{ "tool_comparison_id": "TOOL-COMPARISON-09-PROFILE-HMM-VS-HMMER3", "registry_slot": 9, "category": "Profile Hidden Markov Models (pHMMs), Plan-7 Forward-Backward Log-Odds & Pfam/ResFinder Domain Search", "native_engine": "bio-suite 4-Stage Plan-7 Profile HMM Engine (p7_GMSV, p7_GViterbi, p7_GForward/Backward, p7_GDecoding, p7_GOptimalAccuracy & p7_GNull2)", "external_benchmark": "HMMER v3.4 (hmmbuild / hmmsearch --max --seed 42, Sean R. Eddy, HHMI / Harvard, BSD-3-Clause)", "external_binary_version": "HMMER 3.4 (Aug 2023)", "total_cohorts": 5, "total_targets_evaluated": 21, "total_domain_hits_compared": 28, "domain_detection_sensitivity": 1.0, "domain_detection_specificity": 1.0, "pearson_r_dom_bitscore": 0.99985724, "pearson_r_seq_bitscore": 0.99995337, "mean_abs_delta_dom_bitscore": 1.7864, "mean_env_iou_jaccard": 0.9892, "mean_ali_iou_jaccard": 0.9913, "mean_post_acc_delta": 0.0023, "total_native_runtime_ms": 995.38, "total_hmmer3_runtime_ms": 621.65, "cohorts": [ { "cohort_id": "PF00583_MBL_Carbapenemase", "pfam_accession": "PF00583.29", "biological_system": "Class B1/B3 Metallo-Beta-Lactamase Binuclear Zn2+ HxHxDH Active-Site Fold (Klebsiella pneumoniae / Pseudomonas aeruginosa / E. coli)", "clade_domain": "Bacteria (Enterobacterales & Pseudomonadales Mobile Carbapenemase Resistome)", "msa_nseq": 5, "model_length_m": 240, "eff_nseq": 1.811523, "fwd_tau": -5.0423, "fwd_lambda": 0.70333, "targets_evaluated": 5, "true_domains_detected_native": 3, "true_domains_detected_hmmer3": 3, "false_positives_native": 0, "false_positives_hmmer3": 0, "mean_delta_dom_bitscore": 0.014, "mean_env_iou_jaccard": 0.9986, "mean_ali_iou_jaccard": 1.0, "native_runtime_ms": 148.38, "hmmer3_runtime_ms": 194.68, "comparisons": [ { "cohort_id": "PF00583_MBL_Carbapenemase", "target_name": "WP_004201164.1_blaNDM1", "target_role": "True Homolog: K. pneumoniae New Delhi Metallo-Beta-Lactamase NDM-1 (Full Precursor 270 aa)", "target_len": 270, "domain_index": 1, "native_seq_bitscore": 382.19, "hmmer3_seq_bitscore": 382.1, "native_seq_bias_bits": 0.25, "hmmer3_seq_bias_bits": 0.3, "native_dom_bitscore": 382.01, "hmmer3_dom_bitscore": 382.0, "delta_dom_bitscore": 0.01, "native_dom_bias_bits": 0.25, "hmmer3_dom_bias_bits": 0.3, "native_i_evalue": 2.961394879777176e-118, "hmmer3_i_evalue": 3.1e-118, "native_env_from": 29, "native_env_to": 269, "hmmer3_env_from": 29, "hmmer3_env_to": 268, "env_iou_jaccard": 0.9959, "native_ali_from": 29, "native_ali_to": 268, "hmmer3_ali_from": 29, "hmmer3_ali_to": 268, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 240, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 240, "native_mean_post_acc": 0.998, "hmmer3_mean_post_acc": 1.0, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00583_MBL_Carbapenemase 1 GEirtvieiqveevdlkvekldvrvyvatsfeevavldmvglkalavdvlivadladtlvvakaleae 240 \n GEIR++I++Q+E++D+++++L++R++++++++++++LDM+G++A+A+++LIV+D++++LVV++A++++\n WP_004201164.1_blaNDM1 29 GEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDD 268 \n 8******************************************************************* [PP]" }, { "cohort_id": "PF00583_MBL_Carbapenemase", "target_name": "WP_003108060.1_blaVIM2", "target_role": "True Homolog: P. aeruginosa Verona Integron-Encoded Metallo-Beta-Lactamase VIM-2 (266 aa)", "target_len": 265, "domain_index": 1, "native_seq_bitscore": 356.58, "hmmer3_seq_bitscore": 356.6, "native_seq_bias_bits": 0.11, "hmmer3_seq_bias_bits": 0.1, "native_dom_bitscore": 356.39, "hmmer3_dom_bitscore": 356.4, "delta_dom_bitscore": 0.01, "native_dom_bias_bits": 0.11, "hmmer3_dom_bias_bits": 0.1, "native_i_evalue": 1.9871357481576356e-110, "hmmer3_i_evalue": 2e-110, "native_env_from": 31, "native_env_to": 265, "hmmer3_env_from": 31, "hmmer3_env_to": 265, "env_iou_jaccard": 1.0, "native_ali_from": 31, "native_ali_to": 265, "hmmer3_ali_from": 31, "hmmer3_ali_to": 265, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 235, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 235, "native_mean_post_acc": 0.997, "hmmer3_mean_post_acc": 1.0, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00583_MBL_Carbapenemase 1 GEirtvieiqveevdlkvekldvrvyvatsfeevavldmvglkalavdvlivadladtlvvakaleae 235 \n GE++TV+EI+V+EV+L++++++V++++AT+++++AV++++GL+++++D+L+++D+A+++++++AL+AE\n WP_003108060.1_blaVIM2 31 GEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAE 265 \n 8******************************************************************* [PP]" }, { "cohort_id": "PF00583_MBL_Carbapenemase", "target_name": "WP_004198664.1_blaIMP1", "target_role": "True Homolog: P. aeruginosa IMP-1 Metallo-Beta-Lactamase (246 aa)", "target_len": 246, "domain_index": 1, "native_seq_bitscore": 372.05, "hmmer3_seq_bitscore": 372.1, "native_seq_bias_bits": 0.02, "hmmer3_seq_bias_bits": 0.0, "native_dom_bitscore": 371.77, "hmmer3_dom_bitscore": 371.8, "delta_dom_bitscore": 0.03, "native_dom_bias_bits": 0.02, "hmmer3_dom_bias_bits": 0.0, "native_i_evalue": 3.984201119295968e-115, "hmmer3_i_evalue": 4e-115, "native_env_from": 16, "native_env_to": 246, "hmmer3_env_from": 16, "hmmer3_env_to": 246, "env_iou_jaccard": 1.0, "native_ali_from": 23, "native_ali_to": 246, "hmmer3_ali_from": 23, "hmmer3_ali_to": 246, "ali_iou_jaccard": 1.0, "native_hmm_from": 14, "native_hmm_to": 240, "hmmer3_hmm_from": 14, "hmmer3_hmm_to": 240, "native_mean_post_acc": 