# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- DUF4153 PF13687.6 gi|15027630|ref|NP_149364.1| - 0.69 9.5 14.2 0.8 9.3 14.2 1.1 1 0 0 1 1 1 0 Domain of unknown function (DUF4153) Ribosomal_S13 PF00416.22 gi|15027633|ref|NP_149367.1| - 7e-09 36.2 0.0 1.7e-08 34.9 0.0 1.7 1 0 0 1 1 1 1 Ribosomal protein S13/S18 Ribosomal_S19 PF00203.21 gi|15027635|ref|NP_149369.1| - 5.7e-12 45.3 1.3 6.9e-12 45.1 1.3 1.1 1 0 0 1 1 1 1 Ribosomal protein S19 Ribosomal_L2_C PF03947.18 gi|15027636|ref|NP_149370.1| - 1e-26 93.6 0.0 1.7e-26 92.9 0.0 1.3 1 0 0 1 1 1 1 Ribosomal Proteins L2, C-terminal domain Ribosomal_L2 PF00181.23 gi|15027636|ref|NP_149370.1| - 8.8e-06 25.6 0.5 2.5e-05 24.1 0.5 1.8 1 0 0 1 1 1 1 Ribosomal Proteins L2, RNA binding domain Oxidored_q6 PF01058.22 gi|15027638|ref|NP_149372.1| - 2.8e-19 69.3 0.0 3.5e-19 68.9 0.0 1.1 1 0 0 1 1 1 1 NADH ubiquinone oxidoreductase, 20 Kd subunit Ribosom_S12_S23 PF00164.25 gi|15027639|ref|NP_149373.1| - 4.3e-25 87.5 0.8 5.8e-25 87.1 0.8 1.1 1 0 0 1 1 1 1 Ribosomal protein S12/S23 Ribosomal_S12 PF17487.2 gi|15027639|ref|NP_149373.1| - 0.023 15.4 0.0 0.049 14.4 0.0 1.5 1 1 0 1 1 1 0 Ribosomal protein S12 Proton_antipo_M PF00361.20 gi|15027640|ref|NP_149374.1| - 1.5e-05 24.4 7.2 2.6e-05 23.6 7.2 1.4 1 0 0 1 1 1 1 Proton-conducting membrane transporter DUF1003 PF06210.11 gi|15027640|ref|NP_149374.1| - 0.01 16.0 3.0 0.01 16.0 3.0 1.8 2 1 0 2 2 2 1 Protein of unknown function (DUF1003) Complex1_49kDa PF00346.19 gi|15027641|ref|NP_149375.1| - 2.2e-85 286.0 0.0 3.8e-85 285.3 0.0 1.4 1 1 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 49 Kd subunit RIIa PF02197.17 gi|15027641|ref|NP_149375.1| - 0.11 12.1 0.1 0.24 11.1 0.1 1.5 1 0 0 1 1 1 0 Regulatory subunit of type II PKA R-subunit Ribosomal_S3_C PF00189.20 gi|15027644|ref|NP_149378.1| - 0.033 14.7 0.0 0.06 13.9 0.0 1.4 1 0 0 1 1 1 0 Ribosomal protein S3, C-terminal domain NADHdh PF00146.21 gi|15027646|ref|NP_149380.1| - 1.3e-08 34.6 3.7 1.4e-08 34.4 3.7 1.1 1 0 0 1 1 1 1 NADH dehydrogenase ATP-synt_C PF00137.21 gi|15027647|ref|NP_149381.1| - 1.8e-05 25.0 0.7 2.7e-05 24.4 0.6 1.4 1 1 0 1 1 1 1 ATP synthase subunit C DUF3082 PF11282.8 gi|15027647|ref|NP_149381.1| - 0.046 14.0 0.7 0.046 14.0 0.7 2.1 2 0 0 2 2 2 0 Protein of unknown function (DUF3082) Proton_antipo_M PF00361.20 gi|15027651|ref|NP_149383.1| - 9.8e-06 25.0 29.4 9.8e-06 25.0 29.4 2.1 1 1 0 1 1 1 1 Proton-conducting membrane transporter Ribosomal_L16 PF00252.18 gi|15027652|ref|NP_149386.1| - 3.1e-10 40.2 0.1 3.3e-10 40.1 0.1 1.1 1 0 0 1 1 1 1 Ribosomal protein L16p/L10e Cytochrom_C_asm PF01578.20 gi|15027653|ref|NP_149387.1| - 3.5e-06 27.0 27.2 3.5e-06 27.0 27.2 3.7 3 1 1 4 4 4 1 Cytochrome C assembly protein Pectate_lyase_3 PF12708.7 gi|15027654|ref|NP_149388.1| - 0.082 12.7 1.5 0.14 12.0 0.5 1.8 1 1 1 2 