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.


FAD-linked oxidases, C-terminal domain alignments

These alignments are sequences aligned to the 0046341 model.

Sophisticated options are available for refining alignments:


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Alignments

The numbers along the top are the segment numbers of the HMM states, and each sequence is seperately aligned to the model.
The first sequence is the seed the model was built from.
Upper case letters are aligned, lower case letters are insertions, '-' signifies a deletion and '.' is nothing.

                   10        20        30        40        50        60        70        80        9
                    |         |         |         |         |         |         |         |         
d1diqa1 .pv--FKPFEVIFEDEADIVEIVDALRPLRMSNTIPNSVVIASTLWEAGSAHLTRAQYTTEPGHTPDSVIKQMQKDTGMGAWNLYAALYGTQ
d1e8ga1 ggy---QSYLITLPKDGDLKQAVDIIRPLRLGMALQNVPTIRHILLDAAVLGDKRS-YSSRTEPLSDEELDKIAKQLNLGRWNFYGALYGPE


        0       100       110       120       130       140       150       160       170       180 
        |         |         |         |         |         |         |         |         |         | 
d1diqa1 EQVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGSMWFAPVSEARGSECKKQAAMAKRVLHKYGLD
d1e8ga1 PIRRVLWETIKDAFSAIPGVKFYFPEDTPENSVLRVRDKTMQGIPTYDELKWIDWLPNGAHLFFSPIAKVSGEDAMMQYAVTKKRCQEAGLD


              190       200       210       220       230       240          250       260       270
                |         |         |         |         |         |            |         |         |
d1diqa1 YVAEFIVAPRDMHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSY...GPVKRKLEHAIKRAVDPNNILAPGR
d1e8ga1 FIGTFTVGMREMHHIVCIVFNKKDLIQKRKVQWLMRTLIDDCAANGWGEYRTHLAFMDQIMETYnwnNSSFLRFNEVLKNAVDPNGIIAPGK


                          
                          
d1diqa1 SGI------dlnndf...
d1e8ga1 SGVWPS---qyshvtwkl


Statistics on alignment.   Save alignment.

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Refine alignments

Sophisticated options are available for refining alignments:

Add your sequences to the alignment:
Members of the same: including
Include all superfamily members: , or just those assigned by the selected model:
Initial T99 seed sequence: NoYes

You may enter many sequences at once using
FASTA format:

Upload a multiple sequence FASTA file:




Model: 0046341 (list models)
Initial SAMT99 seed:
Alignment:



Display Options:
Output in FASTA-like format: NoYes
Output column indices: NoYes
Sequence index (number) on each line: NoYes

Max number of insertions shown: (0 does not show insertions)
Characters per line:
Character to show inserts:
Maximum number of sequences:
Exclude sequences shorter than: residues



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Add alignments from genomes

Select below additional genomes you would like to see alignments for, then click on 'Re-Submit'. The genome assignments will be added to this page.


Select to display   Genome
NoYes   Sphaerobolus stellatus v1.0
NoYes   Gloeophyllum trabeumv1.0
NoYes   Daldinia eschscholzii EC12 v1.0
NoYes   Thielavia terrestris NRRL 8126
NoYes   Cryphonectria parasitica - Chestnut blight fungus
NoYes   Verticillium albo-atrum VaMs.102
NoYes   Glomerella graminicola 22
NoYes   Nectria haematococca mpVI
NoYes   Fusarium oxysporum f. sp. lycopersici 4286
NoYes   Fusarium verticillioides 7600
NoYes   Amorphotheca resinae v1.0 - Creosote fungus
NoYes   Botrytis cinerea B05.10
NoYes   Sclerotinia sclerotiorum
NoYes   Microsporum gypseum
NoYes   Zasmidium cellare ATCC 36951 v1.0
NoYes   Dothistroma septosporum
NoYes   Septoria musiva v1.0
NoYes   Coccidioides posadasii RMSCC 3488
NoYes   Coccidioides immitis RS
NoYes   Penicillium chrysogenum Wisconsin 54-1255
NoYes   Aspergillus nidulans FGSC A4
NoYes   Aspergillus sydowii v1.0
NoYes   Aspergillus versicolor v1.0
NoYes   Aspergillus glaucus
NoYes   Aspergillus wentii v1.0
NoYes   Penicillium marneffei ATCC 18224
NoYes   Modestobacter marinus
NoYes   Actinoplanes sp. N902-109
NoYes   Rhodococcus jostii RHA1
NoYes   Candidatus Nitrospira defluvii
NoYes   Sulfuricurvum kujiense DSM 16994
NoYes   Geobacter daltonii FRC-32
NoYes   Geobacter sp. M21
NoYes   Geobacter metallireducens GS-15
NoYes   Stigmatella aurantiaca DW4/3-1
NoYes   Thauera sp. MZ1T
NoYes   Azoarcus sp. KH32C
NoYes   Aromatoleum aromaticum EbN1
NoYes   Burkholderia phytofirmans PsJN
NoYes   Burkholderia phymatum STM815
NoYes   Burkholderia xenovorans LB400
NoYes   Burkholderia sp. RPE64
NoYes   Burkholderia sp. CCGE1002
NoYes   Polaromonas naphthalenivorans CJ2
NoYes   Comamonas testosteroni CNB-2
NoYes   Achromobacter xylosoxidans A8
NoYes   Nitrosospira multiformis ATCC 25196
NoYes   Nitrosomonas eutropha C91
NoYes   Nitrosomonas europaea ATCC 19718
NoYes   Novosphingobium sp. PP1Y
NoYes   Novosphingobium aromaticivorans DSM 12444
NoYes   Sphingobium sp. SYK-6
NoYes   Oceanimonas sp. GK1
NoYes   Nitrosococcus halophilus Nc4
NoYes   Nitrosococcus oceani ATCC 19707
NoYes   Cycloclasticus sp. P1
NoYes   Coccidioides posadasii str. Silveira
NoYes   Coccidioides immitis RMSCC 3703
NoYes   Coccidioides immitis RMSCC 2394
NoYes   Burkholderia phenoliruptrix BR3459a
NoYes   Burkholderia sp. YI23
NoYes   Burkholderia sp. CCGE1003
NoYes   Burkholderia sp. CCGE1001
NoYes   Nitrosomonas sp. AL212
NoYes   Thioflavicoccus mobilis 8321
NoYes   Pseudomonas denitrificans ATCC 13867
NoYes   Pseudomonas putida H8234
NoYes   Cycloclasticus zancles 7-ME
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #2 (meta-genome)
NoYes   Freshwater propionate enrichment of Brocadia fulgida (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden bottom (Fungus garden bottom) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methane enrichment (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2+ (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2- (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   ALL (only advised for small superfamilies)


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