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...

Name of CD :DNA_mis_repair, DNA mismatch repair protein. Also known as the mutL/hexB/PMS1 family.
Pfam ID number : pfam01119
Position of the CD : 147-327 ( CD-Length = 179 residues )
M. musculus : Identities = 390/484 (80%) , Positives = 418/484 (85%), Gaps = 4/484 (0%)


R. norvegicus : Identities = 639/758 (84%) , Positives = 684/758 (89%), Gaps = 3/758 (0%)
D. melanogaster : Identities = 335/751 (44%) , Positives = 453/751 (59%), Gaps = 94/751 (12%)
pairwise alignment
pairwise alignment
pairwise alignment

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

 

[Answer]