# --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- Ribosomal_S13 PF00416.22 gi|114329815|ref|YP_740719.1| - 3.9e-09 37.0 0.0 9.4e-09 35.7 0.0 1.7 1 0 0 1 1 1 1 Ribosomal protein S13/S18 Ribosomal_S19 PF00203.21 gi|114329817|ref|YP_740721.1| - 3.7e-10 39.5 1.4 4.4e-10 39.3 1.4 1.1 1 0 0 1 1 1 1 Ribosomal protein S19 Intein_splicing PF14890.6 gi|114329817|ref|YP_740721.1| - 0.043 13.8 0.2 0.046 13.7 0.2 1.1 1 0 0 1 1 1 0 Intein splicing domain DUF1030 PF06270.11 gi|114329817|ref|YP_740721.1| - 2 8.2 5.0 6.6 6.6 0.5 2.4 1 1 1 2 2 2 0 Protein of unknown function (DUF1030) Ribosomal_L2_C PF03947.18 gi|114329818|ref|YP_740722.1| - 1.2e-25 90.1 0.0 2e-25 89.4 0.0 1.3 1 0 0 1 1 1 1 Ribosomal Proteins L2, C-terminal domain Ribosomal_L2 PF00181.23 gi|114329818|ref|YP_740722.1| - 4.2e-07 29.8 0.2 1.1e-06 28.5 0.2 1.7 1 0 0 1 1 1 1 Ribosomal Proteins L2, RNA binding domain EBV-NA3 PF05009.12 gi|114329819|ref|YP_740723.1| - 0.016 14.7 0.6 0.02 14.5 0.6 1.1 1 0 0 1 1 1 0 Epstein-Barr virus nuclear antigen 3 (EBNA-3) Oxidored_q6 PF01058.22 gi|114329820|ref|YP_740724.1| - 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|114329821|ref|YP_740725.1| - 4.5e-25 87.5 0.9 6e-25 87.1 0.9 1.1 1 0 0 1 1 1 1 Ribosomal protein S12/S23 Ribosomal_S12 PF17487.2 gi|114329821|ref|YP_740725.1| - 0.031 15.0 0.0 0.063 14.0 0.0 1.5 1 1 0 1 1 1 0 Ribosomal protein S12 Proton_antipo_M PF00361.20 gi|114329822|ref|YP_740726.1| - 9e-06 25.1 8.7 1.6e-05 24.3 8.7 1.4 1 0 0 1 1 1 1 Proton-conducting membrane transporter DUF1003 PF06210.11 gi|114329822|ref|YP_740726.1| - 1.1 9.4 7.1 0.26 11.4 3.4 1.9 2 0 0 2 2 2 0 Protein of unknown function (DUF1003) Complex1_49kDa PF00346.19 gi|114329823|ref|YP_740727.1| - 2.1e-85 286.1 0.0 3e-85 285.6 0.0 1.2 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 49 Kd subunit RIIa PF02197.17 gi|114329823|ref|YP_740727.1| - 0.11 12.2 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 DASH_Dad4 PF08650.10 gi|114329823|ref|YP_740727.1| - 3.7 7.6 11.0 18 5.4 6.8 2.7 1 1 1 2 2 2 0 DASH complex subunit Dad4 DUF4312 PF14189.6 gi|114329825|ref|YP_740729.1| - 4.5 7.3 6.9 17 5.5 0.1 2.7 1 1 2 3 3 3 0 Domain of unknown function (DUF4312) Ribosomal_S3_C PF00189.20 gi|114329826|ref|YP_740730.1| - 0.026 15.1 0.0 0.061 13.8 0.0 1.7 2 0 0 2 2 2 0 Ribosomal protein S3, C-terminal domain NADHdh PF00146.21 gi|114329828|ref|YP_740732.1| - 1.5e-08 34.3 3.6 1.7e-08 34.2 3.6 1.0 1 0 0 1 1 1 1 NADH dehydrogenase ATP-synt_C PF00137.21 gi|114329829|ref|YP_740733.1| - 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|114329829|ref|YP_740733.1| - 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) DUF4980 PF16352.5 gi|114329830|ref|YP_740734.1| - 0.015 15.3 0.4 0.015 15.3 0.4 1.9 3 0 0 3 3 3 0 Domain of unknown function (DUF4980) Ribosomal_S7 PF00177.21 gi|114329830|ref|YP_740734.1| - 0.11 12.2 0.0 0.62 9.7 0.0 2.1 1 1 0 1 1 1 0 Ribosomal protein S7p/S5e Proton_antipo_M PF00361.20 gi|114329831|ref|YP_740735.1| - 1.7e-07 30.7 26.1 1.7e-07 30.7 26.1 2.0 2 1 0 2 2 2 1 Proton-conducting membrane transporter Ribosomal_L16 