SUPERFAMILY 1.75 HMM library and genome assignments server

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KaiA/RbsU domain alignments

These alignments are sequences aligned to the 0042633 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        9
                   |         |         |          |         |         |         |         |         
d1q6aa_ .a-MARMSPADKRKLLDELRSIYRTIVLEYFNTDAKVN.ERIDEFVSKAFFADISVSQVLEIHVELMDTFSKQLKLEGRSEDILLDYRLTLI
d1r8ja1 .rFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLN.QSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLI
d1w53a_ md------------FREVIEQRYHQLLSRYIAELTETSlYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSL------------------


        0       100                             
        |         |                             
d1q6aa_ DVIAHLCEMYRRSIPRE-v.....................
d1r8ja1 DVIAHLCEMYRRSIPR--......................
d1w53a_ ------------------pedvfhsldflievmigygmay


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: 0042633 (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   Aspergillus zonatus v1.0
NoYes   Leptolyngbya sp. PCC 7376
NoYes   Pseudanabaena sp. PCC 7367
NoYes   Acaryochloris marina MBIC11017
NoYes   Synechocystis sp. PCC 6803
NoYes   Thermosynechococcus elongatus BP-1
NoYes   Synechococcus sp. PCC 7502
NoYes   Synechococcus sp. PCC 6312
NoYes   Synechococcus sp. CC9311
NoYes   Synechococcus elongatus PCC 7942
NoYes   Microcoleus sp. PCC 7113
NoYes   Trichodesmium erythraeum IMS101
NoYes   Geitlerinema sp. PCC 7407
NoYes   Cyanothece sp. PCC 8802
NoYes   cyanobacterium UCYN-A
NoYes   Halothece sp. PCC 7418
NoYes   Microcystis aeruginosa NIES-843
NoYes   Rivularia sp. PCC 7116
NoYes   Calothrix sp. PCC 7507
NoYes   Anabaena variabilis ATCC 29413
NoYes   'Nostoc azollae' 0708
NoYes   Nostoc sp. PCC 7107
NoYes   Nostoc punctiforme PCC 73102
NoYes   Nostoc sp. PCC 7120
NoYes   Nostoc sp. PCC 7524
NoYes   Anabaena sp. 90
NoYes   Mycobacterium marinum M
NoYes   Moorella thermoacetica ATCC 39073
NoYes   Brevibacillus brevis NBRC 100599
NoYes   Paenibacillus sp. JDR-2
NoYes   Bacillus selenitireducens MLS10
NoYes   Listeria welshimeri serovar 6b str. SLCC5334
NoYes   Listeria innocua Clip11262
NoYes   Listeria seeligeri serovar 1/2b str. SLCC3954
NoYes   Listeria monocytogenes serotype 4b str. CLIP 80459
NoYes   Listeria ivanovii subsp. ivanovii PAM 55
NoYes   Solibacillus silvestris StLB046
NoYes   Lysinibacillus sphaericus C3-41
NoYes   Oceanobacillus iheyensis HTE831
NoYes   Halobacillus halophilus DSM 2266
NoYes   Bacillus sp. JS
NoYes   Bacillus amyloliquefaciens FZB42
NoYes   Bacillus atrophaeus 1942
NoYes   Bacillus subtilis subsp. subtilis str. 168
NoYes   Bacillus licheniformis DSM 13 = ATCC 14580
NoYes   Bacillus halodurans C-125
NoYes   Bacillus pseudofirmus OF4
NoYes   Bacillus clausii KSM-K16
NoYes   Bacillus cellulosilyticus DSM 2522
NoYes   Bacillus pumilus SAFR-032
NoYes   Bacillus megaterium DSM 319
NoYes   Bacillus coagulans 2-6
NoYes   Macrococcus caseolyticus JCSC5402
NoYes   Staphylococcus pseudintermedius HKU10-03
NoYes   Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
NoYes   Staphylococcus lugdunensis HKU09-01
NoYes   Staphylococcus haemolyticus JCSC1435
NoYes   Staphylococcus epidermidis RP62A
NoYes   Staphylococcus carnosus subsp. carnosus TM300
NoYes   Staphylococcus aureus subsp. aureus JH1
NoYes   Staphylococcus aureus
NoYes   Chamaesiphon minutus PCC 6605
NoYes   Synechocystis sp. PCC 6803 substr. PCC-P
NoYes   Synechocystis sp. PCC 6803 substr. PCC-N
NoYes   Synechocystis sp. PCC 6803 substr. GT-I
NoYes   Synechocystis sp. PCC 6803
