ProtSuite Results — d6ce0454e7cb — 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

Skipped

Pfam domain annotation (HMMER)

hmmscan via EBI HMMER API — typically ~1 min

Done

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

Done

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)

Pending

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 Open StructMap

Summary

Length

235 aa

Mol. Weight

26,642 Da

4.44

GRAVY

-0.14

Instability

49.13 (Unstable)

BLAST hits

Domains / motifs

Functional sites

TM helices

Signal peptide

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

Likely 5-15 minutes depending on remote queues.

Sequence Information

Description

sp|O82246|Y2778_ARATH REF/SRPP-like protein At2g47780 OS=Arabidopsis thaliana OX=3702 GN=At2g47780 PE=2 SV=1

Source

RAW

Sequence (235 aa)

MAEDEIVVEEEQSQPQEITPVPPSSSSSPSLVVEDDDEMKLKHLEFIQVAAVYFAACFSTLYELAKDNAGPLKLGVENIEDCVRTVLAPLYEKFHDVPFKLLLFVDRKVDDVFFDVETYVPSLVKQASSQALTVATEVQRTGVVDTTKSIARSVRDKYEPAAEYYAATLWRLLNQLPLFPEVAHLVIPTAFYWSEKYNDAVRYVGDRDYFGAEYLPMIPIEKISDILEQDQCRAD

Physicochemical Properties

Length

235

MW (Da)

26641.84 Da

4.44

GRAVY

-0.14

Aromaticity

0.1064 (10.6%)

Instability Index

49.13

Helix fraction

0.3404 (34.0%)

Sheet fraction

0.4 (40.0%)

Turn fraction

0.2468 (24.7%)

Residue Composition

11.06%

9.36%

8.94%

8.09%

6.38%

5.11%

4.68%

4.26%

3.83%

2.13%

Program
blastp

Database
SWISSPROT

Max hits
10

Returned
0

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 homology search was not run for this job.

BLAST (blastp vs SwissProt) finds homologous proteins and reports percent identity, coverage, and E-value. Re-run the analysis with BLAST enabled to see top hits.

Pipeline — hits per source

Source	Raw parsed	High-conf	Discarded	Final (deduped)
HMMER	1	1	0	1
Phobius	0	0	0	0
CDD	1	1	0	1
ScanProsite	0	0	0	0
UniProtKB	2	2	0	2
InterProScan	1	0	1	0
Waggawagga	0	0	0	0
Total	5	5	0	3

Check annotations below, then click Generate Figure to build the domain architecture diagram.

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
UniProtKB	1–32	Disordered (Region)	Region	—
CDD	35–229	REF (pfam05755) ×3	E-value: 8.41 × 10^-104 (-)	E: 8.4e-104
UniProtKB	1–12	Acidic residues (Compositional bias) low-complexity	Compositional bias	—

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.)

HMMER

1 hits parsed

Status	Type	Interval	Label	E-value / Score
discarded	domain	36–228	PF05755	4.07e-79

CDD

1 hits parsed

Status	Type	Interval	Label	E-value / Score
high-conf	domain	35–229	REF (pfam05755)	8.41e-104

UniProtKB

2 hits parsed

Status	Type	Interval	Label	E-value / Score
high-conf	domain	1–32	Disordered (Region)	—
high-conf	low_complexity	1–12	Acidic residues (Compositional bias)	—

InterProScan/PANTHER

1 hits parsed

Status	Type	Interval	Label	E-value / Score
discarded	family	37–229	Rubber elongation factor (IPR008802)	1.50e-68

Pfam Domain Hits (HMMER)

Raw HMMER results — merged multi-source view in Annotations tab

Domain	Description	Start	End	Length	E-value
PF05755		36	228	193 aa	4.07e-79

Signal Peptide

Phobius

Not detected

SignalP-4.1

Not run

Transmembrane Topology

? via Phobius (EBI)

TM Helices

Topology String

1-235 NON CYTOPLASMIC

No transmembrane helices detected.

