# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- CCDC50_N PF15295.6 lcl|JN383843.1_prot_AEV66631.1_16 - 0.82 9.8 4.4 0.53 10.4 1.5 2.0 2 0 0 2 2 2 0 Coiled-coil domain-containing protein 50 N-terminus PSRP-3_Ycf65 PF04839.13 lcl|JN383843.1_prot_AEV66631.1_16 - 1.1 9.5 3.9 0.36 11.1 0.4 2.1 2 0 0 2 2 2 0 Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) Ribosomal_S2 PF00318.20 lcl|JN383843.1_prot_AEV66638.1_23 - 0.023 13.9 0.0 0.17 11.1 0.0 2.0 2 0 0 2 2 2 0 Ribosomal protein S2 Proton_antipo_M PF00361.20 lcl|JN383843.1_prot_AEV66639.1_24 - 1.4e-53 182.0 30.5 1.4e-53 182.0 30.5 2.9 2 1 1 4 4 4 1 Proton-conducting membrane transporter Dam PF05869.11 lcl|JN383843.1_prot_AEV66641.1_26 - 0.082 12.5 1.2 0.09 12.3 1.2 1.0 1 0 0 1 1 1 0 DNA N-6-adenine-methyltransferase (Dam) Cytochrom_C_asm PF01578.20 lcl|JN383843.1_prot_AEV66646.1_31 - 2.6e-07 30.6 33.2 2.6e-07 30.6 33.2 4.0 3 1 0 3 3 3 1 Cytochrome C assembly protein NADHdh PF00146.21 lcl|JN383843.1_prot_AEV66647.1_32 - 4e-50 170.8 42.5 2.3e-49 168.4 42.5 1.8 1 1 0 1 1 1 1 NADH dehydrogenase PgaD PF13994.6 lcl|JN383843.1_prot_AEV66647.1_32 - 0.88 9.6 0.0 0.88 9.6 0.0 4.1 2 1 2 5 5 5 0 PgaD-like protein VMA21 PF09446.10 lcl|JN383843.1_prot_AEV66648.1_33 - 3.8 7.7 9.4 1.6 8.9 3.4 2.7 3 1 0 3 3 3 0 VMA21-like domain Cytochrome_B PF00033.19 lcl|JN383843.1_prot_AEV66649.1_34 - 4.5e-14 52.7 20.2 5.8e-14 52.3 18.8 2.0 1 1 0 1 1 1 1 Cytochrome b/b6/petB Cytochrom_B_N_2 PF13631.6 lcl|JN383843.1_prot_AEV66649.1_34 - 7.8e-11 42.3 6.1 7.8e-11 42.3 6.1 2.9 3 0 0 3 3 3 1 Cytochrome b(N-terminal)/b6/petB Cytochrom_B_C PF00032.17 lcl|JN383843.1_prot_AEV66649.1_34 - 0.0025 18.1 4.0 0.0025 18.1 4.0 3.3 4 0 0 4 4 4 1 Cytochrome b(C-terminal)/b6/petD Oxidored_q4 PF00507.19 lcl|JN383843.1_prot_AEV66650.1_35 - 5.5e-13 48.9 6.1 5.5e-13 48.9 6.1 1.7 1 1 1 2 2 2 1 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 Cation_ATPase_N PF00690.26 lcl|JN383843.1_prot_AEV66651.1_36 - 0.66 9.7 2.8 0.94 9.2 2.8 1.3 1 0 0 1 1 1 0 Cation transporter/ATPase, N-terminus DUF2683 PF10884.8 lcl|JN383843.1_prot_AEV66652.1_37 - 0.12 12.6 0.0 0.15 12.3 0.0 1.1 1 0 0 1 1 1 0 Protein of unknown function (DUF2683) TMEM189_B_dmain PF10520.9 lcl|JN383843.1_prot_AEV66654.1_39 - 0.036 14.2 0.1 0.038 14.1 0.1 1.1 1 0 0 1 1 1 0 B domain of TMEM189, localisation domain Ribosomal_S7 PF00177.21 lcl|JN383843.1_prot_AEV66655.1_40 - 0.086 12.5 0.0 14 5.3 0.0 2.1 2 0 0 2 2 2 0 Ribosomal protein S7p/S5e ATP-synt_C PF00137.21 lcl|JN383843.1_prot_AEV66658.1_43 - 0.00029 21.1 1.9 0.00037 20.8 1.9 1.2 1 0 0 1 1 1 1 ATP synthase subunit C ABC2_membrane_2 PF12679.7 lcl|JN383843.1_prot_AEV66658.1_43 - 1.2 8.4 7.6 1.4 8.1 7.6 1.0 1 0 0 1 1 1 0 ABC-2 family transporter protein Pet100 PF09803.9 lcl|JN383843.1_prot_AEV66659.1_44 - 1.1 9.8 5.9 2.8 8.5 5.9 1.7 1 1 0 1 1 1 0 Pet100 Ribosomal_S8 PF00410.19 lcl|JN383843.1_prot_AEV66663.1_48 - 6.1e-08 32.7 0.2 7e-08 32.5 0.2 1.0 1 0 0 1 1 1 1 Ribosomal protein S8 NADHdh PF00146.21 lcl|JN383843.1_prot_AEV66665.1_50 - 7e-07 28.8 9.5 7.7e-07 28.7 9.5 1.1 1 0 0 1 1 1 1 NADH dehydrogenase Ribosomal_S14 PF00253.21 lcl|JN383843.1_prot_AEV66666.1_51 - 4.5e-12 45.5 0.8 1.6e-11 43.8 0.2 1.9 2 0 0 2 2 2 1 Ribosomal protein S14p/S29e Complex1_49kDa PF00346.19 lcl|JN383843.1_prot_AEV66667.1_52 - 5.7e-81 271.6 0.0 7.3e-81 271.2 0.0 1.1 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 49 Kd subunit Zn_dep_PLPC PF00882.18 lcl|JN383843.1_prot_AEV66668.1_53 - 