# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- Transposase_20 PF02371.16 gi|73663827|ref|YP_300073.1| - 0.0019 18.5 0.0 0.0024 18.1 0.0 1.2 1 0 0 1 1 1 1 Transposase IS116/IS110/IS902 family DUF1699 PF08004.11 gi|73663828|ref|YP_300074.1| - 1.5e-61 205.8 3.4 1.7e-61 205.6 3.4 1.0 1 0 0 1 1 1 1 Protein of unknown function (DUF1699) Img2 PF05046.14 gi|73663828|ref|YP_300074.1| - 0.0061 16.8 0.1 0.0089 16.3 0.1 1.3 1 0 0 1 1 1 1 Mitochondrial large subunit ribosomal protein (Img2) OrfB_IS605 PF01385.19 gi|73663829|ref|YP_300075.1| - 7.5e-26 90.7 2.1 1e-25 90.3 1.3 1.6 2 0 0 2 2 2 1 Probable transposase OrfB_Zn_ribbon PF07282.11 gi|73663829|ref|YP_300075.1| - 1e-22 79.8 0.5 2.3e-22 78.7 0.5 1.6 1 0 0 1 1 1 1 Putative transposase DNA-binding domain zf-piccolo PF05715.13 gi|73663829|ref|YP_300075.1| - 0.00086 19.4 0.9 0.0018 18.4 0.9 1.5 1 0 0 1 1 1 1 Piccolo Zn-finger HypA PF01155.19 gi|73663829|ref|YP_300075.1| - 0.085 12.9 0.0 0.15 12.0 0.0 1.5 1 0 0 1 1 1 0 Hydrogenase/urease nickel incorporation, metallochaperone, hypA DZR PF12773.7 gi|73663829|ref|YP_300075.1| - 0.11 12.5 0.6 0.21 11.6 0.6 1.4 1 0 0 1 1 1 0 Double zinc ribbon zf-UDP PF14569.6 gi|73663829|ref|YP_300075.1| - 0.44 10.7 1.9 2.4 8.4 1.9 2.1 1 1 0 1 1 1 0 Zinc-binding RING-finger zf-RanBP PF00641.18 gi|73663829|ref|YP_300075.1| - 2 7.8 7.9 6.8 6.1 0.3 2.5 1 1 1 2 2 2 0 Zn-finger in Ran binding protein and others Rubredoxin PF00301.20 gi|73663829|ref|YP_300075.1| - 2.4 8.3 5.1 2.4 8.3 1.0 2.3 2 0 0 2 2 2 0 Rubredoxin Polysacc_synt PF01943.17 gi|73663830|ref|YP_300076.1| - 4.2e-07 29.6 33.6 4.2e-07 29.6 33.6 2.5 2 1 0 2 2 2 1 Polysaccharide biosynthesis protein DUF354 PF04007.12 gi|73663831|ref|YP_300077.1| - 3.4e-09 36.2 0.3 4.5e-09 35.8 0.3 1.1 1 0 0 1 1 1 1 Protein of unknown function (DUF354) Hydrolase_3 PF08282.12 gi|73663831|ref|YP_300077.1| - 0.14 11.9 0.6 0.26 11.0 0.4 1.5 2 0 0 2 2 2 0 haloacid dehalogenase-like hydrolase SQHop_cyclase_C PF13243.6 gi|73663832|ref|YP_300078.1| - 0.0064 15.6 0.1 0.28 10.2 0.0 2.5 2 1 0 2 2 2 2 Squalene-hopene cyclase C-terminal domain Glycos_transf_1 PF00534.20 gi|73663833|ref|YP_300079.1| - 2e-30 105.6 0.0 6.8e-30 103.9 0.0 1.8 2 0 0 2 2 2 1 Glycosyl transferases group 1 Glyco_trans_1_4 PF13692.6 gi|73663833|ref|YP_300079.1| - 2.7e-23 82.9 0.0 4.3e-23 82.2 0.0 1.3 1 0 0 1 1 1 1 Glycosyl transferases group 1 Glyco_transf_4 PF13439.6 gi|73663833|ref|YP_300079.1| - 1.3e-10 41.6 0.0 2.7e-10 40.5 0.0 1.5 1 1 0 1 1 1 1 Glycosyltransferase Family 4 Glyco_trans_1_2 PF13524.6 gi|73663833|ref|YP_300079.1| - 5.3e-06 26.7 0.0 2.7e-05 24.4 0.0 2.2 3 0 0 3 3 3 1 Glycosyl transferases group 1 AAA_31 PF13614.6 gi|73663834|ref|YP_300080.1| - 