# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- DUF1081 PF06448.11 gi|11466255|ref|NP_049570.1| - 0.2 12.0 2.7 0.62 10.5 2.7 1.9 1 0 0 1 1 1 0 Domain of Unknown Function (DUF1081) Ribosomal_S13 PF00416.22 gi|11466256|ref|NP_049571.1| - 7.3e-09 36.1 0.3 1.8e-08 34.9 0.0 1.9 2 0 0 2 2 2 1 Ribosomal protein S13/S18 ApbE PF02424.15 gi|11466256|ref|NP_049571.1| - 0.12 11.9 0.0 0.16 11.5 0.0 1.2 1 0 0 1 1 1 0 ApbE family Ribosomal_S19 PF00203.21 gi|11466258|ref|NP_049573.1| - 4.7e-10 39.2 1.9 5.6e-10 39.0 1.9 1.1 1 0 0 1 1 1 1 Ribosomal protein S19 Ribosomal_L2_C PF03947.18 gi|11466259|ref|NP_049574.1| - 3.4e-27 95.1 0.0 5.4e-27 94.5 0.0 1.2 1 0 0 1 1 1 1 Ribosomal Proteins L2, C-terminal domain Ribosomal_L2 PF00181.23 gi|11466259|ref|NP_049574.1| - 1.8e-06 27.8 1.9 2.7e-06 27.2 0.9 1.9 2 1 1 3 3 3 1 Ribosomal Proteins L2, RNA binding domain Oxidored_q6 PF01058.22 gi|11466261|ref|NP_049576.1| - 2.7e-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|11466262|ref|NP_049577.1| - 2.4e-25 88.3 0.6 3.2e-25 87.9 0.6 1.1 1 0 0 1 1 1 1 Ribosomal protein S12/S23 Ribosomal_S12 PF17487.2 gi|11466262|ref|NP_049577.1| - 0.036 14.8 0.0 0.081 13.7 0.0 1.5 1 1 0 1 1 1 0 Ribosomal protein S12 Proton_antipo_M PF00361.20 gi|11466263|ref|NP_049578.1| - 2.4e-05 23.7 7.7 2.4e-05 23.7 7.7 1.5 2 0 0 2 2 2 1 Proton-conducting membrane transporter Complex1_49kDa PF00346.19 gi|11466264|ref|NP_049579.1| - 8.3e-86 287.4 0.0 1.2e-85 286.9 0.0 1.3 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 49 Kd subunit RIIa PF02197.17 gi|11466264|ref|NP_049579.1| - 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 Cas9_C PF18525.1 gi|11466265|ref|NP_049580.1| - 0.13 12.5 0.0 0.28 11.4 0.0 1.5 1 1 1 2 2 2 0 Cas9 C-terminal domain NADHdh PF00146.21 gi|11466269|ref|NP_049584.1| - 3.3e-08 33.2 4.2 3.6e-08 33.1 4.2 1.1 1 0 0 1 1 1 1 NADH dehydrogenase ATP-synt_C PF00137.21 gi|11466270|ref|NP_049585.1| - 1.2e-05 25.6 1.2 1.6e-05 25.2 1.2 1.2 1 0 0 1 1 1 1 ATP synthase subunit C Phage_int_SAM_4 PF13495.6 gi|11466271|ref|NP_049586.1| - 0.14 12.7 15.7 0.092 13.2 2.8 3.1 3 0 0 3 3 3 0 Phage integrase, N-terminal SAM-like domain Proton_antipo_M PF00361.20 gi|11466272|ref|NP_049587.1| - 5.9e-06 25.7 31.3 5.9e-06 25.7 31.3 2.2 1 1 0 1 1 1 1 Proton-conducting membrane transporter Ribosomal_L16 PF00252.18 gi|11466275|ref|NP_049590.1| - 6.5e-11 42.4 0.2 7e-11 42.3 0.2 1.1 1 0 0 1 1 1 1 Ribosomal protein L16p/L10e Cytochrom_C_asm PF01578.20 gi|11466276|ref|NP_049591.1| - 2.6e-05 24.1 25.2 2.6e-05 24.1 25.2 3.8 2 2 1 3 3 3 1 Cytochrome C assembly protein Oxidored_q4 PF00507.19 gi|11466278|ref|NP_049593.1| - 3.5e-16 59.2 11.6 