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.


GlcG-like alignments

These alignments are sequences aligned to the 0051691 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        80        90
                   |         |         |         |         |         |         |         |         |
d2a2la1 mn--KSQQVQTITLAAAQQMAAAVEKKATEINVAVVFSVVDRGGNTLLIQRMDEAFVSSCDISLNKAWSACSLKQGTHEITSAVQPGQSLYG


               100       110       120       130       140     
                 |         |         |         |         |     
d2a2la1 LQLTNQQRIIIFGGGLPVIFNEQVIGAVGVSGGTVEQDQLLAQCALDCF---sal


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: 0051691 (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   Amorphotheca resinae v1.0 - Creosote fungus
NoYes   Stagonospora nodorum
NoYes   Acaryochloris marina MBIC11017
NoYes   Geodermatophilus obscurus DSM 43160
NoYes   Thermobifida fusca YX
NoYes   Saccharomonospora viridis DSM 43017
NoYes   Propionibacterium propionicum F0230a
NoYes   Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1
NoYes   Rhodococcus jostii RHA1
NoYes   Thermincola potens JR
NoYes   Acetobacterium woodii DSM 1030
NoYes   Eubacterium limosum KIST612
NoYes   [Ruminococcus] torques
NoYes   Clostridium beijerinckii NCIMB 8052
NoYes   Clostridium perfringens ATCC 13124
NoYes   Thermosediminibacter oceani DSM 16646
NoYes   Thermoanaerobacterium xylanolyticum LX-11
NoYes   Halanaerobium hydrogeniformans
NoYes   Geobacillus thermoglucosidasius C56-YS93
NoYes   Bacillus sp. 1NLA3E
NoYes   Flavobacterium psychrophilum JIP02/86
NoYes   Thermovirga lienii DSM 17291
NoYes   Candidatus Solibacter usitatus Ellin6076
NoYes   Granulicella mallensis MP5ACTX8
NoYes   Ilyobacter polytropus DSM 2926
NoYes   Candidatus Methylomirabilis oxyfera
NoYes   Desulfatibacillum alkenivorans AK-01
NoYes   Desulfobacterium autotrophicum HRM2
NoYes   Desulfovibrio magneticus RS-1
NoYes   Desulfovibrio salexigens DSM 2638
NoYes   Burkholderia xenovorans LB400
NoYes   Rhodospirillum rubrum F11
NoYes   Granulibacter bethesdensis CGDNIH1
NoYes   Gluconacetobacter diazotrophicus PAl 5
NoYes   Rhizobium leguminosarum bv. viciae 3841
NoYes   Hyphomicrobium sp. MC1
NoYes   Hyphomicrobium denitrificans ATCC 51888
NoYes   Tolumonas auensis DSM 9187
NoYes   Yersinia enterocolitica subsp. enterocolitica 8081
NoYes   Pectobacterium wasabiae WPP163
NoYes   Pectobacterium sp. SCC3193
NoYes   Escherichia blattae DSM 4481
NoYes   Shigella sonnei Ss046
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
NoYes   Klebsiella oxytoca E718
NoYes   Klebsiella variicola At-22
NoYes   Klebsiella pneumoniae NTUH-K2044
NoYes   Escherichia fergusonii ATCC 35469
NoYes   Citrobacter rodentium ICC168
NoYes   Citrobacter koseri ATCC BAA-895
NoYes   Halopiger xanaduensis SH-6
NoYes   Haloterrigena turkmenica DSM 5511
NoYes   Haloferax volcanii DS2
NoYes   Halalkalicoccus jeotgali B3
NoYes   Rhodococcus erythropolis CCM2595
NoYes   Clostridium perfringens SM101
NoYes   Clostridium perfringens str. 13
NoYes   Clostridium botulinum E3 str. Alaska E43
NoYes   Thermoanaerobacterium saccharolyticum JW/SL-YS485
NoYes   Thermoanaerobacterium thermosaccharolyticum M0795
NoYes   Paenibacillus sp. Y412MC10
NoYes   Geobacillus sp. Y4.1MC1
NoYes   Fusobacterium nucleatum subsp. animalis 4_8
NoYes   Desulfovibrio hydrothermalis AM13 = DSM 14728
NoYes   Desulfovibrio desulfuricans ND132
NoYes   Rhodospirillum rubrum ATCC 11170
NoYes   Gluconacetobacter diazotrophicus PAl 5
NoYes   Rhizobium etli bv. mimosae str. Mim1
NoYes   Hyphomicrobium denitrificans 1NES1
NoYes   Rhodopseudomonas palustris BisB18
NoYes   Vibrio sp. EJY3
NoYes   Yersinia enterocolitica subsp. palearctica 105.5R(r)
NoYes   Yersinia enterocolitica subsp. palearctica Y11
NoYes   Shigella sonnei 53G
NoYes   Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- str. RSK2980
