IndexType of sequence: Sequences are determined by aminoacid sequencing or nucleotide sequencing. Thus, you may search Aminoacid and nucleotide sequences of antibodies.
Note:By using the genetic code you can deduce the aminoacid sequence from the nucleotide sequence. The reverse is not true. Hence, you will find more aminoacid sequences than nucleotide sequences.
Type of chain: Antibodies are composed of two chains: Heavy (H) and Light (L; kappa or lambda). You may search for one of these chains: VH,Vkappa and Vlambda.
Species: This item allows searches by species, for example: human, mouse, pig, frog, etc.
Here you will find the list of all the species that have been used to obtain antibody sequences. In those cases where the species annotation is unambiguous, a link to the Taxonomy Browser of the NCBI has been made.
Note: In some cases you will find redudancies like "frog" and "Xenopus laevis", or even misspellings like "mexcican axolotl" instead of "mexican axolotl". We have inherited these redundancies and misspellings from the original source in order to avoid divergencies with respect to the original source.
Gross Specificity: This item allows searches by the following group of specificities:
Anti-Carbohydrate
Anti-Hapten
Anti-Lipid
Anti-Lipopolysaccharide
Anti-Nucleic Acid
Anti-Peptide
Anti-Protein
Also we have included:
Crossreactive: sequences with more than one fine specificity.
Others: sequences that can not be classified in any one of the above groups.
Undefined: sequences with no specificity annotated.
Fine specificity: The specificity as it has been annotated in the Kabat database.
Here you will find the list of all the fine specificities and their classification in gross specificities. Please send mail for any comments about this classification to almagro@ibt.unam.mx.
Note: As in the species, you will find redudancies and misspellings. For example, there are four different definitions for the specificity "ANTI-(4-HYDROXY-3-NITROPHENYL) ACETYL":
1. ANTI-(4-HYDROXY-3-NITRO-PHENYL) ACETYL ("-" before "PHENYL"),
2. ANTI-(4-HYDROXY-3-NITROPHENY)ACETYL (no "L" after "PHENY"),
3. ANTI-(4-HYDROXY-3-NITROPHENYL) ACETYL (space after "PHENYL)") and
4. ANTI-(4-HYDROXY-3-NITROPHENYL)ACETYL (no space after "PHENYL)").
When the Kabat database was queried in July, 2000 with these definitions, sets of different sequences were obtained.
Definition 1 gave 10 sequences,
Definition 2 gave 75 sequences,
Definition 3 gave 15 sequences and
Definition 4 gave 248 sequences.
Thus, to obtain all of the sequences for the specificity "ANTI-(4-HYDROXY-3-NITROPHENYL) ACETYL", it would be necessary to search the Kabat database using all of the definitions. Again, we have inherited these redundancies and misspellings in order to avoid divergencies with respect to the original source.
Example: Go to the interface and define:
Type of sequence: Aminoacid;
Type of chain: VH;
Species: frog.
Then, Submit.
In July, 2000 we found 112 entries. From the entry 004392 up to the end, the sequence were incomplete.
But, when we defined
Beginning position: 24,
End position: 34 and
% Completeness: 100.
Then, Submit.
We found 44 sequences; those that were complete in the segment within positions 24-34, which is part the CDR-L1 in the Kabat definition (see below).
Note: If you are working with aminoacids then, the numbering schedule you should follow is the Kabat numbering. At nucleotide level, the numbering schedule is continuous.
VH
CDR1 CDR2 CDR3
--------------------- --------------------------------------------------------- ---------------------------------------------------------
Kabat 1 10 20 30 40 50 60 70 80 90 100 110
. . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! a b . . . . ! . . . . ! . . . . ! . . a b c . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . a b c . . ! . . . . ! . . . . ! . . . . ! a b c d e f g h i j k . . . . ! . . . . ! . . .
Nucleotide 1 28 58 88 124 154 193 223 253 292 322 385
...........................!.............................!.............................!...................................!.............................!......................................!.............................!.............................!......................................!.............................!..............................................................!...........
VKappa
CDR1 CDR2 CDR3
--------------------------------------------------- --------------------- ---------------------------------------------
Kabat 1 10 20 30 40 50 60 70 80 90 100
. . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . a b c d e f . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! a b c d e f . . . . ! . . . . ! . a . . .
Nucleotide 1 28 58 106 136 166 196 226 256 286 334
...........................!.............................!...............................................!.............................!.............................!.............................!.............................!.............................!.............................!...............................................!................................
VLambda
CDR1 CDR2 CDR3
--------------------------------------------------- --------------------- ---------------------------------------------
Kabat 1 10 20 30 40 50 60 70 80 90 100
. . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . a b c d e f . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! . . . . ! a b c d e f . . . . ! . . . . ! . a . . .
Nucleotide 1 28 58 106 136 166 196 226 256 286 334
...........................!.............................!...............................................!.............................!.............................!.............................!.............................!.............................!.............................!...............................................!................................
Allows searches of complete antibodies (VH+VL).
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