# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- DUF2070 PF09843.9 gi|299883475|ref|YP_003739026.1| - 4 5.6 22.0 5.3 5.2 22.0 1.1 1 0 0 1 1 1 0 Predicted membrane protein (DUF2070) Spore_Cse60 PF10957.8 gi|299883476|ref|YP_003739027.1| - 0.0055 16.7 0.5 0.011 15.8 0.5 1.5 1 1 0 1 1 1 1 Sporulation protein Cse60 Sigma70_r4_2 PF08281.12 gi|299883477|ref|YP_003739028.1| - 0.00024 20.7 0.0 0.00046 19.8 0.0 1.4 1 0 0 1 1 1 1 Sigma-70, region 4 GerE PF00196.19 gi|299883477|ref|YP_003739028.1| - 0.0017 17.9 0.0 0.0028 17.1 0.0 1.3 1 0 0 1 1 1 1 Bacterial regulatory proteins, luxR family Sigma70_ECF PF07638.11 gi|299883477|ref|YP_003739028.1| - 0.0021 18.0 0.0 0.0025 17.7 0.0 1.3 1 1 0 1 1 1 1 ECF sigma factor Phage_tube PF04985.14 gi|299883477|ref|YP_003739028.1| - 0.017 14.8 0.6 0.024 14.3 0.6 1.2 1 0 0 1 1 1 0 Phage tail tube protein FII HTH_23 PF13384.6 gi|299883477|ref|YP_003739028.1| - 0.025 14.3 0.0 0.043 13.6 0.0 1.3 1 0 0 1 1 1 0 Homeodomain-like domain FERM_M PF00373.18 gi|299883477|ref|YP_003739028.1| - 0.034 14.6 0.0 0.056 13.9 0.0 1.4 1 1 0 1 1 1 0 FERM central domain DUF505 PF04458.12 gi|299883477|ref|YP_003739028.1| - 0.041 12.3 0.1 0.047 12.1 0.1 1.1 1 0 0 1 1 1 0 Protein of unknown function (DUF505) HTH_7 PF02796.15 gi|299883477|ref|YP_003739028.1| - 0.043 13.9 0.0 0.072 13.2 0.0 1.3 1 0 0 1 1 1 0 Helix-turn-helix domain of resolvase Sigma70_r4 PF04545.16 gi|299883477|ref|YP_003739028.1| - 0.17 11.5 0.0 0.41 10.2 0.0 1.7 1 0 0 1 1 1 0 Sigma-70, region 4 HEPN_Apea PF18739.1 gi|299883479|ref|YP_003739030.1| - 0.01 16.3 0.0 0.019 15.4 0.0 1.4 1 0 0 1 1 1 0 Apea-like HEPN DUF1992 PF09350.10 gi|299883479|ref|YP_003739030.1| - 0.069 13.3 0.2 0.55 10.4 0.0 2.6 2 0 0 2 2 2 0 Domain of unknown function (DUF1992) DUF2971 PF11185.8 gi|299883480|ref|YP_003739031.1| - 0.0084 17.2 0.8 0.025 15.8 0.3 2.1 2 1 0 2 2 2 1 Protein of unknown function (DUF2971) DUF4974 PF16344.5 gi|299883480|ref|YP_003739031.1| - 0.16 12.0 1.1 2.9 8.0 0.0 3.2 3 0 0 3 3 3 0 Domain of unknown function (DUF4974) D5_N PF08706.11 gi|299883481|ref|YP_003739032.1| - 8.2e-05 22.9 0.5 0.00024 21.4 0.5 1.9 1 1 0 1 1 1 1 D5 N terminal like AAA_27 PF13514.6 gi|299883481|ref|YP_003739032.1| - 0.087 12.4 0.7 0.61 9.6 0.0 2.2 2 0 0 2 2 2 0 AAA domain DUF643 PF04867.12 gi|299883481|ref|YP_003739032.1| - 0.19 12.4 2.9 12 6.6 0.1 3.6 3 1 1 4 4 4 0 Protein of unknown function (DUF643) RHH_4 PF13467.6 gi|299883482|ref|YP_003739033.1| - 0.11 12.4 0.1 0.81 9.6 0.0 1.9 1 1 1 2 2 2 0 Ribbon-helix-helix domain DUF2312 PF10073.9 gi|299883483|ref|YP_003739034.1| - 0.052 13.2 0.5 0.1 