--- tags: N-exo title: N-exo - Looking into nar/nxr --- [toc] # Summary * [K00370](https://www.genome.jp/dbget-bin/www_bget?K00370) captures alpha subunit of both nitrate reductase (narG/narZ) and nitrite oxidoreducase (nxrA). We had 4 genes annotated as this KO. * [K00371](https://www.genome.jp/dbget-bin/www_bget?K00371) captures beta subunit of both nitrate reductase (narH/narY) and nitrite oxidoreducase (nxrB). We had 6 genes annotated as this one. * I grabbed some reference sequences of narG, narZ, and nxrA and tree'd them with our 4 seqs, and then the same for narH, narY, and nxrB and our 6 genes. (Just to note an observation, there are very few nxr reference sequences compared to nar ones, like tens of thousands of nar ones and only a dozen or so nxr ones.) * From this brief but closer look based on the trees below, it does appear that our 4 K00370 are nitrate reductases (assuming we can trust the annotations in NCBI as being distinguishing between the two – I'm not sure how to ensure that is true...). It's not as clear cut with the 6 K00371, and probably too messy to say, but maybe we only have the nitrate reductases for them too. **Side note** I expected to see more about the similarity or difficulty in distinguishing between these two things when searching, but a quick google search didn't really get me far. Though this paper talks about them as though they used to be thought of as one thing: > *Both nitrite oxidation and nitrate reduction are catalyzed by the membrane-bound nitrite oxidoreductase (NOR) (Tanaka et al. 1983; Sundermeyer-Klinger et al. 1984).* > > From "Close genetic relationship between *Nitrobacter hamburgensis* nitrite oxidoreductase and *Escherichia coli* nitrate reductases" > [Paywal link](https://pubmed.ncbi.nlm.nih.gov/8297210/) > [Sci-Hub link](https://sci-hub.se/10.1007/bf00245305) --- # narG, narZ, nxrA tree (K00370) Our 4 are in black lettering towards the middle (interactive tree [here](https://itol.embl.de/tree/13822922232487411616178912)). This is the one that looks pretty clean to me. Blue labels are nxrA, orange are narG/Z. <a href="https://i.imgur.com/ORw7VNs.png"><img src="https://i.imgur.com/ORw7VNs.png"></a> The same tree with accessions can be seen [here](https://itol.embl.de/tree/13822922232119351616181378) if wanting them. --- # narH, narY, nxrB tree (K00371) Our 6 are in black lettering again (interactive tree [here](https://itol.embl.de/tree/1382292223261341616180039)). <a href="https://i.imgur.com/chAP872.png"><img src="https://i.imgur.com/chAP872.png"></a> As you can see in this one, it's not as clean. Though I'd note that the top one of ours (653281) is on a pretty long, lone branch following the split from the main narH/Y group. Similar to the next one down of ours (841467), which is in a lone clade split off with another narY. Then there are 3 nxrBs (labeled nxrB 7, 12, and 9) mixed in with that major narH/Y clade on the bottom. There is no guarantee these reference sequences are perfectly annotated either. It may be the case that it just isn't that easy to distinguish between these. The same tree with accessions can be seen [here](https://itol.embl.de/tree/1382292223298591616180730) if wanting them. # Log ``` ## trying to split K00370 narG,narZ,nxrA esearch -db protein -query 'nxrA NOT partial' | efetch -format fasta > nxrA-refs.faa # couldn't figure out how to limit search for narG (which as 100,000 in NCBI), so grabbed 15 from the search with this 'narG NOT partial AND ("1200"[SLEN] : "1300"[SLEN])' and put into narG-refs.faa # same done for narZ into narZ-refs.faa, but also added 'NOT Escherichia' to search so i could find some that were from diff tax bit-rename-fasta-headers -i narG-refs.faa -w narG -o narG-refs-renamed.faa bit-rename-fasta-headers -i narZ-refs.faa -w narZ -o narZ-refs-renamed.faa bit-rename-fasta-headers -i nxrA-refs.faa -w nxrA -o nxrA-refs-renamed.faa cat K00370-genes.faa narG-refs-renamed.faa narZ-refs-renamed.faa nxrA-refs-renamed.faa > narG-narZ-nxrA-refs-and-ours.faa muscle -in narG-narZ-nxrA-refs-and-ours.faa -out narG-narZ-nxrA-refs-and-ours-aligned.faa fasttree narG-narZ-nxrA-refs-and-ours-aligned.faa > narG-narZ-nxrA-refs-and-ours.tre # making one without renaming refs so they have their accessions cat K00370-genes.faa narG-refs.faa narZ-refs.faa nxrA-refs.faa > narG-narZ-nxrA-refs-and-ours-not-renamed.faa muscle -in narG-narZ-nxrA-refs-and-ours-not-renamed.faa -out narG-narZ-nxrA-refs-and-ours-not-renamed-aligned.faa fasttree narG-narZ-nxrA-refs-and-ours-not-renamed-aligned.faa > narG-narZ-nxrA-refs-and-ours-not-renamed.tre ## trying to split K00371 narH,narY,nxrB esearch -db protein -query 'nxrB NOT partial' | efetch -format fasta > nxrB-refs.faa # same done for narH and narY as above, just with search string 'narH NOT partial' and 'narY NOT partial', the ones chosen from were all in same length range (and 12 chosen as that's how many nxrB's there were) # narH-refs.faa # narY-refs.faa bit-rename-fasta-headers -i narH-refs.faa -w narH -o narH-refs-renamed.faa bit-rename-fasta-headers -i narY-refs.faa -w narY -o narY-refs-renamed.faa bit-rename-fasta-headers -i nxrB-refs.faa -w nxrB -o nxrB-refs-renamed.faa cat K00371-genes.faa narH-refs-renamed.faa narY-refs-renamed.faa nxrB-refs-renamed.faa > narH-narY-nxrB-refs-and-ours.faa muscle -in narH-narY-nxrB-refs-and-ours.faa -out narH-narY-nxrB-refs-and-ours-aligned.faa fasttree narH-narY-nxrB-refs-and-ours-aligned.faa > narH-narY-nxrB-refs-and-ours.tre # making one without renamed refs # WP_139738682.1 was grabbed from both the narH and narY searches, so removed it from narY cat K00371-genes.faa narH-refs.faa narY-refs.faa nxrB-refs.faa > narH-narY-nxrB-refs-and-ours-not-renamed.faa muscle -in narH-narY-nxrB-refs-and-ours-not-renamed.faa -out narH-narY-nxrB-refs-and-ours-not-renamed-aligned.faa fasttree narH-narY-nxrB-refs-and-ours-not-renamed-aligned.faa > narH-narY-nxrB-refs-and-ours-not-renamed.tre ```