SUPERFAMILY 1.75 HMM library and genome assignments server

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Typo IV secretion system protein TraC alignments

These alignments are sequences aligned to the 0049131 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     
                        |         |         |         |         |         |         |         |     
d1r8ia_ telikqg-------EQLEQMAQQLEQLKSQLETQKNMYESMAKTTNLGDLLGTSTNTLANNLPDNWKEVYSDAMNSSSSVTPSVNSMMGQFN


           90       100       110       120       130       140       150       160       170       
            |         |         |         |         |         |         |         |         |       
d1r8ia_ AEVDDMTPSEAIAYMNKKLAEKGAYDRVMAEKAYNNQMQELSDMQALTEQIKSTPDLKSIADLQARIQTSQGAIQGEQAKLNLMNMLQQSQD


        180        
          |        
d1r8ia_ KLLRAQKDR-a


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: 0049131 (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   Mus musculus 76_38 - House mouse
NoYes   Drosophila ananassae 1.3
NoYes   Dictyostelium purpureum
NoYes   Medicago truncatula - Barrel medic
NoYes   Trichomonas vaginalis
NoYes   Selenomonas sputigena ATCC 35185
NoYes   Prosthecochloris aestuarii DSM 271
NoYes   Zobellia galactanivorans
NoYes   Sulfurospirillum deleyianum DSM 6946
NoYes   Campylobacter hominis ATCC BAA-381
NoYes   Campylobacter lari RM2100
NoYes   Desulfovibrio salexigens DSM 2638
NoYes   Geobacter sp. M21
NoYes   Geobacter metallireducens GS-15
NoYes   Anaeromyxobacter dehalogenans 2CP-1
NoYes   Aromatoleum aromaticum EbN1
NoYes   Candidatus Accumulibacter phosphatis clade IIA str. UW-1
NoYes   Thiomonas arsenitoxydans
NoYes   Leptothrix cholodnii SP-6
NoYes   Burkholderia phytofirmans PsJN
NoYes   Burkholderia phymatum STM815
NoYes   Burkholderia xenovorans LB400
NoYes   Ralstonia eutropha JMP134
NoYes   Cupriavidus necator N-1
NoYes   Burkholderia sp. CCGE1002
NoYes   Burkholderia ambifaria AMMD
NoYes   Burkholderia cenocepacia HI2424
NoYes   Burkholderia multivorans ATCC 17616
NoYes   Burkholderia vietnamiensis G4
NoYes   Verminephrobacter eiseniae EF01-2
NoYes   Polaromonas naphthalenivorans CJ2
NoYes   Variovorax paradoxus S110
NoYes   Acidovorax sp. JS42
NoYes   Acidovorax citrulli AAC00-1
NoYes   Comamonas testosteroni CNB-2
NoYes   Pusillimonas sp. T7-7
NoYes   Advenella kashmirensis WT001
NoYes   Taylorella equigenitalis MCE9
NoYes   Bordetella petrii DSM 12804
NoYes   Bordetella bronchiseptica RB50
NoYes   Achromobacter xylosoxidans A8
NoYes   Achromobacter xylosoxidans
NoYes   Nitrosomonas eutropha C91
NoYes   Methylovorus glucosetrophus SIP3-4
NoYes   Parvularcula bermudensis HTCC2503
NoYes   Asticcacaulis excentricus CB 48
NoYes   Caulobacter sp. K31
NoYes   Phenylobacterium zucineum HLK1
NoYes   Sphingopyxis alaskensis RB2256
NoYes   Novosphingobium sp. PP1Y
NoYes   Sphingobium sp. SYK-6
NoYes   Sphingobium japonicum UT26S
NoYes   Sphingobium chlorophenolicum L-1
NoYes   Sphingomonas sp. MM-1
NoYes   Sphingomonas wittichii RW1
NoYes   Hirschia baltica ATCC 49814
NoYes   Dinoroseobacter shibae DFL 12
NoYes   Ruegeria sp. TM1040
NoYes   Roseobacter denitrificans OCh 114
NoYes   Gluconacetobacter xylinus NBRC 3288
NoYes   Acidiphilium multivorum AIU301
NoYes   Acidiphilium cryptum JF-5
NoYes   Polymorphum gilvum SL003B-26A1
NoYes   Xanthobacter autotrophicus Py2
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   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   Mesorhizobium sp. BNC1
NoYes   Mesorhizobium opportunistum WSM2075
NoYes   Mesorhizobium ciceri biovar biserrulae WSM1271
NoYes   Mesorhizobium loti MAFF303099
NoYes   Oligotropha carboxidovorans OM4
NoYes   Nitrobacter hamburgensis X14
NoYes   Bartonella tribocorum CIP 105476
NoYes   Bartonella henselae str. Houston-1
NoYes   Bartonella grahamii as4aup
NoYes   Bartonella quintana str. Toulouse
NoYes   Oceanimonas sp. GK1
