# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- DUF3391 PF11871.8 gi|119709758|ref|YP_919098.1| - 4.4 7.8 7.0 17 5.9 2.3 2.2 2 0 0 2 2 2 0 Domain of unknown function (DUF3391) CPBP PF02517.16 gi|119709760|ref|YP_919100.1| - 1.8e-05 25.0 9.6 1.8e-05 25.0 9.6 3.6 3 1 0 3 3 3 1 CPBP intramembrane metalloprotease DUF1421 PF07223.11 gi|119709765|ref|YP_919105.1| - 0.051 13.4 0.0 0.11 12.4 0.0 1.6 1 0 0 1 1 1 0 UBA-like domain (DUF1421) zf-RRN7 PF11781.8 gi|119709767|ref|YP_919107.1| - 0.0067 16.1 6.6 0.009 15.7 6.6 1.2 1 0 0 1 1 1 1 Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 Zn_Tnp_IS1595 PF12760.7 gi|119709767|ref|YP_919107.1| - 0.13 12.3 7.3 0.19 11.7 7.3 1.3 1 0 0 1 1 1 0 Transposase zinc-ribbon domain DotD PF16816.5 gi|119709768|ref|YP_919108.1| - 0.15 12.0 0.0 0.21 11.5 0.0 1.2 1 0 0 1 1 1 0 DotD protein RHH_1 PF01402.21 gi|119709770|ref|YP_919110.1| - 0.003 17.4 0.1 0.017 15.0 0.1 2.4 1 0 0 1 1 1 1 Ribbon-helix-helix protein, copG family RHH_3 PF12651.7 gi|119709770|ref|YP_919110.1| - 0.0032 17.4 0.6 0.019 14.9 0.2 2.3 2 0 0 2 2 2 1 Ribbon-helix-helix domain GAS PF13851.6 gi|119709770|ref|YP_919110.1| - 0.01 15.2 2.8 0.011 15.1 0.6 2.0 2 0 0 2 2 2 1 Growth-arrest specific micro-tubule binding RmuC PF02646.16 gi|119709770|ref|YP_919110.1| - 0.025 13.7 0.5 0.21 10.7 0.4 2.3 2 1 0 2 2 2 0 RmuC family Phage_terminase PF10668.9 gi|119709770|ref|YP_919110.1| - 0.034 14.1 0.7 11 6.1 0.2 2.6 2 0 0 2 2 2 0 Phage terminase small subunit CopG_antitoxin PF12441.8 gi|119709770|ref|YP_919110.1| - 0.05 14.1 0.1 0.13 12.8 0.1 1.7 1 0 0 1 1 1 0 CopG antitoxin of type II toxin-antitoxin system LTXXQ PF07813.12 gi|119709770|ref|YP_919110.1| - 0.053 14.3 3.6 0.19 12.4 3.6 2.0 1 1 0 1 1 1 0 LTXXQ motif family protein SKA2 PF16740.5 gi|119709770|ref|YP_919110.1| - 0.059 13.2 0.1 0.17 11.7 0.1 1.7 1 0 0 1 1 1 0 Spindle and kinetochore-associated protein 2 YAcAr PF10686.9 gi|119709770|ref|YP_919110.1| - 0.062 13.3 0.1 0.22 11.5 0.0 2.0 2 0 0 2 2 2 0 YspA, cpYpsA-related SLOG family Surfac_D-trimer PF09006.11 gi|119709770|ref|YP_919110.1| - 0.074 13.0 0.0 0.26 11.2 0.0 2.0 1 1 0 1 1 1 0 Lung surfactant protein D coiled-coil trimerisation PSK_trans_fac PF07704.11 gi|119709770|ref|YP_919110.1| - 0.075 13.8 0.7 0.075 13.8 0.7 3.1 2 2 1 3 3 3 0 Rv0623-like transcription factor APG6_N PF17675.1 gi|119709770|ref|YP_919110.1| - 0.11 13.0 5.0 0.082 13.4 1.4 2.2 2 1 0 2 2 2 0 Apg6 coiled-coil region YabA PF06156.13 gi|119709770|ref|YP_919110.1| - 