SUPERFAMILY 1.75 HMM library and genome assignments server

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PA2201 C-terminal domain-like alignments

These alignments are sequences aligned to the 0052667 model.

Sophisticated options are available for refining alignments:

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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
                   |         |         |         |         |         |         |         |         |

               100       110       120       130       140       150           
                 |         |         |         |         |         |           

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: 0052667 (list models)
Initial SAMT99 seed:

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

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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   Clostridium thermocellum ATCC 27405
NoYes   Ruminococcus albus 7
NoYes   Streptococcus sanguinis SK36
NoYes   Prevotella melaninogenica ATCC 25845
NoYes   Prevotella intermedia 17
NoYes   Bacteroides salanitronis DSM 18170
NoYes   Capnocytophaga canimorsus Cc5
NoYes   Helicobacter hepaticus ATCC 51449
NoYes   Pseudogulbenkiania sp. NH8B
NoYes   Ralstonia solanacearum CFBP2957
NoYes   Verminephrobacter eiseniae EF01-2
NoYes   Acidovorax avenae subsp. avenae ATCC 19860
NoYes   Comamonas testosteroni CNB-2
NoYes   Herbaspirillum seropedicae SmR1
NoYes   Aeromonas hydrophila subsp. hydrophila ATCC 7966
NoYes   Citrobacter rodentium ICC168
NoYes   Pseudomonas brassicacearum subsp. brassicacearum NFM421
NoYes   Pseudomonas protegens Pf-5
NoYes   Pseudomonas aeruginosa UCBPP-PA14
NoYes   Acinetobacter oleivorans DR1
NoYes   Acinetobacter calcoaceticus PHEA-2
NoYes   Acinetobacter baumannii ATCC 17978
NoYes   Clostridium thermocellum DSM 1313
NoYes   Streptococcus equi subsp. zooepidemicus MGCS10565
NoYes   Streptococcus oligofermentans AS 1.3089
NoYes   Bacillus toyonensis BCT-7112
NoYes   Bacillus thuringiensis HD-771
NoYes   Bacillus thuringiensis serovar konkukian str. 97-27
NoYes   Bacillus thuringiensis serovar kurstaki str. HD73
NoYes   Bacillus thuringiensis BMB171
NoYes   Bacillus cereus B4264
NoYes   Bacillus cereus G9842
NoYes   Bacillus cereus ATCC 14579
NoYes   Bacteroides fragilis 638R
NoYes   Ralstonia solanacearum FQY_4
NoYes   Ralstonia solanacearum Po82
NoYes   Ralstonia solanacearum PSI07
NoYes   Ralstonia solanacearum CMR15
NoYes   Ralstonia solanacearum GMI1000
NoYes   Burkholderia sp. KJ006
NoYes   Variovorax paradoxus EPS
NoYes   Pseudomonas monteilii SB3101
NoYes   Pseudomonas monteilii SB3078
NoYes   Pseudomonas putida DOT-T1E
NoYes   Pseudomonas putida S16
NoYes   Pseudomonas putida KT2440
NoYes   Pseudomonas protegens CHA0
NoYes   Pseudomonas poae RE*1-1-14
NoYes   Pseudomonas fluorescens F113
NoYes   Pseudomonas aeruginosa SCV20265
NoYes   Pseudomonas aeruginosa MTB-1
NoYes   Pseudomonas aeruginosa LES431
NoYes   Pseudomonas aeruginosa RP73
NoYes   Pseudomonas aeruginosa B136-33
NoYes   Pseudomonas aeruginosa PA1R
NoYes   Pseudomonas aeruginosa PA1
NoYes   Pseudomonas aeruginosa DK2
NoYes   Pseudomonas aeruginosa NCGM2.S1
NoYes   Pseudomonas aeruginosa M18
NoYes   Pseudomonas aeruginosa LESB58
NoYes   Pseudomonas aeruginosa PA7
NoYes   Pseudomonas aeruginosa PAO1
NoYes   Acinetobacter calcoaceticus ruh2202
NoYes   Acinetobacter johnsonii SH046
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #1 (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #2 (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #3 (meta-genome)
NoYes   Fungus garden combined (combined) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 02(H) (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   Olavius algarvensis endosymbiont metagenome Delta1 (meta-genome)
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
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   TargetDB (Targets)
NoYes   ALL (only advised for small superfamilies)

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