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| # From | |
| cut -f3 permafrost_pathway_orthologs.txt | grep -v ortho | while read ko; do make ${ko}.kegg.faa; done | |
| for i in *kegg.faa; do NAM=$(basename $i .kegg.faa); hmmalign ../profiles/$NAM.hmm $NAM.kegg.faa | awk -vN=$NAM '{if (NR == 2){print "#=GF ID"N"\n#=GF AC "N}else{print $0}}' ; done > alns.stck | |
| mmseqs convertmsa faa/alns.stck ko_msa_db | |
| mmseqs msa2profile ko_msa_db permafrost_ko_profiles --match-mode 1 | |
| # KO | |
| seqkit replace --ignore-case --kv-file <(awk '{print $2"\t"$1}' ko_genes.list) --pattern "(.+)" --replacement "{kv}" <(seqkit replace -p "\s.+" test) > ko_seq.faa | |
| awk '/^>/{split($1,a,":")}{print >> a[2]".fa"}' ../ko_seq.faa | |
| ~/opt/uproc-1.2.0/uproc-makedb model ko_seq.faa koDB |
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| pathway gene orthology | |
| Nitrogen Fixation Nif-specific regulatory protein K02584 | |
| Nitrogen Fixation nitrogen fixation protein NifB K02585 | |
| Nitrogen Fixation nitrogenase molybdenum-iron protein alpha chain [EC:1.18.6.1] K02586 | |
| Nitrogen Fixation nitrogenase molybdenum-cofactor synthesis protein NifE K02587 | |
| Nitrogen Fixation nitrogenase iron protein NifH [EC:1.18.6.1] K02588 | |
| Nitrogen Fixation nitrogen regulatory protein PII 1 K02589 | |
| Nitrogen Fixation nitrogen regulatory protein PII 2 K02590 | |
| Nitrogen Fixation nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1] K02591 | |
| Nitrogen Fixation nitrogenase molybdenum-iron protein NifN K02592 | |
| Nitrate Reduction nitrate reductase 1, alpha subunit [EC:1.7.99.4] K00370 | |
| Nitrate Reduction nitrate reductase 1, beta subunit [EC:1.7.99.4] K00371 | |
| Nitrate Reduction nitrate reductase 1, delta subunit [EC:1.7.99.4] K00373 | |
| Nitrate Reduction nitrate reductase 1, gamma subunit [EC:1.7.99.4] K00374 | |
| Denitrification nitric-oxide reductase, cytochrome b-containing subunit I K04561 | |
| Denitrification nitrous-oxide reductase [EC:1.7.99.6] K00376 | |
| Denitrification nitrous oxidase accessory protein K07218 | |
| Ammonification nitrite reductase (NAD(P)H) large subunit [EC:1.7.1.4] K00362 | |
| Ammonification nitrite reductase (NAD(P)H) small subunit [EC:1.7.1.4] K00363 | |
| Ammonification formate-dependent nitrite reductase, periplasmic cytochrome c552 K03385 | |
| Ammonification formate-dependent nitrite reductase, Fe-S protein K04014 | |
| Ammonification ferredoxin-nitrite reductase [EC:1.7.7.1] K00366 | |
| NADH Dehydrogenase I NADH dehydrogenase [EC:1.6.5.3] K00329 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit A [EC:1.6.5.3] K00330 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit B [EC:1.6.5.3] K00331 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit C [EC:1.6.5.3] K00332 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit D [EC:1.6.5.3] K00333 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit E [EC:1.6.5.3] K00334 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit F [EC:1.6.5.3] K00335 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit G [EC:1.6.5.3] K00336 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit H [EC:1.6.5.3] K00337 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit I [EC:1.6.5.3] K00338 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit J [EC:1.6.5.3] K00339 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit K [EC:1.6.5.3] K00340 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit L [EC:1.6.5.3] K00341 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit M [EC:1.6.5.3] K00342 | |
| NADH Dehydrogenase I NADH dehydrogenase I subunit N [EC:1.6.5.3] K00343 | |
| Pyruvate Dehydrogenase E1 & E2 pyruvate dehydrogenase E1 component subunit alpha [EC:1.2.4.1] K00161 | |