12.3 0.4 1.7 1 1 1 2 2 2 0 Uncharacterized protein conserved in bacteria (DUF2312) DUF2399 PF09664.10 gi|299883484|ref|YP_003739035.1| - 0.0007 19.5 0.0 0.0013 18.7 0.0 1.4 1 0 0 1 1 1 1 Protein of unknown function C-terminus (DUF2399) DUF2644 PF10841.8 gi|299883486|ref|YP_003739037.1| - 0.054 13.7 0.2 0.054 13.7 0.2 1.0 1 0 0 1 1 1 0 Protein of unknown function (DUF2644) Polysacc_deac_1 PF01522.21 gi|299883487|ref|YP_003739038.1| - 1.3e-09 38.0 0.4 7.2e-09 35.6 0.2 2.1 2 1 0 2 2 2 1 Polysaccharide deacetylase SWIM PF04434.17 gi|299883488|ref|YP_003739039.1| - 6.1e-08 32.2 0.8 1.1e-07 31.4 0.2 1.7 2 0 0 2 2 2 1 SWIM zinc finger Mnd1 PF03962.15 gi|299883489|ref|YP_003739040.1| - 0.00072 19.8 0.3 0.014 15.7 0.1 2.0 1 1 1 2 2 2 1 Mnd1 HTH domain BLACT_WH PF17778.1 gi|299883489|ref|YP_003739040.1| - 0.0035 17.3 0.0 0.0062 16.5 0.0 1.4 1 0 0 1 1 1 1 Beta-lactamase associated winged helix domain OmpH PF03938.14 gi|299883490|ref|YP_003739041.1| - 0.017 15.5 2.9 0.037 14.4 2.9 1.6 1 0 0 1 1 1 0 Outer membrane protein (OmpH-like) CC2-LZ PF16516.5 gi|299883490|ref|YP_003739041.1| - 0.022 15.1 5.0 0.043 14.2 5.0 1.6 1 0 0 1 1 1 0 Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator YabA PF06156.13 gi|299883490|ref|YP_003739041.1| - 0.061 14.0 5.0 0.13 12.9 5.0 1.5 1 0 0 1 1 1 0 Initiation control protein YabA Jnk-SapK_ap_N PF09744.9 gi|299883490|ref|YP_003739041.1| - 0.064 13.5 8.8 0.15 12.3 8.8 1.6 1 0 0 1 1 1 0 JNK_SAPK-associated protein-1 Cep57_MT_bd PF06657.13 gi|299883490|ref|YP_003739041.1| - 0.076 13.5 3.0 0.18 12.3 3.0 1.7 1 0 0 1 1 1 0 Centrosome microtubule-binding domain of Cep57 Taxilin PF09728.9 gi|299883490|ref|YP_003739041.1| - 0.13 11.4 8.0 0.5 9.5 7.7 1.8 2 0 0 2 2 2 0 Myosin-like coiled-coil protein HAUS5 PF14817.6 gi|299883490|ref|YP_003739041.1| - 0.2 10.4 6.3 0.29 9.8 6.3 1.2 1 0 0 1 1 1 0 HAUS augmin-like complex subunit 5 CENP-H PF05837.12 gi|299883490|ref|YP_003739041.1| - 0.22 11.9 7.3 0.5 10.8 7.3 1.6 1 0 0 1 1 1 0 Centromere protein H (CENP-H) Spc7 PF08317.11 gi|299883490|ref|YP_003739041.1| - 0.29 10.0 7.7 0.43 9.4 7.7 1.2 1 0 0 1 1 1 0 Spc7 kinetochore protein EzrA PF06160.12 gi|299883490|ref|YP_003739041.1| - 0.31 9.2 7.3 0.4 8.8 7.3 1.1 1 0 0 1 1 1 0 Septation ring formation regulator, EzrA Geminin PF07412.12 gi|299883490|ref|YP_003739041.1| - 0.32 10.7 8.9 0.68 9.6 8.9 1.5 1 0 0 1 1 1 0 Geminin CENP-Q PF13094.6 gi|299883490|ref|YP_003739041.1| - 0.51 10.5 8.8 0.25 11.5 6.1 1.8 2 0 0 2 2 2 0 CENP-Q, a CENPA-CAD centromere complex subunit TMPIT PF07851.13 gi|299883490|ref|YP_003739041.1| - 1.3 8.2 3.4 1.7 7.8 3.4 