Comparative Protein Modelling by SWISS-MODEL

- To make a protein model by homology modelling
- Deadline - 1/4/2002

1. Make a protein structure model of MLH1 based on the protein you find in assignment 7. Show their pairwise alignment.

Ans:

Length = 272

Score = 124 bits (309), Expect = 1e-28
Identities = 81/287 (28 Positives = 144/287 (49 Gaps = 30/287 (10

Query: 25 IQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSK 84
            RPA   KE  EN LDA  T I      GG KLI I DNG GI K  L 
Sbjct:  1 VERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALAL------A 54

Query: 85 LQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAG 144
            S  DL  I   GFRGEALASIS V   T T  TA    A 
Sbjct: 55 IASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAW------------------ 96

Query: 145 NQGTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADV 204
            Q T   V        T    L     E   I E   R               G  V 
Sbjct:  97 -QAYAVTVKPAAHPVGTTLEVLDTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQY 155

Query: 205 RTLPNASTVD-NIRSIFGNAVSRELIEIGCEDKTLAFKMNGYISNANYSVKKC--IFLLF 261
           R  P           I G A       I      L     G     N        I 
Sbjct: 156 RAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLT--LRGWVADPNHTTPALAEIQYCY 213

Query: 262 INHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVH 308
            N R         AI       L     P   L LEI P  V   VH
Sbjct: 214 VNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVSRLVH 260

Length = 271

Score = 118 bits (293), Expect = 8e-27
Identities = 81/282 (28 Positives = 141/282 (49 Gaps = 33/282 (11

Query: 25 IQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSK      84
            RPA   KE  EN LDA  T I      GG KLI I DNG GI K  L 
Sbjct:  1 VERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALAE----- 55

Query: 85 LQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAG 144
                   I   GFRGEALASIS V   T T  TA    A  A           KP A 
Sbjct: 56 --------AIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQA-----YMNVTVKPAAH 102

Query: 145 NQGTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADV 204
             GT   V DL          L     E   I E   R               G  V 
Sbjct: 103 PVGTTLEVLDL----------LRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQY 152

Query: 205 RTLPNASTVD-NIRSIFGNAVSRELIEIGCEDKTLAFKMNGYISNANYSVKKC--IFLLF 261
           R  P           I G A     I        L     G     N        I 
Sbjct: 153 RAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLT--LRGWVADPNHTTPALAEIQYCY 210

Query: 262 INHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNV 303
            N R         AI       L     P   L LEI P  V
Sbjct: 211 VNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQV 252

2. How large is the fragment of MLH1 possible to be modeled?

Ans: N-terminal 40KD fragment

3. Show three rasmol pictures of your model of MLH1?

Ans: