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.


Cloacin translocation domain alignments

These alignments are sequences aligned to the 0039480 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.

                                                                                                    
                                                                                                    
d1jcha2 v...........................................................................................
d1rh1a1 tegidygdtmvvwpstgripggdvkpggssglapsmppgwgdyspqgialvqsvlfpgiirriildkeleegdwsgwsvsvhspwgnekvsa


                     10        20        30        40        50        60        70        80       
                      |         |         |         |         |         |         |         |       
d1jcha2 .....-AAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGPFKFGLWGVALYGVLPSQIAKDDPNMMSKIVTSLPADDITESPVS
d1rh1a1 artvl-ENGLRGGLPEPSRPAAVSFARLEPAS------------------------------------GNEQKIIRLMVTQQLEQVTDIPAS


         90       100       110       120       130               140        150           160      
          |         |         |         |         |                 |          |             |      
d1jcha2 SLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKP........TERPGVFTASI.PGAPVLNISVNNSTPAV....QTLSPGVT
d1rh1a1 QLPAAGNNVPVKYRLTDLMQNGTQYMAIIGGIPMTVPVVDAVPvpdrsrpgTNIKDVYSAPVsPNLPDLVLSVGQMNTPVrsnpEIQEDGVI


         170       180       190       200       210       220       230    
           |         |         |         |         |         |         |    
d1jcha2 NNTDKDVRPAFGTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATH-p.
d1rh1a1 SETGNYVE-AGYTMSSNNHDVIVRFPEGSGVSPLYISAVEILDSNSLSQRQEAENNAKDDFRV---kk


