Table 2 Functional domains present in some hypothetical proteins secreted by R. etli in stationary growth phase

gi|21492958

IPB000209

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes, (serine-carboxyl peptidases).

gi|86355844

IPR010662

The structure shows an alpha-beta hydrolase fold suggesting an enzymatic function for these proteins. The crystal structure from B. subtilis has been solved.

gi|86356671

PDOC00169

Cytochrome c-type centres are also found in the active sites of many enzymes, including cytochrome cd1-nitrite reductase as the N-terminal haem c domain, in quinoprotein alcohol dehydrogenase as the C-terminal domain, in Quinohemoprotein amine dehydrogenase A chain as domains 1 and 2, and in the cytochrome bc1 complex as the cytochrome bc1 domain.

gi|86357010

IPR010221 VCBS

IPR006644 Dystroglycan-type cadherin-like

In animals, cadherin domain-containing proteins are adhesion molecules that modulate a wide variety of processes including cell polarization and migration but they have also been identified in yeast and magnetotactic bacteria. Crystal structures have revealed that multiple cadherin domains form Ca²⁺-dependent rod-like structures with a conserved Ca²⁺-binding pocket at the domain-domain interface.

IPR008009 Putative Ig

This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion. In the Sushi repeat-containing protein (SrpX), this domain is found between two sushi repeats. PKD domains are also found in other proteins, usually in the extracellular parts of proteins involved in interactions with other proteins. For example, domains with a PKD-type fold are found in archaeal surface layer proteins that protect the cell from extreme environments.

IPR005066 Moybdenum cofactor oxidoreductase, dimerisation

The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism.

This domain of about 100 residues is found multiple (up to 35) copies in long proteins from several species of Vibrio, Colwellia, Bradyrhizobium, and Shewanella (hence the name VCBS) and in smaller copy numbers in proteins from several other bacteria. The large protein size and repeat copy numbers, species distribution, and suggested activities oouter membrane adhesin like protein.

gi|86357471

EC:2

IPR013785 Aldolase-type TIM barrel

This entry represents the TIM beta/alpha barrel found in aldolase and related proteins. This TIM barrel usually covers the entire protein structure. Proteins containing this TIM barrel domain include class I aldolases, class I DAHP synthases, class II fructose-bisphosphate aldolases (FBP aldolases), and 5-aminolaevulinate dehydratase (a hybrid of classes I and II aldolases)

IPR006638 Elongator protein 3/MiaB/NifB

This domain is found in MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases

IPR007197 Radical SAM

Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre.

gi|86357955

EC:4.2.3.5

Chorismate synthase catalyzes the last of the seven steps in the shikimate pathway which is used in prokaryotes, fungi and plants for the biosynthesis of aromatic amino acids. It catalyzes the 1,4-trans elimination of the phosphate group from 5-enolpyruvylshikimate-3-phosphate (EPSP) to form chorismate which can then be used in phenylalanine, tyrosine or tryptophan biosynthesis. Chorismate synthase requires the presence of a reduced flavin mononucleotide (FMNH2 or FADH2) for its activity. Chorismate synthase from various sources shows a high degree of sequence conservation. It is a protein of about 360 to 400 amino-acid residues).

gi|86358739

GI:241205844

Integral membrane protein which is thought to regulate cation conductance. A variety of proteins belong to this family. These include the prohibitins, cytoplasmic anti-proliferative proteins and stomatin, an erythrocyte membrane protein. Bacterial HflC protein also belongs to this family.

gi|86360288

PS00495

The apple domain has an N-terminal region that contains four tandem repeats of about 90 amino acids and a C-terminal catalytic domain. The 90 amino-acid repeated domain contains 6 conserved cysteines. It has been shown that three disulphide bonds link the first and sixth, second and fifth, and third and fourth cysteines. This entry contains apple-like domains, which are presented in Plasminogen, Caenorhabditis elegans hypothetical ORFs and the extracellular portion of plant S-locus glycoproteins and S-receptor kinases. The domain is predicted to possess protein-and/or carbohydrate-binding functions.

gi|86360818

PF 06724

This region consists of two a pair of transmembrane helices and occurs three times in each of the family member proteins.

gi|89255303

PF04972

The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate.