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


Length of target sequence: 756 residuesReading user-defined template listExtracting template sequencesRunning pair-wise alignments with target sequence
Sequence identity of templates with target:1BKNA.pdb: 46.05 % identity
1BKNB.pdb: 40.9 % identityLooking for template groups
Global alignment overview:

Taget Sequence: |==================================================|
1BKNA.pdb | -------
1BKNB.pdb | -------

AlignMaster found 1 regions to model separately:
1: Using template(s) 1BKNA.pdb 1BKNB.pdb
Creating Batch files for ProMod (if any):
Batch.1: residues 20 - 146 of submitted sequence.

 

1BKNA
CRYSTAL STRUCTURE OF AN N-TERMINAL 40KD FRAGMENT OF E. COL
DNA MISMATCH REPAIR PROTEIN MUTL
MOL_ID: 1;
MOLECULE: MUTL;
CHAIN: A, B;
FRAGMENT: N-TERMINAL 40KD FRAGMENT;
ENGINEERED: YES
MOL_ID: 1;
ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
STRAIN: K-12;
PLASMID: PTX418;
GENE: MUTL;
EXPRESSION_SYSTEM: ESCHERICHIA COLI;
EXPRESSION_SYSTEM_STRAIN: HMS174 (LAMBDA DE3);
EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
EXPRESSION_SYSTEM_PLASMID: PTX418;
EXPRESSION_SYSTEM_GENE: MUTL
W.YANG,C.BAN
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 TV 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 1BKNB
CRYSTAL STRUCTURE OF AN N-TERMINAL 40KD FRAGMENT OF E. COL
DNA MISMATCH REPAIR PROTEIN MUTL
MOL_ID: 1;
MOLECULE: MUTL;
CHAIN: A, B;
FRAGMENT: N-TERMINAL 40KD FRAGMENT;
ENGINEERED: YES
MOL_ID: 1;
ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
STRAIN: K-12;
PLASMID: PTX418;
GENE: MUTL;
EXPRESSION_SYSTEM: ESCHERICHIA COLI;
EXPRESSION_SYSTEM_STRAIN: HMS174 (LAMBDA DE3);
EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
EXPRESSION_SYSTEM_PLASMID: PTX418;
EXPRESSION_SYSTEM_GENE: MUTL
W.YANG,C.BAN
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
 

SWISS-MODEL > search:MLH1 sequence---SWISS-MODEL Blast ĦiFind the Appropriate Modelling Template(s)Ħj> 1BKNA and 1BKNB as templates


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

272 or 271 residues


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