ProtSuite Results — ba22950c754e — Bioinformatics Lab, Brooklyn College

Analysis Progress

Sequence retrieval

Fetches sequence from UniProt / NCBI or parses your FASTA

Done

Sequence properties

MW, pI, GRAVY, stability — instant local calculation

Done

BLAST homology search

blastp vs SwissProt via NCBI — typically 2–10 min

Done

Pfam domain annotation (HMMER)

hmmscan via EBI HMMER API — typically ~1 min

Error

Signal peptide & TM (Phobius)

Phobius via EBI Job Dispatcher — ~30 sec

Done

Signal peptide (SignalP)

SignalP-4.1 via EBI — independent SP cross-validation, ~30 sec

Skipped

CDD conserved domains (NCBI)

Batch Web CD-Search — typically ~1–2 min

Done

ScanProsite patterns & sites

ExPASy ScanProsite — motifs, active sites, binding sites

Done

UniProtKB feature map

Curated UniProt positional features when an accession is available

Skipped

SMART domain architecture

SMART web adapter — best-effort HTML parsing

Skipped

InterProScan (integrative)

EBI InterProScan — slowest, most comprehensive (~5–8 min)

Done

Coiled-coil prediction (Waggawagga)

Waggawagga — Marcoil/Multicoil2/Ncoils/Paircoil2 heptad-repeat regions (~10–30 sec)

Done

DisorderPred companion

Optional disorder and low-complexity view with IUPred3 / ANCHOR2 comparisons

Skipped

SSPred consensus companion

Optional secondary-structure consensus bundled into the ProtSuite report

Skipped

Merge & deduplicate annotations

Combines all sources into one clean annotation set

Done

Domain architecture figure

PROSITE MyDomains figure (or SVG fallback)

Done

ProtSuite Service Status

BLAST UP

core

NCBI BLAST remote search

HMMER UP

core

Pfam domain scan

Phobius UP

core

Signal peptide and TM topology

CDD UP

core

NCBI conserved domains

ScanProsite UP

core

Patterns and functional sites

UniProtKB features UP

core

Curated UniProt positional features for domains, motifs, regions, and sites

Coils UP

core

Waggawagga coiled-coil prediction (Marcoil/Multicoil2/Ncoils/Paircoil2)

SMART UP

experimental

Best-effort HTML parsing

InterProScan UP

slow

Broad integrative annotation

SignalP UP

core

DTU SignalP-5.0 — independent signal peptide cross-check for Phobius

DisorderPred UP

companion

Companion disorder profile using NetSurf plus IUPred3 / ANCHOR2 comparison.

SSPred consensus UP

companion

Optional secondary-structure consensus bundle using the SSPred service adapters.

Download: JSON report Text summary Domain figure Open StructMap

Summary

Length

265 aa

Mol. Weight

30,689 Da

9.34

GRAVY

-0.1298

Instability

41.57 (Unstable)

BLAST hits

Domains / motifs

Functional sites

TM helices

Signal peptide

Run profile: BLAST, HMMER, Phobius, CDD, ScanProsite, UniProtKB features, Coils, InterProScan

Likely 5-15 minutes depending on remote queues.

Domain Architecture

Download figure

Top BLAST Hit

Transcriptional activator AggR

Escherichia coli

Accession
P43464

E-value
0.00e+00

Identity
100.0%

Coverage
100.0%

Warnings

Hmmer 'NoneType' object has no attribute 'get'

Sequence Information

Description

User-submitted sequence

Source

RAW

Sequence (265 aa)

MKLKQNIEKEIIKINNIRIHQYTVLYTSNCTIDVYTKEGSNTYLRNELIFLERGINISVRLQKKKSTVNPFIAIRLSSDTLRRLKDALMIIYGISKVDACSCPNWSKGIIVADADDSVLDTFKSIDHNDDSRITSDLIYLISKIENNRKIIESIYISAVSFFSDKVRNTIEKDLSKRWTLAIIADEFNVSEITIRKRLESEYITFNQILMQSRMSKAALLLLDNSYQISQISNMIGFSSTSYFIRLFVKHFGITPKQFLTYFKSQ

