# --- 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|297660607|ref|YP_003710318.1| - 2.9e-24 85.8 0.2 8.2e-24 84.3 0.1 1.8 1 1 1 2 2 2 1 Phage integrase family CPSase_L_D3 PF02787.19 gi|297660607|ref|YP_003710318.1| - 0.0047 17.3 0.5 0.04 14.2 0.0 2.6 3 1 0 3 3 3 1 Carbamoyl-phosphate synthetase large chain, oligomerisation domain RHH_3 PF12651.7 gi|297660607|ref|YP_003710318.1| - 0.072 13.1 0.7 0.24 11.4 0.1 2.2 2 0 0 2 2 2 0 Ribbon-helix-helix domain Gp49 PF05973.14 gi|297660608|ref|YP_003710319.1| - 3.6e-08 33.4 0.1 4.5e-08 33.1 0.1 1.1 1 0 0 1 1 1 1 Phage derived protein Gp49-like (DUF891) HTH_26 PF13443.6 gi|297660609|ref|YP_003710320.1| - 0.0062 16.9 0.1 0.11 12.9 0.1 2.3 2 1 0 2 2 2 1 Cro/C1-type HTH DNA-binding domain Imm49 PF15575.6 gi|297660609|ref|YP_003710320.1| - 0.095 12.5 0.0 0.1 12.4 0.0 1.1 1 0 0 1 1 1 0 Immunity protein 49 Stanniocalcin PF03298.13 gi|297660609|ref|YP_003710320.1| - 0.14 11.5 0.0 0.14 11.4 0.0 1.1 1 0 0 1 1 1 0 Stanniocalcin family DDE_Tnp_IS1 PF03400.13 gi|297660610|ref|YP_003710321.1| - 2.2e-07 31.2 0.1 2.3e-07 31.2 0.1 1.1 1 0 0 1 1 1 1 IS1 transposase rve_3 PF13683.6 gi|297660610|ref|YP_003710321.1| - 0.0018 18.0 0.1 0.0024 17.6 0.1 1.3 1 0 0 1 1 1 1 Integrase core domain zf-SAP30 PF13866.6 gi|297660610|ref|YP_003710321.1| - 0.035 14.2 1.5 0.15 12.2 1.5 1.9 1 1 0 1 1 1 0 SAP30 zinc-finger DDE_Tnp_IS1 PF03400.13 gi|297660611|ref|YP_003710322.1| - 1e-11 45.3 0.1 2.8e-11 43.9 0.1 1.6 1 1 0 1 1 1 1 IS1 transposase Zn_Tnp_IS1 PF03811.13 gi|297660611|ref|YP_003710322.1| - 0.00071 19.3 2.7 0.0011 18.7 2.7 1.3 1 0 0 1 1 1 1 InsA N-terminal domain DDE_Tnp_IS240 PF13610.6 gi|297660611|ref|YP_003710322.1| - 0.00087 19.5 0.0 0.0015 18.8 0.0 1.5 1 0 0 1 1 1 1 DDE domain Zn-ribbon_8 PF09723.10 gi|297660611|ref|YP_003710322.1| - 0.19 11.9 1.9 5.4 7.2 0.3 2.5 2 0 0 2 2 2 0 Zinc ribbon domain zf-ISL3 PF14690.6 gi|297660611|ref|YP_003710322.1| - 0.43 11.3 5.4 0.7 10.6 0.7 2.8 3 0 0 3 3 3 0 zinc-finger of transposase IS204/IS1001/IS1096/IS1165 HTH_3 PF01381.22 gi|297660613|ref|YP_003710324.1| - 3e-15 56.0 0.0 4.2e-15 55.5 0.0 1.2 1 0 0 1 1 1 1 Helix-turn-helix HTH_31 PF13560.6 gi|297660613|ref|YP_003710324.1| - 6.3e-09 36.0 0.0 7.6e-09 35.8 0.0 1.0 1 0 0 1 1 1 1 Helix-turn-helix domain HTH_26 PF13443.6 gi|297660613|ref|YP_003710324.1| - 2.7e-06 27.7 0.0 3.4e-06 27.4 0.0 1.1 1 0 0 1 1 1 1 Cro/C1-type HTH DNA-binding domain HTH_19 PF12844.7 gi|297660613|ref|YP_003710324.1| - 0.00069 19.6 0.0 0.0013 18.7 0.0 1.5 1 1 1 2 2 2 1 Helix-turn-helix domain YdaS_antitoxin PF15943.5 gi|297660613|ref|YP_003710324.1| - 0.072 13.0 0.0 0.1 12.5 0.0 1.3 1 0 0 1 1 1 0 Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT HTH_25 PF13413.6 gi|297660613|ref|YP_003710324.1| - 0.08 12.8 0.0 0.11 12.4 0.0 1.4 1 1 0 1 1 1 0 Helix-turn-helix domain Ank_2 PF12796.7 