SUPERFAMILY HMM library and genome assignments server

SUPERFAMILY Assignments for Genomes and Sequence Collections

We provide assignments for 911 distinct genomes. Common species names are provided where available.
The species are organised into five sections:

Model Eukaryotes (176) animals (67), fungi (64), plants (17) and protists (28)
Model Prokaryotes (496) model bacteria (447) and archaea (49)
Strains - Eukaryotes (11); Prokaryotes (228) fungal (10) and plant (1) strains; bacterial (225) and archaeal (3) strains
Eukaryotes - longest transcript per gene (42) versions of eukaryote genomes with splice variants removed
Others incomplete, low coverage or early release genomes, and sequence collections such as UniProt

We put considerable effort into classifying prokaryotes as either model species or strains. Please let us know if you disagree with our classification. The "longest transcript per gene" versions of the eukaryotic genomes may prove useful in eliminating bias from splice variants. A number of duplicate genomes are included. Originally these duplicate genomes used different sequence identifiers.
Please contact superfamily@mrc-lmb.cam.ac.uk to have a genome or some other data set analysed and/or added.
Detailed statistics for each genome are available on the genome statistics page. All data is available for download.


Eukaryotes
Category Organism
Animals Vertebrates Mammals Homo sapiens 49_36k (all transcripts)   (Human)  
Pan troglodytes 49_21h (all transcripts)   (Chimpanzee)  
Pongo pygmaeus 49_1 (all transcripts)   (Bornean orangutan)  
Macaca mulatta 49_10h (all transcripts)   (Rhesus monkey)  
Otolemur garnettii 49_1c (all transcripts)   (Small-eared galago)  
Microcebus murinus 49_1 (all transcripts)   (Gray mouse lemur)  
Rattus norvegicus 49_34s (all transcripts)   (Norway rat)  
Mus musculus 49_37b (all transcripts)   (House mouse)  
Spermophilus tridecemlineatus 49_1e (all transcripts)   (Thirteen-lined ground squirrel)  
Cavia porcellus 49_1c (all transcripts)   (Domestic guinea pig)  
Oryctolagus cuniculus 49_1f (all transcripts)   (Rabbit)  
Ochotona princeps 49_1 (all transcripts)   (American pika)  
Tupaia belangeri 49_1d (all transcripts)   (Northern tree shrew)  
Bos taurus 49_3f (all transcripts)   (Cattle)  
Canis familiaris 49_2g (all transcripts)   (Dog)  
Felis catus 49_1c (all transcripts)   (Domestic cat)  
Equus caballus 49_2 (all transcripts)   (Horse)  
Myotis lucifugus 49_1e (all transcripts)   (Little brown bat)  
Sorex araneus 49_1c (all transcripts)   (European shrew)  
Erinaceus europaeus 49_1c (all transcripts)   (Western European hedgehog)  
Loxodonta africana 49_1d (all transcripts)   (African savanna elephant)  
Echinops telfairi 49_1e (all transcripts)   (Small Madagascar hedgehog)  
Dasypus novemcinctus 49_1f (all transcripts)   (Nine-banded armadillo)  
Monodelphis domestica 49_5d (all transcripts)   (Gray short-tailed opossum)  
Ornithorhynchus anatinus 49_1f (all transcripts)   (Platypus)  
Birds Gallus gallus 49_2g (all transcripts)   (Chicken)  