| Pyruvate Dehydrogenase E1 & E2 pyruvate dehydrogenase E1 component subunit beta [EC:1.2.4.1] K00162 | |
| Pyruvate Dehydrogenase E1 & E2 pyruvate dehydrogenase E1 component [EC:1.2.4.1] K00163 | |
| Pyruvate Dehydrogenase E1 & E2 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC:2.3.1.12] K00627 | |
| Pyruvate Ferridoxin Oxidoreductase pyruvate ferredoxin oxidoreductase, alpha subunit [EC:1.2.7.1] K00169 | |
| Pyruvate Ferridoxin Oxidoreductase pyruvate ferredoxin oxidoreductase, beta subunit [EC:1.2.7.1] K00170 | |
| Pyruvate Ferridoxin Oxidoreductase pyruvate ferredoxin oxidoreductase, delta subunit [EC:1.2.7.1] K00171 | |
| Pyruvate Ferridoxin Oxidoreductase pyruvate ferredoxin oxidoreductase, gamma subunit [EC:1.2.7.1] K00172 | |
| Cellulose Degradation beta-glucosidase K05349 | |
| Cellulose Degradation beta-glucosidase K05350 | |
| Cellulose Degradation beta-glucosidase K01188 | |
| Cellulose Degradation 6-phospho-beta-glucosidase K01222 | |
| Cellulose Degradation 6-phospho-beta-glucosidase K01223 | |
| Cellulose Degradation endoglucanase K01179 | |
| Cellulose Degradation cellobiose phosphorylase K00702 | |
| Cellobiose Transport cellobiose transport system substrate-binding protein K10240 | |
| Cellobiose Transport cellobiose transport system permease protein K10241 | |
| Cellobiose Transport cellobiose transport system permease protein K10242 | |
| Cellobiose Transport cellobiose transport system ATP-binding protein K10243 | |
| Hemi-cellulose Degradation mannan endo-1,4-beta-mannosidase [EC:3.2.1.78] K01218 | |
| Hemi-cellulose Degradation xylose isomerase [EC:5.3.1.5] K01805 | |
| Chitin Degradation putative chitinase K03791 | |
| Chitin Degradation chitinase K01183 | |
| Chitin Degradation chitin deacetylase [EC:3.5.1.41] K01452 | |
| Sugar Utilization L-arabinose isomerase [EC:5.3.1.4] K01804 | |
| Sugar Utilization xylose isomerase [EC:5.3.1.5] K01805 | |
| Sugar Utilization xylulokinase [EC:2.7.1.17] K00854 | |
| Sugar Utilization beta-galactosidase [EC:3.2.1.23] K01190 | |
| Sugar Utilization beta-galactosidase [EC:3.2.1.23] K12308 | |
| Sugar Utilization galactokinase [EC:2.7.1.6] K00849 | |
| Sugar Utilization glucokinase [EC:2.7.1.2] K00845 | |
| Sugar Utilization polyphosphate glucokinase [EC:2.7.1.63] K00886 | |
| Sugar Utilization mannose-6-phosphate isomerase [EC:5.3.1.8] K02793 | |
| Sugar Utilization fructokinase [EC:2.7.1.4] K00847 | |
| Sugar Transporters lactose/L-arabinose transport system substrate-binding protein K10188 | |
| Sugar Transporters lactose/L-arabinose transport system permease protein K10189 | |
| Sugar Transporters lactose/L-arabinose transport system permease protein K10190 | |
| Sugar Transporters putative multiple sugar transport system substrate-binding protein K10546 | |
| Sugar Transporters putative multiple sugar transport system permease protein K10547 | |
| Sugar Transporters putative multiple sugar transport system ATP-binding protein K10548 | |
| Sugar Transporters multiple sugar transport system ATP-binding protein K02023 | |
| Sugar Transporters multiple sugar transport system permease protein K02025 | |
| Sugar Transporters multiple sugar transport system permease protein K02026 | |
| Sugar Transporters multiple sugar transport system substrate-binding protein K02027 | |
| Sugar Transporters D-xylose transport system substrate-binding protein K10543 | |
| Sugar Transporters D-xylose transport system permease protein K10544 | |
| Sugar Transporters D-xylose transport system ATP-binding protein [EC:3.6.3.17] K10545 | |
| Sugar Transporters fructose transport system substrate-binding protein K10552 | |
| Sugar Transporters fructose transport system permease protein K10553 | |
| Sugar Transporters fructose transport system ATP-binding protein K10554 |
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