Supplementary Table 1: Available predictive genome-scale metabolic network reconstructions

Adam M. Feist, Markus J. Herrgard, Ines Thiele, Jennie L. Reed, Bernhard Ø. Palsson "Reconstruction of Biochemical Networks in Microbial Organisms", Nat. Rev. Microbiol. 2009 Feb;7(2):129-43.

Supplementary Table 2 - Common issues encountered during metabolic network reconstruction

This list includes genome-scale metabolic network reconstructions that have been converted into predictive genome-scale models and whose predictive power has been validated against experimental data.

This table is managed and updated by Jared Broddrick (jtb@ucsd.edu). Please send me an email with any missing information.

This page is composed of links to existing, published models. The SBRG makes no guarantee of their completeness or accuracy. Please see the respective publication for that information.

Last updated: 22 February 2018

 

[ Bacteria ] [ Archaea] [ Eukaryota ]

Bacteria

  Organism Strain Organism Genes Version Model Genes Metabolites Reactions Compartments Reference Journal Date
1 Acinetobacter baumannii AYE 3760 AbyMBEL891 650 778 891 2 (c,e) Kim et al. Mol Biosyst 2010/01/23
2 Acinetobacter baylyi ADP1 3287 iAbaylyiV4 774 701 875 3 (c,e,p) Durot et al. BMC Syst Biol 2008/10/09
3 Akkermansia muciniphila BAA-835   iAkkMuc_588 588 540 744   Ottman et al. Appl Environ Microbiol 2017/07/09
4 Amycolatopsis balhimycina   8585   583 647 1363   Vongsangnak et al. Biotechnol Bioeng 2012/01/19
5 Arthrospira platensis NIES-39 6631 nan 620 673 746 3(c,e,p) Yoshikawa et al. PLoS One 2015/12/08
6 Bacillus licheniformis WX-02   iWX1009 1009 1141 1792   Guo et al. Res Microbiol 2016/01/19
7 Bacillus megaterium WSH002     1055 993 1112   Zou et al. J Biotechnol 2013/03/05
8 Bacillus subtilis 168 4114 iBsu1103 1103 1138 1437 2 (c,e) Henry et al. Genome Biol 2009/06/27
9 Bacillus subtilis   4114 model_v3 844 988 1020 2 (c,e) Oh et al. J Biol Chem 2007/06/19
10 Blattabacterium cuenoti Bge   iCG238 364 238 296   Gonzalez-Domenech et al. BMC Microbiol 2012/03/02
11 Blattabacterium cuenoti Pam   iCG230 358 230 289   Gonzalez-Domenech et al. BMC Microbiol 2012/03/02
12 Bordetella pertussis 10536             Budman et al. Biotechnol Prog 2012/12/12
13 Bordetella pertussis Tohama I 3464 iBP1870 762   1675   Branco et al. Appl Environ Microbiol 2017/08/27
14 Buchnera aphidicola APS 574 iGT196 196 240 263 2 (c,e) Thomas et al. BMC Syst Biol 2009/02/24
15 Burkholderia cenocepacia J2315   iKF1028 1028 834 859   Fang et al. BMC Syst Biol 2011/05/26
16 Campylobacter jejuni NCTC 11168     388 467 536   Metris et al. BMC Genomics 2011/11/03
17 Chromohalobacter salexigens DSM 3352 iOA584 584 1411 1386 2 (c,e) Ates et al. BMC Syst Biol 2011/01/22
18 Clostridium acetobutylicum ATCC 824 3848   474 422 552 2 (c,e) Senger and Papoutsakis Biotechnol Bioeng 2008/09/04
19 Clostridium acetobutylicum ATCC 824 3848   432 479 502 2 (c,e) Lee et al. Appl Microbiol Biotechnol 2008/09/02
20 Clostridium beijerinckii NCIMB 8052 5243 iCB925 925 881 938 2(c,e) Milne et al. BMC Syst Biol 2011/08/19
21 Clostridium difficile 630 3968 iMLTC806cdf 806 703 769   Larocque et al. BMC Syst Biol 2014/10/16
