SUPERFAMILY 1.75 HMM library and genome assignments server

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V-region of surface antigen I/II (SA I/II, PAC) alignments

These alignments are sequences aligned to the 0039633 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
                                       |         |         |         |         |         |         |
d1jmma_                 ......QKDLADYPVKLKAYEDEQASIKAALAELEKHKNEDGNLTEPSAQNLVYDLEPNANLSLTTDGKFLKASAV
EG:BRADI2G56750.1:39-80 ledpek----------------------------------------------------------------------


                                80        90       100       110       120       130       140      
                                 |         |         |         |         |         |         |      
d1jmma_                 DDAFSKSTSKAKYVQKILQLDDLDITNLEQSNDVASSMELYGNFGDKAGWSTTVSNNSQVKWGSVLLERGQSATAT
EG:BRADI2G56750.1:39-80 ----------------------------------------------------------------------------


                         150       160       170       180       190       200       210       220  
                           |         |         |         |         |         |         |         |  
d1jmma_                 YTNLQNSYYNGKKISKIVYKYTVDPKSKFQGQKVWLGIFTDPTLGVFASAYTGQVEKNTSIFIKNEFTFYDEDGKP
EG:BRADI2G56750.1:39-80 ----------------------------------------------------------------------------


                             230       240       250       260       270       280       290       3
                               |         |         |         |         |         |         |        
d1jmma_                 INFDNALLSVASLNREHNSIEMAKDYSGKFVKISGSSIGEKNGMIYATDTLNFKQGEGGSRWTMYKNSQAGSGWDS
EG:BRADI2G56750.1:39-80 ---------------------------------------------------------------------WLHNWDE


                        00       310       320       330       340       350       360       370    
                         |         |         |         |         |         |         |         |    
d1jmma_                 SDAPNSWYGAGAIKMSGPNNHVTVGATSATNVMPVSDMPVVPGKDNTDGKKPNIWYSLNGKIRAVNVPKVTKEKPT
EG:BRADI2G56750.1:39-80 FHSPCYYYGVTCDKLSGEVIGVSLSNVS------------------------------------------------


                            
                            
d1jmma_                 PPV.
EG:BRADI2G56750.1:39-80 ---l


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: 0039633 (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   Cryptobacterium curtum DSM 15641
NoYes   Atopobium parvulum DSM 20469
NoYes   Enterococcus sp. 7L76
NoYes   Enterococcus faecalis 62
NoYes   Lactobacillus kefiranofaciens ZW3
NoYes   Lactobacillus salivarius CECT 5713
NoYes   Lactobacillus amylovorus GRL1118
NoYes   Lactobacillus brevis ATCC 367
NoYes   Lactobacillus acidophilus 30SC
NoYes   Lactococcus lactis subsp. cremoris MG1363
NoYes   Streptococcus intermedius JTH08
NoYes   Streptococcus gallolyticus UCN34
NoYes   Streptococcus pasteurianus ATCC 43144
NoYes   Streptococcus macedonicus ACA-DC 198
NoYes   Streptococcus parasanguinis ATCC 15912
NoYes   Streptococcus mutans NN2025
NoYes   Streptococcus sanguinis SK36
NoYes   Streptococcus salivarius 57.I
NoYes   Streptococcus oralis Uo5
NoYes   Streptococcus gordonii str. Challis substr. CH1
NoYes   Enterococcus faecalis str. Symbioflor 1
NoYes   Enterococcus faecalis V583
NoYes   Lactobacillus salivarius UCC118
NoYes   Lactobacillus amylovorus GRL 1112
NoYes   Lactobacillus reuteri TD1
NoYes   Lactobacillus plantarum 16
NoYes   Lactobacillus brevis KB290
NoYes   Lactobacillus acidophilus La-14
NoYes   Lactobacillus acidophilus NCFM
NoYes   Lactococcus lactis subsp. cremoris NZ9000
NoYes   Streptococcus constellatus subsp. pharyngis C1050
NoYes   Streptococcus intermedius B196
NoYes   Streptococcus intermedius C270
NoYes   Streptococcus anginosus C238
NoYes   Streptococcus anginosus C1051
NoYes   Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069
NoYes   Streptococcus gallolyticus subsp. gallolyticus ATCC 43143
NoYes   Streptococcus equi subsp. zooepidemicus ATCC 35246
NoYes   Streptococcus equi subsp. zooepidemicus
NoYes   Streptococcus dysgalactiae subsp. equisimilis ATCC 12394
NoYes   Streptococcus oligofermentans AS 1.3089
NoYes   Streptococcus parasanguinis FW213
NoYes   Streptococcus agalactiae 09mas018883
NoYes   Streptococcus agalactiae NEM316
NoYes   Streptococcus agalactiae 2603V/R
NoYes   Streptococcus mutans GS-5
NoYes   Streptococcus mutans LJ23
NoYes   Streptococcus mutans UA159
NoYes   Streptococcus thermophilus JIM 8232
NoYes   Streptococcus suis T15
NoYes   Streptococcus suis SC070731
NoYes   Streptococcus suis D9
NoYes   Streptococcus suis SS12
NoYes   Streptococcus suis D12
NoYes   Streptococcus suis JS14
NoYes   Streptococcus suis BM407
NoYes   Streptococcus suis SC84
NoYes   Streptococcus suis 98HAH33
NoYes   Streptococcus suis 05ZYH33
NoYes   Streptococcus salivarius CCHSS3
NoYes   Streptococcus salivarius JIM8777
NoYes   Fungus garden combined (combined) (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
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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