NoYes   Cyanobium gracile PCC 6307
NoYes   Dactylococcopsis salina PCC 8305
NoYes   Synechococcus sp. JA-2-3B'a(2-13)
NoYes   Synechococcus sp. JA-3-3Ab
NoYes   Synechococcus sp. CC9902
NoYes   Synechococcus sp. RCC307
NoYes   Synechococcus sp. CC9605
NoYes   Synechococcus sp. WH 8102
NoYes   Synechococcus sp. WH 7803
NoYes   Synechococcus sp. PCC 7002
NoYes   Synechococcus elongatus PCC 6301
NoYes   Crinalium epipsammum PCC 9333
NoYes   Oscillatoria nigro-viridis PCC 7112
NoYes   Oscillatoria acuminata PCC 6304
NoYes   Arthrospira platensis NIES-39
NoYes   Cyanothece sp. PCC 7822
NoYes   Cyanothece sp. PCC 7425
NoYes   Cyanothece sp. PCC 7424
NoYes   Cyanothece sp. ATCC 51142
NoYes   Cyanothece sp. PCC 8801
NoYes   Cyanobacterium aponinum PCC 10605
NoYes   Cyanobacterium stanieri PCC 7202
NoYes   Pleurocapsa minor Pleurocapsa sp. PCC 7327
NoYes   Stanieria cyanosphaera PCC 7437
NoYes   Calothrix parietina Calothrix sp. PCC 6303
NoYes   Cylindrospermum stagnale PCC 7417
NoYes   Anabaena cylindrica PCC 7122
NoYes   Mycobacterium liflandii 128FXT
NoYes   Desulfotomaculum gibsoniae DSM 7213
NoYes   Listeria monocytogenes EGD sequence
NoYes   Listeria monocytogenes N53-1
NoYes   Listeria monocytogenes La111
NoYes   Listeria monocytogenes serotype 4b str. LL195
NoYes   Listeria monocytogenes 07PF0776
NoYes   Listeria monocytogenes M7
NoYes   Listeria monocytogenes J1-220
NoYes   Listeria monocytogenes J1816
NoYes   Listeria monocytogenes SLCC2376
NoYes   Listeria monocytogenes SLCC5850
NoYes   Listeria monocytogenes ATCC 19117
NoYes   Listeria monocytogenes L312
NoYes   Listeria monocytogenes SLCC2479
NoYes   Listeria monocytogenes SLCC7179
NoYes   Listeria monocytogenes SLCC2540
NoYes   Listeria monocytogenes SLCC2378
NoYes   Listeria monocytogenes serotype 1/2b str. SLCC2755
NoYes   Listeria monocytogenes serotype 1/2c str. SLCC2372
NoYes   Listeria monocytogenes serotype 7 str. SLCC2482
NoYes   Listeria monocytogenes 08-5578
NoYes   Listeria monocytogenes 08-5923
NoYes   Listeria monocytogenes L99
NoYes   Listeria monocytogenes HCC23
NoYes   Listeria monocytogenes 10403S
NoYes   Listeria monocytogenes J0161
NoYes   Listeria monocytogenes Finland 1998
NoYes   Listeria monocytogenes FSL R2-561
NoYes   Listeria monocytogenes serotype 4b str. F2365
NoYes   Listeria monocytogenes EGD-e
NoYes   Amphibacillus xylanus NBRC 15112
NoYes   Bacillus amyloliquefaciens subsp. plantarum sequencing
NoYes   Bacillus amyloliquefaciens subsp. plantarum UCMB5033
NoYes   Bacillus amyloliquefaciens subsp. plantarum AS43.3
NoYes   Bacillus amyloliquefaciens subsp. plantarum YAU B9601-Y2
NoYes   Bacillus amyloliquefaciens subsp. plantarum UCMB5113
NoYes   Bacillus amyloliquefaciens subsp. plantarum UCMB5036
NoYes   Bacillus amyloliquefaciens subsp. plantarum CAU B946
NoYes   Bacillus amyloliquefaciens LFB112
NoYes   Bacillus amyloliquefaciens CC178
NoYes   Bacillus amyloliquefaciens Y2
NoYes   Bacillus amyloliquefaciens IT-45
NoYes   Bacillus amyloliquefaciens XH7
NoYes   Bacillus amyloliquefaciens LL3
NoYes   Bacillus amyloliquefaciens TA208
NoYes   Bacillus amyloliquefaciens DSM 7
NoYes   Bacillus licheniformis 9945A
NoYes   Bacillus subtilis PY79
NoYes   Bacillus subtilis XF-1
NoYes   Bacillus subtilis QB928
NoYes   Bacillus subtilis BSn5
NoYes   Bacillus subtilis subsp. subtilis str. BAB-1
NoYes   Bacillus subtilis subsp. subtilis str. BSP1
NoYes   Bacillus subtilis subsp. subtilis str. RO-NN-1
NoYes   Bacillus subtilis subsp. subtilis 6051-HGW
NoYes   Bacillus subtilis subsp. spizizenii TU-B-10
NoYes   Bacillus subtilis subsp. spizizenii str. W23