2 2 0 Pectate lyase superfamily protein Oxidored_q4 PF00507.19 gi|15027655|ref|NP_149389.1| - 9.3e-17 61.0 15.9 1.5e-16 60.4 15.6 1.5 1 1 1 2 2 2 1 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 Complex1_30kDa PF00329.19 gi|15027658|ref|NP_149392.1| - 1.8e-15 57.7 0.0 2.3e-15 57.3 0.0 1.2 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 30 Kd subunit Complex1_30kDa PF00329.19 gi|15027659|ref|NP_149393.1| - 2.1e-15 57.4 0.0 2.8e-15 57.0 0.0 1.2 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 30 Kd subunit Cytochrome_B PF00033.19 gi|15027661|ref|NP_149395.1| - 4.9e-17 62.4 11.5 4.9e-17 62.4 11.5 2.1 2 0 0 2 2 2 1 Cytochrome b/b6/petB Cytochrom_B_N_2 PF13631.6 gi|15027661|ref|NP_149395.1| - 6.1e-14 52.4 5.1 1.4e-13 51.2 5.1 1.6 1 0 0 1 1 1 1 Cytochrome b(N-terminal)/b6/petB Cytochrom_B_C PF00032.17 gi|15027661|ref|NP_149395.1| - 0.0025 18.1 3.7 0.0025 18.1 3.7 3.4 3 1 1 4 4 4 1 Cytochrome b(C-terminal)/b6/petD Proton_antipo_M PF00361.20 gi|15027662|ref|NP_149396.1| - 2.4e-65 220.6 25.2 2.4e-65 220.6 25.2 3.4 3 1 0 3 3 3 1 Proton-conducting membrane transporter Proton_antipo_N PF00662.20 gi|15027662|ref|NP_149396.1| - 6e-05 23.0 4.4 6e-05 23.0 4.4 5.1 5 1 0 5 5 5 2 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus COX2 PF00116.20 gi|15027663|ref|NP_149397.1| - 1e-26 93.2 0.6 9.7e-24 83.6 0.0 2.5 2 0 0 2 2 2 2 Cytochrome C oxidase subunit II, periplasmic domain TAA-Trp-ring PF15401.6 gi|15027663|ref|NP_149397.1| - 0.39 11.2 2.4 0.84 10.1 2.4 1.5 1 0 0 1 1 1 0 Tryptophan-ring motif of head of Trimeric autotransporter adhesin NUFIP1 PF10453.9 gi|15027665|ref|NP_149399.1| - 0.031 14.1 0.1 0.031 14.1 0.1 2.0 3 0 0 3 3 3 0 Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1) COX1 PF00115.20 gi|15027668|ref|NP_149402.1| - 1.4e-92 310.8 62.9 1.8e-70 238.0 54.5 2.1 2 0 0 2 2 2 2 Cytochrome C and Quinol oxidase polypeptide I NADHdh PF00146.21 gi|15027669|ref|NP_149403.1| - 4.1e-63 213.5 21.9 5.5e-63 213.0 21.9 1.1 1 0 0 1 1 1 1 NADH dehydrogenase Ribosomal_L14 PF00238.19 gi|15027671|ref|NP_149405.1| - 8e-20 71.2 0.0 9.6e-20 70.9 0.0 1.0 1 0 0 1 1 1 1 Ribosomal protein L14p/L23e Transposon_TraM PF12508.8 gi|15027671|ref|NP_149405.1| - 0.00032 20.5 0.0 0.00038 20.2 0.0 1.1 1 0 0 1 1 1 1 Conjugative transposon, TraM Proton_antipo_M PF00361.20 gi|15027672|ref|NP_149407.1| - 4.9e-50 170.4 26.7 4.9e-50 170.4 26.7 2.3 2 0 0 2 2 2 1 Proton-conducting membrane transporter # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Tetrahymena_thermophila.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/Tetrahymena_thermophila.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Tetrahymena_thermophila.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/Tetrahymena_thermophila.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 20:01:12 2019 # [ok]