IMGT/DomainGapAlign Documentation

IMGT®, the international ImMunoGeneTics information system®

Introduction

IMGT/DomainGapAlign is part of IMGT®, the international ImMunoGeneTics information system®, the high-quality integrated information system specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MH) of human and other vertebrates species, immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI), created in 1989 by Marie-Paule Lefranc (Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Université Montpellier II and CNRS) and on the Web since July 1995.

IMGT/DomainGapAlign is a tool which analyses amino acid sequences per domain.

IMGT/DomainGapAlign Query page

What IMGT/DomainGapAlign allows?

• To create gaps in your amino acid sequence, according to the IMGT unique numbering, for:
  • the V-REGION or C-DOMAIN of the IG or TR,
  • the V-LIKE-DOMAIN and C-LIKE-DOMAIN of the other IgSF,
  • the G-DOMAIN and C-LIKE-DOMAIN of the MH,
  • the G-LIKE-DOMAIN and C-LIKE-DOMAIN of the other MhSF.
• To align your own amino acid sequence with the IMGT domain directory and to identify:
  • the closest germline IMGT genes and alleles for the V-REGION and J-REGION of the IG or TR,
  • the closest IMGT genes and alleles for the C-DOMAIN of the IG or TR,
  • the closest IMGT gene and allele for the C-LIKE-DOMAIN of the other IgSF,
  • the closest IMGT gene and allele for the G-DOMAIN and C-LIKE-DOMAIN of the MH,
  • the closest IMGT gene and allele for the G-LIKE-DOMAIN and C-LIKE-DOMAIN of the other MhSF.
• To delimit the strands and loops of:
  • the V domains (V-DOMAIN and V-LIKE-DOMAIN),
  • the C domains (C-DOMAIN and C-LIKE-DOMAIN),
  • the G domains (G-DOMAIN and G-LIKE-DOMAIN) platforms,
  • and to delimit the helix of the G domains (G-DOMAIN and G-LIKE-DOMAIN).
• To draw the IMGT Collier de Perles of your V-REGION (V-DOMAIN, see below) or C-DOMAIN by clicking on the name (in green) of your sequence in the alignment.

IMGT/DomainGapAlign Query

Paste or upload your file containing domain sequences in FASTA format. Several sequences can be analysed simultaneously and users can choose how many alignments to display for each sequence. Here are examples of sequences in the required format (variable domain):



>AE000658|TRAV4*01|Homo sapiens|F|V-REGION
LAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEVA
SLFIPADRKSSTLSLPRVSLSDTAVYYCLVGD

Or

>12e8_P|2E8|Mus musculus||VH-CH1
EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEY
VPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSA
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD


Select 'V' for sequences of the variable domains of heavy and light chains. Select 'C' for sequences of the constant domains of heavy and light chains. To delimit the domains (CH1, CH2, CH3) of the heavy chains, an easy way is to check with IMGT Alignments of alleles (in IMGT Repertoire).




In IMGT, the 'domain type' concept has three main concepts: the V type (V for variable), the C type (C for constant) and the G type (G for groove).
'V type' identifies the domain type of domains described as V-DOMAIN and V-LIKE-DOMAIN.
'C type' identifies the domain type of domains described as C-DOMAIN and C-LIKE-DOMAIN.
'G type' identifies the domain type of domains described as G-DOMAIN and G-LIKE-DOMAIN.

Select the species in the drop-down list.

Select the minimum or maximum Smith-Waterman score for the alignments to display (For example, choosing a "Smith-Waterman score above 200" will provide and display alignments whose Smith-Waterman score is superior to 200).

Select the number of alignments to display (Displayed alignments) and tick off the checkbox if you want to display IMGT Colliers de Perles.



V: V-ALPHA, V-BETA, V-DELTA, V-GAMMA, V-KAPPA, V-LAMBDA, V-LIKE.

G: G-ALPHA, G-ALPHA1, G-ALPHA1-LIKE, G-ALPHA2, G-ALPHA2-LIKE, G-BETA.

C: C-ALPHA, C-BETA-1, C-BETA-2, C-DELTA, C-GAMMA-1, C-GAMMA-2, C-GAMMA-3, C-GAMMA-4, C-GAMMA-5, C-GAMMA-6, C-KAPPA, C-LAMBDA, C-LIKE.

IMGT/DomainGapAlign and IMGT/Collier-de-Perles results for V-domain

IMGT/DomainGapAlign gene and allele identification

IMGT/DomainGapAlign identifies the closest germline V-REGION (for 'V') and the closest C-DOMAIN (for 'C').The IMGT gene and allele name of the closest sequence(s) from the IMGT reference directory is (are) provided with a percentage of identity.


