Table IV.
Motif analysis of predicted F-box, Pro-rich, and Cys-rich proteins
| Protein Descriptiona | Groupb | Representative Motifsc | Species Hits from Swiss-Prot/TrEMBLd | Hits to the Arabidopsis Genomee | Hits to the M. truncatula |
|---|---|---|---|---|---|
| F-box associated | 640 | FXIX{2}LGEXGX{2}ESWXKXF | – | 2 | 22 |
| F-box | 630 | [KR]XV[CS]KXW | – | 3 | 1 |
| M. truncatula (3) | |||||
| G. max (3) | |||||
| M. sativa (1) | |||||
| Pro-rich | 5 | SP… (PPV[VYE]K){3,} | T. repens (1) | 0 | 0 |
| Pea (1) | |||||
| C. arietinum (1) | |||||
| Bean (1) | |||||
| Carrot (1) | |||||
| Pro-rich | 485 | SP…PX{5}PX{4}PPXPPX{4}PX{4}P…PX{5}P…PP…P | – | 0 | 0 |
| Pro-rich | 669 | SP…PK…GXIXYQPPT…PXTPX{3}PX{3}PX…PXRPP | – | 0 | 0 |
| SP…CX{5}C…CX{4}C SP…CX{5}C…C…CX{4}CXC | G. orientalis (1) | ||||
| V. faba (5) | |||||
| Cys-rich | 31 | Pea (8) | 8 | 37 | |
| T. repens (1) | |||||
| Scorpion (5) | |||||
| Cys-rich | 645 | SP…C…CX{5}CX{3}C…GXC…CCC | – | 8 | 1 |
| Cys-rich | 38 | SP…CX{3}CX{3}C…CX{3}CX{3}C…CX{3}C | – | 2 | 1 |
| Cys-rich | 36 | SP…CX{5}C…C…CXC…CX{4}CXC | – | 0 | 0 |
| Cys-rich | 40 | SP…C…C…CX{3}C…GXC…CCC | – | 0 | 0 |
| Cys-rich | 41 | SP…C…CX{6}CX{3}C…CX{6}CXCX{2}C | – | 0 | 0 |
| Cys-rich | 655 | SP…CX{6}C…CX{6}C | – | 0 | 1 |
| G. max (1) | |||||
| G. soja (1) | |||||
| M. truncatula (2) | |||||
| Cys-rich | 666 | SP…C…C…C…CXC…C…CX{5}CX{8}CX{12}C | Pea (5) | 6 | 0 |
| L. angustifolius (1) | |||||
| P. vulagaris (1) |
Further descriptions of predicted proteins are provided in the text.
Group numbers are arbitrary identifiers assigned during single-linkage clustering analysis of homologous sequences.
In the representative motifs, single-letter amino acid abbreviations are used. The letters SP in bold designate the signal peptide. X denotes any amino acid. Numbers in curly brackets designate the number of repeats of the previous element. Letters in brackets denote a choice for a single amino acid residue. Three periods designate a gap introduced to optimize alignments. Due to its sequence diversity, two different motifs were used to model members of group 31.
For MAST and HMM analysis against the Swiss-Prot/TrEMBL database an E-value cutoff of 10−4 was used. Regular expression patterns were used to find hits to the Swiss-Prot/TrEMBL database for group 5. The following new abbreviations were used: Trifolium repens (T. repens) and Lupinus angustifolius (L. angustifolius).
Hits to the Arabidopsis and Medicago genomes were identified using either HMM or MAST motifs with an E-value cutoff of 10−4.