0.17 12.5 1.4 2.5 8.8 0.5 2.7 3 1 0 3 3 3 0 Initiation control protein YabA Sigma70_r3 PF04539.16 gi|119709773|ref|YP_919113.1| - 0.0011 19.0 0.0 0.1 12.7 0.0 2.2 2 0 0 2 2 2 1 Sigma-70 region 3 HTH_24 PF13412.6 gi|119709773|ref|YP_919113.1| - 0.0016 18.0 0.0 0.0045 16.5 0.0 1.8 2 0 0 2 2 2 1 Winged helix-turn-helix DNA-binding HTH_38 PF13936.6 gi|119709773|ref|YP_919113.1| - 0.0034 17.1 0.0 0.0089 15.8 0.0 1.7 1 0 0 1 1 1 1 Helix-turn-helix domain FaeA PF04703.12 gi|119709773|ref|YP_919113.1| - 0.019 15.3 0.0 0.032 14.6 0.0 1.3 1 0 0 1 1 1 0 FaeA-like protein TrmB PF01978.19 gi|119709773|ref|YP_919113.1| - 0.11 12.4 0.0 0.2 11.6 0.0 1.4 1 0 0 1 1 1 0 Sugar-specific transcriptional regulator TrmB MerR PF00376.23 gi|119709773|ref|YP_919113.1| - 0.13 12.0 0.2 0.81 9.5 0.2 2.1 1 1 0 1 1 1 0 MerR family regulatory protein YgbB PF02542.16 gi|119709773|ref|YP_919113.1| - 0.21 11.9 0.0 0.3 11.3 0.0 1.2 1 0 0 1 1 1 0 YgbB family DUF1771 PF08590.10 gi|119709774|ref|YP_919114.1| - 0.0016 18.8 0.1 0.0024 18.2 0.1 1.3 1 0 0 1 1 1 1 Domain of unknown function (DUF1771) DOPA_dioxygen PF08883.11 gi|119709774|ref|YP_919114.1| - 0.056 13.6 0.0 0.098 12.8 0.0 1.3 1 0 0 1 1 1 0 Dopa 4,5-dioxygenase family BatA PF07584.11 gi|119709776|ref|YP_919116.1| - 0.045 14.1 0.3 0.045 14.1 0.3 2.3 2 0 0 2 2 2 0 Aerotolerance regulator N-terminal Totivirus_coat PF05518.11 gi|119709776|ref|YP_919116.1| - 0.063 11.3 0.6 0.086 10.9 0.6 1.1 1 0 0 1 1 1 0 Totivirus coat protein DUF4175 PF13779.6 gi|119709776|ref|YP_919116.1| - 0.17 9.7 0.2 0.25 9.2 0.2 1.3 1 0 0 1 1 1 0 Domain of unknown function (DUF4175) TGBp3 PF02495.17 gi|119709776|ref|YP_919116.1| - 0.56 9.9 3.2 1.2 8.8 0.1 2.4 2 0 0 2 2 2 0 Triple gene block 3 DUF641 PF04859.12 gi|119709780|ref|YP_919120.1| - 0.035 14.5 0.2 0.041 14.2 0.2 1.2 1 0 0 1 1 1 0 Plant protein of unknown function (DUF641) HEPN-like_int PF18867.1 gi|119709780|ref|YP_919120.1| - 0.04 13.8 0.0 0.051 13.4 0.0 1.1 1 0 0 1 1 1 0 HEPN-like integron domain APG6_N PF17675.1 gi|119709780|ref|YP_919120.1| - 0.058 13.9 3.7 0.076 13.5 3.7 1.1 1 0 0 1 1 1 0 Apg6 coiled-coil region zf-ISL3 PF14690.6 gi|119709780|ref|YP_919120.1| - 0.067 13.9 0.2 0.12 13.0 0.2 1.4 1 0 0 1 1 1 0 zinc-finger of transposase IS204/IS1001/IS1096/IS1165 PDEase_I_N PF08499.12 gi|119709782|ref|YP_919122.1| - 0.063 13.1 0.0 0.12 12.2 0.0 1.4 1 0 0 1 1 1 0 3'5'-cyclic nucleotide phosphodiesterase N-terminal FUSC_2 PF13515.6 gi|119709783|ref|YP_919123.1| - 0.048 13.8 