Select genomic region:
Overview
1.1

### Identified secondary metabolite regions using strictness 'relaxed'

BGC0001040 (Streptomyces rapamycinicus NRRL 5491)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | T1PKS,NRPS-like,NRPS | 1 | 107,379 | High | rapamycin | NRPS:Type I+PKS

BGC0001040 - Region 1 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 107,379 nt. (total: 107,379 nt) Show pHMM detection rules used
Region on contig edge.
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
MIBiG
Tailoring
MIBiG comparison
KnownClusterBlast
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
External annotation
This annotation was made externally by 'MIBiG' and not by antiSMASH

Name |  | MIBiG
Version |  | 4.0alpha

Type |  | Subregion
Location |  | 1 - 107,380
Label |  | BGC0001040

Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
rapC: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

rapJ: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

rapN: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

rapT: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
rapM: methyltransferase

smcogs
  SMCOG1089: methyltransferase

rapQ: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: deaminase
rapL: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Ligases: ligase synthase
orfDD: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

rapA: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

rapB: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

rapP: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001040.5 |  |  |  | 1.61 | NRPS, PKS | rapamycin | Streptomyces rapamycinicus NRRL 5491
BGC0002135.2 |  |  |  | 1.04 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  |  |  | 1.04 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  |  |  | 1.00 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  |  | 0.97 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 0.95 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  | 0.95 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  |  |  | 0.94 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001825.4 |  |  |  | 0.93 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  |  | 0.93 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001040.5 |  | 1.00 | NRPS, PKS | rapamycin | Streptomyces rapamycinicus NRRL 5491
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 107379:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - Me-ccmal - Me-redmal - ccmal - ccmal - Me-ccmal) + (shikimic_acid - Me-redmal - ccmal - Me-redmal - Me-ccmal) + (Hpr) + (ccmal - ccmal - Me-redmal - mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
rapB: mal - mmal - mmal - mal - mal - mmal
PKS_AT (543..799): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 151.3
  Methoxymalonyl-CoA: 63.6
  inactive: 62.9
  Methylmalonyl-CoA: 40.5
  Isobutyryl-CoA: 20.4
  Acetyl-CoA: 19.1
  fatty_acid: 16.9
  Propionyl-CoA: 16.9
  Ethylmalonyl-CoA: 15.8
  CHC-CoA: 14.3
  Benzoyl-CoA: 10.6
  2-Methylbutyryl-CoA: 9.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2136..2409): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 183.0
  Ethylmalonyl-CoA: 170.3
  Methoxymalonyl-CoA: 144.3
  2-Methylbutyryl-CoA: 89.1
  trans-1,2-CPDA: 88.6
  Propionyl-CoA: 81.6
  CHC-CoA: 75.8
  Malonyl-CoA: 68.2
  Isobutyryl-CoA: 50.1
  Benzoyl-CoA: 39.6
  Acetyl-CoA: 21.8
  3-Methylbutyryl-CoA: 13.9
  inactive: 11.6
  fatty_acid: 8.6

PKS_AT (3779..4052): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 180.0
  Ethylmalonyl-CoA: 171.1
  Methoxymalonyl-CoA: 137.5
  2-Methylbutyryl-CoA: 98.8
  Propionyl-CoA: 89.8
  trans-1,2-CPDA: 84.5
  CHC-CoA: 73.9
  Malonyl-CoA: 67.6
  Isobutyryl-CoA: 41.6
  Benzoyl-CoA: 36.4
  Acetyl-CoA: 25.3
  fatty_acid: 14.3
  3-Methylbutyryl-CoA: 10.2
  inactive: 9.4

PKS_AT (5757..6017): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 151.9
  Methoxymalonyl-CoA: 64.1
  inactive: 62.9
  Methylmalonyl-CoA: 43.3
  Isobutyryl-CoA: 21.0
  Acetyl-CoA: 18.7
  Propionyl-CoA: 18.0
  fatty_acid: 17.1
  Ethylmalonyl-CoA: 15.4
  CHC-CoA: 14.8
  Benzoyl-CoA: 10.2
  2-Methylbutyryl-CoA: 9.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (7383..7638): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 150.0
  inactive: 70.2
  Methoxymalonyl-CoA: 63.9
  Methylmalonyl-CoA: 44.1
  Isobutyryl-CoA: 23.1
  Propionyl-CoA: 17.9
  Acetyl-CoA: 16.7
  fatty_acid: 15.2
  CHC-CoA: 13.1
  Ethylmalonyl-CoA: 12.6
  Benzoyl-CoA: 8.2
  2-Methylbutyryl-CoA: 0.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (9013..9285): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 179.3
  Ethylmalonyl-CoA: 165.6
  Methoxymalonyl-CoA: 143.3
  2-Methylbutyryl-CoA: 90.5
  trans-1,2-CPDA: 86.6
  Propionyl-CoA: 85.2
  CHC-CoA: 77.0
  Malonyl-CoA: 62.9
  Isobutyryl-CoA: 43.6
  Benzoyl-CoA: 37.1
  Acetyl-CoA: 30.5
  3-Methylbutyryl-CoA: 13.2
  inactive: 10.4
  fatty_acid: 8.8

rapA: shikimic_acid - mmal - mal - mmal - mmal
CAL_domain (34..439): shikimic_acid
minowa: shikimic_acid