gi|297660614|ref|YP_003710325.1| - 7.5e-15 55.3 1.2 1.6e-10 41.4 0.0 3.6 4 0 0 4 4 4 2 Ankyrin repeats (3 copies) Ank_4 PF13637.6 gi|297660614|ref|YP_003710325.1| - 3.9e-14 52.8 0.3 0.0073 16.9 0.1 5.7 3 1 2 5 5 5 5 Ankyrin repeats (many copies) Ank_3 PF13606.6 gi|297660614|ref|YP_003710325.1| - 1.8e-13 49.4 1.8 0.0014 19.0 0.0 5.9 5 1 1 6 6 6 3 Ankyrin repeat Ank_5 PF13857.6 gi|297660614|ref|YP_003710325.1| - 3.4e-08 33.6 1.0 0.015 15.6 0.0 4.7 4 1 1 5 5 5 2 Ankyrin repeats (many copies) Ank PF00023.30 gi|297660614|ref|YP_003710325.1| - 4.4e-08 33.2 0.4 1.5 9.4 0.1 4.8 4 1 1 5 5 5 3 Ankyrin repeat MOZART1 PF12554.8 gi|297660614|ref|YP_003710325.1| - 0.1 12.4 0.0 42 4.0 0.0 3.6 3 0 0 3 3 3 0 Mitotic-spindle organizing gamma-tubulin ring associated D5_N PF08706.11 gi|297660619|ref|YP_003710330.1| - 4.7e-16 59.4 0.2 4.7e-16 59.4 0.2 3.5 4 0 0 4 4 4 1 D5 N terminal like ResIII PF04851.15 gi|297660620|ref|YP_003710331.1| - 1.5e-22 80.4 0.0 3.2e-22 79.3 0.0 1.6 2 0 0 2 2 2 1 Type III restriction enzyme, res subunit Helicase_C PF00271.31 gi|297660620|ref|YP_003710331.1| - 1.2e-16 61.0 0.1 3.8e-15 56.2 0.0 2.7 2 0 0 2 2 2 1 Helicase conserved C-terminal domain DEAD PF00270.29 gi|297660620|ref|YP_003710331.1| - 8.7e-08 32.1 0.0 1.8e-07 31.1 0.0 1.6 1 1 0 1 1 1 1 DEAD/DEAH box helicase ERCC3_RAD25_C PF16203.5 gi|297660620|ref|YP_003710331.1| - 0.0082 15.4 0.0 0.014 14.6 0.0 1.3 1 0 0 1 1 1 1 ERCC3/RAD25/XPB C-terminal helicase SWI2_SNF2 PF18766.1 gi|297660620|ref|YP_003710331.1| - 0.041 13.5 0.0 0.08 12.6 0.0 1.5 1 0 0 1 1 1 0 SWI2/SNF2 ATPase MetW PF07021.12 gi|297660620|ref|YP_003710331.1| - 0.085 12.4 0.0 0.26 10.8 0.0 1.8 2 0 0 2 2 2 0 Methionine biosynthesis protein MetW AAA_30 PF13604.6 gi|297660620|ref|YP_003710331.1| - 0.14 11.9 0.0 0.44 10.2 0.0 1.8 2 0 0 2 2 2 0 AAA domain DUF2075 PF09848.9 gi|297660620|ref|YP_003710331.1| - 0.19 10.9 0.1 0.33 10.2 0.1 1.2 1 0 0 1 1 1 0 Uncharacterized conserved protein (DUF2075) HTH_36 PF13730.6 gi|297660621|ref|YP_003710332.1| - 3.1e-07 30.2 0.0 5.8e-07 29.4 0.0 1.4 1 0 0 1 1 1 1 Helix-turn-helix domain HTH_Crp_2 PF13545.6 gi|297660621|ref|YP_003710332.1| - 0.00014 21.8 0.0 0.00032 20.6 0.0 1.6 1 0 0 1 1 1 1 Crp-like helix-turn-helix domain HTH_29 PF13551.6 gi|297660621|ref|YP_003710332.1| - 0.00078 19.4 0.0 0.0019 18.2 0.0 1.6 1 0 0 1 1 1 1 Winged helix-turn helix HTH_23 PF13384.6 gi|297660621|ref|YP_003710332.1| - 0.015 15.0 0.0 0.015 15.0 0.0 1.9 3 0 0 3 3 3 0 Homeodomain-like domain HTH_11 PF08279.12 gi|297660621|ref|YP_003710332.1| - 0.15 12.1 0.0 0.29 11.1 0.0 1.4 1 0 0 1 1 1 0 HTH domain GntR PF00392.21 gi|297660621|ref|YP_003710332.1| - 0.21 11.3 0.0 0.53 10.0 0.0 1.6 1 0 0 1 1 1 0 Bacterial regulatory proteins, gntR family HTH_28 PF13518.6 gi|297660621|ref|YP_003710332.1| - 0.21 11.7 0.8 0.32 11.1 0.0 1.7 2 0 0 2 2 2 0 Helix-turn-helix