PF00252.18 gi|114329834|ref|YP_740738.1| - 5e-11 42.7 0.2 5.3e-11 42.6 0.2 1.1 1 0 0 1 1 1 1 Ribosomal protein L16p/L10e Cytochrom_C_asm PF01578.20 gi|114329835|ref|YP_740739.1| - 4.7e-07 29.8 38.6 4.7e-07 29.8 38.6 4.2 1 1 1 2 2 2 1 Cytochrome C assembly protein SRTM1 PF15872.5 gi|114329835|ref|YP_740739.1| - 0.00015 21.9 1.7 0.00015 21.9 1.7 5.3 6 1 1 7 7 7 1 Serine-rich and transmembrane domain-containing protein 1 Oxidored_q4 PF00507.19 gi|114329837|ref|YP_740741.1| - 1.3e-16 60.6 13.1 1.3e-16 60.6 13.1 1.5 1 1 1 2 2 2 1 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 Complex1_30kDa PF00329.19 gi|114329840|ref|YP_740744.1| - 2.5e-14 53.9 0.0 3.1e-14 53.6 0.0 1.2 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 30 Kd subunit Complex1_30kDa PF00329.19 gi|114329841|ref|YP_740745.1| - 2.5e-14 53.9 0.0 3.1e-14 53.6 0.0 1.2 1 0 0 1 1 1 1 Respiratory-chain NADH dehydrogenase, 30 Kd subunit Cytochrome_B PF00033.19 gi|114329843|ref|YP_740747.1| - 4.9e-17 62.4 11.5 4.9e-17 62.4 11.5 2.0 2 0 0 2 2 2 1 Cytochrome b/b6/petB Cytochrom_B_N_2 PF13631.6 gi|114329843|ref|YP_740747.1| - 5.9e-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|114329843|ref|YP_740747.1| - 0.0036 17.6 3.4 0.0036 17.6 3.4 3.4 3 1 1 4 4 4 1 Cytochrome b(C-terminal)/b6/petD Proton_antipo_M PF00361.20 gi|114329844|ref|YP_740748.1| - 3.7e-65 220.0 25.7 3.7e-65 220.0 25.7 3.3 3 1 0 3 3 3 1 Proton-conducting membrane transporter COX2 PF00116.20 gi|114329845|ref|YP_740749.1| - 1.1e-26 93.1 0.7 9.7e-24 83.6 0.0 2.5 2 0 0 2 2 2 2 Cytochrome C oxidase subunit II, periplasmic domain COX1 PF00115.20 gi|114329850|ref|YP_740754.1| - 1.7e-92 310.6 63.0 1.6e-70 238.1 54.4 2.1 2 0 0 2 2 2 2 Cytochrome C and Quinol oxidase polypeptide I NADHdh PF00146.21 gi|114329851|ref|YP_740755.1| - 1.7e-63 214.7 23.2 2.1e-63 214.4 23.2 1.1 1 0 0 1 1 1 1 NADH dehydrogenase DUF2070 PF09843.9 gi|114329852|ref|YP_740756.1| - 5.6 5.1 30.8 7.2 4.8 30.8 1.1 1 0 0 1 1 1 0 Predicted membrane protein (DUF2070) Ribosomal_L14 PF00238.19 gi|114329853|ref|YP_740757.1| - 1.3e-19 70.4 0.0 1.6e-19 70.2 0.0 1.0 1 0 0 1 1 1 1 Ribosomal protein L14p/L23e Transposon_TraM PF12508.8 gi|114329853|ref|YP_740757.1| - 0.00029 20.6 0.0 0.00034 20.3 0.0 1.2 1 0 0 1 1 1 1 Conjugative transposon, TraM Proton_antipo_M PF00361.20 gi|114329855|ref|YP_740759.1| - 8e-50 169.7 27.7 8e-50 169.7 27.7 2.2 2 0 0 2 2 2 1 Proton-conducting membrane transporter UvrD_C PF13361.6 gi|114329856|ref|YP_740760.1| - 3.5 6.9 11.8 4.7 6.5 11.7 1.3 1 1 0 1 1 1 0 UvrD-like helicase C-terminal domain # # Program: hmmscan # Version: 3.2.1 (June 2018) # Pipeline mode: SCAN # Query file: /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Tetrahymena_malaccensis.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_malaccensis.PFam32-A --tblout /oak/stanford/groups/akundaje/marinovg/genomes/mitochondrial_genomes/Alveolata/Ciliates/Tetrahymena_malaccensis.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_malaccensis.faa # Current dir: /oak/stanford/groups/akundaje/marinovg/genomes # Date: Mon Mar 25 20:01:15 2019 # [ok]