7.1 0.077 13.1 7.1 1.3 1 0 0 1 1 1 0 Fusaric acid resistance protein-like zf-C5HC2 PF02928.16 gi|119709785|ref|YP_919125.1| - 0.07 13.5 0.5 0.14 12.6 0.1 1.7 2 0 0 2 2 2 0 C5HC2 zinc finger DUF1450 PF07293.11 gi|119709785|ref|YP_919125.1| - 0.1 12.4 0.7 0.34 10.7 0.2 1.9 2 0 0 2 2 2 0 Protein of unknown function (DUF1450) FUN14 PF04930.15 gi|119709786|ref|YP_919126.1| - 6e-06 26.6 2.6 7.5e-06 26.3 2.6 1.1 1 0 0 1 1 1 1 FUN14 family SPC12 PF06645.13 gi|119709786|ref|YP_919126.1| - 0.44 10.7 5.0 6.2 7.0 2.8 2.2 2 0 0 2 2 2 0 Microsomal signal peptidase 12 kDa subunit (SPC12) DUF3437 PF11919.8 gi|119709788|ref|YP_919128.1| - 0.18 11.7 0.0 0.19 11.7 0.0 1.2 1 0 0 1 1 1 0 Domain of unknown function (DUF3437) DUF3563 PF12086.8 gi|119709789|ref|YP_919129.1| - 0.081 12.7 0.6 4.8 7.0 0.1 2.2 2 0 0 2 2 2 0 Protein of unknown function (DUF3563) Ku_C PF03730.14 gi|119709789|ref|YP_919129.1| - 0.14 12.9 0.1 0.2 12.4 0.1 1.2 1 0 0 1 1 1 0 Ku70/Ku80 C-terminal arm PSK_trans_fac PF07704.11 gi|119709791|ref|YP_919131.1| - 0.00047 20.9 2.3 0.00068 20.3 2.3 1.3 1 1 0 1 1 1 1 Rv0623-like transcription factor RHH_1 PF01402.21 gi|119709791|ref|YP_919131.1| - 0.0014 18.5 5.2 0.0015 18.4 3.9 1.7 2 0 0 2 2 2 1 Ribbon-helix-helix protein, copG family ParE_toxin PF05016.15 gi|119709791|ref|YP_919131.1| - 0.0015 19.1 0.9 0.0017 18.9 0.9 1.1 1 0 0 1 1 1 1 ParE toxin of type II toxin-antitoxin system, parDE RAC_head PF16717.5 gi|119709791|ref|YP_919131.1| - 0.0047 17.9 0.9 0.005 17.8 0.9 1.1 1 0 0 1 1 1 1 Ribosome-associated complex head domain ADSL_C PF10397.9 gi|119709791|ref|YP_919131.1| - 0.0075 16.8 1.2 0.0075 16.8 1.2 1.1 1 0 0 1 1 1 1 Adenylosuccinate lyase C-terminus TetR_C_11 PF16859.5 gi|119709791|ref|YP_919131.1| - 0.009 16.3 0.1 0.0095 16.2 0.1 1.1 1 0 0 1 1 1 1 Tetracyclin repressor-like, C-terminal domain CPL PF08144.11 gi|119709791|ref|YP_919131.1| - 0.013 15.8 0.3 0.014 15.7 0.3 1.1 1 0 0 1 1 1 0 CPL (NUC119) domain DnaI_N PF07319.11 gi|119709791|ref|YP_919131.1| - 0.013 16.1 0.2 0.016 15.9 0.2 1.1 1 0 0 1 1 1 0 Primosomal protein DnaI N-terminus DUF3818 PF12825.7 gi|119709791|ref|YP_919131.1| - 0.017 14.2 0.5 0.018 14.1 0.5 1.0 1 0 0 1 1 1 0 Domain of unknown function in PX-proteins (DUF3818) Lipoprotein_16 PF03923.13 gi|119709791|ref|YP_919131.1| - 0.023 14.4 0.2 0.026 14.2 0.2 1.3 1 0 0 1 1 1 0 Uncharacterized lipoprotein GerD PF17898.1 gi|119709791|ref|YP_919131.1| - 0.024 14.6 0.3 0.038 13.9 0.3 1.4 1 1 0 1 1 1 0 Spore germination GerD