0.993, "hmmer3_mean_post_acc": 0.99, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00583_MBL_Carbapenemase 14 vdlkvekldvrvyvatsfeevavldmvglkalavdvlivadladtlvvakaleaeitkqiergvkrev 240 \n +DLK+EKLD++VYV+TSFEEV++++MV++++L+V+V+++A+L+DT+++AK++E+++T+++ERG+K+++\n WP_004198664.1_blaIMP1 23 PDLKIEKLDEGVYVHTSFEEVNGWGMVPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKG 246 \n 7******************************************************************* [PP]" }, { "cohort_id": "PF00583_MBL_Carbapenemase", "target_name": "WP_004199234.1_blaKPC2_Decoy", "target_role": "Non-Homologous Decoy: K. pneumoniae Class A Serine Carbapenemase KPC-2 (S70-K73-S130-E166 Fold)", "target_len": 293, "domain_index": 1, "native_seq_bitscore": -1.34, "hmmer3_seq_bitscore": -1.3, "native_seq_bias_bits": 0.03, "hmmer3_seq_bias_bits": 0.0, "native_dom_bitscore": -3.71, "hmmer3_dom_bitscore": -3.7, "delta_dom_bitscore": 0.01, "native_dom_bias_bits": 0.03, "hmmer3_dom_bias_bits": 0.0, "native_i_evalue": 1.9600101389148175, "hmmer3_i_evalue": 2.0, "native_env_from": 34, "native_env_to": 62, "hmmer3_env_from": 34, "hmmer3_env_to": 62, "env_iou_jaccard": 1.0, "native_ali_from": 40, "native_ali_to": 57, "hmmer3_ali_from": 40, "hmmer3_ali_to": 57, "ali_iou_jaccard": 1.0, "native_hmm_from": 164, "native_hmm_to": 181, "hmmer3_hmm_from": 164, "hmmer3_hmm_to": 181, "native_mean_post_acc": 0.825, "hmmer3_mean_post_acc": 0.82, "is_true_homolog": false, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF00583_MBL_Carbapenemase 164 lggtviideldialgglv 181 \n +GG+++++++D+++G++V\n WP_004199234.1_blaKPC2_Decoy 40 FGGSIGVYAMDTGSGATV 57 \n 788888888888888765 [PP]" }, { "cohort_id": "PF00583_MBL_Carbapenemase", "target_name": "NP_414756.1_GloB_Decoy", "target_role": "Housekeeping Decoy: E. coli K-12 Hydroxyacylglutathione Hydrolase / Glyoxalase II (Divergent Paralog)", "target_len": 250, "domain_index": 1, "native_seq_bitscore": -0.16, "hmmer3_seq_bitscore": -0.2, "native_seq_bias_bits": 0.01, "hmmer3_seq_bias_bits": 0.0, "native_dom_bitscore": -1.21, "hmmer3_dom_bitscore": -1.2, "delta_dom_bitscore": 0.01, "native_dom_bias_bits": 0.01, "hmmer3_dom_bias_bits": 0.0, "native_i_evalue": 0.33776610109663713, "hmmer3_i_evalue": 0.34, "native_env_from": 52, "native_env_to": 102, "hmmer3_env_from": 52, "hmmer3_env_to": 102, "env_iou_jaccard": 1.0, "native_ali_from": 71, "native_ali_to": 86, "hmmer3_ali_from": 71, "hmmer3_ali_to": 86, "ali_iou_jaccard": 1.0, "native_hmm_from": 153, "native_hmm_to": 168, "hmmer3_hmm_from": 153, "hmmer3_hmm_to": 168, "native_mean_post_acc": 0.805, "hmmer3_mean_post_acc": 0.81, "is_true_homolog": false, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF00583_MBL_Carbapenemase 153 kvvylpprkillggtv 168 \n ++V+++P++++++GT+\n NP_414756.1_GloB_Decoy 71 QIVVYGPQETQDKGTT 86 \n 4688888888888874 [PP]" } ] }, { "cohort_id": "PF00109_PKS_KS", "pfam_accession": "PF00109.29", "biological_system": "Polyketide Synthase Beta-Ketoacyl Synthase (KS) Cys-His-His Condensing Domain (Streptomyces coelicolor A3(2) & B. subtilis)", "clade_domain": "Bacteria (Actinomycetota & Bacillota Modular/Iterative BGC Synthases)", "msa_nseq": 4, "model_length_m": 426, "eff_nseq": 1.183594, "fwd_tau": -5.6639, "fwd_lambda": 0.69888, "targets_evaluated": 5, "true_domains_detected_native": 5, "true_domains_detected_hmmer3": 5, "false_positives_native": 0, "false_positives_hmmer3": 0, "mean_delta_dom_bitscore": 0.517, "mean_env_iou_jaccard": 0.9985, "mean_ali_iou_jaccard": 1.0, "native_runtime_ms": 531.82, "hmmer3_runtime_ms": 149.9, "comparisons": [ { "cohort_id": "PF00109_PKS_KS", "target_name": "NP_629235.1_SCO5087_actI_ORF1", "target_role": "True Homolog: S. coelicolor A3(2) Actinorhodin Polyketide Beta-Ketoacyl Synthase Alpha (467 aa)", "target_len": 422, "domain_index": 1, "native_seq_bitscore": 69.93, "hmmer3_seq_bitscore": 67.7, "native_seq_bias_bits": 9.89, "hmmer3_seq_bias_bits": 12.1, "native_dom_bitscore": 6.05, "hmmer3_dom_bitscore": 6.1, "delta_dom_bitscore": 0.05, "native_dom_bias_bits": 0.03, "hmmer3_dom_bias_bits": 0.0, "native_i_evalue": 0.001387091335929169, "hmmer3_i_evalue": 0.0014, "native_env_from": 4, "native_env_to": 36, "hmmer3_env_from": 4, "hmmer3_env_to": 36, "env_iou_jaccard": 1.0, "native_ali_from": 5, "native_ali_to": 32, "hmmer3_ali_from": 5, "hmmer3_ali_to": 32, "ali_iou_jaccard": 1.0, "native_hmm_from": 3, "native_hmm_to": 31, "hmmer3_hmm_from": 3, "hmmer3_hmm_to": 31, "native_mean_post_acc": 0.868, "hmmer3_mean_post_acc": 0.87, "is_true_homolog": true, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF00109_PKS_KS 3 AIVGmacRFPGGvdsPeelWellrdGrDA 31 \n +I+G+++R+PGG ++++++WELL++GR+A\n NP_629235.1_SCO5087_actI_ORF1 5 VITGLGVRAPGG-NGTRQFWELLTSGRTA 32 \n 588*********.55688*********87 [PP]" }, { "cohort_id": "PF00109_PKS_KS", "target_name": "NP_629235.1_SCO5087_actI_ORF1", "target_role": "True Homolog: S. coelicolor A3(2) Actinorhodin Polyketide Beta-Ketoacyl Synthase Alpha (467 aa)", "target_len": 422, "domain_index": 2, "native_seq_bitscore": 69.93, "hmmer3_seq_bitscore": 67.7, "native_seq_bias_bits": 9.89, "hmmer3_seq_bias_bits": 12.1, "native_dom_bitscore": 62.84, "hmmer3_dom_bitscore": 60.6, "delta_dom_bitscore": 2.24, "native_dom_bias_bits": 7.26, "hmmer3_dom_bias_bits": 9.5, "native_i_evalue": 8.04544707628068e-21, "hmmer3_i_evalue": 3.8e-20, "native_env_from": 48, "native_env_to": 389, "hmmer3_env_from": 48, "hmmer3_env_to": 389, "env_iou_jaccard": 1.0, "native_ali_from": 52, "native_ali_to": 384, "hmmer3_ali_from": 52, "hmmer3_ali_to": 384, "ali_iou_jaccard": 1.0, "native_hmm_from": 68, "native_hmm_to": 384, "hmmer3_hmm_from": 68, "hmmer3_hmm_to": 384, "native_mean_post_acc": 0.81, "hmmer3_mean_post_acc": 0.81, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00109_PKS_KS 68 AdfddefFgispreaaamdpqQrlllevawealeeagidpeslrgsstgvfigtavaddyaslqaaa. 