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refpkgs.Rmd
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# TreeSAPP reference packages
<!-- Current list of TreeSAPP reference packages, get newest version from https://github.com/hallamlab/RefPkgs/wiki/refpkgs -->
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| Name | Description | Leaf nodes | Pathway | Cycle |
+:================================================================================================================================+:=========================================================================================+:===========+:==============================================+:======+
| [AA10](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/AA10/seed_refpkg/final_outputs) | Auxiliary Activity family 10 | 699 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH101](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH101/seed_refpkg/final_outputs) | Glycoside hydrolase family 101 | 113 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH102](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH102/seed_refpkg/final_outputs) | Glycoside hydrolase family 102 | 727 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH103](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH103/seed_refpkg/final_outputs) | Glycoside hydrolase family 103 | 1145 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH109](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH109/seed_refpkg/final_outputs) | Glycoside hydrolase family 109 | 376 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH115](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH115/seed_refpkg/final_outputs) | Glycoside hydrolase family 115 | 267 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH126](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH126/seed_refpkg/final_outputs) | Glycoside hydrolase family 126 | 112 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH163](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH163/seed_refpkg/final_outputs) | Glycoside hydrolase family 163 | 102 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH67](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH67/seed_refpkg/final_outputs) | Glycoside hydrolase family 67 | 372 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [GH94](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/GH94/seed_refpkg/final_outputs) | Glycoside hydrolase family 94 | 695 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [McrA](https://github.com/hallamlab/RefPkgs/blob/master/Methanogenesis/McrA/MAG_update_RaxML-NG/final_outputs) | Methyl coenzyme M reductase alpha subunit | 424 | Methanogenesis | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [McrA](https://github.com/hallamlab/RefPkgs/blob/master/Methanogenesis/McrA/seed_refpkg/final_outputs) | Methyl coenzyme M reductase alpha subunit | 249 | Methanogenesis | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [McrB](https://github.com/hallamlab/RefPkgs/blob/master/Methanogenesis/McrB/seed_refpkg/final_outputs) | Methyl coenzyme M reductase beta subunit | 110 | Methanogenesis | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [McrG](https://github.com/hallamlab/RefPkgs/blob/master/Methanogenesis/McrG/seed_refpkg/final_outputs) | Methyl coenzyme M reductase gamma subunit | 123 | Methanogenesis | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PHAdeg](https://github.com/hallamlab/RefPkgs/blob/master/Hydrocarbons/PHA_degradation/PHA_depolymerases/final_outputs) | Poly(hydroxyalkanoate) degradation enzymes | 10 | Plastics degradation | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PL11](https://github.com/hallamlab/RefPkgs/blob/master/CAZymes/PL11/seed_refpkg/final_outputs) | Polysaccharide lyase family 11 | 320 | Carbohydrate metabolism | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PuhA](https://github.com/hallamlab/RefPkgs/blob/master/Photosynthesis/PuhA/seed_refpkg/final_outputs) | photosynthetic reaction center H subunit | 47 | Photosynthesis | C |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PilA](https://github.com/hallamlab/RefPkgs/blob/master/Direct_Interspecies_Electron_Transfer/pillin/seed_refpkg/final_outputs) | Type IV pilin N-terminus, including PilA | 70 | Direct interspecies electron transfer | E |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [HydA](https://github.com/hallamlab/RefPkgs/blob/master/Hydrogen/HydA/seed_refpkg/final_outputs) | [FeFe] hydrogenase, group A, B1, B3 | 93 | Hydrogenase | H |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [HgcA](https://github.com/hallamlab/RefPkgs/blob/master/Mercury/HgcA/seed_refpkg/final_outputs) | Methylmercury active enzyme, subunit A | 108 | NA | Hg |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [HgcB](https://github.com/hallamlab/RefPkgs/blob/master/Mercury/HgcB/seed_refpkg/final_outputs) | Methylmercury active enzyme, subunit B | 122 | NA | Hg |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NapA](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Denitrification/NapA/seed_refpkg/final_outputs) | Periplasmic nitrate reductase, large subunit | 765 | Denitrification | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NifD](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Fixation/NifD/seed_refpkg/final_outputs) | nitrogenase molybdenum-iron protein alpha chain | 926 | Nitrogen fixation | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NifH](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Fixation/NifH/seed_refpkg/final_outputs) | Nitrogenase iron protein [TIGR01287,EC:1.18.6.1] | 660 | Nitrogen fixation | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NirK](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Denitrification/NirK/seed_refpkg/final_outputs) | nitrite reductase (NO-forming) | 325 | Denitrification,Annamox | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NirS](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Denitrification/NirS/seed_refpkg/final_outputs) | nitrite reductase (NO-forming) / hydroxylamine reductase | 511 | Denitrification,Annamox | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NorB](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Denitrification/NorB/seed_refpkg/final_outputs) | nitric oxide reductase subunit B | 460 | Denitrification | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NorC](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Denitrification/NorC/seed_refpkg/final_outputs) | nitric oxide reductase subunit C | 173 | Denitrification | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NosZ](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Denitrification/NosZ/seed_refpkg/final_outputs) | Nitrous-oxide reductase (TAT-dependent\|Sec-dependent) | 26 | Denitrification | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NxrA](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Denitrification/NxrA/seed_refpkg/final_outputs) | nitrate reductase / nitrite oxidoreductase, alpha