# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- DUF3973 PF13119.6 gi|8928580|ref|NP_059385.1| - 0.99 9.6 4.2 0.45 10.6 0.6 2.1 1 1 1 2 2 2 0 Domain of unknown function (DUF3973) Proton_antipo_M PF00361.20 gi|8928581|ref|NP_059386.1| - 7.2e-39 133.7 37.2 7.2e-39 133.7 37.2 2.3 2 1 0 2 2 2 1 Proton-conducting membrane transporter Ribosomal_L14 PF00238.19 gi|8928583|ref|NP_059388.1| - 1.6e-23 83.1 0.0 1.8e-23 82.9 0.0 1.0 1 0 0 1 1 1 1 Ribosomal protein L14p/L23e NADHdh PF00146.21 gi|8928585|ref|NP_059390.1| - 6.8e-64 216.0 22.0 8.6e-64 215.7 22.0 1.0 1 0 0 1 1 1 1 NADH dehydrogenase COX1 PF00115.20 gi|8928586|ref|NP_059391.1| - 2e-90 303.8 62.3 3.4e-69 233.8 47.6 2.3 2 0 0 2 2 2 2 Cytochrome C and Quinol oxidase polypeptide I Multi_Drug_Res PF00893.19 gi|8928587|ref|NP_059392.1| - 0.017 15.8 4.5 0.017 15.8 4.5 2.9 3 1 1 4 4 4 0 Small Multidrug Resistance protein DUF2207 PF09972.9 gi|8928588|ref|NP_059393.1| - 0.14 10.9 3.6 0.16 10.7 3.6 1.0 1 0 0 1 1 1 0 Predicted membrane protein (DUF2207) YajC PF02699.15 gi|8928588|ref|NP_059393.1| - 7.3 6.6 6.3 1 9.3 0.2 2.0 2 0 0 2 2 2 0 Preprotein translocase subunit COX2 PF00116.20 gi|8928591|ref|NP_059396.1| - 1.5e-26 92.6 0.6 2.3e-24 85.6 0.0 2.7 2 0 0 2 2 2 2 Cytochrome C oxidase subunit II, periplasmic domain Proton_antipo_M PF00361.20 gi|8928592|ref|NP_059397.1| - 1.9e-64 217.7 26.4 1.9e-64 217.7 26.4 3.1 3 2 0 2 2 2 1 Proton-conducting membrane transporter Proton_antipo_N PF00662.20 gi|8928592|ref|NP_059397.1| - 2.1e-06 27.7 3.8 2.1e-06 27.7 3.8 3.7 3 0 0 3 3 3 1 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus Cytochrome_B PF00033.19 gi|8928593|ref|NP_059398.1| - 2e-11 44.1 14.5 2e-11 44.1 14.5 2.2 2 1 0 2 2 2 1 Cytochrome b/b6/petB Cytochrom_B_N_2 PF13631.6 gi|8928593|ref|NP_059398.1| - 4.1e-10 39.9 5.5 4.1e-10 39.9 5.5 1.6 2 0 0 2 2 2 1 Cytochrome b(N-terminal)/b6/petB DNA_pack_C PF02499.15 gi|8928595|ref|NP_059400.1| - 0.076 12.0 0.1 0.13 11.2 0.1 1.3 1 0 0 1 1 1 0 Probable DNA packing protein, C-terminus SDA1 PF05285.12 gi|8928595|ref|NP_059400.1| - 0.26 10.7 7.9 0.3 10.5 7.9 1.1 1 0 0 1 1 1 0 SDA1 Ribosomal_S13 PF00416.22 gi|8928596|ref|NP_059401.1| - 1.4e-05 25.5 0.0 2.7e-05 24.6 0.0 1.5 1 0 0 1 1 1 1 Ribosomal protein S13/S18 Ribosomal_L2_C PF03947.18 gi|8928598|ref|NP_059403.1| - 8.1e-21 74.5 0.0 1.2e-20 73.9 0.0 1.3 1 0 0 1 1 1 1 Ribosomal Proteins L2, C-terminal domain Oxidored_q6 PF01058.22 gi|8928600|ref|NP_059405.1| - 4.8e-17 62.0 0.1 5.9e-17 61.7 0.1 1.1 1 0 0 1 1 1 1 NADH ubiquinone oxidoreductase, 20 Kd subunit Ribosom_S12_S23 PF00164.25 gi|8928601|ref|NP_059406.1| - 1.5e-23 82.6 1.0 1.9e-23 82.2 1.0 1.1 1 0 0 1 1 1 1 Ribosomal protein