Protein motif scanner
(v1.0.0)Docs
Scan protein sequences for glycosylation, phosphorylation, localization signals, and other biologically important motifs.
Paste a protein sequence or upload FASTA, text, CSV or PDB data, then click Scan motifs. ProteinIQ searches 13 short consensus patterns in the browser. The table shows one row per sequence, with hit counts, positions, matched residues and nearby sequence. Matches are candidates for investigation, not confirmed modifications or functions.
This example contains overlapping N-glycosylation sequons. The description after the FASTA identifier stays out of the sequence.
>sequon-demo protein
NNSTNPSNVTThe sequence has 10 residues, three hits and one distinct motif type. Its Motif hits cell is:
N-glycosylation @1; N-glycosylation @2; N-glycosylation @8The Match ranges and contexts cell is:
N-glycosylation @1-3: NNS (context: NNSTNPSN...); N-glycosylation @2-4: NST (context: NNSTNPSNV...); N-glycosylation @8-10: NVT (context: ...STNPSNVT)NPS at position 5 is excluded because proline occupies the middle position. Fixed-length patterns include overlapping matches. A continuous basic nuclear localization tract is reported once, rather than as shorter matches inside the same tract.
Use separate FASTA headers for separate proteins. Wrapped lines without headers are treated as one sequence.
>amidation-demo
AGRK
>er-demo
MKDEL
>prenylation-demo
MCAAL| Protein ID | Amino acids | Total hits | Unique motifs | Motif hits |
|---|---|---|---|---|
| amidation-demo | 4 | 1 | 1 | Amidation @1 |
| er-demo | 5 | 2 | 2 | SUMOylation @1; ER retention signal @2 |
| prenylation-demo | 5 | 1 | 1 | CAAX prenylation @2 |
The two matches in MKDEL illustrate why context matters: a short SUMO consensus can overlap an ER retrieval signal by chance. KDEL and CAAX are only matched at the end of the supplied sequence. Neither match establishes that the protein reaches the relevant cellular compartment.
| Input | Requirements |
|---|---|
| Protein text | One-letter amino acid codes, uppercase or lowercase. Spaces, line wrapping and position digits are removed. |
| FASTA | Put each sequence on the line after its header. Descriptions remain descriptions. Empty records and text before the first header are rejected. Lines beginning with # are comments. |
| Sequence table | Comma-, semicolon- or tab-delimited data with named ID and sequence columns. Common names such as id, name, accession, sequence and protein_sequence are recognized. Quoted CSV cells are supported. Incomplete or empty sequence rows cause an error. |
| PDB | Protein chains are extracted from observed coordinates. Positions count residues in the extracted sequence from 1, rather than preserving PDB residue numbering. Missing residues and truncated chain ends can affect matches. |
| Files | .fasta, .fa, .fas, .txt, .csv and .pdb, up to 50 MiB per file. One input can contain multiple FASTA records. |
A sequence table can contain:
id,sequence
a,NNST
b,RGDThis produces two rows: a has four residues and two N-glycosylation matches at positions 1 and 2; b has three residues and one RGD match at position 1. For headerless tables or custom column mapping, use CSV to FASTA first.
Gaps, punctuation and internal stop markers are rejected. Removing them could create a motif or shift its position. One terminal * is removed with a warning. Invisible formatting characters and typographic whitespace from pasted documents are normalized, but document file uploads are not supported here.
Ambiguous codes B, X, Z and J are retained and trigger a warning. They can occupy an unrestricted pattern position, so a match such as NXS is uncertain. They do not stand in for a required residue such as asparagine. U and O are retained as one-letter residues. Names belong in FASTA headers: an alphabetic name or accession alone can be mistaken for sequence text. The scanner does not retrieve sequences by accession.
UniProt headers beginning with sp| or tr| use the accession as the protein ID. Other headers use their leading identifier. PDB extraction and ambiguous residues produce page-level warnings; routine case and whitespace cleanup does not.
