SUPERFAMILY 1.75 HMM library and genome assignments server

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DNA clamp 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 24 SUPERFAMILY models representing the DNA clamp superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0050272 1392 2008-09-10 d1vpka2 DNA polymerase III, beta subunit
0053276 2847 2008-09-10 d2pola2 DNA polymerase III, beta subunit
0050271 2786 2008-09-10 d1vpka1 DNA polymerase III, beta subunit
0045418 600 2005-09-08 d2pola1 DNA polymerase III, beta subunit
0050273 744 2008-09-10 d1vpka3 DNA polymerase III, beta subunit
0053277 948 2008-09-10 d2pola3 DNA polymerase III, beta subunit
0036208 15 2005-09-08 d1czda2 DNA polymerase processivity factor
0044284 198 2005-09-08 d1ud9a2 DNA polymerase processivity factor
0035383 15 2005-09-08 d1b77a1 DNA polymerase processivity factor
0043899 9 2005-09-08 d1t6la1 DNA polymerase processivity factor
0048781 214 2008-09-10 d1plqa1 DNA polymerase processivity factor
0038064 196 2005-09-08 d1ge8a2 DNA polymerase processivity factor
0045836 176 2008-09-10 d1axca1 DNA polymerase processivity factor
0036207 15 2005-09-08 d1czda1 DNA polymerase processivity factor
0044283 129 2005-09-08 d1ud9a1 DNA polymerase processivity factor
0035249 113 2005-09-08 d1axca2 DNA polymerase processivity factor
0043400 130 2005-09-08 d1rwza1 DNA polymerase processivity factor
0046967 501 2008-09-10 d1ge8a1 DNA polymerase processivity factor
0036501 16 2005-09-08 d1dmla1 DNA polymerase processivity factor
0035384 15 2005-09-08 d1b77a2 DNA polymerase processivity factor
0043900 9 2005-09-08 d1t6la2 DNA polymerase processivity factor
0049258 735 2008-09-10 d1rwza2 DNA polymerase processivity factor
0042371 147 2005-09-08 d1plqa2 DNA polymerase processivity factor
0046361 14 2008-09-10 d1dmla2 DNA polymerase processivity factor