NoYes   Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. 08-1736
NoYes   Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992
NoYes   Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633
NoYes   Salmonella enterica subsp. enterica Serovar Cubana str. CFSAN002050
NoYes   Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
NoYes   Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
NoYes   Salmonella enterica subsp. enterica serovar Newport str. USMARC-S3124.1
NoYes   Salmonella enterica subsp. enterica serovar Newport str. SL254
NoYes   Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. U288
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. 798
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
NoYes   Salmonella enterica The genome of subsp. enterica serovar Typhimurium str. DT2
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium Definitive Type 104
NoYes   Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12
NoYes   Salmonella enterica subsp. enterica serovar Typhi str. Ty21a
NoYes   Salmonella enterica subsp. enterica serovar Typhi str. CT18
NoYes   Salmonella enterica subsp. enterica serovar Typhi str. Ty2
NoYes   Salmonella enterica serovar Bovismorbificans genomics
NoYes   Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000189
NoYes   Salmonella enterica subsp. enterica serovar Agona str. 24249
NoYes   Salmonella enterica subsp. enterica serovar Agona str. SL483
NoYes   Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
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   Salmonella enterica subsp. enterica serovar Pullorum str. S06004
NoYes   Salmonella enterica subsp. enterica serovar Gallinarum/pullorum str. RKS5078
NoYes   Salmonella enterica subsp. enterica serovar Thompson str. RM6836
NoYes   Klebsiella oxytoca KCTC 1686
NoYes   Klebsiella pneumoniae JM45
NoYes   Klebsiella pneumoniae CG43
NoYes   Klebsiella pneumoniae KCTC 2242
NoYes   Klebsiella pneumoniae 342
NoYes   Klebsiella pneumoniae subsp. pneumoniae 1084
NoYes   Klebsiella pneumoniae subsp. pneumoniae HS11286
NoYes   Klebsiella pneumoniae subsp. pneumoniae MGH 78578
NoYes   Klebsiella pneumoniae subsp. rhinoscleromatis SB3432
NoYes   Escherichia coli E24377A
NoYes   Escherichia coli O83:H1 str. NRG 857C
NoYes   Escherichia coli LF82
NoYes   Escherichia coli ED1a
NoYes   Escherichia coli UMN026
NoYes   Escherichia coli S88
NoYes   Escherichia coli APEC O1
NoYes   Escherichia coli CFT073
NoYes   Escherichia coli O127:H6 str. E2348/69
NoYes   Enterobacter cloacae SCF1
NoYes   4_050719Q (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dendroctonus ponderosae fungus gallery (Hybrid pine) (MPB hybrid gallery) (meta-genome)
NoYes   Fungus garden combined (combined) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden bottom (Fungus garden bottom) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Groundwater dechlorinating community (KB-1) from synthetic mineral medium in Toronto, ON, sample from Site contaminated with chlorinated ethenes
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP16 from Fairy Spring Red Layer (meta-genome)
NoYes   Human Gut Community Subject 7 (meta-genome)
NoYes   Human Gut Community Subject 8 (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Formaldehyde enrichment (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   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   Soil microbial community from bioreactor at Alameda Naval Air Station, CA, contaminated with Chloroethene, Sample 196 (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   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   TargetDB (Targets)
NoYes   The Salmonella enterica Pan-genome (meta-genome)
NoYes   ALL (only advised for small superfamilies)


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