SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins

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Version 1.0

This is the first release of the program. If you observe a bug or suspicious behavior, or get a nonsense result, please send us a note, containing the query alignment and the parameters you've used. Thank you.

Pfam plain text alignment format


The Pfam plain text format is one of the formats, in which aligned sequences from the Pfam database can be retrieved. For the correct work of SDPpred gaps are required to be indicated by dashes and all letters indicating amino acids are required to be in upper case. In this format each line begins with sequence name, followed by the sequence. Thus the alignment looks like this:

GLA_LACLC/1-284       --MDVTW--TVKYITEFVGTALLIIMGNGAVANVELKGTKA-
GLPF_HAEIN/1-249      --MDKSL--KANCIGEFLGTALLIFFGVG-CVAA-LKVAGA-
GLPF_ECOLI/1-251      MSQTSTL--KGQCIAEFLGTGLLIFFGVG-CVAA-LKVAGA-
PDUF_SALTY/1-249      --MNDSL--KAQCGAEFLGTGLFLFFGIG--CLSALKVAGA-
FPS1_YEAST/244-527    KWSSVKNTYLKEFLAEFMGTMVMIIFGSAVVCQVNVAGKIQQ
PI21_ARATH/31-266     ELKKWSF--YRAVIAEFVATLLFLYITVL--TVIGYKIQSD-
PIP1_ATRCA/32-261     ELKLWSF--WRAAIAEFIATLLFLYITVA--TVIGYKKETD-
PIP1_LYCES/45-274     ELSSWSF--YRAGIAEFMATFLFLYITIL--TVMGLKRSDS-
MIP_BOVIN/3-219       ELRSASF--WRAICAEFFASLFYVFFGLG--ASLRWAPGP--
AQP2_HUMAN/3-219      ELRSIAF--SRAVFAEFLATLLFVFFGLG--SALNWPQAL--
AQP1_HUMAN/4-227      EFKKKLF--WRAVVAEFLATTLFVFISIG--SALGFKYPVG-
BIB_DROME/58-273      EIRTLEF--WRSIISECLASFMYVFIVCGAAAGVGVGASVS-
TI11_ARATH/13-234     EATRPDA--LKAALAEFISTLIFVVAGSG--SGMAFNKLTE-
TIP_ANTMA/11-232      DSFSVAS--IKAYVAEFIATLLFVFAGVG--SAIAYNKLTS-
TIPA_PHAVU/13-234     EATHPDS--MRASLAEFASTFIFVFAGEG--SGLALVKIYQ-
TI31_ARATH/16-242     EATHPDS--IRATLAEFLSTFVFVFAAEG--SILSLDKLYW-
NO26_SOYBN/30-244     SLVSVPF--LQKLVAEAVGTYFLIFAGCA---SLVVNENYY-


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