1e-48 165.6 0.0 1.5e-48 165.1 0.0 1.2 1 0 0 1 1 1 1 AAA domain CbiA PF01656.23 gi|73663834|ref|YP_300080.1| - 6.1e-20 71.6 0.0 7.7e-20 71.2 0.0 1.1 1 0 0 1 1 1 1 CobQ/CobB/MinD/ParA nucleotide binding domain Fer4_NifH PF00142.18 gi|73663834|ref|YP_300080.1| - 2.1e-11 43.8 0.1 5.5e-08 32.6 0.1 2.2 2 0 0 2 2 2 2 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family ParA PF10609.9 gi|73663834|ref|YP_300080.1| - 3.3e-10 39.8 1.0 1.3e-09 37.8 1.0 2.0 1 1 0 1 1 1 1 NUBPL iron-transfer P-loop NTPase MipZ PF09140.11 gi|73663834|ref|YP_300080.1| - 1.5e-08 34.2 0.2 5.4e-07 29.2 0.2 2.1 1 1 0 1 1 1 1 ATPase MipZ CBP_BcsQ PF06564.12 gi|73663834|ref|YP_300080.1| - 1.5e-07 31.1 0.0 1.8e-06 27.6 0.0 2.1 2 1 0 2 2 2 1 Cellulose biosynthesis protein BcsQ ArsA_ATPase PF02374.15 gi|73663834|ref|YP_300080.1| - 2.4e-07 30.3 0.7 2.8e-05 23.5 0.3 2.3 2 0 0 2 2 2 2 Anion-transporting ATPase VirC1 PF07015.11 gi|73663834|ref|YP_300080.1| - 0.00077 18.8 0.1 0.0028 17.0 0.1 1.8 2 0 0 2 2 2 1 VirC1 protein SRP54 PF00448.22 gi|73663834|ref|YP_300080.1| - 0.001 18.8 0.1 0.13 11.8 0.1 2.3 2 0 0 2 2 2 1 SRP54-type protein, GTPase domain AAA_25 PF13481.6 gi|73663834|ref|YP_300080.1| - 0.15 11.6 0.0 0.23 11.0 0.0 1.3 1 0 0 1 1 1 0 AAA domain MOZART1 PF12554.8 gi|73663835|ref|YP_300081.1| - 0.18 11.6 0.0 0.25 11.1 0.0 1.2 1 0 0 1 1 1 0 Mitotic-spindle organizing gamma-tubulin ring associated OrfB_IS605 PF01385.19 gi|73663836|ref|YP_300082.1| - 1.6e-27 96.1 0.4 3e-27 95.2 0.4 1.4 1 0 0 1 1 1 1 Probable transposase OrfB_Zn_ribbon PF07282.11 gi|73663836|ref|YP_300082.1| - 4.2e-21 74.6 0.3 7.6e-21 73.8 0.3 1.5 1 0 0 1 1 1 1 Putative transposase DNA-binding domain HTH_OrfB_IS605 PF12323.8 gi|73663836|ref|YP_300082.1| - 1.9e-20 72.1 0.3 3.4e-20 71.2 0.3 1.4 1 0 0 1 1 1 1 Helix-turn-helix domain zf-piccolo PF05715.13 gi|73663836|ref|YP_300082.1| - 0.00052 20.1 0.7 0.0011 19.0 0.7 1.5 1 0 0 1 1 1 1 Piccolo Zn-finger HypA PF01155.19 gi|73663836|ref|YP_300082.1| - 0.073 13.1 0.3 0.14 12.2 0.3 1.6 1 1 0 1 1 1 0 Hydrogenase/urease nickel incorporation, metallochaperone, hypA DZR PF12773.7 gi|73663836|ref|YP_300082.1| - 0.15 12.1 0.5 0.27 11.3 0.5 1.4 1 0 0 1 1 1 0 Double zinc ribbon zf-RanBP PF00641.18 gi|73663836|ref|YP_300082.1| - 6.9 6.1 8.4 17 4.9 0.4 2.6 1 1 1 2 2 2 0 Zn-finger in Ran binding protein and others Glycos_transf_2 PF00535.26 gi|73663837|ref|YP_300083.1| - 8.3e-21 74.5 0.0 1.3e-20 73.9 0.0 1.2 1 0 0 1 1 1 1 Glycosyl transferase family 2 Glyco_tranf_2_3 PF13641.6 gi|73663837|ref|YP_300083.1| - 4.3e-08 33.3 0.0 5.4e-08 33.0 0.0 1.1 1 0 0 1 1 1 1 Glycosyltransferase like family 2 Glyco_tranf_2_4 PF13704.6 gi|73663837|ref|YP_300083.1| - 0.00068 20.1 0.0 0.0012 