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SEED version cvs.1555556707 (3/17/2019 22:5:7) on gum.mcs.anl.gov
The SEED

Subsystem: Alanine_biosynthesis

Author: OlgaZ


Functional Roles
Column Abbrev Functional Role GO Reactions Pre-Computed Publication(s) Relevant Publication(s)
1 AlaR Alanine racemase (EC 5.1.1.1) R00401 Add Publication(s)
2 AlaR_b Alanine racemase, biosynthetic (EC 5.1.1.1) R00401 Add Publication(s)
3 AlaR_c Alanine racemase, catabolic (EC 5.1.1.1) R00401 Add Publication(s)
4 IlvE Branched-chain amino acid aminotransferase (EC 2.6.1.42) R01214 22 Publication(s) Add Publication(s)
5 CDS Cysteine desulfurase (EC 2.8.1.7) 5 Publication(s)
6 IscS Cysteine desulfurase (EC 2.8.1.7), IscS subfamily R07460 Add Publication(s)
7 NifS Cysteine desulfurase (EC 2.8.1.7), NifS subfamily Add Publication(s)
8 SufS Cysteine desulfurase (EC 2.8.1.7), SufS subfamily Add Publication(s)
9 CsdA Cysteine desulfurase CsdA-CsdE (EC 2.8.1.7), main protein CsdA Add Publication(s)
10 AlaB Alanine transaminase (EC 2.6.1.2) R00258 Add Publication(s)
11 IlvY HTH-type transcriptional regulator IlvY Add Publication(s)
12 AvtA Valine--pyruvate aminotransferase (EC 2.6.1.66) R01215 Add Publication(s)
13 AvtA Valine--pyruvate aminotransferase (EC 2.6.1.66) R01215 Add Publication(s)

Subsets of Roles
Subset Includes These Roles
*AlaR 1,2,3
*AvtA 13,13
*IscS 6,5
CDS 6,8,5,7,9
Phoenix 4,13,6,1,2,3,10,13


