B TreeSAPP reference packages

TABLE B.1: Available TreeSAPP reference packages
Name Description Leaf nodes Pathway Cycle
AA10 Auxiliary Activity family 10 699 Carbohydrate metabolism C
GH101 Glycoside hydrolase family 101 113 Carbohydrate metabolism C
GH102 Glycoside hydrolase family 102 727 Carbohydrate metabolism C
GH103 Glycoside hydrolase family 103 1145 Carbohydrate metabolism C
GH109 Glycoside hydrolase family 109 376 Carbohydrate metabolism C
GH115 Glycoside hydrolase family 115 267 Carbohydrate metabolism C
GH126 Glycoside hydrolase family 126 112 Carbohydrate metabolism C
GH163 Glycoside hydrolase family 163 102 Carbohydrate metabolism C
GH67 Glycoside hydrolase family 67 372 Carbohydrate metabolism C
GH94 Glycoside hydrolase family 94 695 Carbohydrate metabolism C
McrA Methyl coenzyme M reductase alpha subunit 424 Methanogenesis C
McrA Methyl coenzyme M reductase alpha subunit 249 Methanogenesis C
McrB Methyl coenzyme M reductase beta subunit 110 Methanogenesis C
McrG Methyl coenzyme M reductase gamma subunit 123 Methanogenesis C
PHAdeg Poly(hydroxyalkanoate) degradation enzymes 10 Plastics degradation C
PL11 Polysaccharide lyase family 11 320 Carbohydrate metabolism C
PuhA photosynthetic reaction center H subunit 47 Photosynthesis C
PilA Type IV pilin N-terminus, including PilA 70 Direct interspecies electron transfer E
HydA [FeFe] hydrogenase, group A, B1, B3 93 Hydrogenase H
HgcA Methylmercury active enzyme, subunit A 108 NA Hg
HgcB Methylmercury active enzyme, subunit B 122 NA Hg
NapA Periplasmic nitrate reductase, large subunit 765 Denitrification N
NifD nitrogenase molybdenum-iron protein alpha chain 926 Nitrogen fixation N
NifH Nitrogenase iron protein [TIGR01287,EC:1.18.6.1] 660 Nitrogen fixation N
NirK nitrite reductase (NO-forming) 325 Denitrification,Annamox N
NirS nitrite reductase (NO-forming) / hydroxylamine reductase 511 Denitrification,Annamox N
NorB nitric oxide reductase subunit B 460 Denitrification N
NorC nitric oxide reductase subunit C 173 Denitrification N
NosZ Nitrous-oxide reductase (TAT-dependent|Sec-dependent) 26 Denitrification N
NxrA nitrate reductase / nitrite oxidoreductase, alpha subunit 658 Nitrification N
NxrB nitrate reductase / nitrite oxidoreductase, beta subunit 648 Nitrification N
XmoA Alpha subunits of copper membrane monooxygenase enzymes 37 Nitrification N
PF00380a Ribosomal protein S9/S16 82 Translation NA
PF00380b Ribosomal protein S9/S16 1065 Translation NA
PF00410a Ribosomal protein S8 155 Translation NA
PF00410b Ribosomal protein S8 1216 Translation NA
PF00687a Ribosomal protein L1p/L10e family 192 Translation NA
PF00687b Ribosomal protein L1p/L10e family 864 Translation NA
PF00750a tRNA synthetases class I (R) 193 Translation NA
PF00750b tRNA synthetases class I (R) 1317 Translation NA
PF00900 Ribosomal family S4e 328 Translation NA
PF01015 Ribosomal S3Ae family 101 Translation NA
PF01092 Ribosomal protein S6e 169 Translation NA
PF01157 Ribosomal protein L21e 74 Translation NA
PF01200 Ribosomal protein S28e 129 Translation NA
PF01280 Ribosomal protein L19e 281 Translation NA
PF01409a tRNA synthetases class II core domain (F) 243 Translation NA
PF01409b tRNA synthetases class II core domain (F) 891 Translation NA
PF01655 Ribosomal protein L32 220 Translation NA
PF01866 Putative diphthamide synthesis protein 229 Translation NA
RpoB RNA polymerase beta subunit 697 Translation NA
CysD sulfate adenylyltransferase (SAT), small subunit 93 Assimilatory sulfate reduction S
CysH phosophoadenylyl-sulfate reductase [PF01507, EC:1.8.4.8|1.8.4.10] 710 Assimilatory sulfate reduction S
CysI_Sir (assimilatory) sulfite reductase (NADPH) hemoprotein, beta subunit|ferredoxin dependent 1055 Assimilatory sulfate reduction S
CysJ sulfite reductase [NADPH] flavoprotein, alpha-component [COG0369, EC:1.8.1.2] 474 Assimilatory sulfate reduction S
CysN Sulfate adenylyltransferase (SAT), large subunit 1221 Assimilatory sulfate reduction S
DsrAB Dissimilatory sulfite reductase, alpha and beta subunits 752 Dissimilatory sulfate reduction and oxidation S
DsrC 341 Dissimilatory sulfate reduction and oxidation S
Sat Sulfate adenylyltransferase [PF01747, EC:2.7.7.4] 254 Dissimilatory sulfate reduction and oxidation S
SoxB S-sulfosulfanyl-L-cysteine sulfohydrolase [TIGR04486] 1012 SOX system S
SoxY Thiosulfate oxidation carrier protein [TIGR04488,ENOG501RH4J] 364 SOX system S
SoxZ Thiosulfate oxidation carrier complex protein [TIGR04490,ENOG501N097] 247 SOX system S