SUPERFAMILY 1.75 HMM library and genome assignments server

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NTF2-like alignments

These alignments are sequences aligned to the 0054672 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        
                      |         |         |          |         |                 |         |        
d2rfra1 ....m-DDLTNLAARLRLLEDREEIRELIARYGPLADSG.DAEALSELWVEDGEYAVVG..FA......TAKGRAAIAALIDGQTHRALMAD
d3b8la1 ..mqc------------PIEDRLAIQDLMIAYAHAVDTVsDIDAVLDVFTEDAVFDLSG..IGlt....PQVGHAGIREFFTNVFAN---MS
d3cu3a1 ...tt-------------TADESAIRAFHRQMIDAWNRG.SGEGFAAPFSETADFITFE..GT......HLKGRKEIAAFHQQAFDTV--VK
d3ef8a1 mtdtn-------------LVEMRAIERMMFDYSYHLDMN.HPEELAALFVEDCEVSYAP..NF......GATGRDAYKKTLEGIGTF---FR
d3ejva1 ....t-------------MADETIILNVLGQYTRAHDRR.DPDAMAALFAPEATIEIVDavGGasrsisRLEGRDAIRVAVRQMMAPHGYRA


        80        90        100       110                       120       130       140       150   
         |         |          |         |                         |         |         |         |   
d2rfra1 GCAHFLGPATVTV.EGDTATARCHSVVFRCVSGTFG................SHRVSANRWTFRRTPAGWRAVRRENALLDG----------
d3b8la1 HHAHYLTNFAVTGyEGDTASMRAYVIGMGVGKDGRA................VTVNGRYFFEVRRTEKGWKATRYTMDFLMP----------
d3cu3a1 GTRLEGEVDFVRFvNSQLALMLVVIRVILPGQTETS................ASRDSLPLYVVTKGDEGWQIEG------------------
d3ef8a1 GTSHHNSNICIDFvSETEANVRSVVLAIHRYTKERPd...............GILYGQYFDTVVKVDGQWKFKRRELRTTMTTDYHV-----
d3ejva1 WSQNVVNAPIIVI.EGDHAVLDAQFMVFSILAAEVPdggwptgtfgaqgrivPIEAGQYRLTLRTVADGWVISAMRIEHR------------


                                               
                                               
d2rfra1 saaarallqf.............................
d3b8la1 lsgtldnak..............................
d3cu3a1 llntrkltlerqfflddfdslsaeaqrqvtdlvaslkqs
d3ef8a1 raanpigrae.............................
d3ejva1 lpmafg.................................


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: 0054672 (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



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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   Anabaena variabilis ATCC 29413
NoYes   Nostoc punctiforme PCC 73102
NoYes   Thermomonospora curvata DSM 43183
NoYes   Rhodococcus jostii RHA1
NoYes   Burkholderia xenovorans LB400
NoYes   Caulobacter sp. K31
NoYes   Novosphingobium sp. PP1Y
NoYes   Novosphingobium aromaticivorans DSM 12444
NoYes   Oscillatoria nigro-viridis PCC 7112
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (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   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)


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