functions-across-genomes-txt

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-script-gen-function-matrix-across-genomes

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

A TAB-delimited output file that describes the distribution of functions across a group of genomes.

General format

With this file type anvi’o may describe the presence-absence of individual functions across genomes, or the frequency of functions. The header of the last column in a functions-across-genomes-txt file will be the name of the function annotation source from which the gene functions were recovered.

Frequency of function hits across genomes

Here is an example output file that shows the frequency of functions across 9 Bifidobacterium genomes:

key B_adolescentis_1_11 B_adolescentis_22L B_adolescentis_6 B_lactis_Bl_04 B_lactis_CNCM_I_2494 B_lactis_DSM_10140 B_longum_JDM301 B_longum_KACC_91563 B_longum_NCIMB8809 COG20_FUNCTION
func_3874a4219ffa 1 1 1 1 1 1 1 1 1 Chromosomal replication initiation ATPase DnaA (DnaA) (PDB:1L8Q)
func_1530552f6b61 1 1 1 1 1 1 1 1 1 DNA polymerase III sliding clamp (beta) subunit, PCNA homolog (DnaN) (PDB:1JQJ)
func_060988dd6d3a 1 1 1 1 1 1 1 1 1 Recombinational DNA repair ATPase RecF (RecF) (PDB:5Z67)
func_46477a763d38 1 1 1 1 1 1 1 1 1 Predicted nucleic acid-binding protein, contains Zn-ribbon domain (includes truncated derivatives)
func_184ca83fe067 2 2 2 2 2 2 2 2 2 DNA gyrase/topoisomerase IV, subunit B (GyrB) (PDB:1EI1)
func_2ee67347f04b 2 2 2 2 2 2 2 2 2 DNA gyrase/topoisomerase IV, subunit A (GyrA) (PDB:1SUU)
func_ff160914972f 1 0 0 0 0 0 3 1 1 Predicted ATPase, archaeal AAA+ ATPase superfamily
func_598325c18ceb 1 0 0 0 0 0 1 1 1 Molybdopterin or thiamine biosynthesis adenylyltransferase (ThiF) (PDB:1ZUD) (PUBMED:32239579)
func_8ce5ff84aa42 14 13 13 10 10 10 22 17 16 Predicted arabinose efflux permease AraJ, MFS family (AraJ) (PDB:4LDS)
func_300e2c6e37e4 1 1 1 1 1 1 1 1 1 Glutamate dehydrogenase/leucine dehydrogenase (GdhA) (PDB:1B3B) (PUBMED:24391520)
func_a666bc87a03f 1 1 1 1 1 1 1 1 1 Large-conductance mechanosensitive channel (MscL) (PDB:2OAR)
func_71379d89f0c6 1 1 1 1 1 1 1 1 1 UTP pyrophosphatase, metal-dependent hydrolase family (YgjP) (PDB:4JIU) (PUBMED:27941785)
func_772efbb7cb2e 2 2 2 2 2 2 2 2 2 Hemolysin-related protein, contains CBS domains, UPF0053 family (TlyC) (PDB:2NQW)
func_5a5bf9735c8a 1 1 1 1 1 1 1 1 1 Carbonic anhydrase (CynT) (PDB:1EKJ) (PUBMED:22081392)
func_1ffc26d0034f 4 4 1 3 3 3 12 13 2 Transposase (or an inactivated derivative) (IS285)
func_0631d9fecae6 2 1 1 1 1 1 2 1 1 Phosphoenolpyruvate carboxylase (Ppc) (PDB:1FIY)
func_62068e09f9f3 2 1 1 0 0 0 1 1 1 Chromosome segregation ATPase Smc (Smc) (PDB:5XG3)
func_f4b8779f6ad8 2 0 0 0 0 0 0 0 0 Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases (PGRP) (PDB:4FET)
func_700652d0a2dd 1 1 1 1 1 1 1 1 1 Uncharacterized membrane protein YjjP, DUF1212 family (YjjP)
(…) (…) (…) (…) (…) (…) (…) (…) (…) (…) (…)

Presence/absence of function hits across genomes

In contrast, here is the presence/absence report for the same data:

key B_adolescentis_1_11 B_adolescentis_22L B_adolescentis_6 B_lactis_Bl_04 B_lactis_CNCM_I_2494 B_lactis_DSM_10140 B_longum_JDM301 B_longum_KACC_91563 B_longum_NCIMB8809 COG20_FUNCTION
func_3874a4219ffa 1 1 1 1 1 1 1 1 1 Chromosomal replication initiation ATPase DnaA (DnaA) (PDB:1L8Q)
func_1530552f6b61 1 1 1 1 1 1 1 1 1 DNA polymerase III sliding clamp (beta) subunit, PCNA homolog (DnaN) (PDB:1JQJ)
func_060988dd6d3a 1 1 1 1 1 1 1 1 1 Recombinational DNA repair ATPase RecF (RecF) (PDB:5Z67)
func_46477a763d38 1 1 1 1 1 1 1 1 1 Predicted nucleic acid-binding protein, contains Zn-ribbon domain (includes truncated derivatives)
func_184ca83fe067 1 1 1 1 1 1 1 1 1 DNA gyrase/topoisomerase IV, subunit B (GyrB) (PDB:1EI1)
func_2ee67347f04b 1 1 1 1 1 1 1 1 1 DNA gyrase/topoisomerase IV, subunit A (GyrA) (PDB:1SUU)
func_ff160914972f 1 0 0 0 0 0 1 1 1 Predicted ATPase, archaeal AAA+ ATPase superfamily
func_598325c18ceb 1 0 0 0 0 0 1 1 1 Molybdopterin or thiamine biosynthesis adenylyltransferase (ThiF) (PDB:1ZUD) (PUBMED:32239579)
func_8ce5ff84aa42 1 1 1 1 1 1 1 1 1 Predicted arabinose efflux permease AraJ, MFS family (AraJ) (PDB:4LDS)
func_300e2c6e37e4 1 1 1 1 1 1 1 1 1 Glutamate dehydrogenase/leucine dehydrogenase (GdhA) (PDB:1B3B) (PUBMED:24391520)
func_a666bc87a03f 1 1 1 1 1 1 1 1 1 Large-conductance mechanosensitive channel (MscL) (PDB:2OAR)
func_71379d89f0c6 1 1 1 1 1 1 1 1 1 UTP pyrophosphatase, metal-dependent hydrolase family (YgjP) (PDB:4JIU) (PUBMED:27941785)
func_772efbb7cb2e 1 1 1 1 1 1 1 1 1 Hemolysin-related protein, contains CBS domains, UPF0053 family (TlyC) (PDB:2NQW)
func_5a5bf9735c8a 1 1 1 1 1 1 1 1 1 Carbonic anhydrase (CynT) (PDB:1EKJ) (PUBMED:22081392)
func_1ffc26d0034f 1 1 1 1 1 1 1 1 1 Transposase (or an inactivated derivative) (IS285)
func_0631d9fecae6 1 1 1 1 1 1 1 1 1 Phosphoenolpyruvate carboxylase (Ppc) (PDB:1FIY)
func_62068e09f9f3 1 1 1 0 0 0 1 1 1 Chromosome segregation ATPase Smc (Smc) (PDB:5XG3)
func_f4b8779f6ad8 1 0 0 0 0 0 0 0 0 Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases (PGRP) (PDB:4FET)
func_700652d0a2dd 1 1 1 1 1 1 1 1 1 Uncharacterized membrane protein YjjP, DUF1212 family (YjjP)
(…) (…) (…) (…) (…) (…) (…) (…) (…) (…) (…)

Edit this file to update this information.