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

Subsystem: Alr_Ahuja

Author:


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)


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