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.

Api92-like alignments

These alignments are sequences aligned to the 0054139 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  
                           |         |         |         |         |         |         |         |  
d2ijra1        ...EWCKNRLEITGRSVFVDIMQQWVTGEEVPLYRHAIQQSIRLFLAGCAGILKPVKCMEYPPFPRLVSHGTGSAVASNLAFQHW
YDR104C:27-119 eiw----------------------------------------------------------------------------------


                     90       100       110       120       130       140       150       160       
                      |         |         |         |         |         |         |         |       
d2ijra1        LDLLLKDAVLDGDTIRQIDRIYLQSGIASVKWETIPEGARQIITQLMARQYPDWFGVASWSSHINGADCWTKLGVMQEHACNCDM
YDR104C:27-119 -----------------------------KQWKKIPEVYEQQPYPLDTNDHIEWMNCQTTQSEYDSRD------FYAFHCFHRRI


               170       180       190       200       210       220       230       240       250  
                 |         |         |         |         |         |         |         |         |  
d2ijra1        LMIIPTRLAIELNGNSQLLTGVSTTHDLYSHLYGMAWPSGQNIIWQRDRINSLRLDFDSPSYPPSAELMGELSAVFDCEIRHWYQ
YDR104C:27-119 DQILKTDNVIDLTEVKDIYQGTRTDYEADKIKYGV--------------------------------------------------


                    260       270       280     
                      |         |         |     
d2ijra1        EPVNGIRGYDCYDRGDHVDSGEYGA---gpf..
YDR104C:27-119 ----------------------------ykeas


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: 0054139 (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   Amphimedon queenslandica
NoYes   Eubacterium siraeum
NoYes   Ruminococcus albus 7
NoYes   Clostridium kluyveri DSM 555
NoYes   Deferribacter desulfuricans SSM1
NoYes   Neisseria gonorrhoeae NCCP11945
NoYes   Gallibacterium anatis UMN179
NoYes   Haemophilus ducreyi 35000HP
NoYes   Photorhabdus asymbiotica
NoYes   Photorhabdus luminescens subsp. laumondii TTO1
NoYes   Xenorhabdus bovienii SS-2004
NoYes   Xenorhabdus nematophila ATCC 19061
NoYes   Proteus mirabilis HI4320
NoYes   Edwardsiella ictaluri 93-146
NoYes   Yersinia pseudotuberculosis IP 31758
NoYes   Yersinia enterocolitica subsp. enterocolitica 8081
NoYes   Serratia sp. ATCC 39006
NoYes   Serratia proteamaculans 568
NoYes   Pantoea sp. At-9b
NoYes   Erwinia sp. Ejp617
NoYes   Erwinia billingiae Eb661
NoYes   Erwinia pyrifoliae Ep1/96
NoYes   Erwinia amylovora ATCC 49946
NoYes   Shigella dysenteriae Sd197
NoYes   Clostridium kluyveri NBRC 12016
NoYes   Acidithiobacillus ferrooxidans ATCC 23270
NoYes   Yersinia pestis Z176003
NoYes   Serratia plymuthica S13
NoYes   Pantoea ananatis LMG 5342
NoYes   Pantoea ananatis PA13
NoYes   Pantoea ananatis AJ13355
NoYes   Erwinia pyrifoliae DSM 12163
NoYes   Shigella flexneri 2002017
NoYes   Shigella flexneri 2a str. 301
NoYes   Salmonella enterica subsp. enterica Serovar Cubana str. CFSAN002050
NoYes   Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. U288
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
NoYes   Salmonella enterica subsp. enterica Serovar Heidelberg str. CFSAN002069
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. 41578
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. SL476
NoYes   Escherichia coli E24377A
NoYes   Escherichia coli E. coli PMV-1
NoYes   Escherichia coli O104:H4 str. 2011C-3493
NoYes   Escherichia coli UM146
NoYes   Escherichia coli Xuzhou21
NoYes   Escherichia coli UMNK88
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli ED1a
NoYes   Escherichia coli UMN026
NoYes   Escherichia coli W
NoYes   Escherichia coli W
NoYes   Escherichia coli SE15
NoYes   Escherichia coli SE11
NoYes   Escherichia coli UTI89
NoYes   Escherichia coli ETEC H10407
NoYes   Escherichia coli O55:H7 str. RM12579
NoYes   Escherichia coli O55:H7 str. CB9615
NoYes   Escherichia coli O26:H11 str. 11368
NoYes   Escherichia coli O157:H7 str. TW14359
NoYes   Escherichia coli O157:H7 str. EC4115
NoYes   Escherichia coli O157:H7 str. Sakai
NoYes   Escherichia coli O157:H7 str. EDL933
NoYes   Enterobacter cloacae subsp. cloacae ATCC 13047
NoYes   Pseudomonas fluorescens A506
NoYes   Atta cephalotes fungus garden (ACEF) (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dendroctonus ponderosae beetle community (MPB hybrid beetle) (Lodgepole pine) (meta-genome)
NoYes   Dendroctonus ponderosae fungus gallery (Hybrid pine) (MPB hybrid gallery) (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Fungus garden combined (combined) (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   Maize field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing corn (Zea may (meta-genome)
NoYes   NCBI 2017_08 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   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   NCBI viral sequences (Viral)
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   TargetDB (Targets)
NoYes   The Salmonella enterica Pan-genome (meta-genome)
NoYes   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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