V.0.1

Phototrophy
TIGR03753	beta-carotene 15,15'-monooxygenase, Brp/Blh family
pf01036 rhodopsin

####REMOVED DUE NON-DISCRIMINATORY MATCHES#####
Peptidase activity
pf01364	Peptidase family C25
pf04151	Bacterial pre-peptidase C-terminal domain
pf03415	Clostripain family
pf04389	Peptidase family M28
pf02163	Peptidase family M50
pf01546	Di- and tripeptidases
pf02073	Leucyl aminopeptidase (aminopeptidase T)
pf00557	Xaa-Pro aminopeptidase
pf03413	Peptidase propeptide and YPEB domain
pf01432	Oligoendopeptidase F
pf00266	Phosphoserine aminotransferase
pf01252	Lipoprotein signal peptidase
pf01433	Aminopeptidase N
pf00246	Zinc carboxypeptidase
pf00717	Peptidase S24-like
pf10502	Peptidase S26
pf04951	D-aminopeptidase
pf05299	M61 glycyl aminopeptidase
#####

Alternative nitrogenase
TIGR01860	nitrogenase vanadium-iron protein, alpha chain vnfD
TIGR01861	nitrogenase iron-iron protein, alpha chain anfD
TIGR02931	Fe-only nitrogenase, beta subunit anfK [also potentially pf00148, Nitrogenase component 1 type Oxidoreductase]
TIGR02932	V-containing nitrogenase, beta subunit vnfK
TIGR02930	V-containing nitrogenase, delta subunit vnfG
TIGR02929	Fe-only nitrogenase, delta subunit anfG
pf03139	Vanadium/alternative nitrogenase delta subunit, targets vnfG (V) and anfG (Fe) alternatives

Ammonia transporter
pf00909 Ammonium Transporter Family (high-affinity ammonia transporter)

DMSP Lyase
PF16867		dddQ
14591		dddP - requires a much more strigent bit score cutoff (recommend >500)
25993		dddD - requires a much more strigent bit score cutoff (recommend >500)
94923		dddK
274874		dddW

DMSP Synthase
4254		dsyB - requires a more strigent bit score cutoff (recommend >260)

Methylphosphonate biosynthesis

####REMOVED DUE NON-DISCRIMINATORY MATCHES#####
Amphibactin biosynthesis
	Multiple SFAM models have exceptionally high bit score matches to reference sequences (>>1000). Both ABO2092 and ABO2903 have common domains and as such share the highest SFAM models
	Recorded the best two models for all references and require both to successfully match for identification
	1544	ABO2902/3 - requires a much more strigent bit score cutoff (recommend >1000)
	27549	ABO2902/3 - requires a much more strigent bit score cutoff (recommend >1000)
#####


Ferrioxamine biosynthesis
	Limited references for comparison. Known to occur as operon in Streptomyces. Each gene matched an SFAM model with at least bit score >200, 3 of 4 top hit is over 500 bit score
	Will required a minimum of 200 bit score for all matches. Check to the presense of all 4 genes in operon
	2219	SCO2782 DesA putative pyridoxal-dependent decarboxylase - requires a more strigent bit score cutoff (recommend >200)
	2732	SCO2783 DesB putative monoxygenase - requires a more strigent bit score cutoff (recommend >200)
	9429	SCO2784 DesC putative acetyltransferase - requires a more strigent bit score cutoff (recommend >200)
	51934	SCO2785 DesD putative siderophore biosynthetic protein	- requires a more strigent bit score cutoff (recommend >200)

Metal Transporters
	TIGR02459	Cobalt transporter CbtB
	TIGR00003	Copper binding HMA (heavy-metal-associated) protein
	TIGR00820	Fe, Zn, Mn permease ZupT
	