Show Phylogenetic Tree
Basic Spreadsheet
Genome ID Organism Variant Code *AlaR IlvE *IscS NifS SufS CsdA AlaB IlvY *AvtA
644279.4 Staphylococcus aureus subsp. aureus 132 [B] C 2214-1 626 1774-5, 1861-5   919        
585143.3 Staphylococcus aureus subsp. aureus 55/2053 [B] C 2621-1 1064 2247-5, 2158-5   1367        
585144.3 Staphylococcus aureus subsp. aureus 58-424 [B] C 2638-1 1075 2183-5   1727        
585145.3 Staphylococcus aureus subsp. aureus 65-1322 [B] C 2619-1 1057 1885-5, 1978-5   1355        
585146.3 Staphylococcus aureus subsp. aureus 68-397 [B] C 2600-1 1062 2156-5, 2244-5   1359        
585147.3 Staphylococcus aureus subsp. aureus A017934/97 [B] C 1620-1 80 1231-5, 1318-5   418        
762962.3 Staphylococcus aureus subsp. aureus ATCC 51811 [B] C 2438-1 140 362-5, 273-5   1157        
585148.3 Staphylococcus aureus subsp. aureus Btn1260 [B] C 1609-1 80 1207-5   387        
585149.6 Staphylococcus aureus subsp. aureus C101 [B] C 2239-1 685 1796-5, 1883-5   981        
585150.3 Staphylococcus aureus subsp. aureus C160 [B] C 2695-1 1105 1882-5   1412        
Genome ID Organism Variant Code *AlaR IlvE *IscS NifS SufS CsdA AlaB IlvY *AvtA
585151.3 Staphylococcus aureus subsp. aureus C427 [B] C 1781-1 174 841-5   449        
93062.19 Staphylococcus aureus subsp. aureus COL [B] C 2009-1 584 1723-5, 1634-5   893        
93062.4 Staphylococcus aureus subsp. aureus COL [B] C 2040-1 1053 1510-5   1070        
585152.3 Staphylococcus aureus subsp. aureus D139 [B] C 2043-1 471 1707-5, 1617-5   757        
585153.3 Staphylococcus aureus subsp. aureus E1410 [B] C 2685-1 1115 1988-5, 1900-5   1414        
681288.4 Staphylococcus aureus subsp. aureus ED98 [B] C 2090-1 507 1620-5   815        
585154.3 Staphylococcus aureus subsp. aureus EMRSA16 [B] C 2122-1 516 1322-5   825        
585155.3 Staphylococcus aureus subsp. aureus H19 [B] C 2686-1 1099 1948-5, 1844-5   2184        
359787.11 Staphylococcus aureus subsp. aureus JH1 [B] C 2192-1 619 1756-5   902        
Genome ID Organism Variant Code *AlaR IlvE *IscS NifS SufS CsdA AlaB IlvY *AvtA
359787.3 Staphylococcus aureus subsp. aureus JH1 [B] C 235-1 2453 1447-5   2525        
359786.13 Staphylococcus aureus subsp. aureus JH9 [B] C 2224-1 629 1779-5   914        
359786.3 Staphylococcus aureus subsp. aureus JH9 [B] C 759-1 2534 271-5   2142        
585156.3 Staphylococcus aureus subsp. aureus M1015 [B] C 1618-1 81 1176-5, 1263-5   379        
585157.3 Staphylococcus aureus subsp. aureus M809 [B] C 1734-1 203 1353-5   540        
585158.3 Staphylococcus aureus subsp. aureus M876 [B] C 2605-1 1055 2228-5, 2141-5   1349        
585159.3 Staphylococcus aureus subsp. aureus M899 [B] C 2168-1 669 1696-5   963        
548470.3 Staphylococcus aureus subsp. aureus MN8 [B] C 2272-1 1545 2423-5, 2511-5   1659        
282458.4 Staphylococcus aureus subsp. aureus MRSA252 [B] C 2163-1 567 1798-5, 1704-5   877        
Genome ID Organism Variant Code *AlaR IlvE *IscS NifS SufS CsdA AlaB IlvY *AvtA
282458.1 Staphylococcus aureus subsp. aureus MRSA252 [B] C 2037-1 531 1609-5   819        
282459.5 Staphylococcus aureus subsp. aureus MSSA476 [B] C 2056-1 534 1706-5, 1619-5   819        
282459.1 Staphylococcus aureus subsp. aureus MSSA476 [B] C 1951-1 507 1543-5   779        
196620.5 Staphylococcus aureus subsp. aureus MW2 [B] C 2070-1 538 1639-5, 1727-5   840        
196620.1 Staphylococcus aureus subsp. aureus MW2 [B] C 1994-1 509 1572-5   797        
418127.6 Staphylococcus aureus subsp. aureus Mu3 [B] C 2113-1 557 1653-5   860        
418127.4 Staphylococcus aureus subsp. aureus Mu3 [B] C 1906-1 520 1496-5   787        
158878.14 Staphylococcus aureus subsp. aureus Mu50 [B] C 2144-1 560 1675-5   869        
585891.3 Staphylococcus aureus subsp. aureus Mu50-omega [B] C 2141-1 559 1672-5   868        
Genome ID Organism Variant Code *AlaR IlvE *IscS NifS SufS CsdA AlaB IlvY *AvtA
158878.1 Staphylococcus aureus subsp. aureus Mu50 [B] C 2070-1 554 1622-5   844        
158879.11 Staphylococcus aureus subsp. aureus N315 [B] C 2028-1 538 1564-5   830        
158879.1 Staphylococcus aureus subsp. aureus N315 [B] C 1940-1 526 1497-5   798        
93061.5 Staphylococcus aureus subsp. aureus NCTC 8325 [B] C 2089-1 482 1575-5, 1664-5   772        
93061.3 Staphylococcus aureus subsp. aureus NCTC 8325 [B] C 2176-1 521 1741-5   814        
548474.3 Staphylococcus aureus subsp. aureus TCH130 [B] C 1959-1 2120 2179-5, 688-5   1402        
548473.3 Staphylococcus aureus subsp. aureus TCH60 [B] C 2499-1 1376 1565-5, 1652-5   1076        
548475.3 Staphylococcus aureus subsp. aureus TCH70 [B] C 2640-1 38 611-5, 700-5   1142        
367830.3 Staphylococcus aureus subsp. aureus USA300 [B] C 328-1 548 393-5   106        
Genome ID Organism Variant Code *AlaR IlvE *IscS NifS SufS CsdA AlaB IlvY *AvtA
451515.3 Staphylococcus aureus subsp. aureus USA300_FPR3757 [B] C 2166-1 601 1724-5, 1813-5   908        
451516.9 Staphylococcus aureus subsp. aureus USA300_TCH1516 [B] C 2155-1 591 1802-5, 1713-5   914        
450394.6 Staphylococcus aureus subsp. aureus USA300_TCH959 [B] C 2642-1 459 880-5, 968-5   42        
585160.3 Staphylococcus aureus subsp. aureus WBG10049 [B] C 1554-1 78 1162-5   374        
585161.3 Staphylococcus aureus subsp. aureus WW2703/97 [B] C 1896-1 417 1344-5   584        
505321.3 Staphylococcus aureus subsp. aureus str. CF-Marseille [B] C 1211-1 1169 2144-5, 437-5   2426        
546342.3 Staphylococcus aureus subsp. aureus str. JKD6008 [B] C 304-1 2683, 2684 934-5, 2067-5   188        
546343.3 Staphylococcus aureus subsp. aureus str. JKD6009 [B] C 1629-1 1031 1132-5, 2412-5   1962        
426430.8 Staphylococcus aureus subsp. aureus str. Newman [B] C 2162-1 563 1653-5, 1742-5   855        
Genome ID Organism Variant Code *AlaR IlvE *IscS NifS SufS CsdA AlaB IlvY *AvtA
426430.6 Staphylococcus aureus subsp. aureus str. Newman [B] C 1922-1 517 1561-5, 1478-5   769        

