SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.

FlgN-like alignments

These alignments are sequences aligned to the 0052781 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        
                                                   |         |         |         |         |        
d2fupa1                              mpdsp-----TLLDLFAEDIGHANQLLQLVDEEFQALERRELPVLQQLLGAKQPLMQQLERNG
mVU_gi|478477796|ref|YP_007708447.1| ....t------LLDLFAEDIGHASQLLQLVDEEFQALERRELPVLQQLLGAKQPLMQQLERNG


                                     60        70        80        90       100       110       120 
                                      |         |         |         |         |         |         | 
d2fupa1                              RARAEILREAGVSLDREGLARYARERADGAELLARGDELGELLERCQQANLRNGRIIRANQAS
mVU_gi|478477796|ref|YP_007708447.1| RARAEILREAGVSLDREGLARYARERADGAELLARGDELGELLERCQQANLRNGRIIRANQAS


                                           130
                                             |
d2fupa1                              TGSLLNILR
mVU_gi|478477796|ref|YP_007708447.1| TGSLLNILR


Statistics on alignment.   Save alignment.

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

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: 0052781 (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   Pseudomonas sp. TKP
NoYes   Pseudomonas fulva 12-X
NoYes   Pseudomonas fluorescens SBW25
NoYes   Pseudomonas mendocina ymp
NoYes   Pseudomonas aeruginosa UCBPP-PA14
NoYes   Pseudomonas denitrificans ATCC 13867
NoYes   Pseudomonas stutzeri CCUG 29243
NoYes   Pseudomonas stutzeri DSM 10701
NoYes   Pseudomonas stutzeri RCH2
NoYes   Pseudomonas poae RE*1-1-14
NoYes   Pseudomonas fluorescens A506
NoYes   Pseudomonas fluorescens R124
NoYes   Pseudomonas fluorescens Pf0-1
NoYes   Pseudomonas resinovorans NBRC 106553
NoYes   Pseudomonas mendocina NK-01
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   Combined (meta-genome)
NoYes   Fungus garden combined (combined) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP17 from Obsidian Pool Prime (meta-genome)
NoYes   Mountain Pine Beetle microbial communities from Grand Prairie, Alberta, sample from Hybrid pine (MPB hybrid beetle) (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-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   TargetDB (Targets)
NoYes   ALL (only advised for small superfamilies)


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