SUPERFAMILY 1.75 HMM library and genome assignments server

Homeodomain-like 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 137 SUPERFAMILY models representing the Homeodomain-like superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0053176 3134 2008-09-10 d2lfba_ Homeodomain
0045889 11097 2008-09-10 d1b72a_ Homeodomain
0048379 4663 2008-09-10 d1nk2p_ Homeodomain
0047583 10991 2008-09-10 d1jgga_ Homeodomain
0050796 3400 2008-09-10 d1x41a1 Homeodomain
0037778 3385 2005-09-08 d1ftza_ Homeodomain
0047358 11358 2008-09-10 d1ig7a_ Homeodomain
0050545 1283 2008-09-10 d1wh5a_ Homeodomain
0047051 11285 2008-09-10 d1gt0c1 Homeodomain
0052257 11392 2008-09-10 d2craa1 Homeodomain
0046702 11184 2008-09-10 d1f43a_ Homeodomain
0045901 11176 2008-09-10 d1b8ib_ Homeodomain
0048540 10949 2008-09-10 d1ocpa_ Homeodomain
0047970 11605 2008-09-10 d1lfup_ Homeodomain
0050573 1373 2008-09-10 d1wi3a_ Homeodomain
0052493 11368 2008-09-10 d2e1oa1 Homeodomain
0036751 3893 2005-09-08 d1e3oc1 Homeodomain
0047179 11093 2008-09-10 d1hdpa_ Homeodomain
0054027 8785 2010-05-31 d2hddb_ Homeodomain
0046802 11923 2008-09-10 d1fjla_ Homeodomain
0046025 11281 2008-09-10 d1bw5a_ Homeodomain
0049336 7257 2008-09-10 d1s7ea1 Homeodomain
0045820 11222 2008-09-10 d1au7a1 Homeodomain
0051641 11644 2008-09-10 d1ztra1 Homeodomain
0040923 3893 2005-09-08 d1mh3a1 Homeodomain
0048195 3570 2008-09-10 d1mnmc_ Homeodomain
0051446 11755 2008-09-10 d1yz8p1 Homeodomain
0050781 9740 2008-09-10 d1x2na1 Homeodomain
0037777 3413 2005-09-08 d1ftta_ Homeodomain
0052309 6690 2008-09-10 d2cufa1 Homeodomain
0035079 3625 2005-09-08 d1akhb_ Homeodomain
0049907 8839 2008-09-10 d1uhsa_ Homeodomain
0052252 9047 2008-09-10 d2cqxa1 Homeodomain
0046399 11332 2008-09-10 d1du6a_ Homeodomain
0045900 4681 2008-09-10 d1b8ia_ Homeodomain
0048818 11272 2008-09-10 d1pufa_ Homeodomain
0050824 3248 2008-09-10 d1x58a1 Homeodomain
0050547 1325 2008-09-10 d1wh7a_ Homeodomain
0053878 4260 2010-05-31 d2ecba1 Homeodomain
0045778 11434 2008-09-10 d1ahdp_ Homeodomain
0051615 4985 2008-09-10 d1zq3p1 Homeodomain
0048162 77 2008-09-10 d1mija_ Homeodomain
0050780 7044 2008-09-10 d1x2ma1 Homeodomain
0052496 1881 2008-09-10 d2ecca1 Homeodomain
0052308 11338 2008-09-10 d2cuea1 Homeodomain
0049809 11 2008-09-10 d1u78a2 Recombinase DNA-binding domain
0052551 31 2008-09-10 d2ezla_ Recombinase DNA-binding domain
0046966 101 2008-09-10 d1gdta1 Recombinase DNA-binding domain
0045264 5 2005-09-08 d2ezia_ Recombinase DNA-binding domain
0049590 15 2008-09-10 d1tc3c_ Recombinase DNA-binding domain
0038534 353 2005-09-08 d1hcra_ Recombinase DNA-binding domain
0052250 4224 2008-09-10 d2cqra1 Myb/SANT domain
0041825 167 2005-09-08 d1ofcx1 Myb/SANT domain
0053777 804 2010-05-31 d2ckxa1 Myb/SANT domain
0050913 2614 2008-09-10 d1xc5a1 Myb/SANT domain
0038474 1888 2005-09-08 d1h8ac1 Myb/SANT domain
0052305 7345 2008-09-10 d2cu7a1 Myb/SANT domain
0034886 1888 2005-09-08 d1a5ja1 Myb/SANT domain
0052249 1847 2008-09-10 d2cqqa1 Myb/SANT domain
0053132 5031 2008-09-10 d2iw5b1 Myb/SANT domain
0038986 1881 2005-09-08 d1idza_ Myb/SANT domain
0050538 2873 2008-09-10 d1wgxa_ Myb/SANT domain
0053698 962 2010-05-31 d2ajea1 Myb/SANT domain
0052177 6085 2008-09-10 d2cjja1 Myb/SANT domain
0038473 1878 2005-09-08 d1h88c2 Myb/SANT domain
0047064 7069 2008-09-10 d1guua_ Myb/SANT domain
0052261 2309 2008-09-10 d2crga1 Myb/SANT domain
0046765 109 2008-09-10 d1fexa_ Myb/SANT domain
0034887 1889 2005-09-08 d1a5ja2 Myb/SANT domain
0049891 1048 2008-09-10 d1ug2a_ Myb/SANT domain
0039196 1603 2005-09-08 d1itya_ DNA-binding domain of telomeric protein
0050954 6417 2008-09-10 d1xg1a1 DNA-binding domain of telomeric protein
0053366 719 2008-09-10 d6paxa2 Paired domain
0048742 1327 2008-09-10 d1pdnc_ Paired domain
0039939 476 2005-09-08 d1k78a1 Paired domain
0053365 797 2008-09-10 d6paxa1 Paired domain
0039940 219 2005-09-08 d1k78a2 Paired domain
0039012 16 2005-09-08 d1igna2 DNA-binding domain of rap1
