Compare human colon cancer gene MLH1 with other genes

- To use ORF finder to translate DNA sequence to protein sequence in all reading frames. -
- To use blastn, blastp, CD search and blast 2 sequence programs for searching and comparison. -

1. Compare MLH1 (answer of assignment 2.6) and mutS (answer of 2.7) sequence.

answer: No significant similarity was found

2. Translate the above two gene sequences to protein sequences.

answer:

>gi|463989|gb|AAC50285.1| hMLH1
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC

>gi|1592569|gb|AAB97931.1| DNA mismatch repair protein [Escherichia coli]
MSAIENFDAHTPMMQQYLKLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRSASAGEPIPMAGIPYHAVENYL
AKLVNQGESVAICEQIGDPATSKGPVERKVVRIVTPGTISDEALLQERQDNLLAAIWQDSKGFAYATLDISSGRFRLSEP
ADRETMAAELQRTNPAELLYAEDFAEMSLIEGRRGLRRRPLWEFEIDTARQQLNLQFGTRDLVGFGVENAPRGLCAAGCL
LQYAKDTQRTTLPHIRSITMEREQDSIIMDAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRHTRV
LLERQQTIGALQDFTAELQPVLRQVGDLERILARLALRTARPRDLARMRHAFQQLPELRAQLETVDSAPVQALREKMGEF
AELRDLLERAIIDTPPVLVRDGGVIASGYNEELDEWRALADGATDYLERLEVRERERTGLDTLKVGFNAVHGYYIQISRG
QSHLAPINYMRRQTLKNAERYIIPELKEYEDKVLTSKGKALALEKQLYEELFDLLLPHLEALQQSASALAELDVLVNLAE
RAYTLNYTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYV
PAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIK
ALTLFATHYFELTQLPEKMEGVANVHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIKRARQKLRELESIS
PNAAATQVDGTQMSLLSVPEETSPAVEALENLDPDSLTPRQALEWIYRLKSLV

3.Perform protein sequence homology searching for MLH1 in GenBank. Give the 10 highest hits.

answer:

GI:13878583, MLH1_Mouse, DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1).
GI:13591989, NP_112315, mismatch repair protein [Rattus norvegicus].
GI:4557757, NP_000240, mutL homolog 1; mutL (E. coli) homolog 1 [Homo sapiens].
GI:466462, AAA17374, (U07418) human homolog of E. coli mutL gene product, Swiss-Prot Accession Number P23367 [Homo sapiens]
GI:604369, AAA85687.1, hMLH1 gene product.[Homo sapiens]
GI:12835158, BAB23172.1, putative [Mus musculus].
GI:13543339, AAH05833.1, Similar to mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2) [Homo sapiens].
GI:7304079, AAF59117.1, Mlh1 gene product [Drosophila melanogaster].
GI:3192877, AAC19117.1, mutL homolog [Drosophila melanogaster].
GI:460627, AAA16835.1, Mlh1p.[Saccharomyces cerevisiae].

4. Compare human MLH1 protein with MLH1 in M. musculus, R. norvegicus and D. melanogaster. Give the pairwise alignment and % of sequence smility.

answer:(link)

Mus musculus Identities = 651/760 (85%), Positives = 693/760 (90%), Gaps = 4/760 (0%)
Rattus norvegicus Identities = 639/758 (84%), Positives = 684/758 (89%), Gaps = 3/758 (0%)
Drosophila melanogaster Identities = 335/751 (44%), Positives = 453/751 (59%), 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.

position: No.147-327 amino acid
name: DNA_mis_repair, DNA mismatch repair protein. Also known as the mutL/hexB/PMS1 pfam family.
ID: pfam01119 (link)

6. Show multiple alignment of MLH1 conserve domain with 5 sequences from the top of the CD alignment.

answer: (link)