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CP088958.1_900
Synechococcus elongatus
Environmental
Core
GLOB
DeepTMHMM: Globular (cytoplasmic)
3 orgs · 3 genera
Homologs in other genera: conserved beyond this protein's own lineage.
Known before
Annotations from existing tools, carried by related sequences — not run on this query
eggNOG
Description
Domain of unknown function (DUF4062)
InterPro · related sequences
Pfam · PF13271
Domain of unknown function (DUF4062)
LLM Annotation
B
DUF4062 domain-containing protein, putative NACHT-family NTPase.
enzyme
the call names none
the enzyme this call names, as read out of it by a second pass
why
The query has a strong DUF4062 domain hit; homologs at 33.0–34.4% identity share this domain. A 100%-identity STRING match belongs to COG5635, described as a predicted NACHT-family NTPase. No biochemical activity, substrate-specific fitness measurements, or coherent conserved pathway neighborhood is provided. The Fitness Browser hit supplies only a hypothetical-protein annotation.
Why this tier
Tier B: the identical STRING homolog provides a named NTPase-family assignment, supporting a qualified family-level annotation alongside the query's DUF4062 domain. The distant E. coli homolog's experimental summary concerns a synonymous mutation and clone phenotypes, without demonstrating this protein's molecular function. Biochemical characterization, fitness measurements, cofitness, and STRING functional partners are absent. Specific ATPase activity and roles in biofilm formation, antibiotic tolerance, or DNA repair are unsupported; neighboring repair-related genes do not establish those functions.
GO terms
1 term
why these terms
The annotation describes the protein as a 'putative NACHT-family NTPase'. The reasoning trace indicates that this assignment is based on a homolog and the protein's domain (DUF4062). While 'putative' and 'family-level' suggest lower confidence, the term 'NTPase' directly maps to 'ribonucleoside triphosphate phosphatase activity' (GO:0017111), which lists 'NTPase activity' as an exact synonym. The trace specifically rejects more specific functions like 'ATPase activity' or roles in biofilm formation and DNA repair due to lack of evidence. Therefore, I assign the most general NTPase activity term. No cellular component or biological process is stated.
molecular function
GO:0017111
ribonucleoside triphosphate phosphatase activity
medium
the extractor's own confidence label, as given
“putative NACHT-family NTPase”
— from the call
Token cost
15,577 total
15,343
Input
234
Output
15,577
Total
✱
Your review — is the call supported by the evidence?
name
Judge the annotation against the evidence below. Pick a verdict, optionally propose a better annotation or add notes, and save. Keys 1–5 pick a verdict; ⌘↵ saves and moves to the next protein in your queue; j / k step through it.
1
supported
the evidence shown to the annotator backs this call
2
overreach
the call claims more than its evidence supports
3
under-called
the evidence supported a more specific call than this
4
wrong
the call is not what this protein does
5
can't tell
the evidence does not settle it either way
propose a corrected annotation
seed from:
the call
DUF4062 domain-containing protein, putative NACHT-family NTPase.