2.5 8.0 9.6 0.21 11.6 2.8 2.5 1 1 0 2 2 2 0 Zinc dependent phospholipase C Ribosomal_S13 PF00416.22 lcl|JN383843.1_prot_AEV66673.1_58 - 0.00059 20.2 1.2 0.00062 20.1 0.1 1.7 2 0 0 2 2 2 1 Ribosomal protein S13/S18 Ribosomal_S19 PF00203.21 lcl|JN383843.1_prot_AEV66674.1_59 - 2.2e-05 24.2 0.0 3.3e-05 23.7 0.0 1.3 1 0 0 1 1 1 1 Ribosomal protein S19 Ribosomal_L2_C PF03947.18 lcl|JN383843.1_prot_AEV66675.1_60 - 4.4e-25 88.3 0.0 6e-25 87.9 0.0 1.2 1 0 0 1 1 1 1 Ribosomal Proteins L2, C-terminal domain Myosin_TH1 PF06017.13 lcl|JN383843.1_prot_AEV66675.1_60 - 0.05 13.3 2.2 0.33 10.6 2.2 1.9 1 1 0 1 1 1 0 Unconventional myosin tail, actin- and lipid-binding Oxidored_q6 PF01058.22 lcl|JN383843.1_prot_AEV66677.1_62 - 4.1e-20 71.9 0.0 5e-20 71.7 0.0 1.1 1 0 0 1 1 1 1 NADH ubiquinone oxidoreductase, 20 Kd subunit Ribosom_S12_S23 PF00164.25 lcl|JN383843.1_prot_AEV66678.1_63 - 4.3e-21 74.7 0.5 5.4e-21 74.3 0.5 1.2 1 0 0 1 1 1 1 Ribosomal protein S12/S23 Proton_antipo_M PF00361.20 lcl|JN383843.1_prot_AEV66679.1_64 - 4.9e-38 131.0 30.7 4.9e-38 131.0 30.7 1.7 1 1 0 1 1 1 1 Proton-conducting membrane transporter Ribosomal_L16 PF00252.18 lcl|JN383843.1_prot_AEV66681.1_66 - 5.8e-19 68.4 0.0 7e-19 68.1 0.0 1.1 1 0 0 1 1 1 1 Ribosomal protein L16p/L10e Proton_antipo_M PF00361.20 lcl|JN383843.1_prot_AEV66682.1_67 - 0.00024 20.4 14.4 0.00024 20.4 14.4 1.8 1 1 1 2 2 2 1 Proton-conducting membrane transporter Complex1_30kDa PF00329.19 lcl|JN383843.1_prot_AEV66686.1_71 - 1.8e-09 38.3 0.0 2.2e-09 38.0 0.0 1.1 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 30 Kd subunit TFIID-18kDa PF02269.16 lcl|JN383843.1_prot_AEV66686.1_71 - 0.029 14.4 0.0 0.039 14.0 0.0 1.2 1 0 0 1 1 1 0 Transcription initiation factor IID, 18kD subunit RNA_pol_I_A49 PF06870.12 lcl|JN383843.1_prot_AEV66690.1_76 - 0.027 13.4 2.2 0.03 13.2 2.2 1.3 1 0 0 1 1 1 0 A49-like RNA polymerase I associated factor YcxB PF14317.6 lcl|JN383843.1_prot_AEV66692.1_78 - 0.011 15.4 0.2 0.011 15.4 0.2 2.3 2 0 0 2 2 2 0 YcxB-like protein Ribosomal_S3_C PF00189.20 lcl|JN383843.1_prot_AEV66694.1_80 - 0.00041 20.8 0.0 0.00063 20.2 0.0 1.3 1 0 0 1 1 1 1 Ribosomal protein S3, C-terminal domain DUF2070 PF09843.9 lcl|JN383843.1_prot_AEV66697.1_83 - 2.7 6.2 11.0 3.3 5.9 11.0 1.0 1 0 0 1 1 1 0 Predicted membrane protein (DUF2070) COX1 PF00115.20 lcl|JN383843.1_prot_AEV66698.1_84 - 5.6e-86 289.1 69.0 2.7e-69 234.1 52.6 3.6 4 0 0 4 4 4 2 Cytochrome C and Quinol oxidase polypeptide I Ribosomal_L14 PF00238.19 lcl|JN383843.1_prot_AEV66700.1_86 - 5.8e-19 68.4 0.0 6.8e-19 68.2 0.0 1.0 1 0 0 1 1 1 1 Ribosomal protein L14p/L23e COX2 PF00116.20 lcl|JN383843.1_prot_AEV66701.1_87 - 1.9e-22 79.4 1.7 6.3e-21 74.5 0.0 2.9 2 0 0 2 2 2 2 Cytochrome C oxidase subunit II, periplasmic domain Glyoxalase_2 PF12681.7 lcl|JN383843.1_prot_AEV66702.1_88 - 0.047 13.6 0.0 0.047 13.6 0.0 1.1 1 0 0 1 1 1 0 Glyoxalase-like domain DUF4525 PF15027.6 lcl|JN383843.1_prot_AEV66709.1_95 - 0.11 12.3 1.9 0.13 12.0 1.9 1.1 1 0 0 1 1 1 0 Domain of unknown function (DUF4525) # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Oxytricha_trifallax.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/mitochondrial_genomes/Alveolata/Ciliates/Oxytricha_trifallax.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Oxytricha_trifallax.PFam32-A.tblout --cpu 20 /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Oxytricha_trifallax.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 19:57:19 2019 # [ok]