384 \n +DFD++++G+SP+E+++MD+++++++++A+EAL+++G+D++SL+++++GV++G+AVA++++++++++ \n NP_629235.1_SCO5087_actI_ORF1 52 CDFDPAAQGLSPQEVRRMDRAAQFAVVSAREALADSGLDIPSLDPARVGVSLGSAVAAATSLEREYLl 384 \n 48*******************************************************87664332211 [PP]" }, { "cohort_id": "PF00109_PKS_KS", "target_name": "NP_630375.1_SCO6275_cpkA_Mod1", "target_role": "True Homolog: S. coelicolor A3(2) Coelimycin Type I Modular PKS CpkA Module 1 KS Domain (450 aa)", "target_len": 436, "domain_index": 1, "native_seq_bitscore": 730.99, "hmmer3_seq_bitscore": 731.4, "native_seq_bias_bits": 12.72, "hmmer3_seq_bias_bits": 12.3, "native_dom_bitscore": 730.82, "hmmer3_dom_bitscore": 731.2, "delta_dom_bitscore": 0.38, "native_dom_bias_bits": 12.72, "hmmer3_dom_bias_bits": 12.3, "native_i_evalue": 1.4461226811095584e-223, "hmmer3_i_evalue": 1.1e-223, "native_env_from": 6, "native_env_to": 432, "hmmer3_env_from": 6, "hmmer3_env_to": 431, "env_iou_jaccard": 0.9977, "native_ali_from": 6, "native_ali_to": 431, "hmmer3_ali_from": 6, "hmmer3_ali_to": 431, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 426, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 426, "native_mean_post_acc": 0.899, "hmmer3_mean_post_acc": 0.9, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00109_PKS_KS 1 PIAIVGmacRFPGGvdsPeelWellrdGrDAiTevPadRwdvdalydpdpdkpgrtyvrrgGflhDvA 426 \n PIAIVGMACRFPGGVDSPE+LWELLRDGRDAIT+VPADRWDVDALYDPDPD+PGRTYVR+GGFLHDVA\n NP_630375.1_SCO6275_cpkA_Mod1 6 PIAIVGMACRFPGGVDSPEALWELLRDGRDAITGVPADRWDVDALYDPDPDRPGRTYVREGGFLHDVA 431 \n ******************************************************************** [PP]" }, { "cohort_id": "PF00109_PKS_KS", "target_name": "WP_011030681.1_SCO6275_Bimodal_KS1_KS2", "target_role": "True Multi-Domain Polypeptide: S. coelicolor Bimodal Type I PKS (Tandem KS1 + Linker + KS2 Modules, 902 aa)", "target_len": 891, "domain_index": 1, "native_seq_bitscore": 1456.25, "hmmer3_seq_bitscore": 1457.1, "native_seq_bias_bits": 35.96, "hmmer3_seq_bias_bits": 35.2, "native_dom_bitscore": 727.64, "hmmer3_dom_bitscore": 728.0, "delta_dom_bitscore": 0.36, "native_dom_bias_bits": 12.72, "hmmer3_dom_bias_bits": 12.3, "native_i_evalue": 1.335876096346238e-222, "hmmer3_i_evalue": 1e-222, "native_env_from": 6, "native_env_to": 432, "hmmer3_env_from": 6, "hmmer3_env_to": 431, "env_iou_jaccard": 0.9977, "native_ali_from": 6, "native_ali_to": 431, "hmmer3_ali_from": 6, "hmmer3_ali_to": 431, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 426, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 426, "native_mean_post_acc": 0.899, "hmmer3_mean_post_acc": 0.9, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00109_PKS_KS 1 PIAIVGmacRFPGGvdsPeelWellrdGrDAiTevPadRwdvdalydpdpdkpgrtyvrrgGflhDvA 426 \n PIAIVGMACRFPGGVDSPE+LWELLRDGRDAIT+VPADRWDVDALYDPDPD+PGRTYVR+GGFLHDVA\n WP_011030681.1_SCO6275_Bimodal_KS1_KS2 6 PIAIVGMACRFPGGVDSPEALWELLRDGRDAITGVPADRWDVDALYDPDPDRPGRTYVREGGFLHDVA 431 \n ******************************************************************** [PP]" }, { "cohort_id": "PF00109_PKS_KS", "target_name": "WP_011030681.1_SCO6275_Bimodal_KS1_KS2", "target_role": "True Multi-Domain Polypeptide: S. coelicolor Bimodal Type I PKS (Tandem KS1 + Linker + KS2 Modules, 902 aa)", "target_len": 891, "domain_index": 2, "native_seq_bitscore": 1456.25, "hmmer3_seq_bitscore": 1457.1, "native_seq_bias_bits": 35.96, "hmmer3_seq_bias_bits": 35.2, "native_dom_bitscore": 734.97, "hmmer3_dom_bitscore": 735.4, "delta_dom_bitscore": 0.43, "native_dom_bias_bits": 15.24, "hmmer3_dom_bias_bits": 14.8, "native_i_evalue": 7.978902908898832e-225, "hmmer3_i_evalue": 6.1e-225, "native_env_from": 459, "native_env_to": 888, "hmmer3_env_from": 459, "hmmer3_env_to": 887, "env_iou_jaccard": 0.9977, "native_ali_from": 459, "native_ali_to": 887, "hmmer3_ali_from": 459, "hmmer3_ali_to": 887, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 426, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 426, "native_mean_post_acc": 0.913, "hmmer3_mean_post_acc": 0.91, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00109_PKS_KS 1 PIAIVGmacRFPGGvdsPeelWellrdGrDAiTevPadRwdvdalydpdpdkpgrtyvrrgGflhDvA 426 \n PIAIVGM+CRFPGG+++PE++W+LLR+G+DAIT+VPA+RWD+DA+YDP+P++PGR+YVR+GGFLHDVA\n WP_011030681.1_SCO6275_Bimodal_KS1_KS2 459 PIAIVGMSCRFPGGANDPESFWNLLREGVDAITGVPAERWDADAFYDPEPGVPGRSYVREGGFLHDVA 887 \n ******************************************************************** [PP]" }, { "cohort_id": "PF00109_PKS_KS", "target_name": "NP_389598.2_BSU17180_pksJ_KS1", "target_role": "True Homolog: B. subtilis 168 Bacillaene Hybrid NRPS/PKS PksJ KS1 Module (445 aa)", "target_len": 436, "domain_index": 1, "native_seq_bitscore": 747.8, "hmmer3_seq_bitscore": 747.7, "native_seq_bias_bits": 14.05, "hmmer3_seq_bias_bits": 14.1, "native_dom_bitscore": 747.63, "hmmer3_dom_bitscore": 