SUPERFAMILY 1.75 HMM library and genome assignments server

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Gam-like alignments

These alignments are sequences aligned to the 0054455 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 
                                      |         |         |         |         |         |         | 
d2p2ua1                     v-IVADIRQAEGALAEIATIDRKVGEIEAQMNEAIDAAKARASQKSAPLLARRKELEDGVATFATLNKTEMF
XP_002614704.1.3285:122-157 .-------------KEEGEVKREVKKEEGEVKEEVNKIKEEAEGE---------------------------


                                   80        90       100       110       120       130       140   
                                    |         |         |         |         |         |         |   
d2p2ua1                     KDRKSLDLGFGTIGFRLSTQIVQMSKITKDMTLERLRQFGISEGIRIKEDVNKEAMQGWPDERLEMVGLKRR
XP_002614704.1.3285:122-157 ------------------------------------------------------------------------


                                150        
                                  |        
d2p2ua1                     TTDAFYIEIN.....
XP_002614704.1.3285:122-157 ----------eglak


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: 0054455 (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   Rhodnius prolixus 22
NoYes   Musa acuminata 22 - Wild Malaysian banana
NoYes   Naegleria gruberi
NoYes   Deinococcus gobiensis I-0
NoYes   Deinococcus proteolyticus MRP
NoYes   Acidaminococcus intestini RyC-MR95
NoYes   Selenomonas ruminantium subsp. lactilytica TAM6421
NoYes   Clostridium thermocellum ATCC 27405
NoYes   butyrate-producing bacterium SS3/4
NoYes   Syntrophobotulus glycolicus DSM 8271
NoYes   Desulfotomaculum ruminis DSM 2154
NoYes   Eubacterium limosum KIST612
NoYes   Clostridium novyi NT
NoYes   Clostridium botulinum A str. ATCC 3502
NoYes   Mahella australiensis 50-1 BON
NoYes   Caldicellulosiruptor owensensis OL
NoYes   Halanaerobium hydrogeniformans
NoYes   Lactobacillus casei ATCC 334
NoYes   Lactobacillus buchneri
NoYes   Lactococcus lactis subsp. cremoris MG1363
NoYes   Listeria innocua Clip11262
NoYes   Geobacillus thermoglucosidasius C56-YS93
NoYes   Bacillus licheniformis DSM 13 = ATCC 14580
NoYes   Bacillus clausii KSM-K16
NoYes   Niastella koreensis GR20-10
NoYes   Marivirga tractuosa DSM 4126
NoYes   Prevotella intermedia 17
NoYes   Alistipes finegoldii DSM 17242
NoYes   Capnocytophaga ochracea DSM 7271
NoYes   Planctomyces limnophilus DSM 3776
NoYes   Opitutus terrae PB90-1
NoYes   Fretibacterium fastidiosum
NoYes   Leptospira interrogans serovar Lai str. IPAV
NoYes   Acidithiobacillus ferrooxidans ATCC 53993
NoYes   Campylobacter hominis ATCC BAA-381
NoYes   Helicobacter hepaticus ATCC 51449
NoYes   Helicobacter felis ATCC 49179
NoYes   Desulfarculus baarsii DSM 2075
NoYes   Syntrophus aciditrophicus SB
NoYes   Desulfatibacillum alkenivorans AK-01
NoYes   Desulfovibrio aespoeensis Aspo-2
NoYes   Desulfovibrio magneticus RS-1
NoYes   Desulfovibrio alaskensis G20
NoYes   Desulfovibrio africanus str. Walvis Bay
NoYes   Neisseria meningitidis FAM18
NoYes   Polaromonas sp. JS666
NoYes   Acidovorax sp. KKS102
NoYes   Sideroxydans lithotrophicus ES-1
NoYes   Magnetococcus marinus MC-1
NoYes   Rhodobacter capsulatus SB 1003
NoYes   Magnetospirillum magneticum AMB-1
NoYes   Azospirillum lipoferum 4B
NoYes   Gallibacterium anatis UMN179
NoYes   Haemophilus parasuis SH0165
NoYes   Haemophilus ducreyi 35000HP
NoYes   Methylococcus capsulatus str. Bath
NoYes   Thioalkalivibrio sulfidophilus HL-EbGr7
NoYes   Citrobacter rodentium ICC168
NoYes   Azotobacter vinelandii DJ
NoYes   Clostridium botulinum BKT015925
NoYes   Clostridium botulinum Ba4 str. 657
NoYes   Clostridium botulinum A2 str. Kyoto
NoYes   Thermoanaerobacterium saccharolyticum JW/SL-YS485
NoYes   Thermoanaerobacterium thermosaccharolyticum M0795
NoYes   Halobacteroides halobius DSM 5150
NoYes   Lactobacillus plantarum subsp. plantarum P-8
NoYes   Lactococcus lactis subsp. lactis KLDS 4.0325
NoYes   Lactococcus lactis subsp. lactis CV56
NoYes   Lactococcus lactis subsp. lactis Il1403
NoYes   Lactococcus lactis subsp. cremoris NZ9000
NoYes   Listeria monocytogenes M7