There are no adjustable motif or model settings. Every run searches the same 13 patterns below.
| Result column | Meaning |
|---|---|
Protein ID | Identifier for the input record. |
Amino acids | Length after formatting cleanup and removal of a terminal stop marker. Ambiguous residues remain in the count. |
Total hits | Number of reported matches, including overlaps between fixed-length matches. |
Unique motifs | Number of different motif types matched. |
Motif hits | Motif names and their 1-based starting positions, sorted by position. |
Match ranges and contexts | Inclusive start and end positions, matched residues, and up to five flanking residues on each side. Ellipses indicate additional sequence beyond the displayed context. |
Sequences with no matches remain in the table with zero counts and No motifs found. The table can be searched and downloaded. Position refers to the start of the pattern, which can differ from the potentially modified residue: for PKA/PKG, the serine or threonine is the fourth residue in the match.
Here, x means one residue, square brackets list allowed residues, and braces list excluded residues. Hyphens separate pattern positions and are not sequence characters.
| Motif | Screening rule | Interpretation |
|---|---|---|
| N-glycosylation | N-{P}-[ST] | Candidate N-linked sequon; the middle residue must not be proline. |
| PKA/PKG phosphorylation | [RK]-[RK]-x-[ST] | Basic consensus preceding a serine or threonine. |
| CK2 phosphorylation | [ST]-x-x-[DE] | Serine or threonine with an acidic residue three positions later. |
| PKC phosphorylation | [ST]-x-[RK] | Simplified basic phosphorylation consensus. |
| N-myristoylation | G-{EDRKHPFYW}-x-x-[STAGCN]-{P} | A sequence candidate searched anywhere, including potential sites exposed after processing. |
| Amidation | x-G-[RK]-[RK] | Candidate residue followed by a glycine donor and a dibasic processing site. |
| RGD cell attachment | R-G-D | Short cell-attachment consensus. |
| Nuclear localization (monopartite) | Four or more consecutive K or R | Basic tract, reported as one maximal match. |
| ER retention signal | [KH]-D-E-L at the C-terminus | KDEL or HDEL retrieval consensus. |
| CAAX prenylation | C-x-x-[ASLIMVT] at the C-terminus | Simplified terminal prenylation rule. |
| Tyrosine sulfation | [ED]-x-x-x-Y | Coarse acidic-context screening rule. |
| GAG attachment | S-G-x-G | Short glycosaminoglycan attachment consensus. |
| SUMOylation | [VILMAFP]-K-x-E | Simplified SUMO consensus around lysine. |
The kinase rules include both serine and threonine acceptors, consistent with the substrate studies summarized in PROSITE's PKA/PKG documentation and CK2 documentation. The amidation rule places glycine immediately after the candidate residue and before two basic residues, as described in PROSITE's amidation documentation and the Bradbury and Smyth review.
Myristoylation requires glycine at an accessible N-terminus, so an internal match only becomes relevant after appropriate processing. The nuclear localization rule detects a basic tract and does not model importin recognition. Tyrosine sulfation depends on a broader context than this coarse rule captures.
A protein motif scanner finds short patterns associated with modification, trafficking, processing or binding. It helps nominate residues for conservation analysis, construct design or experiments. A hit does not establish that a site is modified, accessible or active.
Short motifs occur by chance, especially in long or compositionally biased proteins. Hit counts are not probabilities or significance scores. The scanner does not use structure, evolutionary conservation, enzyme expression, compartment access or confidence scoring. It cannot detect every modification site, signal peptide, domain or protein family.
This fixed set is smaller than the ScanProsite search, which supports the PROSITE collection, profiles and custom patterns. The scanner does not download or search the full PROSITE database, and its simplified rules should not be interpreted as an equivalent annotation service.
| Goal | Tool |
|---|---|
| Screen several short modification and localization consensuses | Protein motif scanner |
| Focus on N-linked sequons and site density | Glycosylation site finder |
| Convert a spreadsheet with custom sequence columns | CSV to FASTA |
| Assemble named sequences from notes | TXT to FASTA |
| Inspect protein composition | Amino acid composition |
No. It identifies a candidate sequon, provided the middle residue is not proline. Accessibility, cellular compartment and other sequence features affect whether the asparagine is modified.
Different patterns can share residues, and repeated copies of one fixed-length pattern can overlap. NNST contains both NNS and NST, starting at positions 1 and 2.
They are the 1-based start of the match. Read the matched residues and the rule to locate a candidate modification site. For example, the PKA/PKG acceptor is three residues after the reported start.
No. It means none of these 13 rules matched the supplied sequence. Many functional features require larger patterns, specialized predictors, structural information or experimental evidence.
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