SUPERFAMILY 1.75 HMM library and genome assignments server

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ARM repeat alignments

These alignments are sequences aligned to the 0048666 model.

Sophisticated options are available for refining alignments:


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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 
                                      |         |         |         |         |         |         | 
d1oyza_ yqkrkaskeyglynqckklnd---------------------DELFRLLDDHNSLKRISSARVLQLRGGQDAVRLAIEFCSDKNYIRRDIGA
d1te4a_ ....................m-----------------------------------------------------------------------


               80        90       100       110       120       130       140       150       160   
                |         |         |         |         |         |         |         |         |   
d1oyza_ FILGQIKICKKCEDNVFNILNNMALNDKSACVRATAIESTAQRCKKNPIYSPKIVEQSQITAFDKSTNVRRATAFAISVINDKATIPLLINL
d1te4a_ --------------------------------------------------------------ADENKWVRRDVSTALSRMGD-EAFEPLLES


            170       180       190       200       210       220       230       240       250     
              |         |         |         |         |         |         |         |         |     
d1oyza_ LKDPNGDVRNWAAFAININKYDNSDIRDCFVEMLQDKNEEVRIEAIIGLSYRKDKRVLSVLCDELKKNTVYDDIIEAAGELGDKTLLPVLDT
d1te4a_ LSNEDWRIRGAAAWIIGNFQ--DERAVEPLIKLLEDDSGFVRSGAARSLEQIGGERVRAAMEKLAETGTGFARKVAVNYL------------


          260       270          
            |         |          
d1oyza_ MLYKFDDNEIITSAIDK----lkrs
d1te4a_ ---------------------eth.


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: 0048666 (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   Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
NoYes   Escherichia fergusonii ATCC 35469
NoYes   Escherichia coli 'BL21-Gold(DE3)pLysS AG'
NoYes   Methanothermobacter marburgensis str. Marburg
NoYes   Methanothermobacter thermautotrophicus str. Delta H
NoYes   Complete genome sequence of Methanobacterium sp. Mb1
NoYes   Salmonella enterica subsp. enterica Serovar Cubana str. CFSAN002050
NoYes   Escherichia coli E24377A
NoYes   Escherichia coli LY180
NoYes   Escherichia coli APEC O78
NoYes   Escherichia coli O104:H4 str. 2009EL-2050
NoYes   Escherichia coli O104:H4 str. 2009EL-2071
NoYes   Escherichia coli O104:H4 str. 2011C-3493
NoYes   Escherichia coli P12b
NoYes   Escherichia coli UMNK88
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli W
NoYes   Escherichia coli W
NoYes   Escherichia coli DH1
NoYes   Escherichia coli DH1
NoYes   Escherichia coli ATCC 8739
NoYes   Escherichia coli BL21(DE3)
NoYes   Escherichia coli BL21(DE3)
NoYes   Escherichia coli SE11
NoYes   Escherichia coli O103:H2 str. 12009
NoYes   Escherichia coli HS
NoYes   Escherichia coli O26:H11 str. 11368
NoYes   Escherichia coli O111:H- str. 11128
NoYes   Escherichia coli O157:H7 str. EDL933
NoYes   Escherichia coli BW2952
NoYes   Escherichia coli str. K-12 substr. MG1655
NoYes   Escherichia coli str. K-12 substr. W3110
NoYes   Escherichia coli str. K-12 substr. DH10B
NoYes   Escherichia coli B str. REL606
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
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   The Salmonella enterica Pan-genome (meta-genome)
NoYes   ALL (only advised for small superfamilies)


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