Amphibians Xenopus laevis   (African clawed frog)  
Xenopus tropicalis 49_41i (all transcripts)   (Western clawed frog)  
Fishes Danio rerio 49_7c (all transcripts)   (Zebrafish)  
Gasterosteus aculeatus 49_1f (all transcripts)   (Three-spined stickleback)  
Oryzias latipes 49_1e (all transcripts)   (Japanese medaka)  
Tetraodon nigroviridis 49_1k (all transcripts)   (Spotted green pufferfish)  
Takifugu rubripes 49_4i (all transcripts)  
Cephalochordata Branchiostoma floridae 1.0   (Florida lancelet)  
Ascidians Ciona savignyi 49_2f (all transcripts)  
Ciona intestinalis 49_2i (all transcripts)  
Echinoderms Strongylocentrotus purpuratus   (Purple sea urchin)  
Cnidarians Nematostella vectensis 1.0   (Starlet sea anemone)  
Annelida Helobdella robusta  
Capitella sp. I  
Insects Flies Drosophila grimshawi 1.2  
Drosophila willistoni 1.2  
Drosophila pseudoobscura 2.2  
Drosophila persimilis 1.2  
Drosophila yakuba 1.2  
Drosophila simulans 1.2  
Drosophila sechellia 1.2  
Drosophila melanogaster FlyBase 5.7 (all transcripts)   (Fruit fly)  
Drosophila melanogaster Ensembl 49_54 (all transcripts)   (Fruit fly)  
Drosophila erecta 1.2  
Drosophila ananassae 1.2  
Drosophila virilis 1.1  
Drosophila mojavensis 1.2  
Aedes aegypti 49_1b (all transcripts)   (Yellow fever mosquito)  
Culex pipiens quinquefasciatus   (Southern house mosquito)  
Anopheles gambiae 49_3j (all transcripts)  
Hymenopterans Nasonia vitripennis   (Jewel wasp)  
Apis mellifera 37.2d (all transcripts)   (Honey bee)  
Butterflies and moths Bombyx mori   (Domestic silkworm)  
Beetles Tribolium castaneum 3.0   (Red flour beetle)  
Crustacea Daphnia pulex   (Common water flea)  
Mollusca Lottia gigantea  
Nematodes Brugia malayi   (Agent of lymphatic filariasis)  
Caenorhabditis elegans WormBase WS147 (all transcripts)   (Nematode)  
Caenorhabditis elegans Ensembl 49_180a (all transcripts)   (Nematode)  
Caenorhabditis briggsae 2  
Placozoa Trichoplax adhaerens  
Choanoflagellida Codonosigidae Monosiga brevicollis  
Fungi Ascomycetes Budding yeasts Candida tropicalis MYA-3404  
Candida parapsilosis  
Candida glabrata  
Candida albicans SC5314  
Yarrowia lipolytica  
Candida lusitaniae ATCC 42720  
Vanderwaltozyma polyspora  
Lodderomyces elongisporus NRRL YB-4239  
Ashbya gossypii 1.0  
Debaromyces hansenii  
Saccharomyces mikatae MIT  
Saccharomyces paradoxus MIT  
Saccharomyces cerevisiae SGD   (Baker's yeast)  
Saccharomyces cerevisiae Ensembl 49_1h (all transcripts)   (Baker's yeast)  
Saccharomyces bayanus MIT  
Candida guilliermondii ATCC 6260  
Pichia stipitis CBS 6054  
Kluyveromyces lactis  
Kluyveromyces waltii  
Fission yeasts Schizosaccharomyces japonicus yFS275  
Schizosaccharomyces pombe   (Fission yeast)  
Sordariomycetes Podospora anserina  
Chaetomium globosum CBS 148.51  
Neurospora crassa 7  
Fusarium oxysporum f. sp. lycopersici 4286  
Nectria haematococca mpVI  
Fusarium verticillioides 7600  
Fusarium graminearum  
Trichoderma atroviride  
Trichoderma reesei 1.2  
Trichoderma virens  
