functions-across-genomes-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)..
🔙 To the main page of anvi’o programs and artifacts.
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.