SUPERFAMILY 1.75 HMM library and genome assignments server

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Galactose oxidase, central domain alignments

These alignments are sequences aligned to the 0047741 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        90
                   |         |         |         |         |         |         |         |         |
d1k3ia3 yt--APQPGLGRWGPTIDLPIVPAAAAIEPTSGRVLMWSSYRNDAFGGSPGGITLTSSWDPSTGIVSDRTVTVTKHDMFCPGISMDGNGQIV


               100       110       120       130       140       150       160       170       180  
                 |         |         |         |         |         |         |         |         |  
d1k3ia3 VTGGNDAKKTSLYDSSSDSWIPGPDMQVARGYQSSATMSDGRVFTIGGSWSGGVFEKNGEVYSPSSKTWTSLPNAKVNPMLTADKQGLYRSD


             190       200       210       220         230       240       250       260       270  
               |         |         |         |           |         |         |         |         |  
d1k3ia3 NHAWLFGWKKGSVFQAGPSTAMNWYYTSGSGDVKSAGKRqsNRGVAPDAMCGNAVMYDAV--KGKILTFGGSPDYQDSDATTNAHIITLGEP


             280       290       300       310       320       330       340       350       360    
               |         |         |         |         |         |         |         |         |    
d1k3ia3 GTSPNTVFASNGLYFARTFHTSVVLPDGSTFITGGQRRGIPFEDSTPVFTPEIYVPEQDTFYKQNPNSIVRVYHSISLLLPDGRVFNGGGGL


           370       380         
             |         |         
d1k3ia3 CGDCTTNHFDAQIFTPNYLYN--sn


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: 0047741 (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



Jump to [ Top of page · Alignments · Refine alignments ]

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   Ustilago maydis
NoYes   Apiospora montagnei NRRL 25634 v1.0
NoYes   Magnaporthe poae ATCC 64411 22
NoYes   Magnaporthe grisea 70-15
NoYes   Podospora anserina
NoYes   Neurospora tetrasperma
NoYes   Neurospora discreta FGSC 8579
NoYes   Neurospora crassa OR74A
NoYes   Verticillium albo-atrum VaMs.102
NoYes   Verticillium dahliae VdLs.17
NoYes   Glomerella graminicola 22
NoYes   Fusarium graminearum
NoYes   Nectria haematococca mpVI
NoYes   Fusarium oxysporum f. sp. lycopersici 4286
NoYes   Fusarium verticillioides 7600
NoYes   Botrytis cinerea B05.10
NoYes   Sclerotinia sclerotiorum
NoYes   Didymella exigua CBS 183.55 v1.0
NoYes   Leptosphaeria maculans 22
NoYes   Setosphaeria turcica v1.0
NoYes   Cochliobolus miyabeanus ATCC 44560 v1.0
NoYes   Cochliobolus victoriae FI3 v1.0
NoYes   Cochliobolus carbonum 26-R-13 v1.0
NoYes   Cochliobolus heterostrophus - Southern corn leaf blight pathogen
NoYes   Alternaria brassicicola
NoYes   Cochliobolus lunatus m118 v2.0
NoYes   Pyrenophora teres f. teres 22
NoYes   Pyrenophora tritici-repentis
NoYes   Stagonospora nodorum
NoYes   Mycosphaerella graminicola IPO323
NoYes   Zasmidium cellare ATCC 36951 v1.0
NoYes   Dothistroma septosporum
NoYes   Penicillium chrysogenum Wisconsin 54-1255
NoYes   Penicillium chrysogenum v1.0
NoYes   Aspergillus fumigatus Af293
NoYes   Aspergillus sydowii v1.0
NoYes   Aspergillus versicolor v1.0
NoYes   Aspergillus glaucus
NoYes   Aspergillus carbonarius ITEM 5010
NoYes   Neosartorya fischeri NRRL 181
NoYes   Aspergillus terreus NIH2624
NoYes   Aspergillus wentii v1.0
NoYes   Aspergillus oryzae RIB40
NoYes   Aspergillus flavus NRRL3357
NoYes   Aspergillus clavatus NRRL 1
NoYes   Penicillium marneffei ATCC 18224
NoYes   Phaeodactylum tricornutumCCAP 1055/1
NoYes   Nostoc punctiforme PCC 73102
NoYes   Actinoplanes sp. SE50/110
NoYes   Sorangium cellulosum 'So ce 56'
NoYes   Stigmatella aurantiaca DW4/3-1
NoYes   Burkholderia sp. RPE64
NoYes   Burkholderia sp. CCGE1002
NoYes   Burkholderia thailandensis E264
NoYes   Burkholderia pseudomallei 1106a
NoYes   Burkholderia mallei SAVP1
NoYes   Variovorax paradoxus S110
NoYes   Methylobacterium chloromethanicum CM4
NoYes   Methylobacterium extorquens AM1
NoYes   Methylobacterium sp. 4-46
NoYes   Aspergillus fumigatus A1163
NoYes   Burkholderia sp. YI23
NoYes   Burkholderia pseudomallei MSHR305
NoYes   Burkholderia pseudomallei NCTC 13179
NoYes   Burkholderia pseudomallei BPC006
NoYes   Burkholderia pseudomallei 1026b
NoYes   Burkholderia pseudomallei MSHR346
NoYes   Burkholderia pseudomallei 668
NoYes   Burkholderia pseudomallei 1710b
NoYes   Burkholderia pseudomallei K96243
NoYes   Burkholderia mallei NCTC 10229
NoYes   Burkholderia mallei NCTC 10247
NoYes   Burkholderia mallei ATCC 23344
NoYes   Combined (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #3 (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   STRING v9.0.5 (STRING)
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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