Magnaporthe grisea 7 r2.3   (Rice blast fungus)  
Eurotiales Neosartorya fischeri NRRL 181  
Aspergillus terreus NIH2624  
Aspergillus fumigatus  
Aspergillus oryzae RIB40  
Aspergillus niger ATCC 1015  
Aspergillus flavus NRRL3357  
Aspergillus clavatus NRRL 1  
Aspergillus nidulans 1 r3.1  
Ascomycetes/Others Botrytis cinerea B05.10  
Sclerotinia sclerotiorum  
Histoplasma capsulatum class NAmI strain WU24  
Coccidioides posadasii RMSCC 3488  
Coccidioides immitis RS  
Uncinocarpus reesii 1704  
Pyrenophora tritici-repentis  
Cochliobolus heterostrophus  
Stagonospora nodorum 1  
Mycosphaerella fijiensis  
Mycosphaerella graminicola  
Basidiomycetes Malassezia globosa CBS 7966  
Ustilago maydis 1 r2  
Puccinia graminis f. sp. tritici CRL 75-36-700-3  
Sporobolomyces roseus  
Coprinopsis cinerea okayama7 130  
Laccaria bicolor  
Phanerochaete chrysosporium 2.1  
Postia placenta  
Cryptococcus neoformans JEC21  
Microsporidians Encephalitozoon cuniculi  
Fungi/Others Rhizopus oryzae RA 99-880  
Phycomyces blakesleeanus  
Batrachochytrium dendrobatidis JEL423  
Mycetozoa Cellular slime mold Dictyostelium discoideum  
Entamoebidae Entamoeba Entamoeba histolytica 1  
Plants Dicotyledons Mustard family Arabidopsis thaliana 8 (all transcripts)   (Thale cress)  
Pea family Medicago truncatula   (Barrel medic)  
Willow family Populus trichocarpa 1.1   (Western balsam poplar)  
Grape family Vitis vinifera   (Wine grape)  
Dicotyledons/Others Carica papaya   (Papaya)  
Monocotyledons Grass family Oryza sativa ssp. japonica 5.0   (Japanese rice)  
Sorghum bicolor   (Sorghum)  
Spikemosses Selaginella moellendorffii  
Mosses Physcomitrella patens subsp. patens  
Green algae Chlorella sp. NC64A  
Volvox carteri f. nagariensis  
Chlamydomonas reinhardtii 3.0  
Ostreococcus lucimarinus CCE9901  
Ostreococcus tauri  
Micromonas sp. CCMP490  
Micromonas sp. RCC299  
Red algae Cyanidioschyzon merolae  
Protists Alveolates Apicomplexa Theileria parva 1  
Theileria annulata  
Plasmodium falciparum 3D7 2.1   (Malaria parasite P. falciparum)  
Plasmodium vivax SaI-1  
Plasmodium knowlesi  
Plasmodium yoelii ssp. yoelii 1  
Plasmodium chabaudi  
Plasmodium berghei ANKA  
Cryptosporidium hominis  
Cryptosporidium parvum Iowa II  
Toxoplasma gondii RH  
Ciliates Paramecium tetraurelia  
Tetrahymena thermophila 1  
Euglenozoa Trypanosoma cruzi  
Trypanosoma brucei  
Leishmania major 100505  
Leishmania infantum JPCM5  
Leishmania braziliensis MHOM/BR/75/M2904  
Parabasalids Trichomonas vaginalis  
stramenopiles Aureococcus anophagefferens  
Phytophthora ramorum 1.0   (Sudden oak death agent)  
Phytophthora sojae 1.0  
Phytophthora infestans T30-4  
Phaeodactylum tricornutum  
Thalassiosira pseudonana  
Diplomonads Giardia lamblia  
Heterolobosea Naegleria gruberi  
Haptophyceae Emiliania huxleyi CCMP1516  

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Prokaryotes
Category Organism
Bacteria Proteobacteria Gamma/enterobacteria Enterobacter sakazakii ATCC BAA-894  
Candidatus Blochmannia pennsylvanicus BPEN  
