 1.3 1 0 0 1 1 1 1 Large polyvalent protein associated domain 26 HIP1_clath_bdg PF16515.5 gi|109644382|ref|YP_659412.1| - 0.015 15.9 0.9 0.017 15.7 0.9 1.1 1 0 0 1 1 1 0 Clathrin-binding domain of Huntingtin-interacting protein 1 CheZ PF04344.13 gi|109644383|ref|YP_659413.1| - 0.0077 16.2 0.0 0.008 16.1 0.0 1.1 1 0 0 1 1 1 1 Chemotaxis phosphatase, CheZ LytR_C PF13399.6 gi|109644383|ref|YP_659413.1| - 0.025 15.6 1.2 0.31 12.0 0.2 2.1 1 1 1 2 2 2 0 LytR cell envelope-related transcriptional attenuator zf-His_Me_endon PF05551.11 gi|109644383|ref|YP_659413.1| - 0.13 12.4 0.0 0.19 11.9 0.0 1.3 1 0 0 1 1 1 0 Zinc-binding loop region of homing endonuclease RVT_3 PF13456.6 gi|109644384|ref|YP_659414.1| - 4e-11 42.8 0.1 5e-11 42.5 0.1 1.1 1 0 0 1 1 1 1 Reverse transcriptase-like RNase_H PF00075.24 gi|109644384|ref|YP_659414.1| - 9.3e-10 38.8 0.3 1.2e-09 38.5 0.3 1.1 1 0 0 1 1 1 1 RNase H PLC-beta_C PF08703.10 gi|109644384|ref|YP_659414.1| - 0.048 13.6 0.0 0.071 13.1 0.0 1.2 1 0 0 1 1 1 0 PLC-beta C terminal HNH PF01844.23 gi|109644385|ref|YP_659415.1| - 1.4e-07 31.6 2.7 2.3e-07 30.9 2.7 1.4 1 0 0 1 1 1 1 HNH endonuclease HNH_5 PF14279.6 gi|109644385|ref|YP_659415.1| - 0.0029 17.4 1.3 0.0057 16.5 1.3 1.5 1 0 0 1 1 1 1 HNH endonuclease ADH_N PF08240.12 gi|109644385|ref|YP_659415.1| - 0.11 12.3 0.4 0.11 12.3 0.4 1.6 1 1 1 2 2 2 0 Alcohol dehydrogenase GroES-like domain Cytochrome_C7 PF14522.6 gi|109644385|ref|YP_659415.1| - 0.21 11.6 7.5 0.69 9.9 5.7 1.8 1 1 0 1 1 1 0 Cytochrome c7 and related cytochrome c Endonuclease_7 PF02945.15 gi|109644385|ref|YP_659415.1| - 0.24 11.4 5.6 0.46 10.4 0.3 2.2 1 1 1 2 2 2 0 Recombination endonuclease VII zf-trcl PF13451.6 gi|109644385|ref|YP_659415.1| - 0.51 10.3 5.6 0.98 9.4 0.8 2.4 2 0 0 2 2 2 0 Probable zinc-ribbon domain D5_N PF08706.11 gi|109644386|ref|YP_659416.1| - 2e-09 37.9 0.1 3.6e-08 33.8 0.1 2.5 1 1 1 2 2 2 1 D5 N terminal like AAA_23 PF13476.6 gi|109644386|ref|YP_659416.1| - 0.073 13.6 0.1 0.29 11.6 0.0 2.0 2 0 0 2 2 2 0 AAA domain Macoilin PF09726.9 gi|109644389|ref|YP_659419.1| - 0.27 9.7 0.6 0.29 9.6 0.6 1.1 1 0 0 1 1 1 0 Macoilin family AAA_31 PF13614.6 gi|109644390|ref|YP_659420.1| - 1.5e-21 77.1 0.0 2.4e-21 76.4 0.0 1.3 1 0 0 1 1 1 1 AAA domain CbiA PF01656.23 gi|109644390|ref|YP_659420.1| - 3e-12 46.7 0.0 4.1e-12 46.3 0.0 1.2 