Prediction, score:
  shikimic_acid: 584.8
  AHBA: 289.8
  fatty_acid: 0.0
  NH2: 0.0
  Acetyl-CoA: 0.0

PKS_AT (1818..2091): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 184.1
  Ethylmalonyl-CoA: 176.5
  Methoxymalonyl-CoA: 141.7
  2-Methylbutyryl-CoA: 97.7
  Propionyl-CoA: 90.2
  trans-1,2-CPDA: 82.6
  CHC-CoA: 76.7
  Malonyl-CoA: 69.9
  Isobutyryl-CoA: 53.4
  Benzoyl-CoA: 44.3
  Acetyl-CoA: 30.3
  fatty_acid: 21.6
  3-Methylbutyryl-CoA: 20.2
  inactive: 12.5

PKS_AT (3796..4056): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 149.8
  inactive: 65.9
  Methoxymalonyl-CoA: 64.0
  Methylmalonyl-CoA: 44.7
  Isobutyryl-CoA: 25.0
  Propionyl-CoA: 18.8
  Acetyl-CoA: 18.7
  fatty_acid: 17.1
  CHC-CoA: 14.8
  Ethylmalonyl-CoA: 12.9
  Benzoyl-CoA: 10.0
  2-Methylbutyryl-CoA: 2.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5387..5659): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 187.3
  Ethylmalonyl-CoA: 174.0
  Methoxymalonyl-CoA: 146.8
  2-Methylbutyryl-CoA: 99.8
  Propionyl-CoA: 90.1
  trans-1,2-CPDA: 87.1
  CHC-CoA: 80.5
  Malonyl-CoA: 75.9
  Isobutyryl-CoA: 46.9
  Benzoyl-CoA: 40.5
  Acetyl-CoA: 22.5
  3-Methylbutyryl-CoA: 15.2
  inactive: 10.2
  fatty_acid: 9.5

PKS_AT (7363..7636): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 186.2
  Ethylmalonyl-CoA: 174.8
  Methoxymalonyl-CoA: 144.4
  2-Methylbutyryl-CoA: 95.2
  Propionyl-CoA: 88.9
  trans-1,2-CPDA: 87.9
  CHC-CoA: 79.1
  Malonyl-CoA: 70.1
  Isobutyryl-CoA: 49.1
  Benzoyl-CoA: 40.1
  Acetyl-CoA: 24.1
  3-Methylbutyryl-CoA: 15.7
  fatty_acid: 12.6
  inactive: 10.1

rapP: Hpr
Search NORINE for peptide: strict or relaxed
AMP-binding (501..898): Hpr
nrpys: Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    pip (Hpr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    DYQYLGHLVK
  Nearest Stachelhaus code(s):
    Hpr DYQYLGHLVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

rapC: mal - mal - mmal - mal
PKS_AT (545..801): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 158.6
  inactive: 66.3
  Methoxymalonyl-CoA: 65.2
  Methylmalonyl-CoA: 43.6
  Isobutyryl-CoA: 21.7
  Propionyl-CoA: 17.5
  Acetyl-CoA: 16.7
  fatty_acid: 15.9
  Ethylmalonyl-CoA: 15.8
  CHC-CoA: 13.3
  Benzoyl-CoA: 11.3
  2-Methylbutyryl-CoA: 8.4
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2132..2387): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 157.9
  Methoxymalonyl-CoA: 67.5
  inactive: 64.5
  Methylmalonyl-CoA: 45.2
  Isobutyryl-CoA: 18.8
  Propionyl-CoA: 17.4
  Ethylmalonyl-CoA: 17.4
  Acetyl-CoA: 16.6
  fatty_acid: 15.9
  CHC-CoA: 13.4
  Benzoyl-CoA: 11.3
  2-Methylbutyryl-CoA: 8.3
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3726..3999): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 187.4
  Ethylmalonyl-CoA: 171.6
  Methoxymalonyl-CoA: 148.3
  2-Methylbutyryl-CoA: 94.7
  trans-1,2-CPDA: 94.4
  Propionyl-CoA: 88.1
  CHC-CoA: 74.5
  Malonyl-CoA: 72.6
  Isobutyryl-CoA: 46.6
  Benzoyl-CoA: 41.6
  Acetyl-CoA: 17.1
  3-Methylbutyryl-CoA: 15.8
  inactive: 11.6
  fatty_acid: 9.8

PKS_AT (5760..6052): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 66.7%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 153.8
  Methoxymalonyl-CoA: 62.3
  inactive: 56.2
  Methylmalonyl-CoA: 47.4
  Propionyl-CoA: 32.6
  Isobutyryl-CoA: 32.3
  fatty_acid: 22.8
  Ethylmalonyl-CoA: 17.7
  Benzoyl-CoA: 10.0
  Acetyl-CoA: 5.2
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -3.1

Link to PARAS substrate predictor