Erwinia carotovora ssp. atroseptica SCRI1043  
Sodalis glossinidius morsitans  
Wigglesworthia glossinidia  
Buchnera aphidicola APS  
Photorhabdus luminescens ssp. laumondii TTO1  
Yersinia pseudotuberculosis IP 32953  
Yersinia pestis CO92  
Yersinia enterocolitica ssp. enterocolitica 8081  
Shigella sonnei Ss046  
Shigella flexneri 2a 2457T  
Shigella dysenteriae Sd197  
Shigella boydii Sb227  
Serratia proteamaculans 568  
Salmonella enterica ssp. enterica ser. Paratyphi A ATCC 9150  
Salmonella typhimurium LT2  
Salmonella typhi  
Klebsiella pneumoniae ssp. pneumoniae MGH 78578  
Escherichia coli K12  
New/updated genome Erwinia tasmaniensis  
Enterobacter sp. 638  
Citrobacter koseri ATCC BAA-895  
Beta Aromatoleum aromaticum EbN1  
Dechloromonas aromatica RCB  
Chromobacterium violaceum ATCC 12472  
Neisseria meningitidis Z2491  
New/updated genome Neisseria gonorrhoeae NCCP11945  
Neisseria gonorrhoeae FA 1090  
Methylobacillus flagellatus KT  
Thiobacillus denitrificans ATCC 25259  
Methylibium petroleiphilum PM1  
Leptothrix cholodnii SP-6  
New/updated genome Cupriavidus taiwanensis  
Ralstonia metallidurans CH34  
Ralstonia eutropha JMP134  
Ralstonia solanacearum GMI1000  
Polynucleobacter sp. QLW-P1DMWA-1  
Polynucleobacter necessarius STIR1  
New/updated genome Burkholderia phymatum STM815  
Burkholderia thailandensis E264  
Burkholderia pseudomallei K96243  
Burkholderia sp. 383  
Burkholderia ambifaria MC40-6  
Burkholderia cepacia AMMD  
Burkholderia cenocepacia AU 1054  
Burkholderia multivorans ATCC 17616  
Burkholderia vietnamiensis G4  
Burkholderia xenovorans LB400  
Burkholderia mallei ATCC 23344  
Verminephrobacter eiseniae EF01-2  
Delftia acidovorans SPH-1  
Polaromonas sp. JS666  
Polaromonas naphthalenivorans CJ2  
Rhodoferax ferrireducens T118  
Acidovorax sp. JS42  
Acidovorax avenae ssp. citrulli AAC00-1  
Herminiimonas arsenicoxydans  
Janthinobacterium sp. Marseille  
Bordetella petrii DSM 12804  
New/updated genome Bordetella avium 197N  
Bordetella pertussis Tohama I  
Bordetella parapertussis 12822  
Bordetella bronchiseptica RB50  
Nitrosospira multiformis ATCC 25196  
Nitrosomonas eutropha C91  
Nitrosomonas europaea ATCC 19718  
Epsilon Arcobacter butzleri RM4018  
Campylobacter hominis ATCC BAA-381  
Campylobacter curvus 525.92  
Campylobacter concisus 13826  
Campylobacter jejuni ssp. jejuni NCTC 11168  
Campylobacter fetus ssp. fetus 82-40  
Sulfurimonas denitrificans DSM 1251  
Wolinella succinogenes DSM 1740  
Helicobacter hepaticus ATCC 51449  
Helicobacter acinonychis Sheeba  
Helicobacter pylori 26695  
Nitratiruptor sp. SB155-2  
Sulfurovum sp. NBC37-1  
Delta Bdellovibrio bacteriovorus HD100  
Syntrophus aciditrophicus SB  
Syntrophobacter fumaroxidans MPOB  
Desulfotalea psychrophila LSv54  
Desulfococcus oleovorans Hxd3  
Lawsonia intracellularis PHE/MN1-00  
Desulfovibrio vulgaris ssp. vulgaris Hildenborough  
Desulfovibrio desulfuricans ssp. desulfuricans G20  
Pelobacter propionicus DSM 2379  
Pelobacter carbinolicus DSM 2380  
