SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

Sigma3 and sigma4 domains of RNA polymerase sigma factors superfamily models

A superfamily is represented by one or more models; usually there is more than one model representing the superfamily. Since each model is built to capture the whole superfamily, they are likely to be overlapping and sometimes are mostly overlapping or even redundant to each other. Also models often do not score their own seed sequence more highly than other sequences in the superfamily, so it is a mistake to think that the model represents the seed sequence.

All models are available for immediate download after obtaining a license by filling in a short online registration form. Licenses are free for academic and commercial purposes.

Plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be viewed for each model by following the model ID link.


All 10 SUPERFAMILY models representing the Sigma3 and sigma4 domains of RNA polymerase sigma factors superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0049223 2179 2008-09-10 d1rp3a1 Sigma3 domain
0047455 2177 2008-09-10 d1iw7f1 Sigma3 domain
0041987 1538 2005-09-08 d1or7a1 Sigma4 domain
0047915 1904 2008-09-10 d1l0oc_ Sigma4 domain
0039239 1111 2005-09-08 d1iw7f2 Sigma4 domain
0049695 1765 2008-09-10 d1ttya_ Sigma4 domain
0049224 7207 2008-09-10 d1rp3a2 Sigma4 domain
0049651 3658 2008-09-10 d1tlhb_ Sigma4 domain
0051096 791 2008-09-10 d1xsva_ YlxM/p13-like
0049340 865 2008-09-10 d1s7oa_ YlxM/p13-like