Pelodictyon phaeoclathratiforme BU-1

Gram-negativeBacilliNon-motileAnaerobic

Kingdom

Pseudomonadati

Phylum

Chlorobiota

Class

Chlorobiia

Order

Chlorobiales

Family

Chlorobiaceae

Genus

Pelodictyon

Description

Pelodictyon phaeoclathhratiforme is a green sulfur bacterium frequently observed in stratified freshwater lakes where light reaches sulfide-containing water layers; it frequently represents the dominant green sulfur bacterium in this habitat. BU 1, the type strain, was isolated from water samples of Buchensee, Germany in 1989. This lake is meromictic, that is the surface and deep waters do not mix; BU 1 was isolated from 9 m deep water. Like all green sulfur bacteria, this species is strictly anaerobic and obligately phototrophic. Photosynthetic pigments comprise mainly bacteriochlorophyll e and isorenieratene/b -isorenieratene plus small amounts of bacteriochlorophyll a. It is actually a brown color. P.phaeoclathratiforme forms net-like microcolonies and has intracellular gas vesicles. Ternary fission, which leads to the formation of ring-shaped and branched colonies, is observed at growth-limiting light intensities. Gas vesicles are proteinaceous hollow rigid structures which occur only in prokaryotic cells which are impermeable to liquid but permeable to gases. Because of their gas content, gas vesicles decrease the density of the cell and may provide neutral or even positive buoyancy if present in sufficient amounts. Like ternary fission, gas vesicles are exclusively observed in cells grown at light intensities below 5 umol photons m-2 s-1. Unlike some cyanobacteria, cells of P.phaeoclathratiforme do not attain positive buoyancy and thus are unlikely to rise to the lake surface and to leave their habitat. The capability of buoyant density regulation offers one explanation for the dominance of P.phaeoclathratiforme in many stratified lakes (modified from http://genome.jgi-psf.org/finished_microbes/pelph/pelph.home.html). (HAMAP: PELPB)

Taxonomy

KingdomPseudomonadati
PhylumChlorobiota
ClassChlorobiia
OrderChlorobiales
FamilyChlorobiaceae
GenusPelodictyon
SpeciesPelodictyon phaeoclathratiforme
StrainBU-1

Profile

Physiology
Gram staining propertiesNegative
ShapeBacilli
MobilityNo
Flagellar presenceYes
Number of membranes2
Image of Pelodictyon phaeoclathratiforme BU-1
Ecology, Host, and Life Cycle
Oxygen requirementsAnaerobic
Optimal temperature15
Temperature rangeMesophilic
HabitatMultiple
Biotic relationshipFree living
Host(s)Not Available
Cell arrangementSingles
SporulationNonsporulating
Energy sourcePhototroph- Photosynthetic
PathogenicityNot Available

Genome Summary

Pelodictyon phaeoclathratiforme BU-1

Accession NumberNC_011060.1

Gene Summary

Adenine Count

Not Available

Thymine Count

Not Available

Guanine Count

Not Available

Cytosine Count

Not Available

Genome Length

Not Available

Protein-coding Genes

2861 genes

Non-Coding Genes

61 genes

# of Chromosomes/Plasmids

1

Genes

NameLocus TagUniProtStrandCoordinatesMolecular Weight
hypothetical proteinPPHA_RS16450Not Available-22084 - 222094627.48
rne/rng family ribonucleasePPHA_RS00110Not Available+22598 - 2428663354.8
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate n-succinyltransferasePPHA_RS00115Not Available+24313 - 2517630860.3
s41 family peptidasePPHA_RS00120Not Available+25181 - 2693864358.0
duf3593 domain-containing proteinPPHA_RS00125Not Available-26929 - 2761525277.5
geranylgeranyl diphosphate reductasePPHA_RS00130Not Available-27616 - 2875842387.6
glycine--trna ligasePPHA_RS00135Not Available-28762 - 3023756560.4
dsre family proteinPPHA_RS00140Not Available+30497 - 3086212878.6
ykgj family cysteine cluster proteinPPHA_RS00145Not Available-30963 - 3173630211.0
hypothetical proteinPPHA_RS00155Not Available+31945 - 3222910734.8

Displaying genes 21 – 30 of 2922 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

57 records
Metabolite IDMetabolite nameStructureCAS number
BASm0000217alpha-ribazoleC14H18N2O4Chemical structure of alpha-ribazoleNot available
Average278.3037Da
Monoisotopic278.126657074Da
BASm00002512-dehydropantoateC6H9O4Chemical structure of 2-dehydropantoateNot available
Average145.1333Da
Monoisotopic145.050083776Da
BASm0000377(S)-malateC4H4O5Chemical structure of (S)-malateNot available
Average132.0716Da
Monoisotopic132.005873238Da
BASm0000387(6R)-5,10-methylene-5,6,7,8-tetrahydrofolateC20H21N7O6Chemical structure of (6R)-5,10-methylene-5,6,7,8-tetrahydrofolateNot available
Average455.432Da
Monoisotopic455.1564286Da
BASm0001717fumarateC4H2O4Chemical structure of fumarateNot available
Average114.0563Da
Monoisotopic113.9953086Da
BASm0001845nicotinateC6H4NO2Chemical structure of nicotinateNot available
Average122.1015Da
Monoisotopic122.0242034Da
BASm0001865diphosphateHO7P2Chemical structure of diphosphateNot available
Average174.95Da
Monoisotopic174.9213971Da
BASm0001921(S)-3-methyl-2-oxopentanoateC6H9O3Chemical structure of (S)-3-methyl-2-oxopentanoate1460-34-0
Average129.1339Da
Monoisotopic129.0551692Da
BASm00021577-cyano-7-deazaguanineC7H5N5OChemical structure of 7-cyano-7-deazaguanineNot available
Average175.1475Da
Monoisotopic175.0494098Da
BASm0002305(S)-2-ethyl-2-hydroxy-3-oxobutanoateC6H9O4Chemical structure of (S)-2-ethyl-2-hydroxy-3-oxobutanoateNot available
Average145.135Da
Monoisotopic145.0506324Da

Displaying 1–10 of 57 metabolites