NoYes   Vibrio sp. Ex25
NoYes   Vibrio harveyi ATCC BAA-1116
NoYes   Vibrio furnissii NCTC 11218
NoYes   Marinobacter adhaerens HP15
NoYes   Marinobacter aquaeolei VT8
NoYes   Alcanivorax borkumensis SK2
NoYes   Halomonas elongata DSM 2581
NoYes   Pseudoxanthomonas spadix BD-a59
NoYes   Xylella fastidiosa M23
NoYes   Xanthomonas axonopodis pv. citri str. 306
NoYes   Xanthomonas albilineans GPE PC73
NoYes   Halothiobacillus neapolitanus c2
NoYes   Thioalkalivibrio sp. K90mix
NoYes   Legionella longbeachae NSW150
NoYes   Legionella pneumophila str. Corby
NoYes   Proteus mirabilis HI4320
NoYes   Edwardsiella tarda EIB202
NoYes   Rahnella aquatilis CIP 78.65 = ATCC 33071
NoYes   Yersinia pseudotuberculosis IP 31758
NoYes   Yersinia enterocolitica subsp. enterocolitica 8081
NoYes   Dickeya zeae Ech1591
NoYes   Pectobacterium sp. SCC3193
NoYes   Pectobacterium atrosepticum SCRI1043
NoYes   Erwinia tasmaniensis Et1/99
NoYes   Cronobacter turicensis z3032
NoYes   Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)
NoYes   Enterobacteriaceae bacterium strain FGI 57
NoYes   Shigella boydii CDC 3083-94
NoYes   Klebsiella pneumoniae NTUH-K2044
NoYes   Citrobacter koseri ATCC BAA-895
NoYes   Azotobacter vinelandii DJ
NoYes   Pseudomonas brassicacearum subsp. brassicacearum NFM421
NoYes   Pseudomonas syringae pv. tomato str. DC3000
NoYes   Pseudomonas aeruginosa UCBPP-PA14
NoYes   Pseudomonas sp. VLB120
NoYes   Acinetobacter baumannii ATCC 17978
NoYes   Arcobacter butzleri 7h1h
NoYes   Campylobacter jejuni subsp. jejuni 00-2544
NoYes   Campylobacter jejuni subsp. jejuni ICDCCJ07001
NoYes   Campylobacter jejuni subsp. jejuni S3
NoYes   Campylobacter jejuni subsp. jejuni IA3902
NoYes   Campylobacter jejuni subsp. jejuni 81-176
NoYes   Campylobacter coli CVM N29710
NoYes   Neisseria gonorrhoeae TCDC-NG08107
NoYes   Burkholderia phenoliruptrix BR3459a
NoYes   Pandoraea pnomenusa 3kgm
NoYes   Ralstonia solanacearum FQY_4
NoYes   Ralstonia solanacearum PSI07
NoYes   Ralstonia solanacearum CMR15
NoYes   Ralstonia solanacearum GMI1000
NoYes   Burkholderia sp. YI23
NoYes   Burkholderia sp. KJ006
NoYes   Burkholderia pseudomallei MSHR305
NoYes   Burkholderia pseudomallei MSHR346
NoYes   Burkholderia pseudomallei K96243
NoYes   Burkholderia ambifaria MC40-6
NoYes   Burkholderia cenocepacia MC0-3
NoYes   Burkholderia cenocepacia J2315
NoYes   Burkholderia multivorans ATCC 17616
NoYes   Alicycliphilus denitrificans BC
NoYes   Variovorax paradoxus B4
NoYes   Taylorella equigenitalis ATCC 35865
NoYes   Bordetella parapertussis Bpp5
NoYes   Achromobacter xylosoxidans NBRC 15126 = ATCC 27061
NoYes   Nitrosomonas sp. AL212
NoYes   Phaeobacter gallaeciensis DSM 17395
NoYes   Phaeobacter gallaeciensis DSM 26640
NoYes   Octadecabacter arcticus 238
NoYes   Rhodobacter sphaeroides ATCC 17025
NoYes   Paracoccus aminophilus JCM 7686
NoYes   Brucella ceti TE10759-12
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 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 leguminosarum bv. trifolii WSM1325
NoYes   Mesorhizobium australicum WSM2073
NoYes   Oligotropha carboxidovorans OM5
NoYes   Oligotropha carboxidovorans OM5
NoYes   Bradyrhizobium sp. BTAi1
NoYes   Bartonella australis Aust/NH1
NoYes   Bartonella vinsonii subsp. berkhoffii str. Winnie
NoYes   Bartonella quintana RM-11
NoYes   Aggregatibacter actinomycetemcomitans ANH9381
NoYes   Aggregatibacter actinomycetemcomitans D11S-1
NoYes   Vibrio fischeri ES114
NoYes   Shewanella sp. ANA-3
NoYes   Stenotrophomonas maltophilia D457
NoYes   Xylella fastidiosa subsp. fastidiosa GB514
NoYes   Xylella fastidiosa 9a5c
NoYes   Xanthomonas campestris pv. vesicatoria str. 85-10
NoYes   Xanthomonas axonopodis pv. citrumelo F1
NoYes   Xanthomonas axonopodis Xac29-1
NoYes   Xanthomonas oryzae pv. oryzae KACC 10331
NoYes   Thioflavicoccus mobilis 8321
NoYes   Legionella pneumophila str. Paris