22 Clostridium ljungdahlii     iHN637 637 698 785   Nagarajan et al. Microb Cell Fact 2013/11/28
23 Clostridium thermocellum ATCC 27405 3307 iSR432 432 525 577 2 (c,e) Roberts et al. BMC Syst Biol 2010/03/24
24 Corynebacterium glutamicum ATCC 13032 3002     411 446 2 (c,e) Kjeldsen and Nielsen Biotechnol Bioeng 2008/11/06
25 Corynebacterium glutamicum ATCC 13032 3002   227 423 502 2 (c,e) Shinfuku et al. Microb Cell Fact 2009/08/04
26 Corynebacterium glutamicum ATCC13032   iC773 773 950 1207   Zhang et al. Biotechnol Biofuels 2017/07/07
27 Corynebacterium glutamicum S9114 3015 iJM658 658 984 1065   Mei et al. Gene 2015/09/24
28 Cyanothece sp. ATCC 51142     iCce806 806   667   Vu et al. PLoS Comput Biol 2012/04/25
29 Cyanothece sp. ATCC 51142     iCyt773         Saha et al. PLoS One 2012/11/08
30 Cyanothece sp. PCC 6803     iSyn731         Saha et al. PLoS One 2012/11/08
31 Dehalococcoides ethenogenes   2061 iAI549 549 549 518 2 (c,e) Ahsanul et al. PLoS Comput Biol 2010/09/03
32 Escherichia coli K-12 4405 iJR904 904 625 931 2 (c,e) Reed et al. Genome Biol 2003/09/04
33 Escherichia coli K-12 MG1655 4405 iJE660 660 438 627 2 (c,e) Edwards and Palsson Proc Natl Acad Sci U S A 2000/05/11
34 Escherichia coli K-12 MG1655 4405 iAF1260 1260 1039 2077 3 (c,e,p) Feist et al. Mol Syst Biol 2007/06/28
35 Escherichia coli K-12 MG1655 4405 iJO1366 1366 1136 2251 3 (c, e, p) Orth et al. Mol Syst Biol 2011/10/13
36 Escherichia coli W (ATCC 9637) 4764 iCA1273 1273 1111 2477 3 (c,e,p) Archer et al. BMC Genomics 2011/01/07
37 Francisella tularensis LVS 1802 iRS605 683 586 605 2 (c,e) Raghunathan et al. BMC Syst Biol 2010/08/25
38 Geobacillus thermoglucosidasius C56-YS93   iGT736 736 1163 1159   Ahmad et al. J Biotechnol 2017/04/08
39 Geobacter metallireducens   3532   747 769 697 2 (c,e) Sun et al. BMC Syst Biol 2009/01/30
40 Geobacter sulfurreducens   3530   588 541 523 2 (c,e) Mahadevan et al. Appl Environ Microbiol 2006/02/08
41 Gluconobacter oxydans 621H   iXW433 433 985 859   Wu et al. Biosystems 2014/01/15
42 Haemophilus influenzae Rd 1775 iJE296 296 343 488 2 (c,e) Edwards and Palsson J Biol Chem 1999/06/11
43 Haemophilus influenzae Rd 1775 iCS400 400 451 461 2 (c,e) Schilling and Palsson J Theor Biol 2000/03/16
44 Helicobacter pylori 26695 1632 iCS291 291 340 388 2 (c,e) Schilling et al. J Bacteriol 2002/07/27
45 Helicobacter pylori 26695 1632 iIT341 341 485 476 2 (c,e) Thiele et al. J Bacteriol 2005/08/04
46 Ketogulonicigenium vulgare WSH-001   iWZ663 663 649 830   Zou et al. J Biotechnol 2012/06/26
47 Klebsiella oxytoca     KoxGSC1457   1099 1457   Park et al. Microb Cell Fact 2013/02/26
48 Klebsiella pneumoniae MGH 78578 5186 iYL1228 1228 1658 1970 3 (c,e,p) Liao et al. J Bacteriol 2011/02/08
49 Lactobacillus plantarum WCFS1 3009   721 531 643 2 (c,e) Teusink et al. J Biol Chem 2006/10/26
50 Lactococcus lactis ssp. lactisIL1403 2310   358 422 621 2 (c,e) Oliveira et al. BMC Microbiol 2005/06/29
51 Lactococcus lactis subsp. cremoris MG1363 2563   518 650 754 2 (c,e) Flahaut et al. Appl Microbiol Biotechnol 2013/08/27