NoYes   Bacillus subtilis subsp. natto BEST195
NoYes   Bacillus licheniformis DSM 13 = ATCC 14580
NoYes   Bacillus infantis NRRL B-14911
NoYes   Bacillus megaterium WSH-002
NoYes   Bacillus megaterium QM B1551
NoYes   Bacillus coagulans 36D1
NoYes   Staphylococcus aureus subsp. aureus MSHR1132
NoYes   Staphylococcus pseudintermedius ED99
NoYes   Staphylococcus pasteuri SP1
NoYes   Staphylococcus lugdunensis N920143
NoYes   Staphylococcus warneri SG1
NoYes   Staphylococcus epidermidis ATCC 12228
NoYes   Staphylococcus aureus CA-347
NoYes   Staphylococcus aureus Bmb9393
NoYes   Staphylococcus aureus M1
NoYes   Staphylococcus aureus 08BA02176
NoYes   Staphylococcus aureus ST228/18412
NoYes   Staphylococcus aureus ST228/18341
NoYes   Staphylococcus aureus ST228/16125
NoYes   Staphylococcus aureus ST228/16035
NoYes   Staphylococcus aureus ST228/15532
NoYes   Staphylococcus aureus ST228/10497
NoYes   Staphylococcus aureus ST228/10388
NoYes   Staphylococcus aureus 04-02981
NoYes   Staphylococcus aureus RF122
NoYes   Staphylococcus aureus subsp. aureus Z172
NoYes   Staphylococcus aureus subsp. aureus 6850
NoYes   Staphylococcus aureus subsp. aureus SA957
NoYes   Staphylococcus aureus subsp. aureus CN1
NoYes   Staphylococcus aureus subsp. aureus SA40
NoYes   Staphylococcus aureus subsp. aureus 11819-97
NoYes   Staphylococcus aureus subsp. aureus M013
NoYes   Staphylococcus aureus subsp. aureus HO 5096 0412
NoYes   Staphylococcus aureus subsp. aureus VC40
NoYes   Staphylococcus aureus subsp. aureus T0131
NoYes   Staphylococcus aureus subsp. aureus LGA251
NoYes   Staphylococcus aureus subsp. aureus ECT-R 2
NoYes   Staphylococcus aureus subsp. aureus JKD6159
NoYes   Staphylococcus aureus subsp. aureus ED133
NoYes   Staphylococcus aureus subsp. aureus ED98
NoYes   Staphylococcus aureus subsp. aureus TW20
NoYes   Staphylococcus aureus subsp. aureus 55/2053
NoYes   Staphylococcus aureus subsp. aureus TCH60
NoYes   Staphylococcus aureus subsp. aureus str. JKD6008
NoYes   Staphylococcus aureus subsp. aureus 71193
NoYes   Staphylococcus aureus subsp. aureus S0385
NoYes   Staphylococcus aureus subsp. aureus str. Newman
NoYes   Staphylococcus aureus subsp. aureus Mu3
NoYes   Staphylococcus aureus subsp. aureus USA300_TCH1516
NoYes   Staphylococcus aureus subsp. aureus USA300_FPR3757
NoYes   Staphylococcus aureus subsp. aureus JH9
NoYes   Staphylococcus aureus subsp. aureus MSSA476
NoYes   Staphylococcus aureus subsp. aureus MRSA252
NoYes   Staphylococcus aureus subsp. aureus MW2
NoYes   Staphylococcus aureus subsp. aureus N315
NoYes   Staphylococcus aureus subsp. aureus Mu50
NoYes   Staphylococcus aureus subsp. aureus COL
NoYes   4_050719Q (meta-genome)
NoYes   5_050719P (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 bottom (Fungus garden bottom) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 01(G) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP15 from Mushroom Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP6 from White Creek Site 3 (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP7 from Chocolate Pots (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methane enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methylamine enrichment (meta-genome)
NoYes   Miscanthus rhizosphere soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Rhizosphere soil sample of Miscanthus x giga (meta-genome)
NoYes   NCBI 2017_08 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   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
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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