{
  "_request": {
    "enabled_modules": [
      "HMMER",
      "Phobius",
      "CDD",
      "ScanProsite",
      "UniProtKB features",
      "Coils",
      "InterProScan"
    ],
    "input_type": "auto",
    "runtime_hint": "Likely 5-15 minutes depending on remote queues.",
    "submitted_at": "2026-10-08T14:00:32.048784+00:00",
    "submitted_value": "\u003esp|O82246|Y2778_ARATH REF/SRPP-like protein At2g47780 OS=Arabidopsis thaliana OX=3702 GN=At2g47780 PE=2 SV=1\r\nMAEDEIVVEEEQSQPQEITPVPPSSSSSPSLVVEDDDEMKLKHLEFIQVAAVYFAACFSTLYELAKDNAGPLKLGVENIEDCVRTVLAP"
  },
  "annotation_debug": {
    "deduped": 3,
    "deduped_per_source": {
      "CDD": 1,
      "HMMER": 1,
      "InterProScan/PANTHER": 1,
      "UniProtKB": 2
    },
    "discarded": 0,
    "filter_log": [],
    "filtered_per_source": {
      "CDD": 1,
      "HMMER": 1,
      "InterProScan/PANTHER": 1,
      "UniProtKB": 2
    },
    "high_confidence": 5,
    "low_confidence": 0,
    "raw_per_source": {
      "CDD": 1,
      "HMMER": 1,
      "InterProScan": 1,
      "Phobius": 0,
      "ScanProsite": 0,
      "UniProtKB": 2,
      "Waggawagga": 0
    },
    "raw_total": 5,
    "validated": 5
  },
  "annotation_summary": {
    "domain_count": 2,
    "has_signal_peptide": false,
    "site_count": 0,
    "source_summary": {
      "CDD": 1,
      "HMMER": 1,
      "InterProScan": 1,
      "Phobius": 0,
      "ScanProsite": 0,
      "UniProtKB": 2,
      "Waggawagga": 0
    },
    "tm_helix_count": 0
  },
  "annotations": [
    {
      "accession": "Region",
      "description": "Disordered",
      "display_priority": 30,
      "e_value": null,
      "end": 32,
      "evidence": "Region",
      "feature_type": "domain",
      "label": "Disordered",
      "score": null,
      "source": "UniProtKB",
      "source_support": [
        "UniProtKB"
      ],
      "start": 1
    },
    {
      "accession": "pfam05755",
      "description": "REF",
      "display_priority": 30,
      "e_value": 8.40747e-104,
      "end": 229,
      "evidence": "E-value: 8.41 \u00d7 10^-104  (-)",
      "feature_type": "domain",
      "label": "REF",
      "score": null,
      "source": "CDD",
      "source_support": [
        "CDD",
        "HMMER",
        "InterProScan/PANTHER"
      ],
      "start": 35
    },
    {
      "accession": "Compositional bias",
      "description": "Acidic residues",
      "display_priority": 50,
      "e_value": null,
      "end": 12,
      "evidence": "Compositional bias",
      "feature_type": "low_complexity",
      "label": "Acidic residues",
      "score": null,
      "source": "UniProtKB",
      "source_support": [
        "UniProtKB"
      ],
      "start": 1
    }
  ],
  "blast": {
    "max_hits_requested": 10
  },
  "companion_disorder": {},
  "companion_sspred": {},
  "completed_at": "2026-10-08 14:03 UTC",
  "figure_ok": false,
  "figure_renderer": "none",
  "hmmer": {
    "domains": [
      {
        "description": "",
        "e_value": 4.071809304287864e-79,
        "name": "PF05755",
        "seq_end": 228,
        "seq_start": 36
      }
    ]
  },
  "job_id": "d6ce0454e7cb",
  "low_confidence_annotations": [],
  "module_errors": {},
  "module_warnings": {},
  "motif_results": [],
  "phobius": {
    "has_signal_peptide": false,
    "signal_peptide_end": 0,
    "tm_count": 0,
    "tm_helices": [],
    "topology": "1-235 NON CYTOPLASMIC"
  },
  "properties": {
    "ambiguous_residues_replaced": 0,
    "amino_acid_count": {
      "A": 21,
      "C": 3,
      "D": 19,
      "E": 22,
      "F": 11,
      "G": 5,
      "H": 3,
      "I": 10,
      "K": 12,
      "L": 22,
      "M": 3,
      "N": 4,
      "P": 15,
      "Q": 10,
      "R": 9,
      "S": 15,
      "T": 11,
      "V": 26,
      "W": 2,
      "Y": 12
    },
    "amino_acid_percent": {
      "A": 8.94,
      "C": 1.28,
      "D": 8.09,
      "E": 9.36,
      "F": 4.68,
      "G": 2.13,
      "H": 1.28,