subunit | 658 | Nitrification | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [NxrB](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Nitrification/NxrB/seed_refpkg/final_outputs) | nitrate reductase / nitrite oxidoreductase, beta subunit | 648 | Nitrification | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [XmoA](https://github.com/hallamlab/RefPkgs/blob/master/Nitrogen_metabolism/Nitrification/XmoA/XmoA_seed/final_outputs) | Alpha subunits of copper membrane monooxygenase enzymes | 37 | Nitrification | N |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00380a](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00380/seed_refpkg_arc/final_outputs) | Ribosomal protein S9/S16 | 82 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00380b](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00380/seed_refpkg_bac/final_outputs) | Ribosomal protein S9/S16 | 1065 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00410a](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00410/seed_refpkg_arc/final_outputs) | Ribosomal protein S8 | 155 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00410b](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00410/seed_refpkg_bac/final_outputs) | Ribosomal protein S8 | 1216 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00687a](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00687/seed_refpkg_arc/final_outputs) | Ribosomal protein L1p/L10e family | 192 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00687b](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00687/seed_refpkg_bac/final_outputs) | Ribosomal protein L1p/L10e family | 864 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00750a](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00750/seed_refpkg_arc/final_outputs) | tRNA synthetases class I (R) | 193 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00750b](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00750/seed_refpkg_bac/final_outputs) | tRNA synthetases class I (R) | 1317 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF00900](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF00900/seed_refpkg/final_outputs) | Ribosomal family S4e | 328 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01015](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01015/seed_refpkg/final_outputs) | Ribosomal S3Ae family | 101 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01092](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01092/seed_refpkg/final_outputs) | Ribosomal protein S6e | 169 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01157](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01157/seed_refpkg/final_outputs) | Ribosomal protein L21e | 74 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01200](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01200/seed_refpkg/final_outputs) | Ribosomal protein S28e | 129 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01280](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01280/seed_refpkg/final_outputs) | Ribosomal protein L19e | 281 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01409a](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01409/seed_refpkg_arc/final_outputs) | tRNA synthetases class II core domain (F) | 243 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01409b](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01409/seed_refpkg_bac/final_outputs) | tRNA synthetases class II core domain (F) | 891 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01655](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01655/seed_refpkg/final_outputs) | Ribosomal protein L32 | 220 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [PF01866](https://github.com/hallamlab/RefPkgs/blob/master/Translation/PF01866/seed_refpkg/final_outputs) | Putative diphthamide synthesis protein | 229 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [RpoB](https://github.com/hallamlab/RefPkgs/blob/master/Translation/RpoB/seed_refpkg/final_outputs) | RNA polymerase beta subunit | 697 | Translation | NA |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [CysD](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/CysD/seed_refpkg/final_outputs) | sulfate adenylyltransferase (SAT), small subunit | 93 | Assimilatory sulfate reduction | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [CysH](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/CysH/seed_refpkg/final_outputs) | phosophoadenylyl-sulfate reductase [PF01507, EC:1.8.4.8\|1.8.4.10] | 710 | Assimilatory sulfate reduction | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [CysI_Sir](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/CysI_Sir/seed_refpkg/final_outputs) | (assimilatory) sulfite reductase (NADPH) hemoprotein, beta subunit\|ferredoxin dependent | 1055 | Assimilatory sulfate reduction | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [CysJ](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/CysJ/seed_refpkg/final_outputs) | sulfite reductase [NADPH] flavoprotein, alpha-component [COG0369, EC:1.8.1.2] | 474 | Assimilatory sulfate reduction | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [CysN](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/CysN/seed_refpkg/final_outputs) | Sulfate adenylyltransferase (SAT), large subunit | 1221 | Assimilatory sulfate reduction | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [DsrAB](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/DsrAB/seed_refpkg/final_outputs) | Dissimilatory sulfite reductase, alpha and beta subunits | 752 | Dissimilatory sulfate reduction and oxidation | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [DsrC](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/DsrC/seed_refpkg/final_outputs) | | 341 | Dissimilatory sulfate reduction and oxidation | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [Sat](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/Sat/seed_refpkg/final_outputs) | Sulfate adenylyltransferase [PF01747, EC:2.7.7.4] | 254 | Dissimilatory sulfate reduction and oxidation | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [SoxB](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/SoxB/seed_refpkg/final_outputs) | S-sulfosulfanyl-L-cysteine sulfohydrolase [TIGR04486] | 1012 | SOX system | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [SoxY](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/SoxY/seed_refpkg/final_outputs) | Thiosulfate oxidation carrier protein [TIGR04488,ENOG501RH4J] | 364 | SOX system | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
| [SoxZ](https://github.com/hallamlab/RefPkgs/blob/master/Sulfur_metabolism/SoxZ/seed_refpkg/final_outputs) | Thiosulfate oxidation carrier complex protein [TIGR04490,ENOG501N097] | 247 | SOX system | S |
+---------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------+------------+-----------------------------------------------+-------+
: (\#tab:reference-packages) Available TreeSAPP reference packages