1.1 1 0 0 1 1 1 0 TMPIT-like protein DUF4407 PF14362.6 gi|299883490|ref|YP_003739041.1| - 2.7 7.3 4.9 4.6 6.5 4.9 1.3 1 0 0 1 1 1 0 Domain of unknown function (DUF4407) DHR10 PF18595.1 gi|299883491|ref|YP_003739042.1| - 0.0021 18.1 1.4 0.0028 17.7 1.4 1.2 1 0 0 1 1 1 1 Designed helical repeat protein 10 domain DUF2570 PF10828.8 gi|299883491|ref|YP_003739042.1| - 0.003 17.4 0.7 0.0036 17.1 0.7 1.1 1 0 0 1 1 1 1 Protein of unknown function (DUF2570) HSBP1 PF06825.12 gi|299883491|ref|YP_003739042.1| - 0.0034 17.2 1.9 0.0083 16.0 0.1 2.0 1 1 1 2 2 2 1 Heat shock factor binding protein 1 HAUS-augmin3 PF14932.6 gi|299883491|ref|YP_003739042.1| - 0.013 15.1 0.8 0.014 15.0 0.8 1.0 1 0 0 1 1 1 0 HAUS augmin-like complex subunit 3 KxDL PF10241.9 gi|299883491|ref|YP_003739042.1| - 0.015 15.6 1.1 0.02 15.1 1.1 1.3 1 1 0 1 1 1 0 Uncharacterized conserved protein Na_Ca_ex_C PF16494.5 gi|299883491|ref|YP_003739042.1| - 0.026 15.0 1.2 0.03 14.8 1.2 1.0 1 0 0 1 1 1 0 C-terminal extension of sodium/calcium exchanger domain DLP_helical PF18709.1 gi|299883491|ref|YP_003739042.1| - 0.028 13.6 1.6 0.028 13.6 1.6 1.0 1 0 0 1 1 1 0 Dynamin-like helical domain BLOC1_2 PF10046.9 gi|299883491|ref|YP_003739042.1| - 0.046 14.0 2.1 0.058 13.7 1.3 1.6 1 1 0 1 1 1 0 Biogenesis of lysosome-related organelles complex-1 subunit 2 USP8_interact PF08941.10 gi|299883491|ref|YP_003739042.1| - 0.092 12.6 0.9 0.1 12.4 0.9 1.1 1 0 0 1 1 1 0 USP8 interacting DUF2076 PF09849.9 gi|299883491|ref|YP_003739042.1| - 0.12 12.4 1.3 0.17 11.9 1.3 1.2 1 0 0 1 1 1 0 Uncharacterized protein conserved in bacteria (DUF2076) SlyX PF04102.12 gi|299883491|ref|YP_003739042.1| - 0.13 12.9 3.9 0.14 12.7 2.9 1.7 1 1 0 1 1 1 0 SlyX Fes1 PF08609.10 gi|299883491|ref|YP_003739042.1| - 0.13 13.2 1.8 0.54 11.2 0.4 2.0 1 1 1 2 2 2 0 Nucleotide exchange factor Fes1 TSC22 PF01166.18 gi|299883491|ref|YP_003739042.1| - 0.13 12.5 2.8 0.22 11.9 0.6 2.0 1 1 1 2 2 2 0 TSC-22/dip/bun family GLTP PF08718.11 gi|299883491|ref|YP_003739042.1| - 0.15 12.4 0.3 0.16 12.3 0.3 1.1 1 0 0 1 1 1 0 Glycolipid transfer protein (GLTP) ABC_tran_CTD PF16326.5 gi|299883491|ref|YP_003739042.1| - 0.17 12.2 4.1 0.31 11.3 4.1 1.5 1 1 0 1 1 1 0 ABC transporter C-terminal domain DivIC PF04977.15 gi|299883491|ref|YP_003739042.1| - 0.31 10.8 4.8 0.45 10.3 4.7 1.5 1 1 0 1 1 1 0 Septum formation initiator DUF1515 PF07439.11 gi|299883491|ref|YP_003739042.1| - 0.37 10.8 3.3 0.7 9.9 3.3 1.4 1 1 0 1 1 1 0 Protein of unknown function (DUF1515) HAUS-augmin3 PF14932.6 gi|299883492|ref|YP_003739043.1| - 0.00096 18.8 6.7 0.0011 18.6 6.7 1.1 1 0 0 1 