IMGT nomenclature is based on the CLASSIFICATION axiom and concepts of IMGT-ONTOLOGY [1]. IMGT gene and allele names were approved by the HUGO Nomenclature Committee (HGNC) and by WHO-IUIS Nomenclature Committee [2]. They are used by Entrez Gene (NCBI), GDB, GeneCards, Ensembl (EBI)...



IMGT/DomainGapAlign Alignment display

IMGT/DomainGapAlign displays your amino acid sequences with IMGT gaps and, for 'V', with delimitations of the FR-IMGT and CDR-IMGT, according to the IMGT unique numbering for V-REGION and V-DOMAIN [3], and for 'C', with delimitation of the strand and loops, according to the IMGT unique numbering for C-DOMAIN [4]. Amino acids in bold represent differences between the closest germline V-REGION (for 'V') or C-DOMAIN (for 'C) and the sequences submitted by users.



IMGT/DomainGapAlign identification and download

IMGT/DomainGapAlign displays your amino acid sequences with IMGT color menu for domains and regions, according to the IMGT Scientific chart. You can display or download your amino acid sequences with or without gaps.



IMGT/DomainGapAlign results summary

A summary of the results is provided as a table and contains following informations:

Sequence name

REGION (V-REGION) identity percentage

CDR-IMGT lengths

Number of different amino acids in CDR1- and CDR2-IMGT

FR-IMGT lengths

Number of different amino acids in FR-IMGT

Total number of amino acids changes in domain


The AA changes are shown in strands and loops and in FR- and CDR-IMGT.



IMGT/DomainGapAlign and IMGT Collier de Perles

IMGT Collier de Perles, on one and two layers, with amino acids changes are generated (complete Collier de Perles, comprising CDR3-IMGT and FR4-IMGT).



IMGT Colliers de Perles on one layer




IMGT Colliers de Perles on two layers




IMGT/Collier-de-Perles tool

The IMGT/Collier-de-Perles tool allows you to choose the CDR-IMGT color type, the Background color, the Amino acid insertions, the CDR3-IMGT lenght and the domain title:

1) CDR-IMGT color type

- For (IGK,IGL,TRA,TRG), CDR-IMGT regions are colored as follows: CDR1-IMGT (blue), CDR2-IMGT (green) and CDR3-IMGT (greenblue).

- For (RPI,IGH,TRB,TRD), CDR-IMGT regions are colored as follows: CDR1-IMGT (red), CDR2-IMGT (orange) and CDR3-IMGT (purple).

2) Background color

- 50% Hydrophobic positions: These positions shown in blue correspond to hydrophobic amino acids (hydropathy index with positive value) and Tryptophan (W) found at a given position in more than 50% of analysed IG and TR sequences.

- 80% hydropathy, volume and physicochemical classes: These positions correspond to positions defined according to the IMGT classes of the 20 common amino acids for the 'hydropathy', 'volume', 'chemical characteristics' properties

3) Domain sequence

- In the Domain sequence window, seize your gaped sequence with the CDR3 and the J amino acids (at least 9 or 10 amino acids beyond the F or W, of the motif F/WGXG respectively, to get the complete J. See Alignments of Alleles for the IGHJ, IGKJ and IGLJ in IMGT Repertoire.

- add gaps in the CDR3-IMGT. If the CDR3-IMGT is <13 amino acid see IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN.

4) In "Your domain title" box (optional), type a clone name (that you would like to be displayed in the figure).

For normal IG and TR domains, you do not need to use the "Amino acid insertions" boxes. These boxes allow to deal with IgSF V-LIKE-DOMAIN and C-LIKE-DOMAIN which have amino acid insertions compared to the IG and TR domains.

IMGT/DomainGapAlign and IMGT/Collier-de-Perles results for C-domain

>SEQ_C_DOM
TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

IMGT/DomainGapAlign gene and allele identification




IMGT/DomainGapAlign Alignment display

IMGT/DomainGapAlign identification and download

IMGT/DomainGapAlign results summary

A summary of the results is provided as a table and contains following informations:

Sequence name

REGION (C-REGION) identity percentage

Total number of amino acids changes in domain

Amino acids changes by Strands, Turns and loops



IMGT/DomainGapAlign and IMGT Collier de Perles

IMGT Collier de Perles, on one and two layers, with amino acids changes are generated (complete Collier de Perles).