eggNOG
Domain of unknown function (DUF4062)
InterPro
Domain of unknown function (DUF4062)
the annotation as you would write it — reasoning goes in notes
notes
save
save & next →
⌘↵
verdict
1
supported
the evidence shown to the annotator backs this call
2
overreach
the call claims more than its evidence supports
3
under-called
the evidence supported a more specific call than this
4
wrong
the call is not what this protein does
5
can't tell
the evidence does not settle it either way
save & next →
notes ↑
back to the full form, for notes or a corrected annotation
Protein Sequence
362 amino acids
Membrane topology
no signal peptide or membrane-spanning segment
DeepTMHMM on this sequence
DeepTMHMM
cytoplasmic 1–362
1–362
Domains
1 InterProScan hits on this sequence, as the annotator saw them
PFAM
6–87
Domain of unknown function DUF4062
Domain of unknown function DUF4062
curated family (HAMAP, PIRSF, NCBIfam, PANTHER)
domain model (Pfam, SMART, PROSITE, PRINTS)
structural (Gene3D, SUPERFAMILY, CDD)
other
Sequence · 362 aa
MEKRYQIFISSTFIDLKDERQAALKAILEIDHMPAGMELFSATDDSAWQLIQDVIDSSDY
YILIVGGRYGSLDEAGLSYTEKEYDYALLTKKPVIPLLHENPDNLPRDKTETDSNAWKKL
QDFRKKVQKKHTCVYWRNADDLKAKVIVGLTSAIKRHPAVGWVRADKVPTETALAEVLSL
KNKITELEKEAALLRDKPPSGTEFLAQGNDKYEIHLSFKSRGKFSIFSHDEDKKYNASIN
LTWNAIFAAVAPSMINEASAHTLRQAFTDFFKRESLKAFQSQKRFENYELVDFSFHKDEI
ETCIVQLRALGLIKENDRKRSVSDTSTYWTLTPYGNTLMVQLRAIKREPLEDEDLDGTAV
ES
Copy sequence
Copy as FASTA
Shown to the annotator
the evidence the call was made from
PaperBLAST
1
Fitness —
no evidence of this kind for this protein
FB homologs
1
InterProScan
1
Homolog domains
2
Neighborhood
2
STRING
orthogroup
Conservation
3 orgs
Topology
GLOB
Not shown to the annotator
structured output behind some of that evidence — for judging the protein, not the call
InterProScan + GO
2
Homolog InterProScan
2
Literature Evidence (PaperBLAST)
Homologs that appear by name in primary research literature, strongest identity first. Each hit shows the source organism, gene ID and literature summary; hits whose citation resolved to a PubMed record carry a direct link, and the rest are marked 'no linked paper' — the homolog and its summary are still real evidence.
34.4%
<40% identity: weak evidence for a specific function
Escherichia coli LF82
The gene LF82_RS22000 is identified as encoding a DUF4062 domain-containing protein in E. coli LF82. The authors describe a specific evolved clone (clone 219) that possesses a synonymous mutation I255I in this gene. This clone was used in the deconstruction of a fusA G604V mutation to test the effects of the fimH L79R mutation on biofilm formation and amikacin tolerance [FIG:Fig7].
LF82_RS22000
PMID 36928386
experimental
PaperBLAST's label for the kind of finding this summary reports
Fitness Browser Homologs
Loci in the Fitness Browser's RB-TnSeq organisms similar to this protein, named by their gene description. The evidence identifies each only by organism and description — two rows alike are not necessarily one gene.
100.0%
≥80% identity: near-certain functional transfer
Synechococcus elongatus PCC 7942
hypothetical protein
InterProScan — This Protein
Domain and motif analysis run directly on this query sequence, as the annotator saw it — not the eggNOG / InterPro annotations carried by related sequences, which are under 'Known before' above.
Database
Domain / Annotation
Position / HMM coords
Query cov
HMM cov
E-value
PFAM
Domain of unknown function DUF4062
6–87/362
(1-82/82)
22.7%
100.0%
3.4e-26
Homolog Domain Architecture
Domains found on HOMOLOGS of this protein, not on the protein itself — the annotator's view of what its relatives carry. Lower identity reaches further but transfers function less surely. Coordinates are on each homolog.
curated family (HAMAP, PIRSF, NCBIfam, PANTHER)
domain model (Pfam, SMART, PROSITE, PRINTS)
structural (Gene3D, SUPERFAMILY, CDD)
other
34.4%
<40% identity: weak evidence for a specific function
Escherichia coli LF82
1 domain
PFAM
6–87
Domain of unknown function DUF4062
Domain of unknown function DUF4062
drawn on the homolog's residues 1–87, the furthest domain end given; the homolog's own length is not in the evidence
33.0%
<40% identity: weak evidence for a specific function
Pseudomonas fluorescens GW456-L13
1 domain
PFAM
6–87
Domain of unknown function DUF4062
Domain of unknown function DUF4062
drawn on the homolog's residues 1–87, the furthest domain end given; the homolog's own length is not in the evidence
Gene Neighborhood (Homolog Context)
The genes flanking a homolog of this protein in its own genome. The coordinates and the neighbours belong to the homolog, not to the query — pick a homolog below, and read its % identity as how far the synteny can be carried back to this protein.