Physicochemical Properties

Length

265

MW (Da)

30689.14 Da

9.34

GRAVY

-0.1298

Aromaticity

0.0981 (9.8%)

Instability Index

41.57

Helix fraction

0.2717 (27.2%)

Sheet fraction

0.4302 (43.0%)

Turn fraction

0.2717 (27.2%)

Residue Composition

14.34%

11.32%

8.68%

8.3%

6.42%

6.04%

5.66%

4.91%

4.53%

4.15%

3.77%

3.4%

2.26%

Program
blastp

Database
SWISSPROT

Max hits
10

Returned
10

SwissProt is the curated section of UniProt — manually annotated, high-quality protein records. Hits here are reliable homologs.
Identity ≥60%: close ortholog | 30–60%: conserved family | <30%: distant or coincidental.

BLAST Hits

Show columns: Accession Protein Organism E-value Identity Coverage Score

Accession	Protein	Organism	E-value	Identity	Coverage	Bit score
P43464	Transcriptional activator AggR	Escherichia coli	0.0	100.0%	100.0%	1374
P25393	HTH-type transcriptional activator CfaD	Escherichia coli	5.48e-126	68.2%	99.6%	927
P16114	DNA-binding dual transcriptional regulator Rns	Escherichia coli	1.63e-124	66.7%	99.6%	917
P43460	HTH-type transcriptional activator CsvR	Escherichia coli	1.19e-119	63.9%	99.6%	885
P0A2T1	Virulence regulon transcriptional activator VirF	Shigella sonnei	6.19e-45	37.1%	93.2%	391
P23774	HTH-type transcriptional activator FapR	Escherichia coli	4.87e-35	29.1%	93.2%	324
Q8FCI7	HTH-type transcriptional regulator GadW	Escherichia coli CFT073	3.96e-19	36.8%	53.6%	213
P63201	HTH-type transcriptional regulator GadW	Shigella flexneri	5.72e-19	36.1%	53.6%	212
P43459	Transcriptional activator PerA	Escherichia coli O127:H6 str. E2348/69	1.23e-17	29.8%	65.3%	204
Q83RF4	HTH-type transcriptional regulator YdeO	Shigella flexneri	1.42e-15	33.3%	48.7%	189

Identity: fraction of aligned positions that are identical. Coverage: query sequence fraction covered by the best alignment. E-value: expected alignments this good by chance; <1e-5 is highly significant. Bit score: normalized alignment quality independent of database size.

Pipeline — hits per source

Source	Raw parsed	High-conf	Discarded	Final (deduped)
HMMER	0	0	0	0
Phobius	0	0	0	0
CDD	1	1	0	1
ScanProsite	2	2	0	2
InterProScan	3	0	3	0
Waggawagga	0	0	0	0
Total	6	6	0	3

Download figure mydomains

Select annotations: 0 selected

E. Custom Annotations

▼ optional — write your own MyDomains commands

How to read and customize the domain architecture diagram

▼

Feature	Format	Reason
Signal peptide	`1,end,2,2,Signal peptide`	Labeled region at N-terminus
TM helix	`start,end,4,1,TM helix`	Distinct structural block
Disulfide bridge	`start,end,2`	Range marks the covalent span; no site pins
Active site	`pos,1`	Pin marker at each catalytic residue
Metal-binding	`pos,0`	Tick at individual ligand residue

A. Domain Architecture & Structural Features

Program	Interval	Name / Accession	Evidence	Confidence
InterProScan/PANTHER	74–258	ARAC-FAMILY TRANSCRIPTIONAL REGULATOR (PTHR43280)	PANTHER PTHR43280 E: 4.80e-24	E: 4.8e-24 Score: 97.1
CDD	177–259	HTH_ARAC (smart00342) ×3	E-value: 9.08 × 10^-26 (-)	E: 9.1e-26
ScanProsite	213–255	HTH_ARAC_FAMILY_1 (PS00041) ×2	PS00041	—

B. Signal Sequence & Topology

No signal peptide or transmembrane helices detected.

C. Functional Sites

	Program	Position	Feature	Evidence	Confidence
None detected. (Run ScanProsite or InterProScan to find ACT_SITE, DISULFID, BINDING residues.)

