General graphical overview of Respiratory subsystems
:http://brucella.uchicago.edu/SubsystemForum/showthread.php?t=95

Variant codes:
1-4 subunit succinate dehydrogenase (2 catalitic+2 anchor subunits), 0r 3 subunits (1.5-cytochrome subunit is missing) or (1.11) 4 subunit succinate dehydrogenase + hypothetical fumarate reductase flavoprotein (hypothetical oxidoreductase, not related??)
2-4 subunit fumarate reductase , or (2.11)- 4 subunits or (2.10)-3-subunits succinate dehydrogenase
3-4 or 3 subunit succinate dehydrogenase and 4 or 3 (or 1-soluble) subunit fumarate reductase
4-3 subunit succinate dehydrogenase and 3 subunit fumarate reductase
5-3 subunit succinate dehydrogenase (or, in some cases, fumarate reductase?)
6-4 subunit succinate dehydrogenase and 3 subunit fumarate reductase
7-3 subunit fumarate reductase
8-2 subunit succinate dehydrogenase or fumarate reductase (only catalitic subunits are present): soluble succinate dehydrogenase?
9-hypothetical fumarate reductase subunit only

Overview and notes:

The super-macromolecular respiratory complex II (succinate:quinone oxidoreductase) couples the oxidation of succinate in the matrix / cytoplasm to the reduction of quinone in the membrane. This function directly connects the Krebs cycle and the aerobic respiratory chain. The complex has been isolated from several sources and appears to be highly homologous in terms of the subunit composition and prosthetic groups. In general, it consists of three to four different subunits and contains one FAD, three distinct types of FeS cluster and one or two protoheme IX as prosthetic groups. FAD binds covalently to the largest flavoprotein subunit (60-75 kDa) and all FeS clusters are probably located in the second largest iron-sulfur subunit (25-30 kDa). These two subunits constitute a peripheral portion of complex II, which can function as a water-soluble succinate dehydrogenase upon release from membranes. In extreme halophile Halobacterium salinarium (f. halobium) and an extreme thermoacidophile Sulfolobus acidocaldarius strain DSM 639 66-kDa flavoprotein subunits derived from their membrane-bound complexes can alone function as a water-soluble succinate dehydrogenases. The reverse reaction has a function in anaerobic respiration as electron acceptor and is known as Fumarate reductase. Succynate dehydrogenase and Fumarate reductase have the same EC number.
For succinate:quinone oxidoreductase activity, however, two (or one in Bacillus subtilis enzyme ) smaller membrane-spanning subunits are required. This lipophilic part of respiratory complex II usually carries one (e.g. mitochondrial, E. coli, and P. denitrificans complexes II) or two protoheme groups (e.g. B. subtilis complex II). Aside from the structural importance, the functional role of protoheme has not been clarified. Protoheme center of the Escherichia coli enzyme is almost fully reduced by succinate and can be re-oxidized by fumarate, and that of highly active Paracoccus denitrificans complex II is not reducible at all ; B. subtilis complex II contains two protoheme centers in a single membrane-anchor subunit (cytochrome b558), of which only one is fully reducible by succinate . The absence of any heme group in Sulfolobus complex II indicates that the low-potential heme b in other respiratory complex II may not be involved in the redox intermediates of the electron transfer from succinate to quinone.
Functional differences of lipophilic subunits may be ,probably, guessed from their sequences. There are quit distant from E.coli cytochrome b-556 groups of anchor proteins ,for instance, in: Bacilli (cytochrome B-558), Patracocci,Xanthomonas and Eucarya (cytochrome B-560),Archaea. Membrane-anchor subunits are less homologous compared to the cases of the flavoprotein and iron-sulfur subunits of mitochondrial and aerobic bacterial respiratory complexes II . From the other side, a comprehensive phylogenetic analysis of the core subunits of succinate:quinone oxidoreductases and quinol:fumarate oxidoreductases show that the classification of the enzymes based on the type of the membrane anchor fully correlates with the specific characteristics of the two core subunits. In general cytochrome B-558 has a highest redox potential and can support both succinate and fumarate reductase activities. Cytochrome B-560 correlates with the lowest fumarate reductase activity of the complex.

Fumarate reductase complex in E.coli contains 2 catalitic subunits , homologous to ones of Succinate oxidoreductase complex and 2 specific hydrophobic anchor proteins. Mutations, physically located within the fumarate reductase anchor domain of E.coli, is manifested by altered catalytic properties, indicating that the intrinsic and extrinsic domains of fumarate reductase are conformationally connected. Helicobacter pylori fumarate reductase is composed by 3 subunits, one of which is cytochrome b polypeptide. Shewanella putrefaciens produces a soluble fumarate reductase ( flavocytochrome c) under anaerobic growth conditions. This protein shares sequence similarity with the catalytic subunits of membrane-bound fumarate reductases from Escherichia coli and works in combination with CymA is an immediate electron donor.

Flavoprotein and iron-sulphur subunits are homologous in Succinate dehydrogenase and Fumarate reductase. I decided to leave annotations for those subunits as Succinate dehydrogenase subunits. Nevertheless, proteins belonging to Fumarate reductase complex can be distinguished by their position in a genome: they always belong to Fumarate reductase anchor (like in E.coli) or Fumarate reductase cytochrome b protein (like in Heliobacter) gene cluster.Sometimes there are only catalitic subunits present in a genome, that likely represent soluble form of fumarate reductase (by analogy to known soluble Shewanella putrefaciens enzyme). I am leaving fumarate-reductase related functions as the spreadsheet entries also because there might be proteins, which particular function could not be distinqueshed.

Succinate dehydrogenase anchor protein is missing in Cyanobacteria and some other organisms. If it is really required in those particular organisms(no experimental data yet) it should be non-ortologous to known ones and is likely not to belong to Succinate dehydrogenase gene cluster, as I found no good candidates looking briefly through related chromosome regions. There is one NCBI record on Nostoc punctiforme SDH anchor protein, which is doubtful;I put it in a separated column. I found few candidates in other organisms in which these functions were missing and annotated them as 'Hypothetical succinate dehydrogenase membrane anchor protein's.

Cytochrome B subunits differ by types of protohaem or other active group(s) they are baring,which is reflected in a protein sequences. Sequence difference is not strong enough to use the latter as a background for a detailed functional assignment. Unless there is experimental evidence, indications from PIR families or high homology to proteins with known properties, we consider those cytochromes to be of b-556 type.

There are no NCBI records regarding cyanobacterial Succinate dehydrogenase cytochrome b subunit. Nevertheless we found an alternative form by long-range homology in Prochlorococci, Synechococcy, Chlorobium as well as in some other bacteria. Synechocystis, Nostoc, Crocosphaera, Trichodesmium and Thermosynechococcus have the second putative alternative candidate for Succinate dehydrogenase cytochrome b subunit, homologous to a new form from Sulfolobus.The latter has a novel Center C composed by Fe2-S2 clusters, which is an inherent redox center in the archaeal complex II (Iwasaki et al,J Biol Chem. 2002 Oct 18;277(42):39642-8.). We annotated it homologs as: putative succinate dehydrogenase subunits C. (Old annotation for the protein from Sulfolobus was: Heterodisulfide reductase. Interesting, that 2-mercaptoethane-sulfonic acid (HS-CoM) was established as one of a direct electron donors for fumarate reductase in Methanobacteria). By analogy to Sulfolobus protein we can suggest that these subunits in cyanobacteria might have only structural but not functional role.