Homolog context:
Genes are laid out left-to-right by genome coordinate, not by direction of transcription; each arrow shows that gene's own strand. The homolog sits in the middle and has no entry of its own in this data, so its own span is not drawn. A short flank means only that fewer genes were reported — it is not a contig end. Hover a gene for its coordinates and KEGG / SwissProt / ModelSEED / MetaCyc assignments.
STRING Association Network
Protein-association network from STRING v12.0, transferred from the best DIAMOND hit into the STRING proteome. STRING's own annotations propagate between species and get noisy, so the matched homolog's annotation is deliberately withheld — read the partners below as corroboration for a function inferred from the other evidence, never as the primary call. Associations supported only by text-mining were removed upstream.
100.0%
≥80% identity: near-certain functional transfer
ABB56903.1
1140.Synpcc7942_0873
Synechococcus elongatus
COG5635
Predicted NTPase, NACHT family domain
conserved in 4,341 species
No functional partners passed STRING's confidence floor for this homolog — the network places it in an orthogroup but links it to nothing specific.
Conservation Breadth
Counted over every homolog the run found, before any panel's display cap. Breadth says a protein is real and under selection; it never says what it does.
3
organisms with a homolog
3
genera
2
organisms other than Synechococcus elongatus
2
other genera
33.0–100.0%
identity range
Homologs reach beyond this protein's genus: evidence it is a real gene under selection — a conserved hypothetical, at the least.
Membrane Topology
DeepTMHMM run on this sequence itself, with the run's own reading of it. Drawn on the sequence above.
Class
GLOB — Globular (cytoplasmic)
Signal peptide
none detected
Membrane helices
none
Path
cytoplasmic 1-362
no signal peptide and no membrane-spanning segment: the protein is predicted to be CYTOPLASMIC (globular).
Not shown to the annotator
InterProScan — Full Scan with GO
The run's complete InterProScan output for this sequence. The annotator saw only the hits with an InterPro entry, and no GO terms; the rest is here for judging the protein, not the call.
2 hits, 1 not in the annotator's text · 0 distinct GO terms
Pfam
6–87
Domain of unknown function (DUF4062)
Domain of unknown function (DUF4062)
Coils
170–197
Coil
Coil
Database
Signature
Position
E-value
InterPro entry
GO
Annotator saw
Pfam
PF13271
Domain of unknown function (DUF4062)
6–87
3.4e-26
IPR025139
Domain of unknown function DUF4062
—
yes
Coils
Coil
Coil
170–197
—
no InterPro entry
—
no
Not shown to the annotator
InterProScan on Homologs
Every homolog of this protein the run scanned — whether for this protein's evidence or for another protein's that shares it. The annotator was given a digest of a few as text (the homolog-domain panel); this is the scan itself, closest homolog first, each on its own length.
curated family (HAMAP, PIRSF, NCBIfam, PANTHER)
domain model (Pfam, SMART, PROSITE, PRINTS)
structural (Gene3D, SUPERFAMILY, CDD)
other
34.4%
<40% identity: weak evidence for a specific function
Escherichia coli LF82
WP_024196728.1
326 aa · found by PaperBLAST
Domain of unknown function DUF4062
2 hits — domain track, entries and GO
Pfam
6–87
Domain of unknown function (DUF4062)
Domain of unknown function (DUF4062)
Coils
170–197
Coil
Coil
Database
Signature
Position
E-value
InterPro entry
GO
Pfam
PF13271
Domain of unknown function (DUF4062)
6–87
1.3e-23
IPR025139
Domain of unknown function DUF4062
—
Coils
Coil
Coil
170–197
—
no InterPro entry
—
33.0%
<40% identity: weak evidence for a specific function
Pseudomonas fluorescens GW456-L13
pseudo13_GW456_L13:PfGW456L13_4141
343 aa · found by FB fitness · FB neighborhood
Domain of unknown function DUF4062
2 hits — domain track, entries and GO
Pfam
6–87
Domain of unknown function (DUF4062)
Domain of unknown function (DUF4062)
Coils
169–199
Coil
Coil
Database
Signature
Position
E-value
InterPro entry
GO
Pfam
PF13271
Domain of unknown function (DUF4062)
6–87
2.2e-25
IPR025139
Domain of unknown function DUF4062
—
Coils
Coil
Coil
169–199
—
no InterPro entry
—
gene-annotate · Dark Protein Atlas