SUPERFAMILY 1.75 HMM library and genome assignments server

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SGNH hydrolase alignments

These alignments are sequences aligned to the 0054858 model.

Sophisticated options are available for refining alignments:


Jump to [ Top of page · Refine alignments · Add alignments from genomes ]

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       
                     |         |         |         |          |         |         |         |       
d3bzwa1 ...c-IQHPWQGKKVGYIGDSITDPNCYGDNIKKYWDFLKEWLG.ITPFVYGISGRQWDDVPRQAEKLKKEHGGEVDAILVFMGTNDYNSSV
d3dc7a1 hvsf--------KRPAWLGDSITANNGLA--TVHYHDILAADWDvERSDNLGISGSTIGSRYDAMAVRYQAIPEDADFIAVFGGVNDYGRDQ


         90       100       110       120       130       140       150       160       170       18
          |         |         |         |         |         |         |         |         |         
d3bzwa1 PIGEWFTEQEEQVLSAHGEMKKMVTRKKRTPVMTQDTYRGRINIGITQLKKLFPDKQIVLLTPLHRSLANFGDKNVQPDESYQNGCGEYIDA
d3dc7a1 PLGQYGD-------------------------CDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGS-----FSAVTNGLGYRQSD


        0       190       200       210       220       230       240             
        |         |         |         |         |         |         |             
d3bzwa1 YVQAIKEAGNIWGIPVIDFNAVTGMNPMVEEQLIYFYDAGYDRLHPDTKGQERMARTLMYQLLA-----lpvaf
d3dc7a1 YEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAAI---YSVDTLHPNNAGHRVIARKLQSFLDSH----f....


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: 0054858 (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   Lactobacillus sakei subsp. sakei 23K
NoYes   Lactobacillus plantarum JDM1
NoYes   Prevotella ruminicola 23
NoYes   Bacteroides salanitronis DSM 18170
NoYes   Bacteroides vulgatus ATCC 8482
NoYes   Bacteroides thetaiotaomicron VPI-5482
NoYes   Pedobacter saltans DSM 12145
NoYes   Lactobacillus plantarum 16
NoYes   Lactobacillus plantarum ZJ316
NoYes   Lactobacillus plantarum subsp. plantarum ST-III
NoYes   Lactobacillus plantarum subsp. plantarum P-8
NoYes   Lactobacillus plantarum WCFS1
NoYes   Bacteroides xylanisolvens XB1A
NoYes   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
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   ALL (only advised for small superfamilies)


Jump to [ Top of page · Alignments · Refine alignments · Add alignments from genomes ]