SUPERFAMILY 1.75 HMM library and genome assignments server

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Chondroitin AC/alginate lyase alignments

These alignments are sequences aligned to the 0048918 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        90 
                  |         |         |         |         |         |         |         |         | 
d1qaza_ g-SHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKIS


              100       110       120       130       140       150       160       170       180   
                |         |         |         |         |         |         |         |         |   
d1qaza_ ATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDT


            190       200       210       220       230       240       250       260       270     
              |         |         |         |         |         |         |         |         |     
d1qaza_ SCCNNHSYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDI


          280       290       300       310       320       330       340       350 
            |         |         |         |         |         |         |         | 
d1qaza_ HSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSATLLAYKP


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: 0048918 (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   Phytophthora capsici
NoYes   Terriglobus saanensis SP1PR4
NoYes   Stenotrophomonas maltophilia K279a
NoYes   Pseudomonas syringae pv. tomato str. DC3000
NoYes   Pseudomonas sp. VLB120
NoYes   Stenotrophomonas maltophilia D457
NoYes   Stenotrophomonas maltophilia JV3
NoYes   Pseudomonas syringae pv. phaseolicola 1448A
NoYes   Pseudomonas syringae pv. syringae B728a
NoYes   Pseudomonas mendocina NK-01
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
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)


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