NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters
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Scaffold Ga0058863_11965738

Scaffold Ga0058863_11965738


Overview

Basic Information
Taxon OID3300004799 Open in IMG/M
Scaffold IDGa0058863_11965738 Open in IMG/M
Source Dataset NameSwitchgrass rhizosphere and bulk soil microbial communities from Kellogg Biological Station, Michigan, USA for expression studies - soil CB-3 (Metagenome Metatranscriptome)
Source Dataset CategoryMetatranscriptome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)1729
Total Scaffold Genes6 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)6 (100.00%)
Novel Protein Genes5 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)5 (100.00%)
Associated Families5

Taxonomy
Not Available(Source: )

Ecosystem & Geography

Source Dataset Ecosystem
Host-Associated → Human → Digestive System → Large Intestine → Fecal → Host-Associated → Switchgrass Rhizosphere And Bulk Soil Microbial Communities From Kellogg Biological Station, Michigan, Usa For Expression Studies

Source Dataset Sampling Location
Location NameKellogg Biological Station, Michigan, USA
CoordinatesLat. (o)42.3912Long. (o)-85.383786Alt. (m)Depth (m)
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F023966Metagenome / Metatranscriptome208Y
F042033Metagenome / Metatranscriptome159Y
F044745Metagenome / Metatranscriptome154Y
F061313Metagenome / Metatranscriptome132Y
F081702Metagenome / Metatranscriptome114Y

Sequences

Protein IDFamilyRBSSequence
Ga0058863_119657381F023966AGGAGGMDPNNRVLSRMGARELTEQEVDAVQGAFVRHTLTPCFIDKKQQLLNGDQSIGECG*
Ga0058863_119657382F061313AGGAGMNDHNRVLVRRGARDLTEKEVEQVCGGLRTATKCSVTAAGAIDGDLHECS*
Ga0058863_119657383F044745GGAMNDQNRVLIRKGARDLNEQEVAMVSGGLRTLTACTLAAAGTLDGDTFHSECGSPDQ*
Ga0058863_119657385F042033GGAMKGRKNMDDQNRVLIRRGARSLNQEEIERVGGGISTTTLCTVPSTTCPNKDGDASIGECGHGC*
Ga0058863_119657386F081702AGGAGMDDQTRVLLRQGSRELSQGEVEQVGGGFNTLSITFGPNGRDGDGSLGES*
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Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"
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