52 Mannheimia succiniciproducens MBEL55E 2384   425 519 686 2 (c,e) Kim et al. Biotechnol Bioeng 2007/04/04
53 Mannheimia succiniciproducens MBEL55E 2384   335 332 373 2 (c,e) Hong et al. Nat Biotechnol 2004/09/21
54 Mycobacterium tuberculosis H37Rv 4402 iNJ661 661 828 939 2 (c,e) Jamshidi and Palsson BMC Syst Biol 2007/06/09
55 Mycobacterium tuberculosis H37Rv 4402 GSMN-TB 726 739 849 2 (c,e) Beste et al. Genome Biol 2007/05/25
56 Mycobacterium tuberculosis H37Rv 4402 iNJ661m 663 838 1049 2 (c,e) Fang et al. BMC Syst Biol 2010/11/26
57 Mycoplasma genitalium G-37 521 iPS189 189 274 262 2 (c,e) Suthers et al. PLoS Comput Biol 2009/02/14
58 Mycoplasma pneumoniae     iJW145 145       Wodke et al. Mol Syst Biol 2013/04/04
59 Neisseria meningitidis serogroup B 2226   555 471 496 2 (c,e) Baart et al. Genome Biol 2007/07/10
60 Oenococcus oeni PSU-1 1864 iSM454 454 536 660   Mendoza et al. Front Microbiol 2017/04/21
61 Piscirickettsia salmonis LF-89 3074 iPS584 584 801 1323   Cortes et al. Front Microbiol 2018/01/13
62 Piscirickettsia salmonis LF-89 2863 iPF215 215 417 445   Fuentealba et al. Bioresour Technol 2016/10/28
63 Porphyromonas gingivalis W83 2015 iVM679   564 679 2 (c,e) Mazumdar et al. J Bacteriol 2008/10/22
64 Pseudomonas aeruginosa PA01 5640 iMO1056 1056 760 883 2 (c,e) Oberhardt et al. J Bacteriol 2008/01/15
65 Pseudomonas fluorescens SBW25   iSB1139 1139 1194 1012   Borgos et al. BMC Syst Biol 2013/03/19
66 Pseudomonas putida KT2440 5350 PpuMBEL1071 900 1044 1071 2 (c,e) Sohn et al. Biotechnol J 2010/06/12
67 Pseudomonas putida KT2440 5350 iJN746 746 911 950 3 (c,p,e) Nogales et al. BMC Syst Biol 2008/09/17
68 Pseudomonas putida KT2440 5350 iJP815 815 886 877 3 (c,p,e) Puchalka et al. PLoS Comput Biol 2008/11/01
69 Pseudomonas stutzeri A1501 4192 iPB890 890 813 1135   Babaei et al. Mol Biosyst 2015/08/26
70 Ralstonia eutropha H16   RehMBEL1391   1171 1391   Park et al. BMC Syst Biol 2011/06/30
71 Ralstonia solanacearum GMI1000 5120 iRP1476 1476 2574 2644 4 (b, c, e, p) Peyraud et al. PLoS Pathog 2016/10/13
72 Rhizobium etli CFN42 3168 iOR363 363 371 387 2 (c,e) Resendis-Antonio et al. PLoS Comput Biol 2007/10/10
73 Rhizobium etli     iOR450 450 377 402   Resendis-Antonio et al. PLoS Comput Biol 2012/10/17
74 Rhodobacter sphaeroides 2.4.1   iRsp1095 1095 796 1158   Imam et al. BMC Syst Biol 2011/07/23
75 Rhodococcus erythropolis               Aggarwal et al. Mol Biosyst 2011/09/14
76 Rhodoferax ferrireducens   4770   744 790 762 2 (c,e) Risso et al. BMC Genomics 2009/09/24
77 Saccharopolyspora erythraea NRRL23338     2075 1646 1482   Licona-Cassani et al. Antonie Van Leeuwenhoek 2012/08/01
78 Salinispora tropica CNB-440 4477 iCC908 908 1317 1373   Contador et al. Antonie Van Leeuwenhoek 2015/10/16
79 Salmonella enterica LT2 4489 STM_v1.0 1270 1119 2201 3 (c,e,p) Thiele et al. BMC Syst Biol 2011/01/20
80 Salmonella enterica LT2 4489 iRR1083 1083 774 1087 2 (c,e) Raghunathan et al. BMC Syst Biol 2009/04/10
81 Salmonella enterica LT2 4489 iMA945 945 1036 1964 2 (c,e) AbuOun et al. J Biol Chem 2009/08/20
82 Shewanella oneidensis MR-1 5066 iSO783 783 634 774 2 (c,e) Pinchuk et al. PLoS Comput Biol 2010/07/01