Geobacter uraniumreducens Rf4  
New/updated genome Geobacter lovleyi SZ  
Geobacter sulfurreducens PCA  
Geobacter metallireducens GS-15  
Sorangium cellulosum So ce 56  
Anaeromyxobacter sp. Fw109-5  
Anaeromyxobacter dehalogenans 2CP-C  
Myxococcus xanthus DK 1622  
Alpha/rickettsias Candidatus Pelagibacter ubique HTCC1062  
Neorickettsia sennetsu Miyayama  
Ehrlichia chaffeensis Arkansas  
Ehrlichia canis Jake  
Ehrlichia ruminantium Welgevonden  
Anaplasma phagocytophilum HZ  
Anaplasma marginale St. Maries  
Orientia tsutsugamushi Boryong  
Rickettsia bellii RML369-C  
Rickettsia canadensis McKiel  
Rickettsia typhi Wilmington  
Rickettsia prowazekii Madrid E  
Rickettsia felis URRWXCal2  
Rickettsia massiliae MTU5  
Rickettsia akari Hartford  
Rickettsia rickettsii Sheila Smith  
Rickettsia conorii Malish 7  
Wolbachia endosymbiont of Drosophila melanogaster  
New/updated genome Wolbachia pipientis  
Alpha/rhizobacteria Xanthobacter autotrophicus Py2  
Azorhizobium caulinodans ORS 571  
Methylobacterium sp. 4-46  
Methylobacterium radiotolerans JCM 2831  
Methylobacterium extorquens PA1  
Ochrobactrum anthropi ATCC 49188  
Brucella canis ATCC 23365  
Brucella suis 1330  
Brucella melitensis 16M  
Brucella ovis ATCC 25840  
Brucella abortus bv. 1 9-941  
Sinorhizobium medicae WSM419  
Sinorhizobium meliloti 1021  
Rhizobium etli CFN 42  
Rhizobium leguminosarum bv. viciae 3841  
Agrobacterium tumefaciens C58  
Parvibaculum lavamentivorans DS-1  
Mesorhizobium sp. BNC1  
Mesorhizobium loti MAFF303099  
Beijerinckia indica ssp. indica ATCC 9039  
Rhodopseudomonas palustris CGA009  
Nitrobacter winogradskyi Nb-255  
Nitrobacter hamburgensis X14  
Bradyrhizobium sp. ORS278  
Bradyrhizobium japonicum USDA 110  
Bartonella tribocorum CIP 105476  
Bartonella henselae Houston-1  
Bartonella quintana Toulouse  
Bartonella bacilliformis KC583  
Proteobacteria/Others Caulobacter sp. K31  
Caulobacter crescentus CB15  
Erythrobacter litoralis HTCC2594  
Sphingopyxis alaskensis RB2256  
Novosphingobium aromaticivorans DSM 12444  
Sphingomonas wittichii RW1  
Zymomonas mobilis ssp. mobilis ZM4  
Maricaulis maris MCS10  
Hyphomonas neptunium ATCC 15444  
Dinoroseobacter shibae DFL 12  
Jannaschia sp. CCS1  
Silicibacter sp. TM1040  
Silicibacter pomeroyi DSS-3  
Roseobacter denitrificans OCh 114  
Rhodobacter sphaeroides 2.4.1  
Paracoccus denitrificans PD1222  
Magnetospirillum magneticum AMB-1  
Rhodospirillum rubrum ATCC 11170  
Granulibacter bethesdensis CGDNIH1  
Gluconacetobacter diazotrophicus PAl 5  
Gluconobacter oxydans 621H  
Haemophilus somnus 129PT  
Mannheimia succiniciproducens MBEL55E  
Pasteurella multocida ssp. multocida Pm70  
Haemophilus ducreyi 35000HP  
Haemophilus influenzae Rd KW20  
Actinobacillus succinogenes 130Z  
Actinobacillus pleuropneumoniae L20  
Aeromonas salmonicida ssp. salmonicida A449  
Aeromonas hydrophila ssp. hydrophila ATCC 7966  
Vibrio fischeri ES114  
Vibrio vulnificus YJ016  
Vibrio parahaemolyticus RIMD 2210633  
Vibrio harveyi ATCC BAA-1116  