CDD

1 hits parsed

Status	Type	Interval	Label	E-value / Score
high-conf	domain	177–259	HTH_ARAC (smart00342)	9.08e-26

ScanProsite

2 hits parsed

Status	Type	Interval	Label	E-value / Score
discarded	motif	164–261	HTH_ARAC_FAMILY_2 (PS01124)	—
high-conf	motif	213–255	HTH_ARAC_FAMILY_1 (PS00041)	—

InterProScan/PROSITE_PATTERNS

1 hits parsed

Status	Type	Interval	Label	E-value / Score
discarded	motif	213–255	HTH domain AraC-type, conserved site (IPR018062)	—

InterProScan/PANTHER

1 hits parsed

Status	Type	Interval	Label	E-value / Score
high-conf	domain	74–258	ARAC-FAMILY TRANSCRIPTIONAL REGULATOR (PTHR43280)	4.80e-24

InterProScan/PROSITE_PROFILES

1 hits parsed

Status	Type	Interval	Label	E-value / Score
discarded	domain	164–261	AraC-like, DNA binding HTH domain (IPR018060)	Score 30.095999

Pfam Domain Annotation

HMMER / Pfam search failed

'NoneType' object has no attribute 'get'

Signal Peptide

Phobius

Not detected

SignalP-4.1

Not run

Transmembrane Topology

? via Phobius (EBI)

TM Helices

Topology String

1-265 NON CYTOPLASMIC

No transmembrane helices detected.