83 Sinorhizobium meliloti     iHZ565 565 522 503   Zhao et al. PLoS One 2012/02/10
84 Sodalis glossinidius       668 690 741   Belda et al. PLoS One 2012/02/01
85 Spirulina platensis C1 PCC9438   iAK692 692 837 875   Klanchui et al. BMC Syst Biol 2012/06/19
86 Staphylococcus aureus 64 strains Varies Multiple (64) Varies Varies Varies   Buffalo et al. Nat Microbiol 2016/10/27
87 Staphylococcus aureus Many 2588   546 1431 1493 2 (c,e) Lee et al. J Bacteriol 2009/04/21
88 Staphylococcus aureus N315 2588 iSB619 619 571 641 2 (c,e) Becker and Palsson BMC Microbiol 2005/03/09
89 Staphylococcus aureus N315 2588 iMH551 551 604 712 2 (c,e) Heinemann et al. Biotechnol Bioeng 2005/09/13
90 Streptococcus pyogenes M49 1701 nan 480 558 576   Levering et al. J Biotechnol 2016/03/13
91 Streptococcus thermophilus LMG18311 1889   429   522 2 (c,e) Pastink et al. Appl Environ Microbiol 2009/04/07
92 Streptomyces clavuligerus   7281 iLT1021 1021 1360 1494 2(e,c) Toro et al. Bioprocess Biosyst Eng 2018/02/07
93 Streptomyces coelicolor A3(2) 7825   789 759 1015 2 (c,e) Alam et al. BMC Genomics 2010/03/27
94 Streptomyces coelicolor A3(2) 7825   700 500 700 2 (c,e) Borodina et al. Genome Res 2005/06/03
95 Streptomyces coelicolor A3(2) 7825 iMK1208 1208 1246 1643 2(e,c) Kim et al. Biotechnol J 2014/03/14
96 Streptomyces lividans TK24       602 702   D'Huys et al. J Biotechnol 2012/05/30
97 Synechococcus elongatus PCC 7942 2723 iJB785 785 768 850 7(e,p,c,u,cm,um,cx) Broddrick et al. Proc Natl Acad Sci U S A 2016/12/03
98 Synechococcus sp PCC 7002   3179 iSyp611         Vu et al. Biotechnol J 2013/04/25
99 Synechococcus sp PCC 7002   3179 nan 728   742 7 (e,c,cx,cm,p,u,um) Hendry et al. Bioresour Technol 2016/04/03
100 Synechococcus sp PCC 7002   3179 iSyp821 821 777 792   Qian et al. Biochim Biophys Acta 2016/12/26
101 Synechocystis sp. PCC6803 PCC6803 3221 iJN678 678 795 863 3(c,p,e) Nogales et al. Proc Natl Acad Sci U S A 2012/02/07
102 Synechocystis sp. PCC6803 PCC6803 3221 iSyn669 669 790 882 2 (c,e) Montagud et al. BMC Syst Biol 2010/11/19
103 Synechocystis sp. PCC6803 PCC6803 3221   677 601 759 6(c,p,e,cx,u,um) Knoop et al. PLoS Comput Biol 2013/07/12
104 Thermoanaerobacter tengcongensis       236 227 253   Tong et al. Mol Biosyst 2013/02/12
105 Thermotoga maritima MSB8 1917   478 503 562 2 (c,e) Zhang et al. Science 2009/09/19
106 Vibrio vulnificus CMCP6 2896 VvuMBEL943 673 792 943 2 (c,e) Kim et al. Mol Syst Biol 2011/01/20
107 Xanthomonas campestris pv. campestris B100     352 338 437   Schatschneider et al. J Biotechnol 2013/02/12
108 Xanthomonas campestris pv. campestris str. B100   iSS352 352 338 447   Schatschneider et al. J Biotechnol 2013/02/12
109 Yersinia pestis 91001 4037 iAN818m 818 825 1020 2 (c,e) Navid and Almaas Mol Biosyst 2009/04/28
110 Yersinia pestis CO92 4306 iPC815 815 963 1678 3 (c,e,p) Charusanti et al. BMC Syst Biol 2011/10/15
111 Zymomonas mobilis ZM1 1929 iEM439 439 658 692 2 (c,e) Motamedian et al. Mol Biosyst 2016/02/18
112 Zymomonas mobilis ZM4 1808 iZM363 363 704 747 2 (c,e) Widiastuti et al. Biotechnol Bioeng 2010/10/23
113 Zymomonas mobilis ZM4 1808 ZmobMBEL601 347 579 601 2 (c,e) Lee et al. Microb Cell Fact 2010/11/26

