SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.


Histone-fold alignments

These alignments are sequences aligned to the 0043120 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        80        90 
                  |         |         |         |         |         |         |         |         | 
d1r4va_ e-TMLRPKGFDKLDHYFRTELDIDLTDETIELLLNSVKAAFGKLFYGAEQRARWNGRDFIALADLNITKALEEHIKNFQKIEQDMGVDELLE
d1wwia1 .----MLMKVAEFERLFRQAAGLDVDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDLPIAKGLQETLQEFRRMDTALELKPVLD


              100       110       120       130        140       150 
                |         |         |         |          |         | 
d1r4va_ YIAFIPPVEMNVGEDLKSEYRNIMGGLLLMHADVIKKATGE.RKPSREAMEFVAQIVDKVF
d1wwia1 ALAALPPLDLEVAEDVRNLLPELAGALVVAYARVLKELDPAlKNPQTEHHERAERVFNLLL


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: 0043120 (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   Anabaena variabilis ATCC 29413
NoYes   Nostoc punctiforme PCC 73102
NoYes   Rubrobacter xylanophilus DSM 9941
NoYes   Frankia alni ACN14a
NoYes   Streptomyces violaceusniger Tu 4113
NoYes   Streptomyces avermitilis MA-4680
NoYes   Streptomyces hygroscopicus subsp. jinggangensis 5008
NoYes   Gordonia bronchialis DSM 43247
NoYes   Rhodococcus jostii RHA1
NoYes   Micrococcus luteus NCTC 2665
NoYes   Oceanithermus profundus DSM 14977
NoYes   Thermus sp. CCB_US3_UF1
NoYes   Thermus scotoductus SA-01
NoYes   Thermus thermophilus HB27
NoYes   Rhodothermus marinus DSM 4252
NoYes   Thermovibrio ammonificans HB-1
NoYes   Persephonella marina EX-H1
NoYes   Aquifex aeolicus VF5
NoYes   Nitratifractor salsuginis DSM 16511
NoYes   Nitratiruptor sp. SB155-2
NoYes   Frankia sp. EuI1c
NoYes   Streptomyces collinus Tu 365
NoYes   Streptomyces hygroscopicus subsp. jinggangensis TL01
NoYes   Rhodococcus erythropolis CCM2595
NoYes   Mycobacterium smegmatis JS623
NoYes   Thermus oshimai JL-2
NoYes   Thermus thermophilus JL-18
NoYes   Thermus thermophilus SG0.5JP17-16
NoYes   Thermus thermophilus HB8
NoYes   Rhodothermus marinus SG0.5JP17-172
NoYes   2_050719S (meta-genome)
NoYes   3_050719R (meta-genome)
NoYes   5_050719P (meta-genome)
NoYes   Bath Hot Springs, planktonic community (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP12 from Calcite Springs, Tower Falls Region (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP13 from Bechler Spring (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
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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