{
  "_request": {
    "enabled_modules": [
      "BLAST",
      "HMMER",
      "Phobius",
      "CDD",
      "ScanProsite",
      "UniProtKB features",
      "Coils",
      "InterProScan"
    ],
    "input_type": "auto",
    "runtime_hint": "Likely 5-15 minutes depending on remote queues.",
    "submitted_at": "2026-07-21T17:44:20.394239+00:00",
    "submitted_value": "MKLKQNIEKEIIKINNIRIHQYTVLYTSNCTIDVYTKEGSNTYLRNELIFLERGINISVRLQKKKSTVNPFIAIRLSSDTLRRLKDALMIIYGISKVDACSCPNWSKGIIVADADDSVLDTFKSIDHNDDSRITSDLIYLISKIENNRKIIESIYISAVSFFSDKVRNTIEKDLSKRWTLAIIADEFNVSEITIRKRLES"
  },
  "annotation_debug": {
    "deduped": 3,
    "deduped_per_source": {
      "CDD": 1,
      "InterProScan/PANTHER": 1,
      "InterProScan/PROSITE_PATTERNS": 1,
      "InterProScan/PROSITE_PROFILES": 1,
      "ScanProsite": 2
    },
    "discarded": 0,
    "filter_log": [],
    "filtered_per_source": {
      "CDD": 1,
      "InterProScan/PANTHER": 1,
      "InterProScan/PROSITE_PATTERNS": 1,
      "InterProScan/PROSITE_PROFILES": 1,
      "ScanProsite": 2
    },
    "high_confidence": 6,
    "low_confidence": 0,
    "raw_per_source": {
      "CDD": 1,
      "HMMER": 0,
      "InterProScan": 3,
      "Phobius": 0,
      "ScanProsite": 2,
      "Waggawagga": 0
    },
    "raw_total": 6,
    "validated": 6
  },
  "annotation_summary": {
    "domain_count": 2,
    "has_signal_peptide": false,
    "site_count": 0,
    "source_summary": {
      "CDD": 1,
      "HMMER": 0,
      "InterProScan": 3,
      "Phobius": 0,
      "ScanProsite": 2,
      "Waggawagga": 0
    },
    "tm_helix_count": 0
  },
  "annotations": [
    {
      "accession": "PTHR43280",
      "description": "ARAC-FAMILY TRANSCRIPTIONAL REGULATOR",
      "display_priority": 30,
      "e_value": 4.8e-24,
      "end": 258,
      "evidence": "PANTHER  PTHR43280  E: 4.80e-24",
      "feature_type": "domain",
      "label": "ARAC-FAMILY TRANSCRIPTIONAL REGULATOR",
      "score": 97.1,
      "source": "InterProScan/PANTHER",
      "source_support": [
        "InterProScan/PANTHER"
      ],
      "start": 74
    },
    {
      "accession": "smart00342",
      "description": "HTH_ARAC",
      "display_priority": 30,
      "e_value": 9.07566e-26,
      "end": 259,
      "evidence": "E-value: 9.08 \u00d7 10^-26  (-)",
      "feature_type": "domain",
      "label": "HTH_ARAC",
      "score": null,
      "source": "CDD",
      "source_support": [
        "ScanProsite",
        "InterProScan/PROSITE_PROFILES",
        "CDD"
      ],
      "start": 177
    },
    {
      "accession": "PS00041",
      "description": "",
      "display_priority": 60,
      "e_value": null,
      "end": 255,
      "evidence": "PS00041",
      "feature_type": "motif",
      "label": "HTH_ARAC_FAMILY_1",
      "score": null,
      "source": "ScanProsite",
      "source_support": [
        "ScanProsite",
        "InterProScan/PROSITE_PATTERNS"
      ],
      "start": 213
    }
  ],
  "blast": {
    "database": "swissprot",
    "hits": [
      {
        "accession": "P43464",
        "coverage_pct": 100.0,
        "e_value": 0.0,
        "identity_pct": 100.0,
        "length": 265,
        "organism": "Escherichia coli",
        "protein_name": "Transcriptional activator AggR",
        "query_end": 265,
        "query_start": 1,
        "score": 1374.0,
        "title": "sp|P43464.1| RecName: Full=Transcriptional activator AggR; AltName: Full=AAF/I regulatory protein [Escherichia coli]"
      },
      {
        "accession": "P25393",
        "coverage_pct": 99.6,
        "e_value": 5.47961e-126,
        "identity_pct": 68.2,
        "length": 265,
        "organism": "Escherichia coli",
        "protein_name": "HTH-type transcriptional activator CfaD",
        "query_end": 264,
        "query_start": 1,
        "score": 927.0,
        "title": "sp|P25393.2| RecName: Full=HTH-type transcriptional activator CfaD; AltName: Full=CFA/I fimbrial subunit D; AltName: Ful"
      },
      {
        "accession": "P16114",
        "coverage_pct": 99.6,
        "e_value": 1.63076e-124,
        "identity_pct": 66.7,
        "length": 265,
        "organism": "Escherichia coli",
        "protein_name": "DNA-binding dual transcriptional regulator Rns",