1 1 1 HAUS augmin-like complex subunit 3 DUF4927 PF16279.5 gi|299883492|ref|YP_003739043.1| - 0.0049 17.9 2.8 0.0066 17.4 2.8 1.2 1 0 0 1 1 1 1 Domain of unknown function (DUF4927) MAD PF05557.13 gi|299883492|ref|YP_003739043.1| - 0.0055 15.1 12.2 0.006 15.0 12.2 1.0 1 0 0 1 1 1 1 Mitotic checkpoint protein ERM PF00769.19 gi|299883492|ref|YP_003739043.1| - 0.0098 15.7 9.9 0.012 15.4 9.9 1.2 1 0 0 1 1 1 1 Ezrin/radixin/moesin family EMP24_GP25L PF01105.24 gi|299883492|ref|YP_003739043.1| - 0.071 13.0 5.9 0.089 12.7 5.9 1.2 1 0 0 1 1 1 0 emp24/gp25L/p24 family/GOLD APG6_N PF17675.1 gi|299883492|ref|YP_003739043.1| - 0.14 12.7 10.7 0.16 12.5 10.7 1.1 1 0 0 1 1 1 0 Apg6 coiled-coil region Sec34 PF04136.15 gi|299883492|ref|YP_003739043.1| - 0.14 12.0 5.6 0.2 11.6 5.6 1.1 1 0 0 1 1 1 0 Sec34-like family 5_nucleotid PF05761.14 gi|299883492|ref|YP_003739043.1| - 0.38 9.6 3.7 0.46 9.3 3.7 1.1 1 0 0 1 1 1 0 5' nucleotidase family V_ATPase_I PF01496.19 gi|299883492|ref|YP_003739043.1| - 1.1 7.1 7.9 1.1 7.1 7.9 1.0 1 0 0 1 1 1 0 V-type ATPase 116kDa subunit family DivIC PF04977.15 gi|299883492|ref|YP_003739043.1| - 6.2 6.7 11.2 4.5 7.1 8.7 1.9 1 1 1 2 2 2 0 Septum formation initiator AAA_23 PF13476.6 gi|299883492|ref|YP_003739043.1| - 6.5 7.2 10.5 7.5 7.0 10.5 1.1 1 0 0 1 1 1 0 AAA domain DUF3368 PF11848.8 gi|299883493|ref|YP_003739044.1| - 0.0013 18.4 0.0 0.0027 17.4 0.0 1.5 1 0 0 1 1 1 1 Domain of unknown function (DUF3368) Se-cys_synth_N PF12390.8 gi|299883493|ref|YP_003739044.1| - 0.031 14.5 0.1 0.11 12.7 0.1 1.9 1 1 1 2 2 2 0 Selenocysteine synthase N terminal UPF0175 PF03683.13 gi|299883494|ref|YP_003739045.1| - 4.7e-09 35.8 0.0 5.1e-09 35.7 0.0 1.1 1 0 0 1 1 1 1 Uncharacterised protein family (UPF0175) Sigma70_r4 PF04545.16 gi|299883494|ref|YP_003739045.1| - 0.0004 19.9 0.6 0.00053 19.5 0.6 1.2 1 0 0 1 1 1 1 Sigma-70, region 4 Ribosomal_S3Ae PF01015.18 gi|299883497|ref|YP_003739048.1| - 0.019 14.6 0.1 0.019 14.6 0.1 1.1 1 0 0 1 1 1 0 Ribosomal S3Ae family Phe_ZIP PF08916.11 gi|299883497|ref|YP_003739048.1| - 0.1 13.3 0.2 0.19 12.5 0.1 1.4 1 1 0 1 1 1 0 Phenylalanine zipper # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Halalkalicoccus_jeotgali_B3_uid50305/NC_014302.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/Halalkalicoccus_jeotgali_B3_uid50305/NC_014302.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Halalkalicoccus_jeotgali_B3_uid50305/NC_014302.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/Halalkalicoccus_jeotgali_B3_uid50305/NC_014302.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 12:16:21 2019 # [ok]