| 1. Compare MLH1 (answer of assignment 2.6) and mutS (answer of 2.7) sequence. |
| No significant similarity was found |
| 2. Translate the above two gene sequences to protein sequences. |
|
MLH1ĄGMSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEG
GLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTK
TADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIATRRKALKNPSEEYGKILEV
VGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAFK
MNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVD
VNVHPTKHEVHFLHEESILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSL
TSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQAIVTEDKTDISSGRARQQD
EEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVEMVEDDSRKE
MTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLL
NTTKLSEELFYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVE
FLKKKAEMLADYFSLEIDEEGNLIGLPLLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLS
KECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIVYKALRSHILPPKHFTEDGNI
LQLANLPDLYKVFERC*
mutSĄG
MSAIENFDAHTPMMQQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLT
KRGASAGEPIPMAGIPYHAVENYLAKLVNQGESVAICEQIGDPATSKGPVERKVVRIVTPGT
ISDEALLQERQDNLLAAIWQDSKGFGYATLDISSGRFRLSEPADRETMAAELQRTNPAELLY
AEDFAEMSLIEGRRGLRRRPLWEFEIDTARQQLNLQFGTRDLVGFGVENAPRGLCAAGCLL
QYAKDTQRTTLPHIRSITMEREQDSIIMDAATRRNLEITQNLAGGAENTLASVLDCTVTPMG
SRMLKRWLHMPVRDTRVLLERQQTIGALQDFTAGLQPVLRQVGDLERILARLALRTARPR
DLARMRHAFQQLPELRAQLETVDSAPVQALREKMGEFAELRDLLERAIIDTPPVLVRDGGV
IASGYNEELDEWRALADGATDYLERLEVRERERTGLDTLKVGFNAVHGYYIQISRGQSHLA
PINYMRRQTLKNAERYIIPELKEYEDKVLTSKGKALALEKQLYEELFDLLLPHLEALQQSAS
ALAELDVLVNLAERAYTLNYTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRML
IITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMV
EMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELT
QLPEKMEGVANVHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIKRARQK
LRELESISPNAAATQVDGTQMSLLSVPEETSPAVEALENLDPDSLTPRQALEWIYRLKSLV*
|
| 3.Perform protein sequence homology searching for MLH1 in GenBank. Give
the 10 highest hits. |
gi|13878583|sp|Q9JK91|MLH1_MOUSE
gi|13591989|ref|NP_112315.1| (NM_031053)
gi|4557757|ref|NP_000240.1| (NM_000249)
gi|466462|gb|AAA17374.1| (U07418)
gi|604369|gb|AAA85687.1| (U17857)
gi|12835158|dbj|BAB23172.1| (AK004105) putative [Mus musculus]
gi|13543339|gb|AAH05833.1|AAH05833 (BC005833)
gi|7304079|gb|AAF59117.1| (AE003838) Mlh1 gene product
gi|3192877|gb|AAC19117.1| (AF068257) mutL homolog
gi|460627|gb|AAA16835.1| (U07187) Mlh1p |
| 4. Compare human MLH1 protein with MLH1 in M. musculus, R. norvegicus
and D. melanogaster. Give the pairwise alignment and % of sequence smility. |
|
M. musculusĄGScore
= 1329 bits (3440), Expect = 0.0
Identities = 670/760 (88%), Positives = 714/760 (93%), Gaps = 4/760 (0%)
R. norvegicusĄGScore
= 1306 bits (3380), Expect = 0.0
Identities = 659/758 (86%), Positives = 707/758 (92%), Gaps = 3/758 (0%)
D. melanogasterĄGScore
= 652 bits (1682), Expect = 0.0
Identities = 348/751 (46%), Positives = 476/751 (63%), Gaps = 94/751 (12%)
|
| 5. Search the conserve domain (CD) for MLH1. Give the position of the
CD, name of CD and Pfam ID number. |
|
positionĄG147-327
nameĄGDNA_mis_repair,
DNA mismatch repair protein. Also known as the mutL/hexB/PMS1 family.
Pfam ID numberĄG01119
|
| 6. Show multiple alignment of MLH1 conserve domain with 5 sequences from
the top of the CD alignment. |
| multiple
alignment of MLH1 conserve domain |
|
|