        "query_end": 264,
        "query_start": 1,
        "score": 917.0,
        "title": "sp|P16114.1| RecName: Full=DNA-binding dual transcriptional regulator Rns; AltName: Full=Regulatory protein Rns [Escheri"
      },
      {
        "accession": "P43460",
        "coverage_pct": 99.6,
        "e_value": 1.1914e-119,
        "identity_pct": 63.9,
        "length": 267,
        "organism": "Escherichia coli",
        "protein_name": "HTH-type transcriptional activator CsvR",
        "query_end": 264,
        "query_start": 1,
        "score": 885.0,
        "title": "sp|P43460.2| RecName: Full=HTH-type transcriptional activator CsvR [Escherichia coli]"
      },
      {
        "accession": "P0A2T1",
        "coverage_pct": 93.2,
        "e_value": 6.18972e-45,
        "identity_pct": 37.1,
        "length": 262,
        "organism": "Shigella sonnei",
        "protein_name": "Virulence regulon transcriptional activator VirF",
        "query_end": 263,
        "query_start": 17,
        "score": 391.0,
        "title": "sp|P0A2T1.1| RecName: Full=Virulence regulon transcriptional activator VirF [Shigella flexneri] \u003esp|P0A2T2.1| RecName: F"
      },
      {
        "accession": "P23774",
        "coverage_pct": 93.2,
        "e_value": 4.87009e-35,
        "identity_pct": 29.1,
        "length": 260,
        "organism": "Escherichia coli",
        "protein_name": "HTH-type transcriptional activator FapR",
        "query_end": 258,
        "query_start": 12,
        "score": 324.0,
        "title": "sp|P23774.2| RecName: Full=HTH-type transcriptional activator FapR; AltName: Full=987P fimbrial operon positive regulato"
      },
      {
        "accession": "Q8FCI7",
        "coverage_pct": 53.6,
        "e_value": 3.95513e-19,
        "identity_pct": 36.8,
        "length": 242,
        "organism": "Escherichia coli CFT073",
        "protein_name": "HTH-type transcriptional regulator GadW",
        "query_end": 258,
        "query_start": 117,
        "score": 213.0,
        "title": "sp|Q8FCI7.1| RecName: Full=HTH-type transcriptional regulator GadW [Escherichia coli CFT073]"
      },
      {
        "accession": "P63201",
        "coverage_pct": 53.6,
        "e_value": 5.71867e-19,
        "identity_pct": 36.1,
        "length": 242,
        "organism": "Shigella flexneri",
        "protein_name": "HTH-type transcriptional regulator GadW",
        "query_end": 258,
        "query_start": 117,
        "score": 212.0,
        "title": "sp|P63201.1| RecName: Full=HTH-type transcriptional regulator GadW [Escherichia coli K-12] \u003esp|P63202.1| RecName: Full=H"
      },
      {
        "accession": "P43459",
        "coverage_pct": 65.3,
        "e_value": 1.23082e-17,
        "identity_pct": 29.8,
        "length": 274,
        "organism": "Escherichia coli O127:H6 str. E2348/69",
        "protein_name": "Transcriptional activator PerA",
        "query_end": 258,
        "query_start": 86,
        "score": 204.0,
        "title": "sp|P43459.2| RecName: Full=Transcriptional activator PerA [Escherichia coli O127:H6 str. E2348/69]"
      },
      {
        "accession": "Q83RF4",
        "coverage_pct": 48.7,
        "e_value": 1.41576e-15,
        "identity_pct": 33.3,
        "length": 253,
        "organism": "Shigella flexneri",
        "protein_name": "HTH-type transcriptional regulator YdeO",
        "query_end": 265,
        "query_start": 137,
        "score": 189.0,
        "title": "sp|Q83RF4.1| RecName: Full=HTH-type transcriptional regulator YdeO [Shigella flexneri]"
      }
    ],
    "max_hits_requested": 10
  },
  "companion_disorder": {},
  "companion_sspred": {},
  "completed_at": "2026-07-21 17:45 UTC",
  "figure_generated_at": "2026-07-21 23:06:34 UTC",
  "figure_ok": true,
  "figure_renderer": "mydomains",
  "figure_source": "prosite",
  "hmmer": {},
  "job_id": "ba22950c754e",
  "low_confidence_annotations": [],
  "module_errors": {
    "hmmer": "\u0027NoneType\u0027 object has no attribute \u0027get\u0027"
  },
  "module_warnings": {},
  "motif_results": [],
  "phobius": {
    "has_signal_peptide": false,
    "signal_peptide_end": 0,
    "tm_count": 0,
