HOMEWORK4

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.

→MLH1 protein sequence mutS protein sequence

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

→ref|NP_000240.1| mutL homolog 1; mutL (E. coli) homolog 1 [Homo sapiens]

gb|AAA17374.1| (U07418) human homolog of E. coli mutL gene product

gb|AAA85687.1| (U17857) hMLH1 gene product [Homo sapiens]

sp|Q9JK91|MLH1_MOUSE DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1).

ref|NP_112315.1| mismatch repair protein [Rattus norvegicus ]

dbj|BAB23172.1| (AK004105) putative [Mus musculus]

gb|AAH05833.1|AAH05833 (BC005833) Similar to mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2) [Homo sapiens].

gb|AAF59117.1| (AE003838) Mlh1 gene product [Drosophila melanogaster].

gb|AAC19117.1| (AF068257) mutL homolog [Drosophila melanogaster].

ref|NP_192653.1| MLH1 protein [Arabidopsis thaliana]

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

M.musculus

sp|Q9JK91|MLH1_MOUSE DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1)
gb|AAF64514.1|AF250844_1 (AF250844) MutL homolog 1 protein [Mus musculus]
Length = 760

Score = 1329 bits (3440), Expect = 0.0
Identities = 670/760 (88%), Positives = 714/760 (93%), Gaps = 4/760 (0%)

R. norvegicus

ref|NP_112315.1| mismatch repair protein [Rattus norvegicus]
sp|P97679|MLH1_RAT DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1)
gb|AAB38506.1| (U80054) mismatch repair protein [Rattus norvegicus]
Length = 757

Score = 1306 bits (3380), Expect = 0.0
Identities = 659/758 (86%), Positives = 707/758 (92%), Gaps = 3/758 (0%)

D. melanogaster

gb|AAF59117.1| (AE003838) Mlh1 gene product [Drosophila melanogaster]
Length = 664

Score = 644 bits (1662), Expect = 0.0
Identities = 345/751 (45%), Positives = 472/751 (61%), 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:147~325a.a.

name: DNA_mis_repair, DNA mismatch repair protein. Also known as the mutL/hexB/PMS1 family.

Pfam ID: 01119

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

→ answers