(Last Update: 04/20/00 )
Question: how far down the list of possible homologs should I go? For example, is DING_ECOLI a probable homolog? It is named in Swissprot as "probable ATP-dependent helicase DING", and has as synonym "DNA-damage-inducible protein G". What about YOAA_ECOLI and YOAA_HAEIN? They are also ATP-dependent helicases in the DING subfamily.
All the bacterial matches are fairly weak helicase matches. They are unlikely to serve the same function as XPD.
Organism | Score file | Most likely homolog | E-value | Alignment |
---|---|---|---|---|
Deinococcus radiodurans | drad.dist | gi|6459005|gb|AAF10831.1|AE001973_4 | 2.5e-06 | |
Microplasma genitalium | geni.dist | MG073 :excinuclease ABC subunit B (uvrB) E.coli | 3.6e-06 |
Organism | Score file | Most likely homolog | Alignment |
---|---|---|---|
Aeropyrum pernix |
aero.dist | gi|5103961|dbj|BAA79277.1| | |
Archaeoglobus fulgidus |
aful.dist | gi|2650581 (N-terminus only) | |
Methanobacterium thermoautotrophicum |
thermo.dist | gi|2622454 (MTH1347) | |
Methanococcus jannaschii | jann.dist | gi|1591610|gb|AAB98945.1| (MJ0942) | |
Pyrococcus abyssi | pabyssi.dist | gi|5458763|emb|CAB50250.1| | |
Pyrococcus horikoshii | pyrohori.dist | gi|3257105|gnl|PID|d1030731 |
nucleotide change | aa/splice allele1,allele2 | comments | references |
---|---|---|---|
xeroderma pigmentosum | |||
L461V,del716-730 (null?) | |||
G47R | |||
R683W | |||
Y542C | |||
R616P (null?) | |||
R683W | |||
R616P (null?) | |||
R683W | |||
R616W (null?) | |||
R683Q | |||
Q726ter | |||
R601L | |||
D234N | |||
R683W | |||
del36->61 (null?) | |||
R683W | |||
R616P | |||
R683W | |||
L461V, del716->730(null?) | |||
197fs/ter (null) | |||
S541R | |||
XP-CS combined | |||
G675R | |||
669fs->708ter | |||
G602D | |||
trichothiodystropy | |||
R112H | |||
del488->493,del460->493 (null?) | |||
730fs->744ter | |||
del488->493,del460->493 (null?) | |||
R112H | |||
R112H | |||
del482 (null?) | |||
D673G | |||
R722W | |||
L461V, del716->730(null?) | |||
R112H | |||
del121->159 (exon6) (null?) | |||
C259Y | |||
R722W | |||
L461V, del716->730(null?) | |||
R722W | |||
L461V, del716->730(null?) | |||
R658H | |||
R658H | |||
R658C, K751Q | |||
G713R | |||
L461V, del716->730(null?) | |||
A725P |
How should references be handled? MEDLINE pointers?
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