Spreadsheet Options


















notes

  Alanine biosynthesis I is established only by existence of the relevant 
enzymes. Its contribution to alanine synthesis remains speculative because 
alanine auxotrophs have not yet been isolated. Because alanine but not valine 
represses AvtA, its primary purpose is probably synthesis of L-alanine.

The alanine biosyntheis III pathway, mediated by cysteine desulfurase activity 
is required to donate sulfane sulfur for the synthesis of Fe-S clusters, 
thiamine, thionucleosides in tRNAs, biotin, lipoic acid, and molybdopterin 
probably contributes only a minor amount of the cell's alanine requirement, as 
judged by the cell's total requirement for sulfane sulfur.

In many eubacteria, alanine racemase occurs as a homodimer. These subunits 
constitute a major and minor component. In E coli these genes are denoted as 
dadX (major) and alr(minor).

Bioinformatic analyses currently recognize the AvtA structure as similar to the 
class I  or class I/II structures of ATs, which represent the most common types 
of ATs present in C. glutamicum. Nevertheless, AvtA is the only AT with 
exceptionally high activity toward L-alanine as an amino donor instead of 
preferably using L-glutamate.

===========REFERENCES:=============

1. Karp, P.D. (2003)The MetaCyc Metabolic Pathway Database in: Metabolic 
Engineering, B. Kholodenko and H. Westerhoff eds., Horizon Scientific Press.

2. Wang MD, Liu L, Wang BM, Berg CM. Cloning and characterization of the 
Escherichia coli K-12 alanine-valine transaminase (avtA) gene.J Bacteriol. 1987 
Sep;169(9):4228-34.PMID: 3040683

3. Marienhagen J, Kennerknecht N, Sahm H, Eggeling L. Functional analysis of all 
aminotransferase proteins inferred from the genome sequence of Corynebacterium 
glutamicum. J Bacteriol. 2005 Nov;187(22):7639-46. PMID: 16267288

4. Mihara H, Esaki N. Bacterial cysteine desulfurases: their function and 
mechanisms.Appl Microbiol Biotechnol. 2002 Oct;60(1-2):12-23. Epub 2002 Sep 4. 
Review.PMID: 12382038