SUPERFAMILY 1.75 HMM library and genome assignments server

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Colicin Ia, N-terminal domain alignments

These alignments are sequences aligned to the 0053400 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     
                                      |         |         |         |               |         |     
d1ciia2                      EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSD......IEKRDKEITAYKNTLSAQ
ENSBTAP00000047378:1075-1264 ----------------------------------GRDWCPVSPSREDllsrieLEKLSEENTLLKNELGRI


                                70         80        90       100       110       120       130     
                                 |          |         |         |         |         |         |     
d1ciia2                      QKENE.NKRTEAGKRLSAAIAAREKDENTLKTLRAGNADAADITRQEFRLLQAELREYGFRTEIAGYDALR
ENSBTAP00000047378:1075-1264 QQELEaSERTEAAQRKDIEVLKRDKE---------KACSEMEELRTQSQKCRDELSQLNHRVLQLGEEAST


                               140       150       160       170       180       190       200      
                                 |         |         |         |         |         |         |      
d1ciia2                      LHTESRMLFADADSLRISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELEKNGGAA
ENSBTAP00000047378:1075-1264 HQTQSEK-------SPVTVQLLTHRLEEAELREELQGNQIQKLELELDRVTR-------------------


                              210       220       230       240       250       260       270       
                                |         |         |         |         |         |         |       
d1ciia2                      LAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALTRAEQQLTQQKNTPDGKTIVSPEKFPGR
ENSBTAP00000047378:1075-1264 ----DRQSLRL--AQSQLREALEESRNQLYGATQRLQLAQSQHTQRVQQLR--------------------


                             280       290       300       310       320       330       340       3
                               |         |         |         |         |         |         |        
d1ciia2                      SSTNDSIVVSGDPRFAGTIKITTSAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEV
ENSBTAP00000047378:1075-1264 -----------------------------------------------------------------------


                             50       360       370       380       390       400       410       42
                              |         |         |         |         |         |         |         
d1ciia2                      AEWDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEKENIRNQLSGINQKIAEEKR
ENSBTAP00000047378:1075-1264 -----------------------------------------------------------------------


                             0         
                             |         
d1ciia2                      KQDELKATK.
ENSBTAP00000047378:1075-1264 ---------e


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: 0053400 (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   Xenorhabdus nematophila ATCC 19061
NoYes   Serratia plymuthica S13
NoYes   Serratia liquefaciens ATCC 27592
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 SE11
NoYes   Escherichia coli O55:H7 str. RM12579
NoYes   Escherichia coli O55:H7 str. CB9615
NoYes   NCBI 2017_08 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   The Salmonella enterica Pan-genome (meta-genome)
NoYes   ALL (only advised for small superfamilies)


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