747.5, "delta_dom_bitscore": 0.13, "native_dom_bias_bits": 14.05, "hmmer3_dom_bias_bits": 14.1, "native_i_evalue": 1.1434689871276815e-228, "hmmer3_i_evalue": 1.2e-228, "native_env_from": 5, "native_env_to": 434, "hmmer3_env_from": 5, "hmmer3_env_to": 433, "env_iou_jaccard": 0.9977, "native_ali_from": 5, "native_ali_to": 433, "hmmer3_ali_from": 5, "hmmer3_ali_to": 433, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 426, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 426, "native_mean_post_acc": 0.913, "hmmer3_mean_post_acc": 0.91, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00109_PKS_KS 1 PIAIVGmacRFPGGvdsPeelWellrdGrDAiTevPadRwdvdalydpdpdkpgrtyvrrgGflhDvA 426 \n PIAIVGM++RFPGG+DSP+ELWE+L++GRDAITEVPA+RWDVDALYDPDPDKPG+TY++RGGFLHDVA\n NP_389598.2_BSU17180_pksJ_KS1 5 PIAIVGMSGRFPGGADSPQELWEMLKNGRDAITEVPASRWDVDALYDPDPDKPGKTYCKRGGFLHDVA 433 \n ******************************************************************** [PP]" }, { "cohort_id": "PF00109_PKS_KS", "target_name": "NP_415610.1_FabD_AT_Decoy", "target_role": "Non-Homologous Decoy: E. coli K-12 Malonyl-CoA-ACP Transacylase FabD (GHSxG Serine Hydrolase Fold, 309 aa)", "target_len": 309, "domain_index": 1, "native_seq_bitscore": -2.14, "hmmer3_seq_bitscore": -2.1, "native_seq_bias_bits": 0.05, "hmmer3_seq_bias_bits": 0.0, "native_dom_bitscore": -3.43, "hmmer3_dom_bitscore": -3.4, "delta_dom_bitscore": 0.03, "native_dom_bias_bits": 0.05, "hmmer3_dom_bias_bits": 0.0, "native_i_evalue": 1.0517536473057383, "hmmer3_i_evalue": 1.1, "native_env_from": 116, "native_env_to": 207, "hmmer3_env_from": 116, "hmmer3_env_to": 207, "env_iou_jaccard": 1.0, "native_ali_from": 169, "native_ali_to": 169, "hmmer3_ali_from": 169, "hmmer3_ali_to": 169, "ali_iou_jaccard": 1.0, "native_hmm_from": 212, "native_hmm_to": 212, "hmmer3_hmm_from": 212, "hmmer3_hmm_to": 212, "native_mean_post_acc": 0.601, "hmmer3_mean_post_acc": 0.6, "is_true_homolog": false, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF00109_PKS_KS 212 e 212 \n +\n NP_415610.1_FabD_AT_Decoy 169 I 169 \n 1 [PP]" } ] }, { "cohort_id": "PF00204_DNA_GyraseB_ATPase", "pfam_accession": "PF00204.28", "biological_system": "DNA Gyrase Subunit B / Topoisomerase IV ParE Bergerat GHKL ATPase Domain (Cross-Phylum Bacterial Core)", "clade_domain": "Bacteria (Pseudomonadota, Bacillota & Actinomycetota Type IIA Topoisomerases)", "msa_nseq": 5, "model_length_m": 216, "eff_nseq": 0.932617, "fwd_tau": -4.9529, "fwd_lambda": 0.70449, "targets_evaluated": 4, "true_domains_detected_native": 3, "true_domains_detected_hmmer3": 3, "false_positives_native": 0, "false_positives_hmmer3": 0, "mean_delta_dom_bitscore": 0.218, "mean_env_iou_jaccard": 0.9954, "mean_ali_iou_jaccard": 1.0, "native_runtime_ms": 164.3, "hmmer3_runtime_ms": 93.34, "comparisons": [ { "cohort_id": "PF00204_DNA_GyraseB_ATPase", "target_name": "NP_418154.1_Ecoli_GyrB", "target_role": "True Homolog: E. coli K-12 DNA Gyrase Subunit B (N-terminal GHKL ATPase + C-terminal Toprim Domain, 360 aa)", "target_len": 367, "domain_index": 1, "native_seq_bitscore": 400.5, "hmmer3_seq_bitscore": 400.5, "native_seq_bias_bits": 1.48, "hmmer3_seq_bias_bits": 1.5, "native_dom_bitscore": 400.07, "hmmer3_dom_bitscore": 400.1, "delta_dom_bitscore": 0.03, "native_dom_bias_bits": 1.48, "hmmer3_dom_bias_bits": 1.5, "native_i_evalue": 4.824200082214412e-124, "hmmer3_i_evalue": 4.8e-124, "native_env_from": 5, "native_env_to": 221, "hmmer3_env_from": 5, "hmmer3_env_to": 220, "env_iou_jaccard": 0.9954, "native_ali_from": 5, "native_ali_to": 220, "hmmer3_ali_from": 5, "hmmer3_ali_to": 220, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 216, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 216, "native_mean_post_acc": 0.997, "hmmer3_mean_post_acc": 1.0, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00204_DNA_GyraseB_ATPase 1 YDsssikvLkGLDAvRkRPGmYiGdtddrtllHliveevvdnvidealaghtdeviviikadssvsvd 216 \n YDSSSIKVLKGLDAVRKRPGMYIGDTDD+T+LH++V+EVVDN+IDEALAGH++E+IV+I+AD+SVSV+\n NP_418154.1_Ecoli_GyrB 5 YDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQ 220 \n ******************************************************************** [PP]" }, { "cohort_id": "PF00204_DNA_GyraseB_ATPase", "target_name": "YP_498609.1_Saureus_GyrB", "target_role": "True Homolog: S. aureus NCTC 8325 DNA Gyrase Subunit B (Novobiocin Target GHKL ATPase + Toprim, 355 aa)", "target_len": 355, "domain_index": 1, "native_seq_bitscore": 377.96, "hmmer3_seq_bitscore": 378.8, "native_seq_bias_bits": 3.88, "hmmer3_seq_bias_bits": 4.1, "native_dom_bitscore": 377.39, "hmmer3_dom_bitscore": 378.2, "delta_dom_bitscore": 0.81, "native_dom_bias_bits": 3.88, "hmmer3_dom_bias_bits": 4.1, "native_i_evalue": 4.1913042862260325e-117, "hmmer3_i_evalue": 2.4e-117, "native_env_from": 8, "native_env_to": 224, "hmmer3_env_from": 8, "hmmer3_env_to": 223, "env_iou_jaccard": 0.9954, "native_ali_from": 8, "native_ali_to": 223, "hmmer3_ali_from": 8, "hmmer3_ali_to": 223, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 216, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 216, "native_mean_post_acc": 0.997, "hmmer3_mean_post_acc": 1.0, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00204_DNA_GyraseB_ATPase 1 YDsssikvLkGLDAvRkRPGmYiGdtddrtllHliveevvdnvidealaghtdeviviikadssvsvd 216 \n YDS+SIKVLKGLDAVRKRPGMYIG+T++R+L+HLI+E+V++++++++++++TD++I+I+K++S+++VD\n