Vibrio cholerae O1 biov. eltor N16961  
Photobacterium profundum SS9  
Psychromonas ingrahamii 37  
Idiomarina loihiensis L2TR  
Shewanella loihica PV-4  
Shewanella halifaxensis HAW-EB4  
Shewanella sediminis HAW-EB3  
Shewanella denitrificans OS217  
Shewanella pealeana ATCC 700345  
Shewanella oneidensis MR-1  
Shewanella baltica OS155  
Shewanella woodyi ATCC 51908  
Shewanella sp. MR-7  
Shewanella amazonensis SB2B  
Shewanella frigidimarina NCIMB 400  
Shewanella putrefaciens CN-32  
Colwellia psychrerythraea 34H  
Pseudoalteromonas atlantica T6c  
Pseudoalteromonas haloplanktis TAC125  
Saccharophagus degradans 2-40  
Marinobacter aquaeolei VT8  
Hahella chejuensis KCTC 2396  
Alcanivorax borkumensis SK2  
Marinomonas sp. MWYL1  
Chromohalobacter salexigens DSM 3043  
Methylococcus capsulatus Bath  
Dichelobacter nodosus VCS1703A  
New/updated genome Stenotrophomonas maltophilia R551-3  
Xylella fastidiosa 9a5c  
Xanthomonas axonopodis pv. citri 306  
Xanthomonas oryzae pv. oryzae KACC10331  
Xanthomonas campestris pv. campestris ATCC 33913  
Alkalilimnicola ehrlichei MLHE-1  
Halorhodospira halophila SL1  
Nitrosococcus oceani ATCC 19707  
Coxiella burnetii RSA 493  
Legionella pneumophila ssp. pneumophila Philadelphia 1  
Baumannia cicadellinicola Hc  
Candidatus Carsonella ruddii PV  
Candidatus Vesicomyosocius okutanii HA  
Candidatus Ruthia magnifica Cm  
Pseudomonas entomophila L48  
Pseudomonas syringae pv. tomato DC3000  
Pseudomonas stutzeri A1501  
Pseudomonas putida KT2440  
Pseudomonas fluorescens Pf-5  
Pseudomonas mendocina ymp  
Pseudomonas aeruginosa PAO1  
New/updated genome Cellvibrio japonicus Ueda107  
Psychrobacter sp. PRwf-1  
Psychrobacter arcticus 273-4  
Psychrobacter cryohalolentis K5  
Acinetobacter sp. ADP1  
Acinetobacter baumannii ATCC 17978  
Thiomicrospira crunogena XCL-2  
Francisella philomiragia ssp. philomiragia ATCC 25017  
Francisella tularensis ssp. tularensis SCHU S4  
Acidobacteria Solibacter usitatus Ellin6076  
Acidobacteria bacterium Ellin345  
Firmicutes Bacillales Exiguobacterium sibiricum 255-15  
Listeria welshimeri ser. 6b SLCC5334  
Listeria innocua Clip11262  
Listeria monocytogenes EGD-e  
Lysinibacillus sphaericus C3-41  
Oceanobacillus iheyensis HTE831  
Geobacillus thermodenitrificans NG80-2  
Geobacillus kaustophilus HTA426  
Bacillus halodurans C-125  
Bacillus weihenstephanensis KBAB4  
Bacillus thuringiensis ser. konkukian 97-27  
Bacillus cereus ATCC 14579  
Bacillus anthracis Ames Ancestor  
Bacillus clausii KSM-K16  
Bacillus subtilis ssp. subtilis 168  
Bacillus pumilus SAFR-032  
Bacillus licheniformis ATCC 14580  
Bacillus amyloliquefaciens FZB42  
Staphylococcus saprophyticus ssp. saprophyticus ATCC 15305  
Staphylococcus haemolyticus JCSC1435  
Staphylococcus epidermidis RP62A  
Staphylococcus aureus ssp. aureus NCTC 8325  
Lactobacillales Enterococcus faecalis V583  
Oenococcus oeni PSU-1  
Leuconostoc citreum KM20  
Leuconostoc mesenteroides ssp. mesenteroides ATCC 8293  
Lactobacillus johnsonii NCC