1 0 0 1 1 1 1 CobQ/CobB/MinD/ParA nucleotide binding domain MipZ PF09140.11 gi|109644390|ref|YP_659420.1| - 8e-11 41.7 0.0 3.9e-06 26.4 0.0 2.2 1 1 1 2 2 2 2 ATPase MipZ CBP_BcsQ PF06564.12 gi|109644390|ref|YP_659420.1| - 4.2e-06 26.4 1.2 0.00014 21.4 0.4 2.4 2 1 0 2 2 2 1 Cellulose biosynthesis protein BcsQ ArsA_ATPase PF02374.15 gi|109644390|ref|YP_659420.1| - 0.00037 19.8 0.2 0.00072 18.8 0.1 1.6 2 0 0 2 2 2 1 Anion-transporting ATPase ParA PF10609.9 gi|109644390|ref|YP_659420.1| - 0.0029 17.1 1.9 0.0031 17.0 0.2 1.8 2 0 0 2 2 2 1 NUBPL iron-transfer P-loop NTPase Myb_DNA-binding PF00249.31 gi|109644390|ref|YP_659420.1| - 0.07 13.3 0.0 0.18 12.0 0.0 1.7 1 0 0 1 1 1 0 Myb-like DNA-binding domain DUF853 PF05872.12 gi|109644390|ref|YP_659420.1| - 0.1 11.1 0.2 0.15 10.6 0.2 1.3 1 0 0 1 1 1 0 Bacterial protein of unknown function (DUF853) SRP54 PF00448.22 gi|109644390|ref|YP_659420.1| - 0.41 10.2 2.7 0.66 9.6 0.1 2.5 3 1 0 3 3 3 0 SRP54-type protein, GTPase domain AAA_25 PF13481.6 gi|109644390|ref|YP_659420.1| - 1.9 8.0 5.2 16 5.0 2.6 3.0 2 1 0 2 2 2 0 AAA domain Nterm_IS4 PF13006.7 gi|109644391|ref|YP_659421.1| - 0.0031 17.7 0.0 0.005 17.0 0.0 1.3 1 0 0 1 1 1 1 Insertion element 4 transposase N-terminal T2SSF PF00482.23 gi|109644391|ref|YP_659421.1| - 0.019 14.9 0.1 0.028 14.4 0.1 1.4 1 0 0 1 1 1 0 Type II secretion system (T2SS), protein F RHH_1 PF01402.21 gi|109644391|ref|YP_659421.1| - 1.1 9.3 0.0 1.1 9.3 0.0 4.0 5 0 0 5 5 5 0 Ribbon-helix-helix protein, copG family AIM3 PF17096.5 gi|109644394|ref|YP_659424.1| - 0.025 15.5 0.1 0.037 15.0 0.1 1.2 1 0 0 1 1 1 0 Altered inheritance of mitochondria protein 3 Mrr_cat PF04471.12 gi|109644396|ref|YP_659426.1| - 4.3e-23 81.5 0.1 7.2e-23 80.8 0.1 1.4 1 0 0 1 1 1 1 Restriction endonuclease WYL PF13280.6 gi|109644396|ref|YP_659426.1| - 1.2e-19 71.0 4.4 1.2e-18 67.7 1.1 2.7 2 2 0 3 3 3 1 WYL domain Mrr_cat_2 PF13156.6 gi|109644396|ref|YP_659426.1| - 2.2e-15 56.7 0.3 1.4e-14 54.1 0.3 2.1 2 0 0 2 2 2 1 Restriction endonuclease Mrr_cat_2 PF13156.6 gi|109644397|ref|YP_659427.1| - 1.7e-24 86.1 0.5 2.6e-24 85.5 0.5 1.3 1 0 0 1 1 1 1 Restriction endonuclease Mrr_cat PF04471.12 gi|109644397|ref|YP_659427.1| - 6.1e-22 77.8 0.0 8.5e-22 77.3 0.0 1.2 1 0 0 1 1 1 1 Restriction endonuclease DUF4352 PF11611.8 gi|109644398|ref|YP_659428.1| - 5.2e-09 