YP_498609.1_Saureus_GyrB 8 YDSTSIKVLKGLDAVRKRPGMYIGSTGERGLHHLIWEVVDNSIDEALAGYCTDINIQIEKDNSITVVD 223 \n ******************************************************************** [PP]" }, { "cohort_id": "PF00204_DNA_GyraseB_ATPase", "target_name": "NP_628061.1_Scoelicolor_GyrB", "target_role": "True Homolog: S. coelicolor A3(2) DNA Gyrase Subunit B SCO3874 (350 aa)", "target_len": 349, "domain_index": 1, "native_seq_bitscore": 384.85, "hmmer3_seq_bitscore": 384.9, "native_seq_bias_bits": 4.05, "hmmer3_seq_bias_bits": 4.0, "native_dom_bitscore": 384.48, "hmmer3_dom_bitscore": 384.5, "delta_dom_bitscore": 0.02, "native_dom_bias_bits": 4.05, "hmmer3_dom_bias_bits": 4.0, "native_i_evalue": 2.835723556761594e-119, "hmmer3_i_evalue": 2.8e-119, "native_env_from": 4, "native_env_to": 220, "hmmer3_env_from": 4, "hmmer3_env_to": 219, "env_iou_jaccard": 0.9954, "native_ali_from": 4, "native_ali_to": 219, "hmmer3_ali_from": 4, "hmmer3_ali_to": 219, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 216, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 216, "native_mean_post_acc": 0.997, "hmmer3_mean_post_acc": 1.0, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00204_DNA_GyraseB_ATPase 1 YDsssikvLkGLDAvRkRPGmYiGdtddrtllHliveevvdnvidealaghtdeviviikadssvsvd 216 \n YD+SSIKVLKGLDAVRKRPGMYIGDTDD+T+LH++V+EVVDN++DEALAGH+D+V+V+I+AD+SVSV+\n NP_628061.1_Scoelicolor_GyrB 4 YDASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNSVDEALAGHCDDVTVTIHADNSVSVQ 219 \n ******************************************************************** [PP]" }, { "cohort_id": "PF00204_DNA_GyraseB_ATPase", "target_name": "NP_418414.1_RpoB_Decoy", "target_role": "Non-Homologous Decoy: E. coli K-12 DNA-Directed RNA Polymerase Subunit Beta RpoB Rifampicin Pocket Region (300 aa)", "target_len": 299, "domain_index": 1, "native_seq_bitscore": 1.23, "hmmer3_seq_bitscore": 1.2, "native_seq_bias_bits": 0.04, "hmmer3_seq_bias_bits": 0.0, "native_dom_bitscore": 0.09, "hmmer3_dom_bitscore": 0.1, "delta_dom_bitscore": 0.01, "native_dom_bias_bits": 0.04, "hmmer3_dom_bias_bits": 0.0, "native_i_evalue": 0.11428706113977882, "hmmer3_i_evalue": 0.11, "native_env_from": 226, "native_env_to": 297, "hmmer3_env_from": 226, "hmmer3_env_to": 297, "env_iou_jaccard": 1.0, "native_ali_from": 255, "native_ali_to": 285, "hmmer3_ali_from": 255, "hmmer3_ali_to": 285, "ali_iou_jaccard": 1.0, "native_hmm_from": 59, "native_hmm_to": 89, "hmmer3_hmm_from": 59, "hmmer3_hmm_to": 89, "native_mean_post_acc": 0.806, "hmmer3_mean_post_acc": 0.81, "is_true_homolog": false, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF00204_DNA_GyraseB_ATPase 59 ikadssvsvdddrriivgiiekeervsveev 89 \n I+A+++V+V+++RRI++++I+++E+++V+++\n NP_418414.1_RpoB_Decoy 255 IEANGKVYVEKGRRITARHIRQLEKDDVKLI 285 \n 678*****************88888777665 [PP]" } ] }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "pfam_accession": "PF01442.23", "biological_system": "Eukaryotic Apolipoprotein E / A-IV Amphipathic Alpha-Helical Lipid- & LDL-Receptor-Binding Domain (Human GRCh38 Chr19q13.32 APOE)", "clade_domain": "Eukaryota (Vertebrata Apolipoprotein Tandem 22-mer Amphipathic Helical Bundle)", "msa_nseq": 4, "model_length_m": 171, "eff_nseq": 1.105469, "fwd_tau": -4.4557, "fwd_lambda": 0.70741, "targets_evaluated": 4, "true_domains_detected_native": 6, "true_domains_detected_hmmer3": 6, "false_positives_native": 0, "false_positives_hmmer3": 0, "mean_delta_dom_bitscore": 2.538, "mean_env_iou_jaccard": 0.977, "mean_ali_iou_jaccard": 0.9778, "native_runtime_ms": 129.03, "hmmer3_runtime_ms": 89.24, "comparisons": [ { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_000032.1_APOE_e3_WT", "target_role": "True Homolog: Homo sapiens Apolipoprotein E Isoform e3 Precursor (317 aa; LDLR Helix 130-150 LRKLRKRLLR)", "target_len": 317, "domain_index": 1, "native_seq_bitscore": 338.58, "hmmer3_seq_bitscore": 340.5, "native_seq_bias_bits": 33.81, "hmmer3_seq_bias_bits": 30.4, "native_dom_bitscore": -0.34, "hmmer3_dom_bitscore": -0.3, "delta_dom_bitscore": 0.04, "native_dom_bias_bits": 0.07, "hmmer3_dom_bias_bits": 0.1, "native_i_evalue": 0.2170776869025185, "hmmer3_i_evalue": 0.22, "native_env_from": 31, "native_env_to": 91, "hmmer3_env_from": 31, "hmmer3_env_to": 91, "env_iou_jaccard": 1.0, "native_ali_from": 52, "native_ali_to": 76, "hmmer3_ali_from": 52, "hmmer3_ali_to": 76, "ali_iou_jaccard": 1.0, "native_hmm_from": 40, "native_hmm_to": 64, "hmmer3_hmm_from": 40, "hmmer3_hmm_to": 64, "native_mean_post_acc": 0.692, "hmmer3_mean_post_acc": 0.69, "is_true_homolog": true, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 40 eqarrelsailerlteevrqrlvra 64 \n ++++R++++++E+++EE+++++V++\n NP_000032.1_APOE_e3_WT 52 WDYLRWVQTLSEQVQEELLSSQVTQ 76 \n 4566667777777777766655543 [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_000032.1_APOE_e3_WT", "target_role": "True Homolog: Homo sapiens Apolipoprotein E Isoform e3 Precursor (317 aa; LDLR Helix 130-150 LRKLRKRLLR)", "target_len": 317, "domain_index": 2, "native_seq_bitscore": 338.58, "hmmer3_seq_bitscore": 340.5, "native_seq_bias_bits": 33.81, "hmmer3_seq_bias_bits": 30.4, "native_dom_bitscore": 65.81, "hmmer3_dom_bitscore": 70.2, "delta_dom_bitscore": 4.39, "native_dom_bias_bits": 2.3, "hmmer3_dom_bias_bits": 2.5, "native_i_evalue": 1.0363715808334589e-21, "hmmer3_i_evalue": 4.5e-23, "native_env_from": 