central core domain PEP-utilisers_N PF05524.13 gi|119709791|ref|YP_919131.1| - 0.025 14.7 1.0 0.03 14.5 1.0 1.0 1 0 0 1 1 1 0 PEP-utilising enzyme, N-terminal NEMO PF11577.8 gi|119709791|ref|YP_919131.1| - 0.026 14.5 1.9 0.032 14.3 1.9 1.2 1 0 0 1 1 1 0 NF-kappa-B essential modulator NEMO RPN7 PF10602.9 gi|119709791|ref|YP_919131.1| - 0.033 13.9 1.9 0.041 13.6 1.9 1.1 1 0 0 1 1 1 0 26S proteasome subunit RPN7 AAA_32 PF13654.6 gi|119709791|ref|YP_919131.1| - 0.039 12.8 1.0 0.04 12.7 1.0 1.0 1 0 0 1 1 1 0 AAA domain XH PF03469.14 gi|119709791|ref|YP_919131.1| - 0.042 13.8 0.8 0.056 13.4 0.7 1.4 1 1 1 2 2 2 0 XH domain T6SS_VipA PF05591.12 gi|119709791|ref|YP_919131.1| - 0.044 13.6 2.0 0.049 13.4 2.0 1.1 1 0 0 1 1 1 0 Type VI secretion system, VipA, VC_A0107 or Hcp2 DUF445 PF04286.12 gi|119709791|ref|YP_919131.1| - 0.046 13.5 1.1 0.047 13.5 1.1 1.0 1 0 0 1 1 1 0 Protein of unknown function (DUF445) Sec3_C_2 PF15278.6 gi|119709791|ref|YP_919131.1| - 0.049 14.0 0.5 0.062 13.7 0.5 1.2 1 0 0 1 1 1 0 Sec3 exocyst complex subunit MethyTransf_Reg PF10119.9 gi|119709791|ref|YP_919131.1| - 0.065 13.9 0.2 0.073 13.8 0.2 1.2 1 0 0 1 1 1 0 Predicted methyltransferase regulatory domain Taeniidae_ag PF05596.11 gi|119709791|ref|YP_919131.1| - 0.075 13.0 2.0 0.18 11.8 1.5 1.7 2 0 0 2 2 2 0 Taeniidae antigen RNase_J_C PF17770.1 gi|119709791|ref|YP_919131.1| - 0.078 14.0 0.3 0.093 13.8 0.3 1.2 1 0 0 1 1 1 0 Ribonuclease J C-terminal domain COMP PF11598.8 gi|119709791|ref|YP_919131.1| - 0.089 13.3 4.2 0.11 13.0 2.2 2.1 2 1 0 2 2 2 0 Cartilage oligomeric matrix protein Se-cys_synth_N PF12390.8 gi|119709791|ref|YP_919131.1| - 0.18 12.0 2.1 7.5 6.9 2.1 2.7 1 1 0 1 1 1 0 Selenocysteine synthase N terminal Regulator_TrmB PF11495.8 gi|119709792|ref|YP_919132.1| - 0.045 12.9 0.3 0.05 12.8 0.3 1.0 1 0 0 1 1 1 0 Archaeal transcriptional regulator TrmB ERCC3_RAD25_C PF16203.5 gi|119709793|ref|YP_919133.1| - 2e-14 53.4 0.0 3.5e-12 46.1 0.0 2.3 1 1 0 1 1 1 1 ERCC3/RAD25/XPB C-terminal helicase Helicase_C PF00271.31 gi|119709793|ref|YP_919133.1| - 6.2e-10 39.4 0.0 1.4e-09 38.3 0.0 1.6 1 0 0 1 1 1 1 Helicase conserved C-terminal domain ResIII PF04851.15 gi|119709793|ref|YP_919133.1| - 8.5e-10 38.9 0.0 7.2e-09 35.9 0.0 2.5 2 1 0 2 2 2 1 Type III restriction enzyme, res subunit DEAD PF00270.29 gi|119709793|ref|YP_919133.1| - 1.3e-08 34.8 0.0 4.6e-08 33.0 0.0 1.9 1 0 0 1 1 1 1 DEAD/DEAH box helicase TelA PF05816.11 gi|119709793|ref|YP_919133.1| - 0.00051 19.2 0.3 