S12/S23 Complex1_49kDa PF00346.19 gi|8928603|ref|NP_059408.1| - 2.6e-88 295.7 0.0 3.2e-88 295.3 0.0 1.1 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 49 Kd subunit DUF4404 PF14357.6 gi|8928603|ref|NP_059408.1| - 0.17 12.5 0.0 0.44 11.2 0.0 1.6 1 0 0 1 1 1 0 Domain of unknown function (DUF4404) Ribosomal_S14 PF00253.21 gi|8928604|ref|NP_059409.1| - 1.7e-08 34.1 0.1 3.7e-08 33.0 0.1 1.5 1 0 0 1 1 1 1 Ribosomal protein S14p/S29e POTRA_1 PF08478.10 gi|8928605|ref|NP_059410.1| - 0.093 13.0 0.0 0.13 12.6 0.0 1.3 1 0 0 1 1 1 0 POTRA domain, FtsQ-type BBL5 PF07289.11 gi|8928605|ref|NP_059410.1| - 0.36 9.8 5.0 0.4 9.7 5.0 1.0 1 0 0 1 1 1 0 Bardet-Biedl syndrome 5 protein LPAM_2 PF13627.6 gi|8928608|ref|NP_059413.1| - 0.11 12.4 1.5 0.26 11.2 1.5 1.7 1 0 0 1 1 1 0 Prokaryotic lipoprotein-attachment site DUF1772 PF08592.11 gi|8928609|ref|NP_059414.1| - 0.18 12.1 4.5 0.13 12.6 2.8 1.5 1 1 0 1 1 1 0 Domain of unknown function (DUF1772) DUF2569 PF10754.9 gi|8928609|ref|NP_059414.1| - 0.25 11.8 12.5 3.4 8.1 7.6 2.8 1 1 1 2 2 2 0 Protein of unknown function (DUF2569) ATP-synt_C PF00137.21 gi|8928610|ref|NP_059415.1| - 5.2e-07 29.9 4.6 7.3e-07 29.4 4.6 1.3 1 0 0 1 1 1 1 ATP synthase subunit C DUF3082 PF11282.8 gi|8928610|ref|NP_059415.1| - 5.6 7.3 10.2 3.7 7.8 1.9 2.2 2 1 0 2 2 2 0 Protein of unknown function (DUF3082) NADHdh PF00146.21 gi|8928612|ref|NP_059417.1| - 0.02 14.2 0.2 0.026 13.9 0.2 1.1 1 0 0 1 1 1 0 NADH dehydrogenase FA_desaturase PF00487.24 gi|8928613|ref|NP_059418.1| - 6.6 6.5 16.4 7.7 6.3 16.4 1.2 1 0 0 1 1 1 0 Fatty acid desaturase DUF5325 PF17259.2 gi|8928616|ref|NP_059421.1| - 0.079 12.9 1.7 0.14 12.0 1.7 1.4 1 0 0 1 1 1 0 Family of unknown function (DUF5325) Ribosomal_L16 PF00252.18 gi|8928617|ref|NP_059422.1| - 6e-08 32.8 0.1 8.7e-08 32.2 0.1 1.3 1 0 0 1 1 1 1 Ribosomal protein L16p/L10e Cytochrom_C_asm PF01578.20 gi|8928619|ref|NP_059424.1| - 6.6e-11 42.4 20.4 1.2e-08 35.0 9.8 2.3 2 0 0 2 2 2 2 Cytochrome C assembly protein Oxidored_q4 PF00507.19 gi|8928621|ref|NP_059426.1| - 2.7e-13 49.9 15.3 2.7e-13 49.9 15.3 1.7 1 1 1 2 2 2 1 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 Complex1_30kDa PF00329.19 gi|8928623|ref|NP_059428.1| - 2.5e-07 31.3 0.0 3.2e-07 31.0 0.0 1.2 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 30 Kd subunit # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Paramecium_aurelia.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/Paramecium_aurelia.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Paramecium_aurelia.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/Paramecium_aurelia.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 19:57:04 2019 # [ok]