95, "native_env_to": 149, "hmmer3_env_from": 95, "hmmer3_env_to": 152, "env_iou_jaccard": 0.9483, "native_ali_from": 95, "native_ali_to": 149, "hmmer3_ali_from": 95, "hmmer3_ali_to": 152, "ali_iou_jaccard": 0.9483, "native_hmm_from": 1, "native_hmm_to": 55, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 58, "native_mean_post_acc": 0.99, "hmmer3_mean_post_acc": 0.99, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 1 ElEEllvrlAeelRkllkkelrdAddllkadavdlanaleqarrelsailerlte 55 \n ELEE+L+++AEE+R++L+KEL++A+++L+AD++D++++L+Q+R+E++A+L+++TE\n NP_000032.1_APOE_e3_WT 95 ELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTE 149 \n 8*****************************************************7 [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_000032.1_APOE_e3_WT", "target_role": "True Homolog: Homo sapiens Apolipoprotein E Isoform e3 Precursor (317 aa; LDLR Helix 130-150 LRKLRKRLLR)", "target_len": 317, "domain_index": 3, "native_seq_bitscore": 338.58, "hmmer3_seq_bitscore": 340.5, "native_seq_bias_bits": 33.81, "hmmer3_seq_bias_bits": 30.4, "native_dom_bitscore": 278.14, "hmmer3_dom_bitscore": 283.5, "delta_dom_bitscore": 5.36, "native_dom_bias_bits": 20.08, "hmmer3_dom_bias_bits": 20.2, "native_i_evalue": 6.048108490007871e-87, "hmmer3_i_evalue": 1.4e-88, "native_env_from": 150, "native_env_to": 317, "hmmer3_env_from": 147, "hmmer3_env_to": 317, "env_iou_jaccard": 0.9825, "native_ali_from": 150, "native_ali_to": 317, "hmmer3_ali_from": 148, "hmmer3_ali_to": 317, "ali_iou_jaccard": 0.9882, "native_hmm_from": 4, "native_hmm_to": 171, "hmmer3_hmm_from": 2, "hmmer3_hmm_to": 171, "native_mean_post_acc": 0.997, "hmmer3_mean_post_acc": 1.0, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 4 EllvrlAeelRkllkkelrdAddllkadavdlanaleqarrelsailerlteevrqrlvralrkgrka 171 \n EL+VRLA++LRKL+K++LRDADDL+K++AV++A+A+E+A+R+LSAI+ERL+++V+Q++VRA+++G++A\n NP_000032.1_APOE_e3_WT 150 ELRVRLASHLRKLRKRLLRDADDLQKRLAVYQAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLA 317 \n 8******************************************************************* [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_000032.1_APOE_Christchurch_R136S", "target_role": "True Homolog: Homo sapiens Apolipoprotein E Christchurch Variant (R136S Mature / R154S Precursor HSPG-Shielded Allele, 317 aa)", "target_len": 317, "domain_index": 1, "native_seq_bitscore": 336.38, "hmmer3_seq_bitscore": 338.3, "native_seq_bias_bits": 32.85, "hmmer3_seq_bias_bits": 29.4, "native_dom_bitscore": -0.34, "hmmer3_dom_bitscore": -0.3, "delta_dom_bitscore": 0.04, "native_dom_bias_bits": 0.07, "hmmer3_dom_bias_bits": 0.1, "native_i_evalue": 0.2170776869025185, "hmmer3_i_evalue": 0.22, "native_env_from": 31, "native_env_to": 91, "hmmer3_env_from": 31, "hmmer3_env_to": 91, "env_iou_jaccard": 1.0, "native_ali_from": 52, "native_ali_to": 76, "hmmer3_ali_from": 52, "hmmer3_ali_to": 76, "ali_iou_jaccard": 1.0, "native_hmm_from": 40, "native_hmm_to": 64, "hmmer3_hmm_from": 40, "hmmer3_hmm_to": 64, "native_mean_post_acc": 0.692, "hmmer3_mean_post_acc": 0.69, "is_true_homolog": true, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 40 eqarrelsailerlteevrqrlvra 64 \n ++++R++++++E+++EE+++++V++\n NP_000032.1_APOE_Christchurch_R136S 52 WDYLRWVQTLSEQVQEELLSSQVTQ 76 \n 4566667777777777766655543 [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_000032.1_APOE_Christchurch_R136S", "target_role": "True Homolog: Homo sapiens Apolipoprotein E Christchurch Variant (R136S Mature / R154S Precursor HSPG-Shielded Allele, 317 aa)", "target_len": 317, "domain_index": 2, "native_seq_bitscore": 336.38, "hmmer3_seq_bitscore": 338.3, "native_seq_bias_bits": 32.85, "hmmer3_seq_bias_bits": 29.4, "native_dom_bitscore": 65.81, "hmmer3_dom_bitscore": 70.2, "delta_dom_bitscore": 4.39, "native_dom_bias_bits": 2.3, "hmmer3_dom_bias_bits": 2.5, "native_i_evalue": 1.0363715808334589e-21, "hmmer3_i_evalue": 4.5e-23, "native_env_from": 95, "native_env_to": 149, "hmmer3_env_from": 95, "hmmer3_env_to": 152, "env_iou_jaccard": 0.9483, "native_ali_from": 95, "native_ali_to": 149, "hmmer3_ali_from": 95, "hmmer3_ali_to": 152, "ali_iou_jaccard": 0.9483, "native_hmm_from": 1, "native_hmm_to": 55, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 58, "native_mean_post_acc": 0.99, "hmmer3_mean_post_acc": 0.99, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 1 ElEEllvrlAeelRkllkkelrdAddllkadavdlanaleqarrelsailerlte 55 \n ELEE+L+++AEE+R++L+KEL++A+++L+AD++D++++L+Q+R+E++A+L+++TE\n NP_000032.1_APOE_Christchurch_R136S 95 ELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTE 149 \n 8*****************************************************7 [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_000032.1_APOE_Christchurch_R136S", "target_role": "True Homolog: Homo sapiens Apolipoprotein E Christchurch Variant (R136S Mature / R154S Precursor HSPG-Shielded Allele, 317 aa)", "target_len": 317, "domain_index": 3, "native_seq_bitscore": 336.38, "hmmer3_seq_bitscore": 338.3, "native_seq_bias_bits": 32.85, "hmmer3_seq_bias_bits": 29.4, "native_dom_bitscore": 275.94, "hmmer3_dom_bitscore": 281.3, "delta_dom_bitscore": 5.36, "native_dom_bias_bits": 19.12, "hmmer3_dom_bias_bits": 19.2, "native_i_evalue": 2.8631954504114776e-86, "hmmer3_i_evalue": 6.6e-88, "native_env_from": 150, "native_env_to": 317, "hmmer3_env_from": 147, "hmmer3_env_to": 