0.00088 18.4 0.3 1.3 1 0 0 1 1 1 1 Toxic anion resistance protein (TelA) SecA_DEAD PF07517.14 gi|119709793|ref|YP_919133.1| - 0.005 16.2 0.9 0.016 14.5 0.0 1.9 2 0 0 2 2 2 1 SecA DEAD-like domain AAA_30 PF13604.6 gi|119709793|ref|YP_919133.1| - 0.033 13.9 0.1 0.48 10.1 0.0 2.5 2 0 0 2 2 2 0 AAA domain Not3 PF04065.15 gi|119709793|ref|YP_919133.1| - 0.14 11.5 3.7 0.56 9.6 0.7 2.2 2 0 0 2 2 2 0 Not1 N-terminal domain, CCR4-Not complex component DUF3909 PF13077.6 gi|119709795|ref|YP_919135.1| - 0.042 14.0 0.8 0.077 13.2 0.2 1.6 1 1 0 1 1 1 0 Protein of unknown function (DUF3909) P22_Tail-4 PF11650.8 gi|119709795|ref|YP_919135.1| - 0.14 12.1 0.6 0.2 11.6 0.6 1.2 1 0 0 1 1 1 0 P22 tail accessory factor S-layer PF07752.11 gi|119709798|ref|YP_919138.1| - 0.058 12.5 0.2 0.066 12.3 0.2 1.0 1 0 0 1 1 1 0 S-layer protein Ecotin PF03974.13 gi|119709799|ref|YP_919139.1| - 0.016 15.2 0.0 0.028 14.4 0.0 1.5 1 1 0 1 1 1 0 Ecotin DUF4979 PF16351.5 gi|119709799|ref|YP_919139.1| - 0.12 12.6 0.0 0.17 12.1 0.0 1.2 1 0 0 1 1 1 0 Domain of unknown function (DUF4979) UL41A PF17591.2 gi|119709805|ref|YP_919145.1| - 0.04 14.0 0.6 0.089 12.9 0.1 1.9 1 1 0 1 1 1 0 Herpesvirus UL41A Imm70 PF15601.6 gi|119709805|ref|YP_919145.1| - 0.15 11.6 0.0 0.22 11.1 0.0 1.3 1 0 0 1 1 1 0 Immunity protein 70 zf_C2H2_10 PF18414.1 gi|119709807|ref|YP_919147.1| - 0.93 9.1 3.7 8.1 6.1 0.1 2.3 2 0 0 2 2 2 0 C2H2 type zinc-finger Vitellogenin_N PF01347.22 gi|119709808|ref|YP_919148.1| - 0.03 12.7 0.0 0.47 8.8 0.0 1.9 1 1 1 2 2 2 0 Lipoprotein amino terminal region Phage_integrase PF00589.22 gi|119709809|ref|YP_919149.1| - 3.4e-34 118.1 0.0 5.7e-34 117.4 0.0 1.4 1 0 0 1 1 1 1 Phage integrase family Phage_int_SAM_1 PF02899.17 gi|119709809|ref|YP_919149.1| - 2.9e-05 24.3 0.5 0.0016 18.7 0.0 3.1 2 2 1 3 3 3 1 Phage integrase, N-terminal SAM-like domain DUF4224 PF13986.6 gi|119709809|ref|YP_919149.1| - 0.12 12.3 0.0 0.33 10.9 0.0 1.7 1 0 0 1 1 1 0 Domain of unknown function (DUF4224) # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Thermofilum_pendens_Hrk_5_uid58563/NC_008696.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/Crenarchaeota/Thermofilum_pendens_Hrk_5_uid58563/NC_008696.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Thermofilum_pendens_Hrk_5_uid58563/NC_008696.PFam32-A.tblout --cpu 20 /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Thermofilum_pendens_Hrk_5_uid58563/NC_008696.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 11:52:57 2019 # [ok]