From 22 To 2292 Length 2271
Length: 756 aa
M S F V A G V I
R R L D E T V V N R I A A G E V I Q R P A N A I K E
M I E N C L D A K S T S I Q V I V K E G G L K L I Q I Q D N G T G I
R K E D L D I V C E R F T T S K L Q S F E D L A S I S T Y G F R G E A L A
S I S H V A H V T I T T K T AD G K C A Y R A S Y S D G K L K A P P K P C A
G N Q G T Q ITV E D L F Y N I A T R R K A L K N P S E E Y G K I L E V V G
R Y S V H N A G I S F S V K K Q G E T V A D V R T L P N A S T V D N I R S
I F G N A V S R E L I E I G C E D K T L A F K M
N G Y I S N A N Y S V K K C I F L L F I N H R L V E S T S L R K A I E T V
Y A A Y L P K N T H P F L Y L S L E I S P Q N V D V N V H P T K H E V H F
L H E E S I L E R V Q Q H I E S K L L G S N S S R M
Y F T Q T L L P G L A G P S G E M V K S T T S
L T S S S T S G S S D K V Y A H Q M V R T D S
R E Q K L D A F L Q P L S K P L S S Q P Q A I V T E D K T D I S S G R A R
Q Q D E E M L E L P A P A E V A A K N Q S L E
G D T T K G T S E M S E K R G P T S S N P R K
R H R E D S D V E M V E D D S R K E M
T A A C T P R R R I I N L T S V L S L Q E E I N E Q G H E V L R E M
L H N H S F V G C V N P Q W A L A Q H Q T K L Y L L N T T K L S E E L F Y
Q I L I Y D F A N F G V L R L S E P A P L F D L A M
L A L D S P E S G W T E E D G P K E G L A E Y I V E F L K K K A E
M L A D Y F S L E I D E E G N L I G L P L L I D N Y V P P L E G L P
I F I L R L A T E V N W D E E K E C F E S L S K E C A M
F Y S I R K Q Y I S E E S T L S G Q Q S E V P G S I P N S W K W T V E H I
V Y K A L R S H I L P P K H F T E D G N I L Q L A N L P D L Y
K V F E R C *
mutS
From 679 To 3240 Length 2562
Length: 853 aa
M S A I E N F D A H T P
M M Q Q Y L R L K A Q H P E I L L F Y R M
G D F Y E L F Y D D A K R A S Q L L D I S L T K R G A S A G E P I P M
A G I P Y H A V E N Y L A K L V N Q G E S V A I C E Q I G D P A T S K G P
V E R K V V R I V T P G T I S D E A L L Q E R Q D N L L A A I W Q D S K G
F G Y A T L D I S S G R F R L S E P A D R E T M
A A E L Q R T N P A E L L Y A E D F A E M S L
I E G R R G L R R R P L W E F E I D T A R Q Q L N L Q F G T R D L V G F G
V E N A P R G L C A A G C L L Q Y A K D T Q R T T L P H I R S I T M
E R E Q D S I I M D A A T R R N L E I T Q N L
A G G A E N T L A S V L D C T VT PM G S R M
L K R W L H M P V R D T R V L L E R Q Q T I G
A L Q D F T A G L Q P V L R Q V G D L E R I L A R L A L R T A R P R D L A
R M R H A F Q Q L P E L R A Q L E T V D S A P
V Q A L R E K M G E F A E L R D L L E R A I I
D T P P V L V R D G G V I A S G Y N E E L D E W R A L A D G A T D Y L E R
L E V R E R E R T G L D T L K V G F N A V H G Y Y I Q I S R G Q S H L A P
I N Y M R R Q T L K N A E R Y I I P E L K E Y
E D K V L T S K G K A L A L E K Q L Y E E L F D L L L P H L E A L Q Q S A
S A L A E L D V L V N L A E R A Y T L N Y T C P T F I D K P G I R I T E G
R H P V V E Q V L N E P F I A N P L N L S P Q R R M
L I I T G PNM G G K S T Y M
R Q T A L I A L M A Y I G S Y V P A Q K V E I
G P I D R I F T R V G A A D D L A S G R S T F M
V E M T E T A N I L H N A T E Y S L VL
M D E I G R G T S T Y D G L S L A W A C A E N L A N K I K A L T L F
A T H Y F E L T Q L P E K M E G V A N V H L D
A L E H G D T I A F M H S V Q D G A A S K S Y
G L A V A A L A G V P K E V I K R A R Q K L R E L E S I S P N A A A T Q V
D G T Q M S L L S V P E E T S P A V E A L E N
L D P D S L T P R Q A L E W I Y R L K S L V *
E Value
0.0
0.0
0.0
e-137
e-137
5e-53
6e-53
1e-50
2e-47
1e-46
Score (bits)
1459
1458
1445
487
487
208
208
200
189
187
Sequences producing significant alignments:
gi|4557757mutL homolog 1; mutL (E. coli) homolog 1 [Homo sapien...