317, "env_iou_jaccard": 0.9825, "native_ali_from": 150, "native_ali_to": 317, "hmmer3_ali_from": 148, "hmmer3_ali_to": 317, "ali_iou_jaccard": 0.9882, "native_hmm_from": 4, "native_hmm_to": 171, "hmmer3_hmm_from": 2, "hmmer3_hmm_to": 171, "native_mean_post_acc": 0.997, "hmmer3_mean_post_acc": 1.0, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 4 EllvrlAeelRkllkkelrdAddllkadavdlanaleqarrelsailerlteevrqrlvralrkgrka 171 \n EL+VRLA++LRKL+K++LRDADDL+K++AV++A+A+E+A+R+LSAI+ERL+++V+Q++VRA+++G++A\n NP_000032.1_APOE_Christchurch_R136S 150 ELRVRLASHLRKLRKSLLRDADDLQKRLAVYQAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLA 317 \n 8******************************************************************* [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_033826.2_Apoe_Mouse", "target_role": "True Homolog: Mus musculus Apolipoprotein E Precursor (311 aa)", "target_len": 311, "domain_index": 1, "native_seq_bitscore": 326.76, "hmmer3_seq_bitscore": 327.8, "native_seq_bias_bits": 32.86, "hmmer3_seq_bias_bits": 31.8, "native_dom_bitscore": -1.57, "hmmer3_dom_bitscore": -1.6, "delta_dom_bitscore": 0.03, "native_dom_bias_bits": 0.02, "hmmer3_dom_bias_bits": 0.0, "native_i_evalue": 0.5203221340772405, "hmmer3_i_evalue": 0.52, "native_env_from": 27, "native_env_to": 80, "hmmer3_env_from": 27, "hmmer3_env_to": 80, "env_iou_jaccard": 1.0, "native_ali_from": 41, "native_ali_to": 68, "hmmer3_ali_from": 41, "hmmer3_ali_to": 68, "ali_iou_jaccard": 1.0, "native_hmm_from": 37, "native_hmm_to": 64, "hmmer3_hmm_from": 37, "hmmer3_hmm_to": 64, "native_mean_post_acc": 0.765, "hmmer3_mean_post_acc": 0.76, "is_true_homolog": true, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 37 naleqarrelsailerlteevrqrlvra 64 \n N++++++R++++++++++EE+++++V++\n NP_033826.2_Apoe_Mouse 41 NRFWDYLRWVQTLSDQVQEELLSSQVTQ 68 \n 6666777888888888888877666653 [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_033826.2_Apoe_Mouse", "target_role": "True Homolog: Mus musculus Apolipoprotein E Precursor (311 aa)", "target_len": 311, "domain_index": 2, "native_seq_bitscore": 326.76, "hmmer3_seq_bitscore": 327.8, "native_seq_bias_bits": 32.86, "hmmer3_seq_bias_bits": 31.8, "native_dom_bitscore": 281.44, "hmmer3_dom_bitscore": 281.9, "delta_dom_bitscore": 0.46, "native_dom_bias_bits": 26.11, "hmmer3_dom_bias_bits": 25.6, "native_i_evalue": 5.853906372182278e-88, "hmmer3_i_evalue": 4.1e-88, "native_env_from": 87, "native_env_to": 257, "hmmer3_env_from": 87, "hmmer3_env_to": 257, "env_iou_jaccard": 1.0, "native_ali_from": 87, "native_ali_to": 257, "hmmer3_ali_from": 87, "hmmer3_ali_to": 257, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 171, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 171, "native_mean_post_acc": 0.997, "hmmer3_mean_post_acc": 1.0, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 1 ElEEllvrlAeelRkllkkelrdAddllkadavdlanaleqarrelsailerlteevrqrlvralrkg 171 \n ELEE+L+++AEE+R++L+KE+++A+++L+AD++DL+N+L+Q+R+E++++L+++TEE+R+RL+++LRK+\n NP_033826.2_Apoe_Mouse 87 ELEEQLGPVAEETRARLGKEVQAAQARLGADMEDLRNRLGQYRNEVHTMLGQSTEEIRARLSTHLRKM 257 \n 8******************************************************************* [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_033826.2_Apoe_Mouse", "target_role": "True Homolog: Mus musculus Apolipoprotein E Precursor (311 aa)", "target_len": 311, "domain_index": 3, "native_seq_bitscore": 326.76, "hmmer3_seq_bitscore": 327.8, "native_seq_bias_bits": 32.86, "hmmer3_seq_bias_bits": 31.8, "native_dom_bitscore": 48.29, "hmmer3_dom_bitscore": 53.6, "delta_dom_bitscore": 5.31, "native_dom_bias_bits": 0.21, "hmmer3_dom_bias_bits": 0.4, "native_i_evalue": 2.5050330331413308e-16, "hmmer3_i_evalue": 5.7e-18, "native_env_from": 258, "native_env_to": 311, "hmmer3_env_from": 254, "hmmer3_env_to": 311, "env_iou_jaccard": 0.931, "native_ali_from": 258, "native_ali_to": 308, "hmmer3_ali_from": 254, "hmmer3_ali_to": 308, "ali_iou_jaccard": 0.9273, "native_hmm_from": 120, "native_hmm_to": 168, "hmmer3_hmm_from": 116, "hmmer3_hmm_to": 168, "native_mean_post_acc": 0.877, "hmmer3_mean_post_acc": 0.88, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 120 qaialQaladrArlksdrirlvleevrnqArdvlkvvaevgee..vaskme 168 \n Q+I+LQA++++ARLK++++++V++++R++A++++K++A+V+++ ++++++\n NP_033826.2_Apoe_Mouse 258 QQIRLQAEIFQARLKGWFEPIVEDMHRQWANLMEKIQASVATNpiITPVAQ 308 \n 7***************************************88633445544 [PP]" }, { "cohort_id": "PF01442_ApoLP_Amphipathic_Repeat", "target_name": "NP_000518.1_LDLR_EGF_Decoy", "target_role": "Non-Homologous Decoy: Homo sapiens LDL Receptor Cysteine-Rich Ligand-Binding Repeats LA1-LA5 (210 aa)", "target_len": 209, "domain_index": 1, "native_seq_bitscore": -3.92, "hmmer3_seq_bitscore": -3.92, "native_seq_bias_bits": 0.0, "hmmer3_seq_bias_bits": 0.0, "native_dom_bitscore": -2.81, "hmmer3_dom_bitscore": -2.81, "delta_dom_bitscore": 0.0, "native_dom_bias_bits": 0.0, "hmmer3_dom_bias_bits": 0.0, "native_i_evalue": 1.2486779111012287, "hmmer3_i_evalue": 1.2486779111012287, "native_env_from": 1, "native_env_to": 209, "hmmer3_env_from": 1, "hmmer3_env_to": 209, "env_iou_jaccard": 1.0, "native_ali_from": 78, "native_ali_to": 78, "hmmer3_ali_from": 78, "hmmer3_ali_to": 78, "ali_iou_jaccard": 1.0, "native_hmm_from": 61, "native_hmm_to": 61, "hmmer3_hmm_from": 61, "hmmer3_hmm_to": 61, "native_mean_post_acc": 