Eukaryota

  Organism Strain Organism Genes Version Model Genes Metabolites Reactions Compartments Reference Journal Date
1 Arabidopsis thaliana   27379 AraGEM 1419 1748 1567 6 (c,e,m, de et al. Plant Physiol 2010/01/02
2 Aspergillus nidulans   9451 iHD666 666 732 794 4 (c,e,m,o) David et al. BMC Genomics 2008/04/15
3 Aspergillus niger CBS 513.88 14165 iMA871 871 1045 1190 3 (c,e,m) Andersen et al. Mol Syst Biol 2008/03/28
4 Aspergillus niger   14165 iHL1210 1210 1254 1764 3 (c,e,m,x) Lu et al. Biotechnol Bioeng 2016/10/04
5 Aspergillus oryzae RIB40 12074   1314 1073 1053 3 (c,e,m,x) Vongsangnak et al. BMC Genomics 2008/05/27
6 Aspergillus terreus NIH2624 10406 iJL1454 1454 1155 1451 3 (c,e,m) Liu et al. Mol Biosyst 2013/04/30
7 Brassica napus         262 313   Pilalis et al. Biotechnol Bioeng 2011/02/22
8 Caenorhabditis elegans     iCEL1273 1273   1985   Yilmaz and Walhout Cell Syst 2016/05/24
9 Candida glabrata     iNX804 804 1025 1287   Xu et al. Mol Biosyst 2012/11/23
10 Candida tropicalis     iCT646 645 1146 1421   Mishra et al. Biotechnol Bioeng 2016/02/26
11 Chlamydomonas reinhardtii   16709 AlgaGEM 866 1862 1725 4 (c,e,m,o) Dal'Molin et al. BMC Genomics 2012/03/06
12 Chlamydomonas reinhardtii   16709 iRC1080 1080 1068 2190 10 (c, e, h, s, f, x, g, m, n, u) Chang et al. Mol Syst Biol 2011/08/04
13 Chlorella variabilis   9879 iAJ526 526 1236 1455   Juneja et al. Bioresour Technol 2016/03/21
14 Chlorella vulgaris UTEX395 7100 iCZ843 843 1770 2286 6(e,c,m,h,u,o) Zuniga et al. Plant Physiol 2016/07/04
15 Cordyceps militaris   9651 iWV1170 1170 894 1267 5 (p,c,m,x,e) Vongsangnak et al. Gene 2017/05/18
16 Cryptosporidium hominis   3884 iNV213 213   540 2 (c,e) Vanee et al. Chem Biodivers 2010/05/22
17 Drosophila melongaster   15431 fly_model         Feala et al. BMC Syst Biol 2009/09/11
18 Homo sapiens   28783 Recon 1 1496 2766 3311 8 (c,e,m,x Duarte et al. Proc Natl Acad Sci U S A 2007/02/03
19 Homo sapiens   28783 Recon 2.2 1675 5324 7785 8 (c,e,m,x,im) Swainston et al. Metabolomics 2016/07/01
20 Homo sapiens   28783 Recon3D 3288 4140 13543 8 (c,e,m,x Brunk et al. Nat Biotechnol 2018/02/20
21 Homo sapiens   28783 Recon 2 1789 5063 7440   Thiele et al. Nat Biotechnol 2013/03/05
22 Kluyveromyces lactis     iOD907 907 1476 1867   Dias et al. Biotechnol J 2014/04/30
23 Leishmania donovani BPK282A1 8135 iMS604 604 1135 1159 8 (c,m,glycosome, acidocalcisome,r,n,f,e) Sharma et al. Mol Biosyst 2017/04/04
24 Leishmania major Friedlin 8370 iAC560 560 1101 1112 8 (a,f,y,c, Chavali et al. Mol Syst Biol 2008/03/28
25 Mucor circinelloides     iWV1213 1213 1413 1326 5(c,e,p,b,m) Vongsangnak et al. Gene 2016/02/26
26 Mus musculus   28287   473 872 1220 3 (c,e,m) Sheikh et al. Biotechnol Prog 2005/05/21
27 Mus musculus   28287   724 1287 1494 3 (c,e,m) Selvarasu et al. Mol Biosyst 2009/12/22
28 Mus musculus   28287 iMM1415 1415 2774 3726 8 (c,e,g,l, Sigurdsson et al. BMC Syst Biol 2010/10/21
29 Mus musculus   28287   1399 2179 2037 3 (c,e,m) Quek and Nielsen Genome Inform 2008/01/01