IMGT Colliers de Perles on one layer




IMGT Colliers de Perles on two layers

IMGT/DomainGapAlign and IMGT/Collier-de-Perles results for G-domain

>pMH75
FRPWFLEYCKSECHFYNTTQRVRLLVRYFYNLELNLRFDSDVGEFRAVTELGQPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRR

IMGT/DomainGapAlign gene and allele identification




IMGT/DomainGapAlign Alignment display

IMGT/DomainGapAlign identification and download

4.4 IMGT/DomainGapAlign results summary

A summary of the results is provided as a table and contains following informations:

Sequence name

REGION (G-REGION) identity percentage

Total number of amino acids changes in domain

Amino acids changes by Strands, Turns and loops



IMGT/DomainGapAlign and IMGT Collier de Perles

IMGT Collier de Perles, on one and two layers, with amino acids changes are generated.



IMGT Colliers de Perles on one layer




IMGT Colliers de Perles on one layer (with AA changes)

IMGT/Collier-de-Perles tool for G-DOMAIN

First select Domain type: Groove(G)

1. IMGT/DomainGapAlign steps

Before using IMGT/Colliers-de-Perles for G-domain, align your sequences against the human ones using IMGT/DomainGapAlign to be sure to localize the gaps at the right positions (including the gaps at the beginning of the sequences).

Model for MH class I gaps

>HLA-A*0102 G-ALPHA1
..........GSHSMRY.FSTSVSRPGSGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRA.......PWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSED..

>HLA-A*0102 G-ALPHA2
..........GSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNED..LRSWTAAD.......MAAQITKRKWEAV.HAAEQRRVYLEGRCVDGLRRYLENGKETLQRT

Model for MH class II gaps

>HLA-DRA*0101 G-ALPHA
........IKEEHVIIQ.AEFYLNP....DQSGEFMFDFDGDEIFHVDMA..KKETVWRL.......EEFGR....FASFEAQGALANIAVDKANLEIMTKRSNYTPITN...

>HLA-DRB1*0101 G-BETA
......GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSD..VGEYRAVT.......ELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRR........

Note that IMGT/DomainGapAlign provide more sequences, but be aware that in these alignments the numbering includes gaps for MH1, MH2 and RPI-MH1Like like comparison.

2. IMGT/Collier-de-Perles steps

In Make Your Own IMGT Collier de Perles page (IMGT/Collier-de-Perles), select Domain type: Groove(G).
For MH1, click 'Link G-DOMAINs'.
Paste in the 'Domain 1 sequence' window the sequence of G-ALPHA1 (for MH1) or G-ALPHA (for MH2).
Paste in the 'Domain 2 sequence' window the sequence of G-ALPHA2 (for MH1) or G-BETA (for MH2).










The IMGT "Colliers de Perles" obtained are respectively as follow:

IMGT/DomainGapAlign and IMGT/Collier-de-Perles results for S-domain

>SEQ_S_DOM
PAVESRLVGGSSICEGTVEVRQGAQWAALCDSSSARSSLRWEEVCREQQCGSVNSYRVLDAGDPTSRGLFCPHQKLSQCHELWERNSYCKKVFVTCQD

IMGT/DomainGapAlign gene and allele identification




IMGT/DomainGapAlign Alignment display

IMGT/DomainGapAlign identification and download

IMGT/DomainGapAlign results summary

A summary of the results is provided as a table and contains following informations:

Sequence name

REGION (S-REGION) identity percentage

Total number of amino acids changes in domain

Amino acids changes by Strands, Turns and loops



IMGT/DomainGapAlign and IMGT Collier de Perles

IMGT Collier de Perles, on one and two layers, with amino acids changes are generated (complete Collier de Perles).



IMGT Colliers de Perles on one layer




IMGT Colliers de Perles on two layers

References

Version

4.10.3 (2021-12-06)

• Solve problem of V-DOMAIN with CDR3-IMGT more than 31 AA length: the 'CDR_lengths' value is more consistent now.

4.10.2 (2021-01-26)

• Take into account the 'Smith-Waterman score above' parameter

4.10.1 (2021-01-22)

• Minor maintenance

4.10.0 (2019-05-06)

• Revised interface (HTML/CSS/Javascript)
• Improve alignment rendering
• Reduce inconsistency with the corresponding 'Results summary'
• Improved link to IMGT/Collier-de-Perles when there are insertions

4.9.2 (2016-09-26)

• Handle A and F domains

4.9.1 (2013-12-19)

• Update linking to IMGT/GENE-DB
• Javascript fixes (species selection)
• Internal changes

4.9.0 (2013-04-06)

• Handle both mixed-case (upper/lower) input sequence
• For V-DOMAIN, show V and J reference allele alignment separetely
• More internal changes

Created:

10/12/06

IMGT/DomainGapAlign development:

IMGT/DomainGapAlign was implemented by Quentin Kaas (2005) and has been developed since 2006 by François Ehrenmann, and since 2011 by Patrice Duroux

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