19.4 0.0 1.5 1 0 0 1 1 1 1 Glycosyl transferase family 2 Glyco_tranf_2_2 PF10111.9 gi|73663837|ref|YP_300083.1| - 0.02 14.4 0.0 0.032 13.7 0.0 1.3 1 0 0 1 1 1 0 Glycosyltransferase like family 2 Laminin_G_3 PF13385.6 gi|73663838|ref|YP_300084.1| - 5.5e-25 88.3 10.5 6.8e-14 52.3 1.1 5.6 4 2 0 4 4 4 2 Concanavalin A-like lectin/glucanases superfamily PKD PF00801.20 gi|73663838|ref|YP_300084.1| - 4e-19 68.2 13.0 1.9e-12 46.8 4.2 6.2 9 0 0 9 9 9 2 PKD domain DUF4399 PF14347.6 gi|73663838|ref|YP_300084.1| - 7.5e-07 29.4 7.1 6.4 7.2 0.0 8.5 9 0 0 9 9 9 1 Domain of unknown function (DUF4399) KTSC PF13619.6 gi|73663838|ref|YP_300084.1| - 0.00068 19.4 0.1 77 3.2 0.0 5.8 5 0 0 5 5 5 0 KTSC domain ASH PF15780.5 gi|73663838|ref|YP_300084.1| - 0.0059 16.8 18.6 6.7 7.0 0.1 7.3 5 1 2 7 7 7 2 Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin PKD_3 PF16820.5 gi|73663838|ref|YP_300084.1| - 0.76 9.6 3.1 4.8 7.0 0.2 3.6 4 0 0 4 4 4 0 PKD-like domain CopC PF04234.12 gi|73663838|ref|YP_300084.1| - 0.81 10.8 18.4 0.29 12.2 0.4 5.9 7 2 0 7 7 7 0 CopC domain OrfB_IS605 PF01385.19 gi|73663839|ref|YP_300085.1| - 7.3e-26 90.8 1.3 1.8e-25 89.5 1.3 1.6 1 0 0 1 1 1 1 Probable transposase OrfB_Zn_ribbon PF07282.11 gi|73663839|ref|YP_300085.1| - 1.8e-22 79.1 0.5 3.6e-22 78.0 0.5 1.6 1 0 0 1 1 1 1 Putative transposase DNA-binding domain HTH_OrfB_IS605 PF12323.8 gi|73663839|ref|YP_300085.1| - 9.4e-21 73.0 0.5 2.1e-20 71.9 0.5 1.6 1 0 0 1 1 1 1 Helix-turn-helix domain zf-piccolo PF05715.13 gi|73663839|ref|YP_300085.1| - 0.0024 18.0 2.6 0.0026 17.9 0.9 1.9 2 0 0 2 2 2 1 Piccolo Zn-finger HypA PF01155.19 gi|73663839|ref|YP_300085.1| - 0.13 12.3 0.0 0.25 11.4 0.0 1.5 1 0 0 1 1 1 0 Hydrogenase/urease nickel incorporation, metallochaperone, hypA zf-RanBP PF00641.18 gi|73663839|ref|YP_300085.1| - 3.3 7.1 7.8 9.1 5.7 0.3 2.5 1 1 1 2 2 2 0 Zn-finger in Ran binding protein and others Y1_Tnp PF01797.16 gi|73663840|ref|YP_300086.1| - 3.9e-26 91.5 1.5 4.2e-26 91.4 1.5 1.0 1 0 0 1 1 1 1 Transposase IS200 like Castor1_N PF18700.1 gi|73663841|ref|YP_300087.1| - 0.94 9.3 4.2 0.68 9.8 0.6 2.6 2 0 0 2 2 2 0 Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain Hexapep PF00132.24 gi|73663842|ref|YP_300088.1| - 1.2e-17 62.9 24.0 7.8e-09 34.9 7.3 3.6 3 1 1 4 4 4 3 Bacterial transferase hexapeptide (six repeats) Hexapep_2 PF14602.6 gi|73663842|ref|YP_300088.1| - 9.2e-10 38.1 20.4 7.7e-06 25.6 7.6 3.6 3 0 0 3 3 3 3 Hexapeptide repeat of succinyl-transferase Phage_integrase PF00589.22 gi|73663843|ref|YP_300089.1| - 1.2e-07 31.7 0.3 6.8e-07 29.2 0.3 1.9 1 1 0 1 1 1 1 Phage integrase family CPSase_L_D3 PF02787.19 gi|73663843|ref|YP_300089.1| - 0.084 13.2 0.2 0.17 12.2 0.2 1.5 1 0 0 1 