    "tm_helices": [],
    "topology": "1-265 NON CYTOPLASMIC"
  },
  "properties": {
    "ambiguous_residues_replaced": 0,
    "amino_acid_count": {
      "A": 10,
      "C": 3,
      "D": 16,
      "E": 12,
      "F": 13,
      "G": 6,
      "H": 3,
      "I": 38,
      "K": 22,
      "L": 23,
      "M": 5,
      "N": 17,
      "P": 3,
      "Q": 9,
      "R": 15,
      "S": 30,
      "T": 16,
      "V": 11,
      "W": 2,
      "Y": 11
    },
    "amino_acid_percent": {
      "A": 3.77,
      "C": 1.13,
      "D": 6.04,
      "E": 4.53,
      "F": 4.91,
      "G": 2.26,
      "H": 1.13,
      "I": 14.34,
      "K": 8.3,
      "L": 8.68,
      "M": 1.89,
      "N": 6.42,
      "P": 1.13,
      "Q": 3.4,
      "R": 5.66,
      "S": 11.32,
      "T": 6.04,
      "V": 4.15,
      "W": 0.75,
      "Y": 4.15
    },
    "aromaticity": 0.0981,
    "gravy": -0.1298,
    "helix_fraction": 0.2717,
    "instability_index": 41.57,
    "is_stable": false,
    "isoelectric_point": 9.34,
    "length": 265,
    "molecular_weight_da": 30689.14,
    "sheet_fraction": 0.4302,
    "turn_fraction": 0.2717
  },
  "raw_annotations": [
    {
      "accession": "smart00342",
      "description": "HTH_ARAC",
      "display_priority": 60,
      "e_value": 9.07566e-26,
      "end": 259,
      "evidence": "E-value: 9.08 \u00d7 10^-26  (-)",
      "feature_type": "domain",
      "label": "HTH_ARAC",
      "score": null,
      "source": "CDD",
      "source_support": [
        "CDD"
      ],
      "start": 177
    },
    {
      "accession": "PS01124",
      "description": "",
      "display_priority": 60,
      "e_value": null,
      "end": 261,
      "evidence": "PS01124",
      "feature_type": "motif",
      "label": "HTH_ARAC_FAMILY_2",
      "score": null,
      "source": "ScanProsite",
      "source_support": [
        "ScanProsite"
      ],
      "start": 164
    },
    {
      "accession": "PS00041",
      "description": "",
      "display_priority": 60,
      "e_value": null,
      "end": 255,
      "evidence": "PS00041",
      "feature_type": "motif",
      "label": "HTH_ARAC_FAMILY_1",
      "score": null,
      "source": "ScanProsite",
      "source_support": [
        "ScanProsite"
      ],
      "start": 213
    },
    {
      "accession": "IPR018062",
      "description": "HTH domain AraC-type, conserved site",
      "display_priority": 60,
      "e_value": null,
      "end": 255,
      "evidence": "PROSITE_PATTERNS  IPR018062",
      "feature_type": "motif",
      "label": "HTH domain AraC-type, conserved site",
      "score": null,
      "source": "InterProScan/PROSITE_PATTERNS",
      "source_support": [
        "InterProScan/PROSITE_PATTERNS"
      ],
      "start": 213
    },
    {
      "accession": "PTHR43280",
      "description": "ARAC-FAMILY TRANSCRIPTIONAL REGULATOR",
      "display_priority": 60,
      "e_value": 4.8e-24,
      "end": 258,
      "evidence": "PANTHER  PTHR43280  E: 4.80e-24",
      "feature_type": "domain",
      "label": "ARAC-FAMILY TRANSCRIPTIONAL REGULATOR",
      "score": 97.1,
      "source": "InterProScan/PANTHER",
      "source_support": [
        "InterProScan/PANTHER"
      ],
      "start": 74
    },
    {
      "accession": "IPR018060",
      "description": "AraC-like, DNA binding HTH domain",
      "display_priority": 60,
      "e_value": null,
      "end": 261,
      "evidence": "PROSITE_PROFILES  IPR018060  Score: 30.1",
      "feature_type": "domain",
      "label": "AraC-like, DNA binding HTH domain",
      "score": 30.095999,
      "source": "InterProScan/PROSITE_PROFILES",
      "source_support": [
        "InterProScan/PROSITE_PROFILES"
      ],
      "start": 164
    }
  ],
  "retrieval": {
    "error": "",
    "header": "User-submitted sequence",
    "organism": "",
    "sequence": "MKLKQNIEKEIIKINNIRIHQYTVLYTSNCTIDVYTKEGSNTYLRNELIFLERGINISVRLQKKKSTVNPFIAIRLSSDTLRRLKDALMIIYGISKVDACSCPNWSKGIIVADADDSVLDTFKSIDHNDDSRITSDLIYLISKIENNRKIIESIYISAVSFFSDKVRNTIEKDLSKRWTLAIIADEFNVSEITIRKRLESEYITFNQILMQSRMSKAALLLLDNSYQISQISNMIGFSSTSYFIRLFVKHFGITPKQFLTYFKSQ",
    "source": "raw",
    "status": "ok"
  },
  "signalp": {},
  "uniprot_features": {}
}

Analysis Results

HMMER / Pfam search failed