NoYes   Legionella pneumophila str. Lens
NoYes   Legionella pneumophila subsp. pneumophila LPE509
NoYes   Legionella pneumophila subsp. pneumophila str. Thunder Bay
NoYes   Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NoYes   Legionella pneumophila subsp. pneumophila
NoYes   Legionella pneumophila subsp. pneumophila
NoYes   Legionella pneumophila 2300/99 Alcoy
NoYes   Rahnella aquatilis HX2
NoYes   Yersinia pseudotuberculosis IP 32953
NoYes   Yersinia pestis biovar Microtus str. 91001
NoYes   Dickeya dadantii Ech586
NoYes   Dickeya dadantii 3937
NoYes   Pantoea ananatis AJ13355
NoYes   Cronobacter sakazakii ATCC BAA-894
NoYes   Shigella flexneri 2a str. 2457T
NoYes   Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633
NoYes   Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853
NoYes   Salmonella enterica subsp. enterica serovar Agona str. SL483
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   Klebsiella oxytoca KCTC 1686
NoYes   Klebsiella pneumoniae 342
NoYes   Klebsiella pneumoniae subsp. pneumoniae 1084
NoYes   Klebsiella pneumoniae subsp. pneumoniae HS11286
NoYes   Enterobacter aerogenes EA1509E
NoYes   Escherichia coli E. coli PMV-1
NoYes   Escherichia coli JJ1886
NoYes   Escherichia coli Xuzhou21
NoYes   Escherichia coli ED1a
NoYes   Escherichia coli UMN026
NoYes   Escherichia coli HS
NoYes   Escherichia coli O157:H7 str. EC4115
NoYes   Enterobacter cloacae subsp. cloacae ATCC 13047
NoYes   Azotobacter vinelandii CA6
NoYes   Azotobacter vinelandii CA
NoYes   Pseudomonas denitrificans ATCC 13867
NoYes   Pseudomonas syringae pv. phaseolicola 1448A
NoYes   Pseudomonas monteilii SB3078
NoYes   Pseudomonas putida H8234
NoYes   Pseudomonas putida DOT-T1E
NoYes   Pseudomonas putida S16
NoYes   Pseudomonas fluorescens A506
NoYes   Pseudomonas aeruginosa SCV20265
NoYes   Pseudomonas aeruginosa B136-33
NoYes   Pseudomonas aeruginosa NCGM2.S1
NoYes   Acinetobacter baumannii ATCC 19606
NoYes   Methylophaga sp. JAM7
NoYes   Cycloclasticus zancles 7-ME
NoYes   Vibrio campbellii ATCC BAA-1116
NoYes   2_050719S (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   5_050719P (meta-genome)
NoYes   Activated sludge plasmid pool Morges-2009 (Newbler) (meta-genome)
NoYes   Activated sludge plasmid pool Visp-2009 (Newbler) (meta-genome)
NoYes   Air microbial communities Singapore indoor air filters 1 (meta-genome)
NoYes   Air microbial communities Singapore indoor air filters 2 (meta-genome)
NoYes   Atta cephalotes fungus garden (ACEF) (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Crater Hills (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dendroctonus ponderosae beetle community (MPB hybrid beetle) (Lodgepole pine) (meta-genome)
NoYes   Dendroctonus ponderosae fungus gallery (Hybrid pine) (MPB hybrid gallery) (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (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   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #3 (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   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   Marine anammox bioreactor enriched for Scalindua species (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Formate 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   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   Protozoadb 2010_08 (Protozoadb)
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   Sludge/Australian, Phrap Assembly (meta-genome)
NoYes   Sludge/US, Jazz Assembly (meta-genome)
NoYes   Sludge/US, Phrap Assembly (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 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   Uranium Contaminated Groundwater FW106 (meta-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   The Salmonella enterica Pan-genome (meta-genome)
NoYes   ALL (only advised for small superfamilies)


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