Plant NRAMP family database · release 1

A searchable atlas for plant NRAMP evolution.

Integrating NRAMP homologs and annotations from red algae, green algae, charophytes, bryophytes, lycophytes, ferns, gymnosperms, basal angiosperms, monocots, and dicots for comparative browsing, phylogenetic analysis, and N-terminal dileucine-like motif research.

Dataset signature

One curated family, several biological views.

Built around 504 master annotations, complete protein and CDS sequences, motif/TM1 coordinates, multiple sequence alignments, and a Newick phylogeny.

—NRAMP records

—plant groups

—motif +

Coverage—NRAMP protein records

Taxonomy—species / source labels

Motif—motif-positive records

TM1 detail—motif + TM1 coordinate rows

Dataset overview

Lineage breadth and annotation balance

All statistics are calculated directly from the supplied master table. Clade-Y and Clade-X naming is used consistently across every module.

Records by plant group

Ten representative plant lineages

10 groups

NRAMP clade composition

Display names used throughout the database

clade profile

—records

Predicted localization

DeepLoc category distribution

Data readiness

Files connected in this release

Complete: 504 annotation rows, 504 protein sequences, 504 CDS sequences, a 504-sequence alignment and a 504-leaf phylogenetic tree.

Motif/TM1: 140 motif-positive records; 129 include motif sequence, motif coordinates and first transmembrane-helix coordinates.

Sequences: — available directly from the supplied FASTA files.

Browse records

Filter the NRAMP collection

Combine species, plant group, NRAMP clade, predicted localization, and motif filters, then open any record to inspect its sequences and full annotation.

Gene / protein ID	Species	Group	Length	Clade	Motif	DeepLoc

—

Motif module

N-terminal dileucine-like motif

Motif and TM1 coordinates come from the supplied absolute-position table. Missing coordinates remain unassigned rather than inferred.

Clade-Y enrichment

Motif-positive NRAMPs form a focused Clade-Y annotation layer.

[D/E]xxxL[L/I]

All 129 records in the coordinate table belong to Clade-Y, enabling comparison of motif start positions, distance to TM1, and distribution across plant groups.

Positive—motif-positive records

Coordinates—detailed position rows

Before TM1—motifs before first TM helix

Clade—coordinate-row clade

Motif start positions

Distribution across coordinate rows

Motif-positive records by group

Presence counts from the master table

Coordinate records

Open a row to inspect its complete record.

129 rows

Protein ID	Motif	Position	TM1	Distance	Group

Phylogeny module

NRAMP phylogeny and annotation map

The supplied Newick tree is rendered with all 504 leaves and aligned annotation tracks for plant group, clade, DeepLoc prediction, and motif status.

Clade × annotation matrix

Motif and localization composition by NRAMP clade

Clade	Records	Motif +	PM-like	Endo-like	Motif ratio

Full annotated tree

Scroll inside the frame to inspect all 504 leaves. Hover over an annotation block to view its value.

Download SVG

GroupCladeDeepLocMotif status

Downloads

Data and source files

Download the supplied source files under reusable standard names, or export the current filtered result set from the Browse module.

CSV · generated

Integrated annotation table

504 records with displayed clade names and decoded duplication types.

Download TSV · source

NRAMP master table

Original group, species, clade, localization, network and duplication fields.

Download XLSX · source

Original annotation form

The supplied 504-row annotation workbook.

Download XLSX · source

Motif / TM1 coordinates

129 records with motif and first transmembrane-helix coordinates.

Download XLSX · source

Protein lengths

Protein IDs and lengths for all 504 records.

Download FASTA · 504 proteins

NRAMP protein sequences

Complete supplied protein sequence collection.

Download FASTA · 504 CDS

NRAMP CDS sequences

Complete supplied CDS sequence collection keyed by protein ID.

Download FASTA · alignment

Full NRAMP alignment

The supplied N120 alignment for all 504 sequences.

Download FASTA · Clade-Y

Clade-Y alignment

The supplied 163-sequence Clade-Y alignment.

Download NEWICK · source

Phylogenetic tree

Supplied tree topology, support labels and branch lengths.

Download SVG · generated

Annotated tree figure

504-leaf tree with group, clade, localization and motif strips.

Download

CSV · live view

Current filtered records

Export the exact result set selected in Browse.

About the database

Scope and provenance

A static, portable release built directly from the supplied study files.

This database integrates and presents the plant NRAMP homologs identified in this study together with their associated annotations across ten representative plant groups. Records can be browsed by species, plant group, NRAMP clade, predicted localization, and motif status. Each entry includes a gene/protein identifier, species, protein length, clade, localization, motif and TM1 coordinates, duplication type, protein sequence, and CDS sequence. The phylogeny module aligns tree topology with group, clade, localization, and motif annotations, while the download module provides annotation tables, sequences, alignments, and tree files.

Data boundary: The current master table provides a unified pepid only, so Gene ID and Protein ID display the same source identifier. Species-level complete CDS, protein, GFF3, and genome files can be added in a later release.

Duplication type legend

Numeric genetype codes are decoded throughout the database.

Code	Displayed type
0	singleton
1	dispersed
2	proximal
3	tandem
4	whole-genome duplication-derived