      "I": 4.26,
      "K": 5.11,
      "L": 9.36,
      "M": 1.28,
      "N": 1.7,
      "P": 6.38,
      "Q": 4.26,
      "R": 3.83,
      "S": 6.38,
      "T": 4.68,
      "V": 11.06,
      "W": 0.85,
      "Y": 5.11
    },
    "aromaticity": 0.1064,
    "gravy": -0.14,
    "helix_fraction": 0.3404,
    "instability_index": 49.13,
    "is_stable": false,
    "isoelectric_point": 4.44,
    "length": 235,
    "molecular_weight_da": 26641.84,
    "sheet_fraction": 0.4,
    "turn_fraction": 0.2468
  },
  "raw_annotations": [
    {
      "accession": "PF05755",
      "description": "",
      "display_priority": 30,
      "e_value": 4.071809304287864e-79,
      "end": 228,
      "evidence": "HMMER/Pfam  PF05755",
      "feature_type": "domain",
      "label": "PF05755",
      "score": null,
      "source": "HMMER",
      "source_support": [
        "HMMER"
      ],
      "start": 36
    },
    {
      "accession": "pfam05755",
      "description": "REF",
      "display_priority": 60,
      "e_value": 8.40747e-104,
      "end": 229,
      "evidence": "E-value: 8.41 \u00d7 10^-104  (-)",
      "feature_type": "domain",
      "label": "REF",
      "score": null,
      "source": "CDD",
      "source_support": [
        "CDD"
      ],
      "start": 35
    },
    {
      "accession": "Region",
      "description": "Disordered",
      "display_priority": 30,
      "e_value": null,
      "end": 32,
      "evidence": "Region",
      "feature_type": "domain",
      "label": "Disordered",
      "score": null,
      "source": "UniProtKB",
      "source_support": [
        "UniProtKB"
      ],
      "start": 1
    },
    {
      "accession": "Compositional bias",
      "description": "Acidic residues",
      "display_priority": 30,
      "e_value": null,
      "end": 12,
      "evidence": "Compositional bias",
      "feature_type": "low_complexity",
      "label": "Acidic residues",
      "score": null,
      "source": "UniProtKB",
      "source_support": [
        "UniProtKB"
      ],
      "start": 1
    },
    {
      "accession": "IPR008802",
      "description": "Rubber elongation factor",
      "display_priority": 60,
      "e_value": 1.5e-68,
      "end": 229,
      "evidence": "PANTHER  IPR008802  E: 1.50e-68",
      "feature_type": "family",
      "label": "Rubber elongation factor",
      "score": 242.8,
      "source": "InterProScan/PANTHER",
      "source_support": [
        "InterProScan/PANTHER"
      ],
      "start": 37
    }
  ],
  "retrieval": {
    "error": "",
    "header": "sp|O82246|Y2778_ARATH REF/SRPP-like protein At2g47780 OS=Arabidopsis thaliana OX=3702 GN=At2g47780 PE=2 SV=1",
    "organism": "",
    "sequence": "MAEDEIVVEEEQSQPQEITPVPPSSSSSPSLVVEDDDEMKLKHLEFIQVAAVYFAACFSTLYELAKDNAGPLKLGVENIEDCVRTVLAPLYEKFHDVPFKLLLFVDRKVDDVFFDVETYVPSLVKQASSQALTVATEVQRTGVVDTTKSIARSVRDKYEPAAEYYAATLWRLLNQLPLFPEVAHLVIPTAFYWSEKYNDAVRYVGDRDYFGAEYLPMIPIEKISDILEQDQCRAD",
    "source": "raw",
    "status": "ok"
  },
  "signalp": {},
  "uniprot_features": {
    "accession": "O82246",
    "annotations": [
      {
        "accession": "Region",
        "description": "Disordered",
        "display_priority": 30,
        "e_value": null,
        "end": 32,
        "evidence": "Region",
        "feature_type": "domain",
        "label": "Disordered",
        "score": null,
        "source": "UniProtKB",
        "source_support": [
          "UniProtKB"
        ],
        "start": 1
      },
      {
        "accession": "Compositional bias",
        "description": "Acidic residues",
        "display_priority": 30,
        "e_value": null,
        "end": 12,
        "evidence": "Compositional bias",
        "feature_type": "low_complexity",
        "label": "Acidic residues",
        "score": null,
        "source": "UniProtKB",
        "source_support": [
          "UniProtKB"
        ],
        "start": 1
      }
    ]
  }
}

Analysis Results