1 1 0 Carbamoyl-phosphate synthetase large chain, oligomerisation domain DUF4494 PF14902.6 gi|73663843|ref|YP_300089.1| - 0.13 12.1 0.9 0.23 11.3 0.9 1.3 1 0 0 1 1 1 0 Domain of unknown function (DUF4494) Cdc6_C PF09079.11 gi|73663844|ref|YP_300090.1| - 6.7e-13 48.4 0.1 1.9e-12 47.0 0.1 1.7 1 0 0 1 1 1 1 CDC6, C terminal winged helix domain AAA PF00004.29 gi|73663844|ref|YP_300090.1| - 1.8e-08 34.9 0.0 3.6e-08 33.9 0.0 1.5 1 0 0 1 1 1 1 ATPase family associated with various cellular activities (AAA) AAA_22 PF13401.6 gi|73663844|ref|YP_300090.1| - 1.8e-05 25.0 0.0 4e-05 23.9 0.0 1.6 1 0 0 1 1 1 1 AAA domain NACHT PF05729.12 gi|73663844|ref|YP_300090.1| - 8e-05 22.6 0.0 0.00016 21.6 0.0 1.5 1 0 0 1 1 1 1 NACHT domain ATPase_2 PF01637.18 gi|73663844|ref|YP_300090.1| - 0.00039 20.4 5.2 0.0023 17.9 0.9 2.6 2 1 0 2 2 2 1 ATPase domain predominantly from Archaea AAA_16 PF13191.6 gi|73663844|ref|YP_300090.1| - 0.00048 20.6 0.0 0.0024 18.3 0.0 2.1 1 1 1 2 2 2 1 AAA ATPase domain Ribosomal_L7Ae PF01248.26 gi|73663844|ref|YP_300090.1| - 0.0028 17.3 0.2 0.0085 15.8 0.2 1.8 1 0 0 1 1 1 1 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family AAA_2 PF07724.14 gi|73663844|ref|YP_300090.1| - 0.0085 16.2 0.0 0.016 15.3 0.0 1.4 1 0 0 1 1 1 1 AAA domain (Cdc48 subfamily) RNA_helicase PF00910.22 gi|73663844|ref|YP_300090.1| - 0.011 16.1 0.6 0.64 10.4 0.3 3.1 2 1 0 2 2 2 0 RNA helicase TniB PF05621.11 gi|73663844|ref|YP_300090.1| - 0.012 15.0 0.1 0.023 14.1 0.1 1.4 1 0 0 1 1 1 0 Bacterial TniB protein NB-ARC PF00931.22 gi|73663844|ref|YP_300090.1| - 0.069 12.3 0.2 0.25 10.5 0.1 2.1 1 1 1 2 2 2 0 NB-ARC domain AAA_assoc_2 PF16193.5 gi|73663844|ref|YP_300090.1| - 0.075 13.4 0.1 0.19 12.1 0.1 1.7 1 0 0 1 1 1 0 AAA C-terminal domain AAA_24 PF13479.6 gi|73663844|ref|YP_300090.1| - 0.081 12.6 0.0 0.17 11.6 0.0 1.6 1 0 0 1 1 1 0 AAA domain DUF2075 PF09848.9 gi|73663844|ref|YP_300090.1| - 0.11 11.7 0.0 0.16 11.2 0.0 1.2 1 0 0 1 1 1 0 Uncharacterized conserved protein (DUF2075) AAA_19 PF13245.6 gi|73663844|ref|YP_300090.1| - 0.17 12.2 0.0 0.45 10.8 0.0 1.6 1 0 0 1 1 1 0 AAA domain CM_2 PF01817.21 gi|73663844|ref|YP_300090.1| - 0.25 11.7 4.2 49 4.4 0.1 3.8 4 0 0 4 4 4 0 Chorismate mutase type II # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosarcina_barkeri_Fusaro_uid57715/NC_007349.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/Methanosarcina_barkeri_Fusaro_uid57715/NC_007349.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosarcina_barkeri_Fusaro_uid57715/NC_007349.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/Methanosarcina_barkeri_Fusaro_uid57715/NC_007349.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 15:49:31 2019 # [ok]