binding-frequencies-txt
Table of Contents
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
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.