Team:Heidelberg/Templates/NRPS-W-20a

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== Tool selection for domain prediciton ==
== Tool selection for domain prediciton ==

Latest revision as of 03:48, 29 October 2013

Tool selection for domain prediciton

We tried to determine, which tool would be most appropriate for automated determination of domains. Thus we used the first CDS of the teicoplanin NRPS, as curated in the NRPS-PKS (SBSPKS) database. We then compared the automated prediction with the tool of Maryland, as well as antiSMASH2.


A domain T domain C domain A domain T domain E domain
Start End Start End Start End Start End Start End Start End
NRPS-PKS 1 491 505 564 604 1021 1015 1511 1526 1584 1608 2053
Maryland 18 503 504 567 599 1012 1008 1524 1524 1587 1604 2063
antiSMASH 35 426 502 567 598 891 1056 1447 1522 1589 1602 1896
pfam 15 478 504 566 598 891 1036 1498 1524 1586 1620 (as C) 1896 (as C)

Note that Pfam can't differentiate between C and E domains. Pfam also does not return any predictions in regard to A-domain specificity. antiSMASH is able to predict the A-domain specificities as annotated in NRPS-PKS, while Maryland's tool can only predict the second A-domain (Tyrosine), while the first is incorrectly predicted to be specific for Leucine (curated: HpG, 4-hydroxyphenyl glycine).

The same analysis was also repeated for thaxtomin.

A domain NM domain T domain C domain
Start End Start End Start End Start End
NRPS-PKS 1 506 509 712 944 1005 1029 1458
Maryland 5 521 468 879 942 1006 1028 1455
antiSMASH 42 445 511 732 940 1007 1025 1325
pfam 22 486 538 638 942 1006 1023 1326

In this case, both tools correctly predict the L-Phenylalanine specificity of the A-domain.

Analysis of tycC from the tyrocidine-cluster.

C domain A domain T domain C domain A domain T domain C domain A domain T domain C domain A domain T domain C domain A domain T domain C domain A domain T domain TE domain
Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End Start End
Marahiel (C-T), Ilia (A-T), Philipp (C-A) 953 963 1033 1050 1345 1990 2000 2070 2087 3028 3038 3108 3125 3571 4063 4073 4143 4160 5107 5117 5187 5204 6150 6160 6230 6247
NRPS-PKS 13 447 442 957 972 1036 1058 1483 1478 1994 2009 2073 2095 2520 2515 3032 3048 3111 3133 3558 3553 4066 4082 4146 4168 4593 4588 5111 5126 5190 5212 5639 5636 6151 6169 6233 6256 6466
Maryland 8 438 441 964 972 1036 1053 1474 1477 2001 2009 2073 2090 2511 2516 3039 3047 3111 3128 3549 3552 4074 4082 4146 4163 4584 4587 5118 5126 5190 5207 5630 5637 6160 6169 6233 6254 6482
antiSMASH 8 305 490 887 970 1039 1054 1339 1526 1924 2007 2075 2090 2376 2563 2962 3045 3113 3128 3413 3601 3997 4080 4149 4165 4449 4636 5041 5124 5193 5208 5494 5682 6083 6167 6236 6253 6482
pfam 7 306 470 944 972 1036 1052 1341 1506 1981 2009 2073 2089 2378 2543 3019 3047 3111 3127 3416 3581 4054 4082 4146 4162 4450 4616 5098 5126 5190 5206 5495 5662 6141 6169 6233 6254 6482

In regards to prediction of A-domain specificity, antiSMASH predictions and the curated NRPS-PKS amino acids were the same. On the other hand, Maryland predicted did not get any hit for A6 (Leu) and for A1/A3 respectively it predicted to possible amino acids (Asn+Asp compared to Asn / Tyr + Trp compared to Tyr in antiSMASH and NRPS-PKS).

TycB3 C-A domain

Clustal Omega MSA of different C-A domain borders of Tyrocidine cluster with annotation (prediction) of the start of the A domain according to different tools.
Clustal Omega MSA of different C-A domain borders of Tyrocidine cluster with annotation (prediction) of the end of the C domain according to different tools.
C domain A domain
Start End Start End
paper primer position 2520 (MLTAA..)
NRPS-PKS 2100 2527 2540 3029
Maryland 2095 2518 2521 3039
antiSMASH 2096 2381 2570 2961
pfam 2094 2383 2550 3019

Inegration of antiSMASH

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