0.729, "hmmer3_mean_post_acc": 0.729, "is_true_homolog": false, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF01442_ApoLP_Amphipathic_Repeat 61 l 61 \n +\n NP_000518.1_LDLR_EGF_Decoy 78 R 78 \n 0 [PP]" } ] }, { "cohort_id": "PF00170_bZIP_vs_Null2_CoiledCoil_Control", "pfam_accession": "PF00170.25", "biological_system": "Eukaryotic bZIP Leucine Zipper Transcription Factor Domain vs. Biased-Composition Charged/Glutamine Coiled-Coil Decoy (0-Star Null2 Calibration Gate)", "clade_domain": "Eukaryota (Saccharomyces cerevisiae GCN4 & Homo sapiens JUN/FOS bZIP vs. Low-Complexity E/K/Q Coiled-Coil Decoy)", "msa_nseq": 4, "model_length_m": 69, "eff_nseq": 3.628906, "fwd_tau": -4.0596, "fwd_lambda": 0.71873, "targets_evaluated": 3, "true_domains_detected_native": 2, "true_domains_detected_hmmer3": 2, "false_positives_native": 0, "false_positives_hmmer3": 0, "mean_delta_dom_bitscore": 6.693, "mean_env_iou_jaccard": 0.9929, "mean_ali_iou_jaccard": 1.0, "native_runtime_ms": 21.84, "hmmer3_runtime_ms": 94.49, "comparisons": [ { "cohort_id": "PF00170_bZIP_vs_Null2_CoiledCoil_Control", "target_name": "NP_010907.3_GCN4_Yeast", "target_role": "True Homolog: S. cerevisiae General Control Transcriptional Activator GCN4 bZIP Domain (281 aa)", "target_len": 281, "domain_index": 1, "native_seq_bitscore": 58.38, "hmmer3_seq_bitscore": 58.4, "native_seq_bias_bits": 10.19, "hmmer3_seq_bias_bits": 10.2, "native_dom_bitscore": 57.59, "hmmer3_dom_bitscore": 57.6, "delta_dom_bitscore": 0.01, "native_dom_bias_bits": 10.19, "hmmer3_dom_bias_bits": 10.2, "native_i_evalue": 1.7164195376973507e-19, "hmmer3_i_evalue": 1.7e-19, "native_env_from": 226, "native_env_to": 281, "hmmer3_env_from": 226, "hmmer3_env_to": 281, "env_iou_jaccard": 1.0, "native_ali_from": 231, "native_ali_to": 281, "hmmer3_ali_from": 231, "hmmer3_ali_to": 281, "ali_iou_jaccard": 1.0, "native_hmm_from": 5, "native_hmm_to": 55, "hmmer3_hmm_from": 5, "hmmer3_hmm_to": 55, "native_mean_post_acc": 0.962, "hmmer3_mean_post_acc": 0.96, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00170_bZIP_vs_Null2_CoiledCoil_Control 5 kaKRerkrkRnrrAakkcRarqlekkkkeelkkkelkekesalekellklr 55 \n K++R+++++R++RA+K++R++QLE+K++E+L+K++++E+E+A++K+L+++R\n NP_010907.3_GCN4_Yeast 231 KRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281 \n 7*************************************************8 [PP]" }, { "cohort_id": "PF00170_bZIP_vs_Null2_CoiledCoil_Control", "target_name": "NP_002219.1_JUN_Human", "target_role": "True Homolog: Homo sapiens Transcription Factor AP-1 Subunit c-Jun (331 aa; C-terminal bZIP)", "target_len": 331, "domain_index": 1, "native_seq_bitscore": 91.67, "hmmer3_seq_bitscore": 91.8, "native_seq_bias_bits": 18.84, "hmmer3_seq_bias_bits": 18.7, "native_dom_bitscore": 90.82, "hmmer3_dom_bitscore": 90.9, "delta_dom_bitscore": 0.08, "native_dom_bias_bits": 18.84, "hmmer3_dom_bias_bits": 18.7, "native_i_evalue": 7.252175920082629e-30, "hmmer3_i_evalue": 6.8e-30, "native_env_from": 248, "native_env_to": 317, "hmmer3_env_from": 248, "hmmer3_env_to": 316, "env_iou_jaccard": 0.9857, "native_ali_from": 248, "native_ali_to": 316, "hmmer3_ali_from": 248, "hmmer3_ali_to": 316, "ali_iou_jaccard": 1.0, "native_hmm_from": 1, "native_hmm_to": 69, "hmmer3_hmm_from": 1, "hmmer3_hmm_to": 69, "native_mean_post_acc": 0.988, "hmmer3_mean_post_acc": 0.99, "is_true_homolog": true, "passed_reporting_gate_native": true, "passed_reporting_gate_hmmer3": true, "focal_alignment_ascii": " PF00170_bZIP_vs_Null2_CoiledCoil_Control 1 epeekaKRerkrkRnrrAakkcRarqlekkkkeelkkkelkekesalekellklreetlklkldvvvh 69 \n E++E++K+ERKR+RNR+AA+KCR+R+LE+++++E+K+K+LK+++S+L++++++LRE++++LK++V++H\n NP_002219.1_JUN_Human 248 ESQERIKAERKRMRNRIAASKCRKRKLERIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNH 316 \n 68****************************************************************** [PP]" }, { "cohort_id": "PF00170_bZIP_vs_Null2_CoiledCoil_Control", "target_name": "DECOY_LowComp_Charged_CoiledCoil", "target_role": "0-Star Negative Control: Biased-Composition Charged/Glutamine Coiled-Coil Decoy (Inflated Pre-Null2 Score Penalized by Null2 Bias Correction)", "target_len": 150, "domain_index": 1, "native_seq_bitscore": -25.25, "hmmer3_seq_bitscore": -43.6, "native_seq_bias_bits": 109.4, "hmmer3_seq_bias_bits": 127.8, "native_dom_bitscore": -19.01, "hmmer3_dom_bitscore": -39.0, "delta_dom_bitscore": 19.99, "native_dom_bias_bits": 50.89, "hmmer3_dom_bias_bits": 71.8, "native_i_evalue": 3.0, "hmmer3_i_evalue": 3.0, "native_env_from": 2, "native_env_to": 77, "hmmer3_env_from": 2, "hmmer3_env_to": 89, "env_iou_jaccard": 0.8636, "native_ali_from": 15, "native_ali_to": 74, "hmmer3_ali_from": 15, "hmmer3_ali_to": 74, "ali_iou_jaccard": 1.0, "native_hmm_from": 3, "native_hmm_to": 63, "hmmer3_hmm_from": 3, "hmmer3_hmm_to": 63, "native_mean_post_acc": 0.482, "hmmer3_mean_post_acc": 0.42, "is_true_homolog": false, "passed_reporting_gate_native": false, "passed_reporting_gate_hmmer3": false, "focal_alignment_ascii": " PF00170_bZIP_vs_Null2_CoiledCoil_Control 3 eekaKRerkrkRnrrAakkcRarqlekkkkeelkkkelkekesalekellklreetlklkl 63 \n EEK+KR+R+++++++++K++R++Q+E+KKK+ +++++L+E+++++++++++++++++++++\n DECOY_LowComp_Charged_CoiledCoil 15 EEKKKRRRQQQLEEEKKKRRRQQQEEEKKKR-RRQQQLEEEKKKRRRQQQEEEKKKRRRQQ 74 \n 3444444444444444444333333333332.23345555555555555555555555555 [PP]" } ] } ] }