Microbial 'omics


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binding-frequencies-txt [artifact]

Table of Contents

TXT

A TXT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-run-interacdome

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

When the user runs anvi-run-interacdome, it stores binding frequencies directly into the contigs-db as misc-data-amino-acids. Yet anvi-run-interacdome also outputs tabular data directly accessible by the user–this data is what is meant by binding-frequencies-txt.

Specifically, this artifact refers to 2 files named INTERACDOME-match_state_contributors.txt and INTERACDOME-domain_hits.txt (the INTERACDOME prefix can be changed with -O).

INTERACDOME-match_state_contributors.txt displays the binding frequencies in the following format:

gene_callers_id codon_order_in_gene pfam_id match_state ligand binding_freq
1 169 PF00534 22 ADP 0.687948
1 169 PF13692 8 ADP 0.595441
1 174 PF00534 27 ADP 0.735759
1 174 PF13692 14 ADP 0.595441
1 184 PF00534 37 ADP 0.0697656
1 184 PF13692 24 ADP 0.101399
1 186 PF00534 39 ADP 0.0697656
1 186 PF13692 26 ADP 0.101399
1 187 PF13692 27 ADP 0.201761
1 189 PF00534 47 ADP 0.0697656

Each binding frequency is associated with both the exact residue of the user’s gene sequences (from their contigs-db) and the exact match states (from the Pfam database) that contributed the binding frequency.

INTERACDOME-match_state_contributors.txt is a parsed summary of the hmmsearch output in the following format:

pfam_name pfam_id corresponding_gene_call domain qual score bias c-evalue i-evalue hmm_start hmm_stop hmm_bounds ali_start ali_stop ali_bounds env_start env_stop env_bounds mean_post_prob match_state_align comparison_align sequence_align version
Beta_elim_lyase PF01212 1762 1 ! 20.9 0.1 1e-08 3.5e-06 33 169 .. 44 177 .. 34 215 .. 0.72 tvnrLedavaelfgke..aalfvpqGtaAnsill.kill.qr..geevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA ++ +++ael+ + f+ Gt +++ l + + +r g+ +i++ h +et + g +l ++ +++G +++e+l+++i++ e i + +++v n+ G++ +++e+ ev +a+ +i++h+D+ LLQQARKQIAELINVSanEIYFTSGGTEGDNWVLkGTAIeKRefGNHIIISAVEHPAVTETAEQLVELGFELSYAPVDKEGRVKVEELQKLIRK—–ETILVSVMAVNNE–VGTIQPIKEISEV–LAEFPKIHFHVDAV 20
PAPS_reduct PF01507 1541 1 ! 36.1 0.1 3.6e-13 1.3e-10 2 164 .. 21 231 .. 20 234 .. 0.79 lvvsvsgGkdslVllhLalkafkpv….pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgs.slyee.aaeriaKveplkk……………………………aLekldedall..tGaRrdesksraklpiveidedfek………slrvfPllnWteedvwqyilrenipynpLydqgfr + +s+sgGkds +++La + ++ ++ ++ + ++ t++f++++e+ +++ +++ ++++ + + +++ + + + e+ + p k e++ ++a+ +G+R++es +r++ +++ +++ + ++Pl++W+ d+w+ + +++yn +y++ ++ VYFSFSGGKDSGLMVQLANLVAEKLdrnfDLLILNIEANYTATVDFIKKIEQLPRVKNIYHFCLPFFEDNNTSFFQPQwKMWDPsEKEKWIHSLP–KnaitleniddglkkyyslsngnpdrflryfqnwYKEQYPQSAIScgVGIRAQESLHRHSAVTKGENKYKNRcwinitlegNILFYPLFDWKVGDIWAATFKCELEYNYIYEKMYK 18
Ank_2 PF12796 1756 1 ! 32.2 0 6.7e-12 2.3e-09 29 84 .] 74 135 .. 53 135 .. 0.85 aLhyAakngnleivklLle…h.a..adndgrtpLhyAarsghleivklLlekgadinlkd aL Aa + +++ vk +l+ + + +d +g+tpL +A+ ++ +ei+k L+++gadinl++ ALLEAANQRDTKKVKEILQdttYqVdeVDTEGNTPLNIAVHNNDIEIAKALIDRGADINLQN 6
Ank_2 PF12796 1756 2 ! 28.5 0 9.5e-11 3.3e-08 22 75 .. 199 265 .. 195 267 .] 0.76 pn..k.ngktaLhyAak..ngnl…eivklLleha…..adndgrtpLhyAarsghleivklLle ++ + +g taL+ A+ +gn +ivklL+e++ dn+grt++ yA ++g++ei k+L + IDfqNdFGYTALIEAVGlrEGNQlyqDIVKLLMENGadqsiKDNSGRTAMDYANQKGYTEISKILAQ 6
IGPS PF00218 1615 1 ! 20.6 0.1 1.2e-08 4e-06 202 249 .. 195 242 .. 73 248 .. 0.88 LaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvek +++lv+++++++ae i+t+e+++++k+ gv ++ vG +++r ++ +k IKQLVQENICVIAEGKIHTPEQARQIKKLGVAGIVVGGAITRPQEIAK 20
Ribosomal_L33 PF00471 1562 1 ! 66.6 1.5 1.1e-22 3.7e-20 2 47 .] 4 49 .] 3 49 .] 0.97 kvtLeCteCksrnYtttknkrntperLelkKYcprcrkhtlhkEtK +++LeC e+++r Y t+knkrn+perLelkKY p++r++ ++kE K NIILECVETGERLYLTSKNKRNNPERLELKKYSPKLRRRAIFKEVK 19
Ribosomal_S14 PF00253 1565 1 ! 83.3 0.1 3.9e-28 1.3e-25 2 54 .] 36 88 .. 35 88 .. 0.98 laklprnssptrirnrCrvtGrprGvirkfgLsRicfRelAlkgelpGvkKaS laklpr+s+p+r+r r++ +GrprG++rkfg+sRi+fRel ++g +pGvkKaS LAKLPRDSNPNRLRLRDQTDGRPRGYMRKFGMSRIKFRELDHQGLIPGVKKAS 20
Polysacc_synt_C PF14667 1593 1 ! 61.4 19.2 5.4e-21 1.9e-18 2 139 .. 371 516 .. 370 519 .. 0.83 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl…llrrllkpllaalvmgivvylllllllglllla…al..alllavlvgalvYllllll L+ ++s+ +l+++t++ siLq+l +k+a+ ++ i++l+kli+++++i+lf +G +iat+++ ++++++ +++l+r++ i++ ++ +++ +++vm i+ +l+l+++ ++ + +l + l +++g++v+ + l++ LSATIISTSLLGIFTIVLSILQALSFHKKAMQITSITLLLKLIIQIPCIYLFKGYGLSIATIICTMFTTIIAYRFLSRKFDINPikyNRKYYSRLVYSTIVMTILSLLMLKIISSVYKFEstlQLffLISLIGCLGGVVFSVTLFR 5

For each hit, this table includes how good the hit was, the alignment of the user gene to the exact HMM match states, and more! In fact, it includes all of hte domain hit summary information, the sequence of the consensus match states, the comparison string for the hit, and the sequence of the user’s gene.

For more information, check out this blogpost.

Edit this file to update this information.