SUPERFAMILY 1.75 HMM library and genome assignments server

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TmoB-like alignments

These alignments are sequences aligned to the 0043826 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   
                 |         |         |         |         |         |         |         |   
d1t0qc_ TFPIMSNFERDFVIQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFMD


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: 0043826 (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   Pseudonocardia dioxanivorans CB1190
NoYes   Gordonia polyisoprenivorans VH2
NoYes   Thermomicrobium roseum DSM 5159
NoYes   Sulfobacillus acidophilus DSM 10332
NoYes   Kyrpidia tusciae DSM 2912
NoYes   Dechloromonas aromatica RCB
NoYes   Pandoraea sp. RB-44
NoYes   Methylibium petroleiphilum PM1
NoYes   Ralstonia eutropha JMP134
NoYes   Cupriavidus taiwanensis LMG 19424
NoYes   Cupriavidus metallidurans CH34
NoYes   Cupriavidus necator N-1
NoYes   Ralstonia pickettii 12D
NoYes   Burkholderia sp. CCGE1002
NoYes   Xanthobacter autotrophicus Py2
NoYes   Hyphomicrobium sp. MC1
NoYes   Pseudoxanthomonas spadix BD-a59
NoYes   Frankia sp. CcI3
NoYes   Sulfobacillus acidophilus TPY
NoYes   Burkholderia phenoliruptrix BR3459a
NoYes   Pandoraea pnomenusa 3kgm
NoYes   Ralstonia pickettii 12J
NoYes   Bradyrhizobium sp. BTAi1
NoYes   Bradyrhizobium oligotrophicum S58
NoYes   Cycloclasticus zancles 7-ME
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   Sludge/Australian, Phrap Assembly (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2- (Oak Ridge ambient) (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
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)


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