30 Neurospora crassa       836       Dreyfuss et al. PLoS Comput Biol 2013/08/13
31 Penicillium chrysogenum Wisconsin 54-1255     1006   1471   Agren et al. PLoS Comput Biol 2013/04/05
32 Phaeodactylum tricornutum CCAP 1055/1 12280 nan 607 587 849 5(e,c,m,h,x) Kim et al. Plant J 2015/11/22
33 Phaeodactylum tricornutum CCAP 1055/1 12280 iLB1027 1027 2172 4456 6 (e,c,h,u,x,m) Levering et al. PLoS One 2016/05/07
34 Pichia pastoris DSMZ 70382 5450 PpaMBEL1254 540 1147 1254 8 (c,e,g,m Sohn et al. Biotechnol J 2010/05/27
35 Pichia pastoris GS115 5313 iLC915 915 899 1423 7 (c,m,p,v,r,g,n) Caspeta et al. BMC Syst Biol 2012/04/05
36 Pichia stipitis CBS 6054 5841 iSS884 884 992 1332 4 (c,m,p,v) Caspeta et al. BMC Syst Biol 2012/04/05
37 Pichia pastoris GS115 5313 iPP668 668 1177 1361 8 (c,e,g,m Chung et al. Microb Cell Fact 2010/07/03
38 Pichia pastoris GS115 5313 iRY1243 1243 1094 2407 9 (c,m,x,r,n,e,g,v,i) Ye et al. Bioresour Bioprocess 2017/05/27
39 Pichia pastoris   5450 iMT1026 1026 1689 2035 8(c,m,x,e,r,g,v,n) Tomas-Gamisans et al. PLoS One 2016/01/27
40 Plasmodium falciparum 3D7 5615   579 1622 1375 6 (c,i,m,n,r,v) Huthmacher et al. BMC Syst Biol 2010/09/03
41 Plasmodium falciparum 3D7 5615   366 616 1001 4 (c,e,i,m) Plata et al. Mol Syst Biol 2010/09/09
42 Saccharomyces cerevisiae Sc288 6183 iAZ900 900 1597 1240 8 (c,e,r,g,m,n,p,v) Zomorrodi and Maranas BMC Syst Biol 2010/12/31
43 Saccharomyces cerevisiae Sc288 6183 iFF708 708 584 1175 3 (c,e,m) Forster et al. Genome Res 2003/02/05
44 Saccharomyces cerevisiae Sc288 6183 iMM904 904 713 1412 8(c,e,m,x Mo et al. BMC Syst Biol 2009/03/27
45 Saccharomyces cerevisiae Sc288 6183 iND750 750 646 1149 8 (c,e,m, Duarte et al. Genome Res 2004/06/16
46 Saccharomyces cerevisiae Sc288 6183 iIN800 800 1013 1446 3(c,e,m) Nookaew et al. BMC Syst Biol 2008/08/09
47 Saccharomyces cerevisiae Sc288 6183 iLL672 672 636 1038 3 (c,e,m) Kuepfer et al. Genome Res 2005/10/06
48 Saccharomyces cerevisiae Sc288 6183 iMH805/775 832 1168 1857 15(c,e,g,m,n, r Herrgard et al. Nat Biotechnol 2008/10/11
49 Saccharomyces cerevisiae Sc288 6183 iTO977 977 1353 1566 4 Osterlund et al. BMC Syst Biol 2013/05/02
50 Saccharomyces pombe Sz-0205 4940 SpoMBEL1693 605 1744 1693 8(c,e,m,x Sohn et al. Biotechnol J 2010/06/12
51 Scheffersomyces stipitis CBS 6054 5816 iTL885 885 589 1240 3(c,e,m) Liu et al. Biotechnol Biofuels 2012/09/25
52 Schizochytrium limacinum SR21   iCY1170_DHA 1170 1659 1769   Ye et al. BMC Genomics 2015/10/18
53 Schizosaccharomyces pombe Sz-0205 4940 SpoMBEL1693 605 1744 1693 8(c,e,m,x Sohn et al. BMC Syst Biol 2012/05/29
54 Toxoplasma gondii   382   382 384 571 5 (a,c, rm, m, mm) Song et al. Mol Syst Biol 2013/11/20
55 Yarrowia lipolytica     iNL895 895 1847 2002 16 Loira et al. BMC Syst Biol 2012/05/09
56 Yarrowia lipolytica     iYL619_PCP 619 843 1142   Pan and Hua PLoS One 2012/12/14
57 Zea mays     iRS1563 1563 1825 1985   Saha et al. PLoS One 2011/07/15