domain HTH_17 PF12728.7 gi|297660622|ref|YP_003710333.1| - 0.0088 16.2 0.0 0.013 15.6 0.0 1.3 1 0 0 1 1 1 1 Helix-turn-helix domain Phage_integrase PF00589.22 gi|297660623|ref|YP_003710334.1| - 1.8e-06 27.9 0.0 4.9e-06 26.4 0.0 1.7 1 0 0 1 1 1 1 Phage integrase family SNF2_assoc PF08455.10 gi|297660623|ref|YP_003710334.1| - 0.0081 15.2 1.0 0.012 14.7 1.0 1.2 1 0 0 1 1 1 1 Bacterial SNF2 helicase associated AAA_31 PF13614.6 gi|297660625|ref|YP_003710336.1| - 7.2e-20 71.6 0.2 1.6e-10 41.2 0.0 2.1 1 1 1 2 2 2 2 AAA domain CbiA PF01656.23 gi|297660625|ref|YP_003710336.1| - 9.3e-13 48.4 0.1 5.3e-12 45.9 0.1 1.9 1 1 0 1 1 1 1 CobQ/CobB/MinD/ParA nucleotide binding domain VirC1 PF07015.11 gi|297660625|ref|YP_003710336.1| - 4.2e-06 26.2 0.1 2e-05 24.0 0.1 1.8 1 1 0 1 1 1 1 VirC1 protein CBP_BcsQ PF06564.12 gi|297660625|ref|YP_003710336.1| - 2.3e-05 24.0 0.0 0.36 10.3 0.0 2.8 2 1 0 2 2 2 2 Cellulose biosynthesis protein BcsQ MipZ PF09140.11 gi|297660625|ref|YP_003710336.1| - 4.4e-05 22.9 0.1 0.062 12.6 0.0 2.2 2 0 0 2 2 2 2 ATPase MipZ ParA PF10609.9 gi|297660625|ref|YP_003710336.1| - 8.7e-05 22.1 1.3 0.042 13.3 0.1 2.3 2 1 0 2 2 2 2 NUBPL iron-transfer P-loop NTPase Fer4_NifH PF00142.18 gi|297660625|ref|YP_003710336.1| - 0.00011 21.7 0.0 0.02 14.3 0.0 2.1 2 0 0 2 2 2 2 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family SRP54 PF00448.22 gi|297660625|ref|YP_003710336.1| - 0.0034 17.0 0.0 0.005 16.5 0.0 1.3 1 0 0 1 1 1 1 SRP54-type protein, GTPase domain AAA_24 PF13479.6 gi|297660625|ref|YP_003710336.1| - 0.018 14.8 0.0 0.027 14.2 0.0 1.2 1 0 0 1 1 1 0 AAA domain P63C PF10546.9 gi|297660626|ref|YP_003710337.1| - 0.11 13.1 0.4 0.29 11.7 0.1 1.9 2 1 0 2 2 2 0 P63C domain PSK_trans_fac PF07704.11 gi|297660627|ref|YP_003710338.1| - 0.00047 20.9 0.5 0.00056 20.6 0.5 1.2 1 0 0 1 1 1 1 Rv0623-like transcription factor Paz_1 PF18349.1 gi|297660627|ref|YP_003710338.1| - 0.0047 16.9 0.1 0.0049 16.8 0.1 1.1 1 0 0 1 1 1 1 PAZ domain ACP_PD PF04336.12 gi|297660627|ref|YP_003710338.1| - 0.0081 16.6 0.4 0.01 16.2 0.4 1.1 1 0 0 1 1 1 1 Acyl carrier protein phosphodiesterase CENP-B_N PF04218.13 gi|297660627|ref|YP_003710338.1| - 0.054 13.1 0.1 0.077 12.6 0.1 1.3 1 0 0 1 1 1 0 CENP-B N-terminal DNA-binding domain PemK_toxin PF02452.17 gi|297660628|ref|YP_003710339.1| - 2.9e-24 85.6 0.0 3.2e-24 85.5 0.0 1.0 1 0 0 1 1 1 1 PemK-like, MazF-like toxin of type II toxin-antitoxin system # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/NC_014226.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/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/NC_014226.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/NC_014226.PFam32-A.tblout --cpu 20 /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/NC_014226.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Sun Mar 24 04:11:56 2019 # [ok]