SUPERFAMILY 1.75 HMM library and genome assignments server

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IpaD-like alignments

These alignments are sequences aligned to the 0053138 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     
                        |         |         |         |         |         |         |         |     
d2izpa1 .......MTDDDLRAAGVDRRVPEQKLGAAIDEFASLRLPDRIDGRFVDGRRANLTVFDDARVAVRGHARAQRNLLERLETELLGGTLDTAG
d2j0oa1 hpvssltMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRHEYPINKDARELLHSAPKEAE------LD
d2ym9c_ ......t-------------------------------------------------------------------------------------


           90       100        110       120       130       140         150       160            17
            |         |          |         |         |         |           |         |              
d2izpa1 DEGGIQPDPILQGLVDVIG.QGKSDIDAYATIVEGLTKYFQSVADVMSKLQDYISAK..DDKNMKIDGGKIKALIQQVIDHL.....PTMQL
d2j0oa1 GDQMISHRELWAKIANSINdINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGgnDGNSVKLQVNSLKKALEELKEKY.....KDKPL
d2ym9c_ ----ISDAEIWDMVSQNISaIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGk.DGNTVKLDVTSLKNDLNSLVNKYnqinsNTVLF


        0                       180           190       200       210              220       230    
        |                         |             |         |         |                |         |    
d2izpa1 P......KG..........ADIARWRKELGDAVSI....SDSGVVTINPDKLIKMRDSLPPDG.......TVWDTARYQAWNTAFSGQKDNI
d2j0oa1 YpanntvSQ..........EQANKWLTELGGTIGKvsqkNGGYVVSINMTPIDNMLKSLDNLGgnge...VVLDNAKYQAWNAGFSAEDETM
d2ym9c_ P......AQsgsgvkvateAEARQWLSELNLPNSClksyGSGYVVTVDLTPLQKMVQDIDGLGapgkdskLEMDNAKYQAWQSGFKAQEENM


           240       250       260                 
             |         |         |                 
d2izpa1 QNDVQTLVEKYSHQNSNFDNLVKVLSGAISTLT..........
d2j0oa1 KNNLQTLVQKYSNANSIFDNLVKVLSSTISSC-..........
d2ym9c_ KTTLQTLTQKYSNANSLYDNLVKVLSSTISSS-letaksflqg


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: 0053138 (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   Drosophila suzukii
NoYes   Pandoraea sp. RB-44
NoYes   Chromobacterium violaceum ATCC 12472
NoYes   Burkholderia thailandensis E264
NoYes   Burkholderia pseudomallei 1106a
NoYes   Xanthomonas albilineans GPE PC73
NoYes   Providencia stuartii MRSN 2154
NoYes   Proteus mirabilis HI4320
NoYes   Yersinia enterocolitica subsp. enterocolitica 8081
NoYes   Sodalis glossinidius str. 'morsitans'
NoYes   Erwinia tasmaniensis Et1/99
NoYes   Erwinia sp. Ejp617
NoYes   Erwinia pyrifoliae Ep1/96
NoYes   Erwinia amylovora ATCC 49946
NoYes   Shigella sonnei Ss046
NoYes   Shigella dysenteriae Sd197
NoYes   Shigella boydii CDC 3083-94
NoYes   Salmonella bongori NCTC 12419
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
NoYes   Pseudomonas sp. UW4
NoYes   Clostridium saccharoperbutylacetonicum N1-4(HMT)
NoYes   Pandoraea pnomenusa 3kgm
NoYes   Burkholderia thailandensis MSMB121
NoYes   Burkholderia pseudomallei MSHR305
NoYes   Burkholderia pseudomallei NCTC 13179
NoYes   Burkholderia pseudomallei BPC006
NoYes   Burkholderia pseudomallei 1026b
NoYes   Burkholderia pseudomallei 668
NoYes   Burkholderia pseudomallei 1710b
NoYes   Burkholderia pseudomallei K96243
NoYes   Burkholderia mallei NCTC 10229
NoYes   Burkholderia mallei NCTC 10247
NoYes   Burkholderia mallei ATCC 23344
NoYes   Proteus mirabilis BB2000
NoYes   Morganella morganii subsp. morganii KT
NoYes   Erwinia pyrifoliae DSM 12163
NoYes   Erwinia amylovora CFBP1430
NoYes   Shigella sonnei 53G
NoYes   Shigella flexneri 2002017
NoYes   Shigella flexneri 2a str. 301
NoYes   Shigella dysenteriae 1617
NoYes   Salmonella bongori N268-08
NoYes   Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- str. RSK2980
NoYes   Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. 08-1736
NoYes   Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992
NoYes   Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633
NoYes   Salmonella enterica subsp. enterica Serovar Cubana str. CFSAN002050
NoYes   Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
NoYes   Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
NoYes   Salmonella enterica subsp. enterica serovar Newport str. USMARC-S3124.1
NoYes   Salmonella enterica subsp. enterica serovar Newport str. SL254
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. U288
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. 798
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
NoYes   Salmonella enterica The genome of subsp. enterica serovar Typhimurium str. DT2
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium Definitive Type 104
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   Salmonella enterica serovar Bovismorbificans genomics
NoYes   Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000189
NoYes   Salmonella enterica subsp. enterica serovar Agona str. 24249
NoYes   Salmonella enterica subsp. enterica serovar Agona str. SL483
NoYes   Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
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   Salmonella enterica subsp. enterica serovar Heidelberg str. SL476
NoYes   Salmonella enterica subsp. enterica serovar Pullorum str. S06004
NoYes   Salmonella enterica subsp. enterica serovar Gallinarum/pullorum str. CDC1983-67
NoYes   Salmonella enterica subsp. enterica serovar Gallinarum/pullorum str. RKS5078
NoYes   Salmonella enterica subsp. enterica serovar Thompson str. RM6836
NoYes   Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
NoYes   Escherichia coli O7:K1 str. CE10
NoYes   Escherichia coli 042
NoYes   Escherichia coli IAI39
NoYes   Escherichia coli UMN026
NoYes   Escherichia coli SMS-3-5
NoYes   Pseudomonas fluorescens F113
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   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   simHC - Simulated High Complexity Metagenome (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)


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