0047361 1015 2008-09-10 d1igna1 DNA-binding domain of rap1
0047440 208 2008-09-10 d1iufa2 Centromere-binding
0047203 305 2008-09-10 d1hlva2 Centromere-binding
0047439 22 2008-09-10 d1iufa1 Centromere-binding
0047202 60 2008-09-10 d1hlva1 Centromere-binding
0046275 8950 2008-09-10 d1d5ya2 AraC type transcriptional activator
0035607 2739 2005-09-08 d1bl0a1 AraC type transcriptional activator
0036286 2269 2005-09-08 d1d5ya1 AraC type transcriptional activator
0045977 7625 2008-09-10 d1bl0a2 AraC type transcriptional activator
0049392 9335 2008-09-10 d1sgma1 Tetracyclin repressor-like, N-terminal domain
0052877 11367 2008-09-10 d2gena1 Tetracyclin repressor-like, N-terminal domain
0051466 9607 2008-09-10 d1z0xa1 Tetracyclin repressor-like, N-terminal domain
0052830 11786 2008-09-10 d2g3ba1 Tetracyclin repressor-like, N-terminal domain
0052647 12025 2008-09-10 d2fbqa1 Tetracyclin repressor-like, N-terminal domain
0054860 10095 2010-05-31 d3c07a1 Tetracyclin repressor-like, N-terminal domain
0054157 8061 2010-05-31 d2iu5a1 Tetracyclin repressor-like, N-terminal domain
0049910 12876 2008-09-10 d1ui5a1 Tetracyclin repressor-like, N-terminal domain
0049545 11479 2008-09-10 d1t56a1 Tetracyclin repressor-like, N-terminal domain
0053204 11374 2008-09-10 d2np5a1 Tetracyclin repressor-like, N-terminal domain
0049195 10840 2008-09-10 d1rkta1 Tetracyclin repressor-like, N-terminal domain
0053065 9945 2008-09-10 d2i10a1 Tetracyclin repressor-like, N-terminal domain
0045724 9757 2008-09-10 d1a6ia1 Tetracyclin repressor-like, N-terminal domain
0051585 6046 2008-09-10 d1zk8a1 Tetracyclin repressor-like, N-terminal domain
0052845 6847 2008-09-10 d2g7la1 Tetracyclin repressor-like, N-terminal domain
0050079 7708 2008-09-10 d1v7ba1 Tetracyclin repressor-like, N-terminal domain
0048725 11449 2008-09-10 d1pb6a1 Tetracyclin repressor-like, N-terminal domain
0052798 9885 2008-09-10 d2fx0a1 Tetracyclin repressor-like, N-terminal domain
0054374 9623 2010-05-31 d2oi8a1 Tetracyclin repressor-like, N-terminal domain
0054072 9250 2010-05-31 d2hyja1 Tetracyclin repressor-like, N-terminal domain
0049523 8007 2008-09-10 d1t33a1 Tetracyclin repressor-like, N-terminal domain
0053202 10673 2008-09-10 d2np3a1 Tetracyclin repressor-like, N-terminal domain
0052885 9418 2008-09-10 d2gfna1 Tetracyclin repressor-like, N-terminal domain
0051514 12339 2008-09-10 d1z77a1 Tetracyclin repressor-like, N-terminal domain
0052843 4509 2008-09-10 d2g7ga1 Tetracyclin repressor-like, N-terminal domain
0047677 10163 2008-09-10 d1jt6a1 Tetracyclin repressor-like, N-terminal domain
0052655 10674 2008-09-10 d2fd5a1 Tetracyclin repressor-like, N-terminal domain
0052393 9750 2008-09-10 d2d6ya1 Tetracyclin repressor-like, N-terminal domain
0053235 10954 2008-09-10 d2o7oa1 Tetracyclin repressor-like, N-terminal domain
0053096 7944 2008-09-10 d2id3a1 Tetracyclin repressor-like, N-terminal domain
0052848 9850 2008-09-10 d2g7sa1 Tetracyclin repressor-like, N-terminal domain
0052742 10427 2008-09-10 d2fq4a1 Tetracyclin repressor-like, N-terminal domain
0054341 7930 2010-05-31 d2o7ta1 Tetracyclin repressor-like, N-terminal domain
0050188 12461 2008-09-10 d1vi0a1 Tetracyclin repressor-like, N-terminal domain
0054048 7711 2010-05-31 d2hkua1 Tetracyclin repressor-like, N-terminal domain
0047429 419 2008-09-10 d1irza_ GARP response regulators
0048440 1677 2008-09-10 d1ntca_ FIS-like
0049952 1576 2008-09-10 d1umqa_ FIS-like
0037176 120 2005-09-08 d1etob_ FIS-like
0046907 2101 2008-09-10 d1g2ha_ FIS-like
0048555 192 2008-09-10 d1ofcx2 SLIDE domain
0049236 157 2008-09-10 d1rr7a_ Middle operon regulator, Mor
0052194 526 2008-09-10 d2coba1 Psq domain
0052856 297 2008-09-10 d2ga1a1 Alr1493-like
0051803 4 2008-09-10 d2ao9a1 Nanomeric phage protein-like
0052312 196 2008-09-10 d2cuja1 SWIRM domain
0052741 292 2008-09-10 d2fq3a1 SWIRM domain
0052200 336 2008-09-10 d2coma1 SWIRM domain
0054226 2209 2010-05-31 d2jn6a1 Cgl2762-like
0054327 1588 2010-05-31 d2o3fa1 RpiR-like