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: 0039480 (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   Candidatus Saccharimonas aalborgensis
NoYes   Vibrio harveyi ATCC BAA-1116
NoYes   Vibrio parahaemolyticus RIMD 2210633
NoYes   Vibrio anguillarum 775
NoYes   Marinobacter aquaeolei VT8
NoYes   Photorhabdus asymbiotica
NoYes   Photorhabdus luminescens subsp. laumondii TTO1
NoYes   Xenorhabdus bovienii SS-2004
NoYes   Providencia stuartii MRSN 2154
NoYes   Proteus mirabilis HI4320
NoYes   Rahnella sp. Y9602
NoYes   Rahnella aquatilis CIP 78.65 = ATCC 33071
NoYes   Yersinia pseudotuberculosis IP 31758
NoYes   Yersinia pestis Pestoides F
NoYes   Serratia proteamaculans 568
NoYes   Pectobacterium wasabiae WPP163
NoYes   Pectobacterium sp. SCC3193
NoYes   Pectobacterium atrosepticum SCRI1043
NoYes   Pantoea sp. At-9b
NoYes   Erwinia tasmaniensis Et1/99
NoYes   Enterobacteriaceae bacterium strain FGI 57
NoYes   Enterobacter aerogenes KCTC 2190
NoYes   Enterobacter asburiae LF7a
NoYes   Enterobacter cloacae subsp. dissolvens SDM
NoYes   Citrobacter koseri ATCC BAA-895
NoYes   Pseudomonas sp. TKP
NoYes   Pseudomonas sp. UW4
NoYes   Pseudomonas brassicacearum subsp. brassicacearum NFM421
NoYes   Pseudomonas syringae pv. tomato str. DC3000
NoYes   Pseudomonas fluorescens SBW25
NoYes   Pseudomonas aeruginosa UCBPP-PA14
NoYes   Vibrio anguillarum Listonella anguillarum M3
NoYes   Rahnella aquatilis HX2
NoYes   Yersinia pseudotuberculosis PB1/+
NoYes   Yersinia pseudotuberculosis YPIII
NoYes   Yersinia pseudotuberculosis IP 32953
NoYes   Yersinia pestis biovar Microtus str. 91001
NoYes   Yersinia pestis A1122
NoYes   Yersinia pestis Z176003
NoYes   Yersinia pestis D182038
NoYes   Yersinia pestis D106004
NoYes   Yersinia pestis biovar Medievalis str. Harbin 35
NoYes   Yersinia pestis Nepal516
NoYes   Yersinia pestis Antiqua
NoYes   Yersinia pestis Angola
NoYes   Yersinia pestis CO92
NoYes   Yersinia pestis KIM10+
NoYes   Yersinia enterocolitica subsp. palearctica 105.5R(r)
NoYes   Yersinia enterocolitica subsp. palearctica Y11
NoYes   Serratia plymuthica S13
NoYes   Serratia plymuthica 4Rx13
NoYes   Serratia marcescens WW4
NoYes   Serratia liquefaciens ATCC 27592
NoYes   Pectobacterium carotovorum subsp. carotovorum PCC21
NoYes   Shigella flexneri 2002017
NoYes   Salmonella bongori N268-08
NoYes   Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- str. RSK2980
NoYes   Klebsiella pneumoniae JM45
NoYes   Klebsiella pneumoniae subsp. pneumoniae HS11286
NoYes   Klebsiella pneumoniae subsp. pneumoniae MGH 78578
NoYes   Klebsiella pneumoniae subsp. rhinoscleromatis SB3432
NoYes   Enterobacter aerogenes EA1509E
NoYes   Escherichia coli E. coli PMV-1
NoYes   Escherichia coli JJ1886
NoYes   Escherichia coli NA114
NoYes   Escherichia coli str. 'clone D i2'
NoYes   Escherichia coli str. 'clone D i14'
NoYes   Escherichia coli UM146
NoYes   Escherichia coli IHE3034
NoYes   Escherichia coli O83:H1 str. NRG 857C
NoYes   Escherichia coli ABU 83972
NoYes   Escherichia coli LF82
NoYes   Escherichia coli ED1a
NoYes   Escherichia coli S88
NoYes   Escherichia coli SMS-3-5
NoYes   Escherichia coli SE15
NoYes   Escherichia coli APEC O1
NoYes   Escherichia coli UTI89
NoYes   Escherichia coli 536
NoYes   Escherichia coli O111:H- str. 11128
NoYes   Enterobacter cloacae subsp. cloacae ENHKU01
NoYes   Enterobacter cloacae subsp. cloacae NCTC 9394
NoYes   Enterobacter cloacae subsp. cloacae ATCC 13047
NoYes   Pseudomonas syringae pv. phaseolicola 1448A
NoYes   Pseudomonas syringae pv. syringae B728a
NoYes   Pseudomonas monteilii SB3101
NoYes   Pseudomonas monteilii SB3078
NoYes   Pseudomonas putida HB3267
NoYes   Pseudomonas putida S16
NoYes   Pseudomonas putida BIRD-1
NoYes   Pseudomonas putida ND6
NoYes   Pseudomonas putida KT2440
NoYes   Pseudomonas putida GB-1
NoYes   Pseudomonas poae RE*1-1-14
NoYes   Pseudomonas fluorescens F113
NoYes   Pseudomonas fluorescens A506
NoYes   Pseudomonas fluorescens R124
NoYes   Pseudomonas fluorescens Pf0-1
NoYes   Pseudomonas aeruginosa SCV20265
NoYes   Pseudomonas aeruginosa MTB-1
NoYes   Pseudomonas aeruginosa LES431
NoYes   Pseudomonas aeruginosa RP73
NoYes   Pseudomonas aeruginosa B136-33
NoYes   Pseudomonas aeruginosa PA1R
NoYes   Pseudomonas aeruginosa PA1
NoYes   Pseudomonas aeruginosa DK2
NoYes   Pseudomonas aeruginosa NCGM2.S1
NoYes   Pseudomonas aeruginosa M18
NoYes   Pseudomonas aeruginosa LESB58
NoYes   Pseudomonas aeruginosa PA7
NoYes   Pseudomonas aeruginosa PAO1
NoYes   Nicotiana benthamiana 0.4.4
NoYes   Vibrio campbellii ATCC BAA-1116
NoYes   Atta cephalotes fungus garden (ACEF) (meta-genome)
NoYes   Combined (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   Endophytic microbiome from Rice (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   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   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (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   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   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 ]