1.
Compare MLH1 (answer of assignment 2.6) and mutS (answer of
2.7) sequence.
No
significant alignment.
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2.
Translate the above two gene sequences to protein sequences.
MLH1
>lcl|Sequence
1 ORF:22..2292 Frame +1
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRK
EDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPK
PCAGNQGTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNA
STVDNIRSIFGNAVSRELIEIGCEDKTLAFKMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVY
AAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIESKLLGSNSSRMYFTQTLLP
GLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQAIVTEDKTDIS
SGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVEMVEDDSRKEM
TAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEI
DEEGNLIGLPLLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQ
QSEVPGSIPNSWKWTVEHIVYKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC*
mutS
>lcl|Sequence 1 ORF:1..2562 Frame +1
MSAIENFDAHTPMMQQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGEPIPMAG
IPYHAVENYLAKLVNQGESVAICEQIGDPATSKGPVERKVVRIVTPGTISDEALLQERQDNLLAAIWQDS
KGFGYATLDISSGRFRLSEPADRETMAAELQRTNPAELLYAEDFAEMSLIEGRRGLRRRPLWEFEIDTAR
QQLNLQFGTRDLVGFGVENAPRGLCAAGCLLQYAKDTQRTTLPHIRSITMEREQDSIIMDAATRRNLEIT
QNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQQTIGALQDFTAGLQPVLRQVGDLER
ILARLALRTARPRDLARMRHAFQQLPELRAQLETVDSAPVQALREKMGEFAELRDLLERAIIDTPPVLVR
DGGVIASGYNEELDEWRALADGATDYLERLEVRERERTGLDTLKVGFNAVHGYYIQISRGQSHLAPINYM
RRQTLKNAERYIIPELKEYEDKVLTSKGKALALEKQLYEELFDLLLPHLEALQQSASALAELDVLVNLAE
RAYTLNYTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQTALI
ALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTS
TYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHGDTIAFMHSVQDGAASKS
YGLAVAALAGVPKEVIKRARQKLRELESISPNAAATQVDGTQMSLLSVPEETSPAVEALENLDPDSLTPR
QALEWIYRLKSLV*
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3.Perform
protein sequence homology searching for MLH1 in GenBank. Give
the 10 highest hits.
blastb
of MLH1
Score
E
Sequences producing significant alignments: (bits) Value
- gi|13878583|sp|Q9JK91|MLH1_MOUSE
DNA MISMATCH REPAIR PROTEI... 1292 0.0
- gi|13591989|ref|NP_112315.1|
mismatch repair protein [Rattu... 1289 0.0
- gi|4557757|ref|NP_000240.1|
mutL homolog 1; mutL (E. coli) ... 1467 0.0
- gi|466462|gb|AAA17374.1|
(U07418) human homolog of E. coli ... 1466 0.0
- gi|604369|gb|AAA85687.1|
(U17857) hMLH1 gene product [Homo ... 1453 0.0
- gi|12835158|dbj|BAB23172.1|
(AK004105) putative [Mus musculus] 753 0.0
- gi|13543339|gb|AAH05833.1|AAH05833
(BC005833) Similar to mu... 731 0.0
- gi|7304079|gb|AAF59117.1|
(AE003838) Mlh1 gene product [Dro... 615 e-175
- gi|3192877|gb|AAC19117.1|
(AF068257) mutL homolog [Drosophi... 608 e-173
- gi|460627|gb|AAA16835.1|
(U07187) Mlh1p [Saccharomyces cere... 471 e-132
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4.
Compare human MLH1 protein with MLH1 in M. musculus, R. norvegicus
and D. melanogaster. Give the pairwise alignment and % of
sequence smility.
human MLH1 protein with
- MLH1
in M. musculus Identities = 651/760 (85%), Positives = 693/760
(90%), Gaps = 4/760 (0%)
- MLH1
in R. norvegicus Identities = 639/758 (84%), Positives =
684/758 (89%), Gaps = 3/758 (0%)
- MLH1
in D. melanogaster Identities = 335/751 (44%), Positives
= 453/751 (59%), Gaps = 94/751 (12%)
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5.
Search the conserve domain (CD) for MLH1. Give the position
of the CD, name of CD and Pfam ID number.
conserved domain database
position:
No.147-179 amino acid
name: DNA_mis_repair, DNA mismatch repair protein. Also known
as the mutL/hexB/PMS1 pfam family.
ID: pfam01119
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6.
Show multiple alignment of MLH1 conserve domain with 5 sequences
from the top of the CD alignment.
multiple
alignment of MLH1 conserve domain
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