Archaea

  Organism Strain Organism Genes Version Model Genes Metabolites Reactions Compartments Reference Journal Date
1 Halobacterium salinarum R-1 2867   490 557 711 2 (c,e) Gonzalez et al. Mol Biosyst 2008/01/24
2 Methanococcus maripaludis S2 1722 iMM518 518 556 570 2 (e,c) Goyal et al. Mol Biosyst 2014/02/21
3 Methanosarcina acetivorans C2A 4540 iVS941 941 708 705 2 (c,e) Satish et al. BMC Syst Biol 2011/02/18
4 Methanosarcina acetivorans C2A 4540 iMB745 745 715 756 2 (c,e) Benedict et al. J Bacteriol 2011/12/06
5 Methanosarcina barkeri Fusaro 5072 iAF692 692 558 619 2 (c,e) Feist et al. Mol Syst Biol 2006/06/02
6 Methanosarcina barkeri Fusaro 5072 iMG746 746 719 741 2 (c,e) Gonnerman et al. Biotechnol J 2013/02/20
7 Natronomonas pharaonis DSM 2160 2892   654 597 683 2 (c,e) Gonzalez et al. PLoS Comput Biol 2010/06/15
8 Sulfolobus solfataricus P2 2977     705 718   Ulas et al. PLoS One 2012/09/07

 

File Attachments: 

File cth.iSR432.xml

File iAZ900_noCyles.xml