3.5e-16 59.2 11.6 1.3 1 1 0 1 1 1 1 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 Phage_holin_2_3 PF16080.5 gi|11466278|ref|NP_049593.1| - 0.0089 15.8 0.6 0.017 14.8 0.6 1.5 1 0 0 1 1 1 1 Bacteriophage holin family HP1 Complex1_30kDa PF00329.19 gi|11466281|ref|NP_049596.1| - 1.3e-14 54.8 0.0 1.7e-14 54.5 0.0 1.2 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 30 Kd subunit Cytochrome_B PF00033.19 gi|11466283|ref|NP_049598.1| - 1.7e-16 60.6 11.0 1.7e-16 60.6 11.0 2.0 2 0 0 2 2 2 1 Cytochrome b/b6/petB Cytochrom_B_N_2 PF13631.6 gi|11466283|ref|NP_049598.1| - 2.6e-13 50.3 5.8 6.5e-13 49.0 5.8 1.6 1 0 0 1 1 1 1 Cytochrome b(N-terminal)/b6/petB Cytochrom_B_C PF00032.17 gi|11466283|ref|NP_049598.1| - 0.0014 18.8 2.9 0.0014 18.8 2.9 3.4 3 1 1 4 4 4 1 Cytochrome b(C-terminal)/b6/petD Proton_antipo_M PF00361.20 gi|11466284|ref|NP_049599.1| - 7.9e-65 219.0 26.6 7.9e-65 219.0 26.6 3.9 4 1 1 5 5 5 1 Proton-conducting membrane transporter Proton_antipo_N PF00662.20 gi|11466284|ref|NP_049599.1| - 3.1e-05 24.0 4.6 3.1e-05 24.0 4.6 4.5 5 1 0 5 5 5 1 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus COX2 PF00116.20 gi|11466285|ref|NP_049600.1| - 1.4e-27 96.0 4.0 9.7e-24 83.6 0.0 3.3 2 1 1 3 3 3 3 Cytochrome C oxidase subunit II, periplasmic domain Bromodomain PF00439.25 gi|11466285|ref|NP_049600.1| - 0.018 15.1 0.3 0.062 13.4 0.3 2.1 1 0 0 1 1 1 0 Bromodomain FA_desaturase PF00487.24 gi|11466287|ref|NP_049602.1| - 1.6 8.5 10.9 0.16 11.8 6.4 1.6 2 0 0 2 2 2 0 Fatty acid desaturase COX1 PF00115.20 gi|11466290|ref|NP_049605.1| - 4.6e-92 309.1 63.1 3.3e-70 237.1 54.4 2.1 2 0 0 2 2 2 2 Cytochrome C and Quinol oxidase polypeptide I NADHdh PF00146.21 gi|11466291|ref|NP_049606.1| - 6.9e-64 216.0 23.4 9.6e-64 215.5 23.4 1.1 1 0 0 1 1 1 1 NADH dehydrogenase DUF2070 PF09843.9 gi|11466292|ref|NP_049607.1| - 6.1 5.0 23.5 8.2 4.6 23.5 1.1 1 0 0 1 1 1 0 Predicted membrane protein (DUF2070) Ribosomal_L14 PF00238.19 gi|11466293|ref|NP_049608.1| - 4.3e-22 78.5 0.0 5.1e-22 78.2 0.0 1.0 1 0 0 1 1 1 1 Ribosomal protein L14p/L23e Transposon_TraM PF12508.8 gi|11466293|ref|NP_049608.1| - 0.0014 18.3 0.0 0.0016 18.1 0.0 1.2 1 0 0 1 1 1 1 Conjugative transposon, TraM Proton_antipo_M PF00361.20 gi|11466295|ref|NP_049610.1| - 1.2e-48 165.8 26.7 1.2e-48 165.8 26.7 2.3 2 1 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_pyriformis.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_pyriformis.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Tetrahymena_pyriformis.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_pyriformis.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 20:01:16 2019 # [ok]