SUPERFAMILY 1.75 HMM library and genome assignments server

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AGR C 984p-like alignments

These alignments are sequences aligned to the 0054345 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 
                  |         |         |         |         |         |         |         |         | 
d2o8sa1 v-TSTYTSYRLISQDIGKSLERVSKQPDVARETEYYREKIGSVKSIDDFMADTRLYNYALKAHGLEDMAYAKAFIRKVLTEGASDKNAFANK


              100       110       120       130       140       150       160       170       180   
                |         |         |         |         |         |         |         |         |   
d2o8sa1 LSDNRYAELAKSLDFAGLGAAATATEAAKSGVIGNYARQTLEQEAGDDNNGVRLALYFERKAPTIKSGLDFLADDALAQVFRTTFNLPDAFA


            190       200       210       220      
              |         |         |         |      
d2o8sa1 AADVDKQAALIEKSINIKDLQDPEKVGKLLERFTIMWEMQN-p


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: 0054345 (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   Hyphomonas neptunium ATCC 15444
NoYes   Dinoroseobacter shibae DFL 12
NoYes   Phaeobacter gallaeciensis 2.10
NoYes   Pseudovibrio sp. FO-BEG1
NoYes   Jannaschia sp. CCS1
NoYes   Ruegeria sp. TM1040
NoYes   Ruegeria pomeroyi DSS-3
NoYes   Ketogulonicigenium vulgare Y25
NoYes   Ketogulonigenium vulgarum WSH-001
NoYes   Roseobacter litoralis Och 149
NoYes   Rhodobacter sphaeroides ATCC 17029
NoYes   Rhodobacter capsulatus SB 1003
NoYes   Paracoccus denitrificans PD1222
NoYes   Rhodospirillum centenum SW
NoYes   Azospirillum lipoferum 4B
NoYes   Azospirillum sp. B510
NoYes   Azospirillum brasilense Sp245
NoYes   Gluconacetobacter diazotrophicus PAl 5
NoYes   Acidiphilium multivorum AIU301
NoYes   Acidiphilium cryptum JF-5
NoYes   Gluconobacter oxydans 621H
NoYes   Polymorphum gilvum SL003B-26A1
NoYes   Azorhizobium caulinodans ORS 571
NoYes   Methylobacterium chloromethanicum CM4
NoYes   Methylobacterium extorquens AM1
NoYes   Methylobacterium sp. 4-46
NoYes   Methylobacterium populi BJ001
NoYes   Methylobacterium radiotolerans JCM 2831
NoYes   Ochrobactrum anthropi ATCC 49188
NoYes   Brucella microti CCM 4915
NoYes   Brucella pinnipedialis B2/94
NoYes   Brucella canis ATCC 23365
NoYes   Brucella suis ATCC 23445
NoYes   Brucella melitensis ATCC 23457
NoYes   Brucella ovis ATCC 25840
NoYes   Brucella abortus S19
NoYes   Sinorhizobium fredii NGR234
NoYes   Sinorhizobium medicae WSM419
NoYes   Sinorhizobium meliloti AK83
NoYes   Genome sequence of Rhizobium sp. strain IRBG74
NoYes   Rhizobium etli CIAT 652
NoYes   Rhizobium leguminosarum bv. viciae 3841
NoYes   Agrobacterium tumefaciens str. C58
NoYes   Agrobacterium radiobacter K84
NoYes   Agrobacterium sp. H13-3
NoYes   Agrobacterium vitis S4
NoYes   Candidatus Liberibacter asiaticus str. psy62
NoYes   Mesorhizobium sp. BNC1
NoYes   Mesorhizobium opportunistum WSM2075
NoYes   Mesorhizobium ciceri biovar biserrulae WSM1271
NoYes   Mesorhizobium loti MAFF303099
NoYes   Methylocella silvestris BL2
NoYes   Beijerinckia indica subsp. indica ATCC 9039
NoYes   Rhodomicrobium vannielii ATCC 17100
NoYes   Hyphomicrobium sp. MC1
NoYes   Hyphomicrobium denitrificans ATCC 51888
NoYes   Rhodopseudomonas palustris BisA53
NoYes   Bradyrhizobium japonicum USDA 110
NoYes   Bartonella clarridgeiae 73
NoYes   Bartonella bacilliformis KC583
NoYes   Phaeobacter gallaeciensis DSM 17395
NoYes   Phaeobacter gallaeciensis DSM 26640
NoYes   Leisingera methylohalidivorans DSM 14336
NoYes   Rhodobacter sphaeroides KD131
NoYes   Rhodobacter sphaeroides 2.4.1
NoYes   Paracoccus aminophilus JCM 7686
NoYes   Gluconacetobacter diazotrophicus PAl 5
NoYes   Gluconobacter oxydans H24
NoYes   Methylobacterium extorquens DM4
NoYes   Methylobacterium extorquens PA1
NoYes   Brucella ceti TE10759-12
NoYes   Brucella ceti TE28753-12
NoYes   Brucella canis HSK A52141
NoYes   Brucella suis VBI22
NoYes   Brucella suis 1330
NoYes   Brucella suis 1330
NoYes   Brucella melitensis NI
NoYes   Brucella melitensis M5-90
NoYes   Brucella melitensis M28
NoYes   Brucella melitensis bv. 1 str. 16M
NoYes   Brucella abortus A13334
NoYes   Brucella melitensis biovar Abortus 2308
NoYes   Brucella abortus bv. 1 str. 9-941
NoYes   Sinorhizobium fredii USDA 257
NoYes   Sinorhizobium fredii HH103
NoYes   Sinorhizobium meliloti 2011
NoYes   Sinorhizobium meliloti GR4
NoYes   Sinorhizobium meliloti Rm41
NoYes   Sinorhizobium meliloti SM11
NoYes   Sinorhizobium meliloti BL225C
NoYes   Sinorhizobium meliloti 1021
NoYes   Rhizobium etli CFN 42
NoYes   Rhizobium etli bv. mimosae str. Mim1
NoYes   Rhizobium tropici CIAT 899
NoYes   Rhizobium leguminosarum bv. trifolii WSM2304
NoYes   Rhizobium leguminosarum bv. trifolii WSM1325
NoYes   Liberibacter crescens BT-1
NoYes   Candidatus Liberibacter solanacearum CLso-ZC1
NoYes   Candidatus Liberibacter americanus str. Sao Paulo
NoYes   Candidatus Liberibacter asiaticus str. gxpsy
NoYes   Mesorhizobium australicum WSM2073
NoYes   Hyphomicrobium nitrativorans NL23
NoYes   Hyphomicrobium denitrificans 1NES1
NoYes   Rhodopseudomonas palustris BisB18
NoYes   Bradyrhizobium sp. S23321
NoYes   Bradyrhizobium japonicum USDA 6
NoYes   Ricinus communis - Castor bean
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Endophytic microbiome from Rice (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #1 (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #2 (meta-genome)
NoYes   Freshwater propionate enrichment of Brocadia fulgida (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 01(G) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 04(N) (meta-genome)
NoYes   Maize field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing corn (Zea may (meta-genome)
NoYes   Maize rhizosphere soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Soil sample from rhizosphere of corn (Zea mays))< (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 1 Maryland Estuary CO2- (Maryland Estuary ambient) (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2+ (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2- (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 4 Nevada Test Site Crust CO2- (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2+ (Oak Ridge elevated CO2) (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2- (Oak Ridge ambient) (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   Global Ocean Sampling Expedition (GOS)
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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