NoYes   Listeria monocytogenes J1-220
NoYes   Listeria monocytogenes SLCC2479
NoYes   Listeria monocytogenes SLCC2540
NoYes   Listeria monocytogenes serotype 1/2c str. SLCC2372
NoYes   Listeria monocytogenes 08-5578
NoYes   Listeria monocytogenes 08-5923
NoYes   Listeria monocytogenes L99
NoYes   Listeria monocytogenes HCC23
NoYes   Listeria monocytogenes FSL R2-561
NoYes   Bacillus licheniformis 9945A
NoYes   Bacillus subtilis subsp. natto BEST195
NoYes   Bacillus licheniformis DSM 13 = ATCC 14580
NoYes   Bacillus thuringiensis HD-771
NoYes   Staphylococcus aureus CA-347
NoYes   Staphylococcus aureus Bmb9393
NoYes   Staphylococcus aureus subsp. aureus Z172
NoYes   Staphylococcus aureus subsp. aureus SA957
NoYes   Staphylococcus aureus subsp. aureus M013
NoYes   Staphylococcus aureus subsp. aureus str. JKD6008
NoYes   Staphylococcus aureus subsp. aureus NCTC 8325
NoYes   Riemerella anatipestifer RA-CH-1
NoYes   Leptospira interrogans serovar Lai str. 56601
NoYes   Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
NoYes   Fusobacterium nucleatum subsp. vincentii 3_1_36A2
NoYes   Acidithiobacillus ferrooxidans ATCC 23270
NoYes   Campylobacter jejuni RM1221
NoYes   Campylobacter jejuni subsp. jejuni 00-2544
NoYes   Campylobacter jejuni subsp. jejuni 00-2538
NoYes   Campylobacter jejuni subsp. jejuni 00-2425
NoYes   Campylobacter jejuni subsp. jejuni ICDCCJ07001
NoYes   Campylobacter jejuni subsp. jejuni S3
NoYes   Desulfovibrio vulgaris RCH1
NoYes   Desulfovibrio vulgaris str. 'Miyazaki F'
NoYes   Desulfovibrio vulgaris str. Hildenborough
NoYes   Geobacter sp. M18
NoYes   Neisseria meningitidis WUE 2594
NoYes   Neisseria meningitidis G2136
NoYes   Neisseria meningitidis M01-240355
NoYes   Neisseria meningitidis 8013
NoYes   Neisseria meningitidis 053442
NoYes   Neisseria meningitidis Z2491
NoYes   Rhodopseudomonas palustris TIE-1
NoYes   Mannheimia succiniciproducens MBEL55E
NoYes   Bibersteinia trehalosi USDA-ARS-USMARC-192
NoYes   Mannheimia haemolytica USMARC_2286
NoYes   Mannheimia haemolytica M42548
NoYes   Mannheimia haemolytica D174
NoYes   Mannheimia haemolytica D153
NoYes   Mannheimia haemolytica USDA-ARS-USMARC-183
NoYes   Haemophilus parasuis ZJ0906
NoYes   Haemophilus influenzae F3031
NoYes   Haemophilus influenzae Rd KW20
NoYes   Shigella sonnei 53G
NoYes   Salmonella bongori N268-08
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   Enterobacter aerogenes EA1509E
NoYes   Escherichia coli JJ1886
NoYes   Escherichia coli LY180
NoYes   Escherichia coli O7:K1 str. CE10
NoYes   Escherichia coli NA114
NoYes   Escherichia coli ABU 83972
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli IAI39
NoYes   Escherichia coli W
NoYes   Escherichia coli W
NoYes   Escherichia coli SE11
NoYes   Escherichia coli O157:H7 str. Sakai
NoYes   Azotobacter vinelandii CA6
NoYes   Azotobacter vinelandii CA
NoYes   Pseudomonas aeruginosa LES431
NoYes   Pseudomonas aeruginosa NCGM2.S1
NoYes   Pseudomonas aeruginosa LESB58
NoYes   Acinetobacter baumannii BJAB0715
NoYes   Acinetobacter baumannii TCDC-AB0715
NoYes   Acinetobacter baumannii MDR-ZJ06
NoYes   Activated sludge plasmid pool Morges-2009 (Newbler) (meta-genome)
NoYes   Dendroctonus ponderosae beetle community (MPB hybrid beetle) (Lodgepole pine) (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Freshwater propionate enrichment of Brocadia fulgida (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Hindgut microbiome of Nasutitermes sp. (Costa Rica) (meta-genome)
NoYes   Human Gut Community Subject 8 (meta-genome)
NoYes   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methanol enrichment (meta-genome)
NoYes   Miscanthus field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing Miscanthu (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2- (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   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Wastewater Terephthalate-degrading communities from Bioreactor (meta-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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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