SUPERFAMILY 1.75 HMM library and genome assignments server

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lambda repressor-like DNA-binding domains alignments

These alignments are sequences aligned to the 0045765 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       
                                          |         |         |         |         |         |       
d1adra_ .........................MNTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKG
d1nera_ .......csnekardwhradviagl--------------KKRKLSLSALSRQFGYAPTTLANALERH-WPKGE--QIIANALETKPEV----
d1rioa_ stkkkpltqeqledarrlkaiyekk-------------KNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFSPS
d1rzsa_ ..............mykkdvidhfg-------------------TQRAVAKALGISDAAVSQWK----------------------------
d2croa_ ........................m---QTLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK-RPRFLFEIAMALNCDPVWLQYG
d3orca_ ................eqritlkdy---------------AMRFGQTKTAKDLGVYQSAINKA-----------------------------


         70                                       
          |                                       
d1adra_ DLS------qtnvay...........................
d1nera_ ---------iwpsryqage.......................
d1rioa_ ---------iareiyemyeavhhhhhh...............
d1rzsa_ ---------evipekdayrleivtagalkyqenayrqaa...
d2croa_ ---------t................................
d3orca_ ---------ihagrkifltinadgsvyaeevkdgevkpfpsn


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

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FASTA format:

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Model: 0045765 (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   Adineta vaga
NoYes   Amphimedon queenslandica
NoYes   Escherichia coli 'BL21-Gold(DE3)pLysS AG'
NoYes   Salmonella enterica subsp. enterica Serovar Heidelberg str. CFSAN002069
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. B182
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. 41578
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. SL476
NoYes   Escherichia coli LY180
NoYes   Escherichia coli O7:K1 str. CE10
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 UM146
NoYes   Escherichia coli 042
NoYes   Escherichia coli Xuzhou21
NoYes   Escherichia coli IHE3034
NoYes   Escherichia coli UMNK88
NoYes   Escherichia coli O83:H1 str. NRG 857C
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli LF82
NoYes   Escherichia coli ED1a
NoYes   Escherichia coli 55989
NoYes   Escherichia coli S88
NoYes   Escherichia coli W
NoYes   Escherichia coli W
NoYes   Escherichia coli BL21(DE3)
NoYes   Escherichia coli BL21(DE3)
NoYes   Escherichia coli APEC O1
NoYes   Escherichia coli UTI89
NoYes   Escherichia coli HS
NoYes   Escherichia coli O55:H7 str. CB9615
NoYes   Escherichia coli O26:H11 str. 11368
NoYes   Escherichia coli O127:H6 str. E2348/69
NoYes   Escherichia coli O157:H7 str. TW14359
NoYes   Escherichia coli O157:H7 str. EC4115
NoYes   Escherichia coli O157:H7 str. Sakai
NoYes   Escherichia coli O157:H7 str. EDL933
NoYes   Escherichia coli BW2952
NoYes   Enterobacter cloacae subsp. cloacae ATCC 13047
NoYes   Activated sludge plasmid pool Visp-2009 (Newbler) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP16 from Fairy Spring Red Layer (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   NCBI viral sequences (Viral)
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   The Salmonella enterica Pan-genome (meta-genome)
NoYes   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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