SUPERFAMILY 1.75 HMM library and genome assignments server

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Colicin alignments

These alignments are sequences aligned to the 0034942 model.

Sophisticated options are available for refining alignments:

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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   
                                                                  |         |         |         |   
d1a87a_                                            .....s-AKVGEITITPDNSKPGRYISSNPEYSLLAKLIDAESIKGTEV
jgi|Picme1|105890|estExt_fgenesh1_pg.C_5_t20079  .....a-------------------------------------------
jgi|Naegr1|63187|fgeneshNG_pg.scaffold_6000031   stekqv-------------------------------------------
GS_02720                                         .....a-------------------------------------------
GS_02720                                         ......-------------------------------------------
GS_02720                                         ..ykel-------------DERVKLLSPRANDPLQS--RPFFEATRLRA
GS_03675                                         .dsgkp----------------GRYLPTNKDKLIKGLIQSIDDH--SGT

                                                        50        60        70        80            
                                                         |         |         |         |            
d1a87a_                                            YTFHTRKGQYVKVTVPDSNIDKMRVDYVNWKGPKYNNKLVK....RFVS
jgi|Picme1|105890|estExt_fgenesh1_pg.C_5_t20079  -----------------------------------------....----
jgi|Naegr1|63187|fgeneshNG_pg.scaffold_6000031   -----------------------------------------....----
GS_02720                                         -------------------------DITQIQKAISQVSNNRnagiARVH
GS_02720                                         ------EEKQKQVTASETRLNQISSEINGIQEAISQANNKRstavSRIH
GS_02720                                         RAGDEMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRstavSRIH
GS_03675                                         YTIHYTGGAVATVTVPNGDVNKMNVHYNIGSGPS-------....----

                                                   90       100       110       120       130       
                                                    |         |         |         |         |       
d1a87a_                                            QFLLFRKEEKEKNEKEALLKASELVSGMGDKLGEYLGVKYKNVAKEVAN
jgi|Picme1|105890|estExt_fgenesh1_pg.C_5_t20079  ----------------------------------------QQLSNDLAT
jgi|Naegr1|63187|fgeneshNG_pg.scaffold_6000031   --------------------------------------------EKLQT
GS_02720                                         DAEDNLKTAQTNLLNSQIKDAVN--------------------------
GS_03675                                         ------SEFKAENEANAVNDAISKVNDFYKELASKYGDK----------

                                                   140       150       160       170       180      
                                                     |         |         |         |         |      
d1a87a_                                            DIKNFHGRNIRSYNEAMASLNKVLANPKMKVNKSDKDAIVNAWKQVNAK
jgi|Naegr1|63187|fgeneshNG_pg.scaffold_6000031   QLTNLAGTQVEEADQAINLMGKIRDDLNVKLNENTENSLFNMMKVL---
GS_02720                                         KSK---GKKIGNVNEALAAFEKYKDVLNKKFSKADRDAIFNALASVKYD
GS_02720                                         KSK---GKKISNVNEALAAFEKYKDVLNKKFSKADRDAIFNALEAVKYE
GS_02720                                         -------------------------------------------------
GS_03675                                         -------------------------------------------------

                                                    190       200       210       220       230     
                                                      |         |         |         |         |     
d1a87a_                                            DMANKIGNLGKAFKVADLAIKVEKIREKSIEGYNTGNWGPLLLEVESWI
jgi|Picme1|105890|estExt_fgenesh1_pg.C_5_t20079  DTFNNIQRF----------------------------------------
jgi|Naegr1|63187|fgeneshNG_pg.scaffold_6000031   --GENNRQLIDDYHIVSEVLLAHNNIKKTIEKLET--------------
GS_02720                                         DWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDT--------------
GS_02720                                         -------------------------------------------------
GS_03675                                         -------------------------------------------------

                                                     240       250       260       270        280   
                                                       |         |         |         |          |   
d1a87a_                                            IGGVVAGVAISLFGAVLSFLPISGLAVTALGVIGI.MTISYLSSFIDAN
jgi|Picme1|105890|estExt_fgenesh1_pg.C_5_t20079  -----------------------------------.-------------
jgi|Naegr1|63187|fgeneshNG_pg.scaffold_6000031   -----------------------------------.-------------
GS_02720                                         VDAGVSYVVVLLFSVLAG---------TTLGIWGIaIVTGILCAFIDKN
GS_02720                                         -----------------------------------.-------------
GS_02720                                         -----------------------------------.-------------
GS_03675                                         -----------------------------------.-------------

d1a87a_                                            RVSNINNIISSV--ir
jgi|Picme1|105890|estExt_fgenesh1_pg.C_5_t20079  --------------qs
jgi|Naegr1|63187|fgeneshNG_pg.scaffold_6000031   --------------..
GS_02720                                         KLNTINEVLGI---..
GS_02720                                         --------------e.
GS_02720                                         --------------a.
GS_03675                                         --------------r.

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: 0034942 (list models)
Initial SAMT99 seed:

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   Pichia membranifaciensv1.0
NoYes   Naegleria gruberi
NoYes   Geobacillus thermoglucosidasius C56-YS93
NoYes   Photorhabdus asymbiotica
NoYes   Proteus mirabilis HI4320
NoYes   Erwinia tasmaniensis Et1/99
NoYes   Erwinia sp. Ejp617
NoYes   Erwinia pyrifoliae Ep1/96
NoYes   Erwinia amylovora ATCC 49946
NoYes   Shigella sonnei Ss046
NoYes   Enterobacter sp. 638
NoYes   Citrobacter rodentium ICC168
NoYes   Pseudomonas fluorescens SBW25
NoYes   Pseudomonas aeruginosa UCBPP-PA14
NoYes   Ascaris suum Victoria/Ghent - Pig roundworm
NoYes   Gloeobacter kilaueensis Gloeobacter sp. JS
NoYes   Geobacillus sp. Y4.1MC1
NoYes   Mannheimia haemolytica USMARC_2286
NoYes   Mannheimia haemolytica M42548
NoYes   Mannheimia haemolytica D174
NoYes   Mannheimia haemolytica D171
NoYes   Mannheimia haemolytica D153
NoYes   Mannheimia haemolytica USDA-ARS-USMARC-183
NoYes   Mannheimia haemolytica USDA-ARS-USMARC-185
NoYes   Morganella morganii subsp. morganii KT
NoYes   Rahnella aquatilis HX2
NoYes   Serratia plymuthica S13
NoYes   Serratia plymuthica 4Rx13
NoYes   Serratia marcescens WW4
NoYes   Erwinia pyrifoliae DSM 12163
NoYes   Erwinia amylovora CFBP1430
NoYes   Shigella sonnei 53G
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
NoYes   Salmonella enterica subsp. enterica Serovar Heidelberg str. CFSAN002069
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. 41578
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. SL476
NoYes   Escherichia coli UMNK88
NoYes   Escherichia coli S88
NoYes   Escherichia coli SMS-3-5
NoYes   Escherichia coli SE11
NoYes   Escherichia coli O55:H7 str. RM12579
NoYes   Escherichia coli O55:H7 str. CB9615
NoYes   Pseudomonas fluorescens A506
NoYes   Pseudomonas aeruginosa PAO1
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   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   NCBI 2017_08 genome
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   STRING v9.0.5 (STRING)
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   The Salmonella enterica Pan-genome (meta-genome)
NoYes   ALL (only advised for small superfamilies)

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