gi|466462|gb|AAA17374.1|(U07418) human homolog of E. coli mutL ...
gi|604369|gb|AAA85687.1|(U17857) hMLH1 gene product [Homo sapiens]
gi|460627|gb|AAA16835.1|(U07187) Mlh1p [Saccharomyces cerevisiae]
gi|6323819MutL homolog, forms a complex with Pms1p and Msh2p to...
gi|127552|sp|P23367|MUTL_ECOLIDNA MISMATCH REPAIR PROTEIN
MUTL ...
gi|1171080|sp|P44494|MUTL_HAEINDNA MISMATCH REPAIR PROTEIN MUTL...
gi|127553|sp|P14161|MUTL_SALTYDNA MISMATCH REPAIR PROTEIN MUTL ...
gi|123083|sp|P14160|HEXB_STRPNDNA MISMATCH REPAIR PROTEIN HEXB ...
gi|1709188|sp|P49850|MUTL_BACSUDNA MISMATCH REPAIR PROTEIN MUTL...
Assignment 4
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.
Ans : No significant similarity was found.
2. Translate the above two gene sequences to protein sequences.
Ans : MLH1
3.Perform protein sequence homology searching for MLH1 in GenBank. Give the 10 highest hits.
Ans :
4. Compare human MLH1 protein with MLH1 in M. musculus, R. norvegicus and D. melanogaster. Give the pairwise alignment and % of sequence smility.
Ans :
5. Search the conserve domain (CD) for MLH1. Give the position of the CD, name of CD and Pfam ID number.
Ans :
6. Show multiple alignment of MLH1 conserve domain with 5 sequences from the top of the CD alignment.
Ans :
10 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....| consensus 1 GTTVEVRDLFYNLPVRRKFLKSPKKEFRKILDLLQRYALIHPNVSFSLTKEGKALLQLKT 60 query 147 GTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRT 206 1B63_A 144 GTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRA 203 gi 730028 147 GTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRT 206 gi 3192877 149 GTIICIEDLFYNMPQRRQALRSPAEEFQRLSEVLARYAVHNPRVGFTLRKQGDAQPALRT 208 |
70 80 90 100 110 120 ....*....|....*....|....*....|....*....|....*....|....*....| consensus 61 SP--S-SLKERIRSVFGTAVLKNLIPF--E--EKDGDFRIEGFISSPNVSR-SSRDRQFL 112 query 207 LP--NaSTVDNIRSIFGNAVSRELIEIgcE--DKTLAFKMNGYISNANYSV--KKCIFLL 260 1B63_A 204 VPegG-QKERRLGAICGTAFLEQALAI--E--WQHGDLTLRGWVADPNHTTpALAEIQYC 258 gi 730028 207 LPn-A-STVDNIRSIFGNAVSRELIEI--GceDKTLAFKMNGYISNANYSV--KKCIFLL 260 gi 3192877 209 PVa-S-SRSENIRIIYGAAISKELLEF--ShrDEVYKFEAECLITQVNYSA--KKCQMLL 262 |
130 140 150 160 170 180 ....*....|....*....|....*....|....*....|....*....|....*....| consensus 113 FINGRPVEDKLLLKAIREVYATYLPRGRYPVFVLNLELPPELVDVNVHPDKKEVRLLKEE 172 query 261 FINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE 320 1B63_A 259 YVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSR 318 gi 730028 261 FINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE 320 gi 3192877 263 FINQRLVESTALRTSVDSIYATYLPRGHHPFVYMSLTLPPQNLDVNVHPTKHEVHFLYQE 322 |
....*.. consensus 173 EILDLIK 179 query 321 SILERVQ 327 1B63_A 319 LVHDFIY 325 gi 730028 321 SILERVQ 327 gi 3192877 323 EIVDSIK 329 |