36.4 0.1 5e-07 30.1 0.2 2.3 2 0 0 2 2 2 1 Domain of unknown function (DUF4352) CARDB PF07705.11 gi|109644398|ref|YP_659428.1| - 0.016 15.5 0.0 0.091 13.0 0.0 2.2 2 1 0 2 2 2 0 CARDB DUF3558 PF12079.8 gi|109644398|ref|YP_659428.1| - 0.075 13.0 2.0 0.12 12.3 2.0 1.3 1 0 0 1 1 1 0 Protein of unknown function (DUF3558) Phage_holin_2_4 PF16082.5 gi|109644399|ref|YP_659429.1| - 0.86 9.4 5.2 1.3 8.8 5.2 1.4 1 0 0 1 1 1 0 Bacteriophage holin family, superfamily II-like DUF4352 PF11611.8 gi|109644400|ref|YP_659430.1| - 0.00032 21.0 0.0 0.47 10.8 0.0 2.1 2 0 0 2 2 2 2 Domain of unknown function (DUF4352) Resolvase PF00239.21 gi|109644401|ref|YP_659431.1| - 4.6e-35 120.9 2.6 4.6e-35 120.9 2.6 1.7 2 0 0 2 2 2 1 Resolvase, N terminal domain HTH_29 PF13551.6 gi|109644401|ref|YP_659431.1| - 0.0051 16.8 0.2 0.02 14.9 0.2 2.0 1 0 0 1 1 1 1 Winged helix-turn helix HTH_23 PF13384.6 gi|109644401|ref|YP_659431.1| - 0.017 14.9 0.2 0.057 13.2 0.2 2.0 1 0 0 1 1 1 0 Homeodomain-like domain Mg_chelatase_C PF13335.6 gi|109644401|ref|YP_659431.1| - 0.017 15.8 6.4 0.038 14.6 0.3 2.3 2 0 0 2 2 2 0 Magnesium chelatase, subunit ChlI C-terminal HTH_28 PF13518.6 gi|109644401|ref|YP_659431.1| - 0.018 15.2 0.1 0.046 13.9 0.1 1.6 1 0 0 1 1 1 0 Helix-turn-helix domain Phage_NinH PF06322.11 gi|109644401|ref|YP_659431.1| - 0.086 12.7 0.2 0.18 11.7 0.2 1.5 1 0 0 1 1 1 0 Phage NinH protein HTH_3 PF01381.22 gi|109644401|ref|YP_659431.1| - 0.099 12.7 0.1 0.23 11.5 0.1 1.6 1 0 0 1 1 1 0 Helix-turn-helix SurA_N_3 PF13624.6 gi|109644401|ref|YP_659431.1| - 0.27 11.0 2.9 0.35 10.6 0.5 2.1 2 0 0 2 2 2 0 SurA N-terminal domain CAP PF00188.26 gi|109644402|ref|YP_659432.1| - 5.9e-12 46.5 0.3 9.7e-12 45.8 0.3 1.4 1 0 0 1 1 1 1 Cysteine-rich secretory protein family VAPB_antitox PF02697.14 gi|109644403|ref|YP_659433.1| - 0.01 16.6 0.1 0.04 14.7 0.1 1.9 2 0 0 2 2 2 0 Putative antitoxin # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloquadratum_walsbyi_DSM_16790_uid58673/NC_008213.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_DSM_16790_uid58673/NC_008213.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloquadratum_walsbyi_DSM_16790_uid58673/NC_008213.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_DSM_16790_uid58673/NC_008213.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 12:41:27 2019 # [ok]