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:a.MLH1:
    22 atgtcgttcgtggcaggggttattcggcggctggacgagacagtg
        M  S  F  V  A  G  V  I  R  R  L  D  E  T  V 
     67 gtgaaccgcatcgcggcgggggaagttatccagcggccagctaat
        V  N  R  I  A  A  G  E  V  I  Q  R  P  A  N 
    112 gctatcaaagagatgattgagaactgtttagatgcaaaatccaca
        A  I  K  E  M  I  E  N  C  L  D  A  K  S  T 
    157 agtattcaagtgattgttaaagagggaggcctgaagttgattcag
        S  I  Q  V  I  V  K  E  G  G  L  K  L  I  Q 
    202 atccaagacaatggcaccgggatcaggaaagaagatctggatatt
        I  Q  D  N  G  T  G  I  R  K  E  D  L  D  I 
    247 gtatgtgaaaggttcactactagtaaactgcagtcctttgaggat
        V  C  E  R  F  T  T  S  K  L  Q  S  F  E  D 
    292 ttagccagtatttctacctatggctttcgaggtgaggctttggcc
        L  A  S  I  S  T  Y  G  F  R  G  E  A  L  A 
    337 agcataagccatgtggctcatgttactattacaacgaaaacagct
        S  I  S  H  V  A  H  V  T  I  T  T  K  T  A 
    382 gatggaaagtgtgcatacagagcaagttactcagatggaaaactg
        D  G  K  C  A  Y  R  A  S  Y  S  D  G  K  L 
    427 aaagcccctcctaaaccatgtgctggcaatcaagggacccagatc
        K  A  P  P  K  P  C  A  G  N  Q  G  T  Q  I 
    472 acggtggaggaccttttttacaacatagccacgaggagaaaagct
        T  V  E  D  L  F  Y  N  I  A  T  R  R  K  A 
    517 ttaaaaaatccaagtgaagaatatgggaaaattttggaagttgtt
        L  K  N  P  S  E  E  Y  G  K  I  L  E  V  V 
    562 ggcaggtattcagtacacaatgcaggcattagtttctcagttaaa
        G  R  Y  S  V  H  N  A  G  I  S  F  S  V  K 
    607 aaacaaggagagacagtagctgatgttaggacactacccaatgcc
        K  Q  G  E  T  V  A  D  V  R  T  L  P  N  A 
    652 tcaaccgtggacaatattcgctccatctttggaaatgctgttagt
        S  T  V  D  N  I  R  S  I  F  G  N  A  V  S 
    697 cgagaactgatagaaattggatgtgaggataaaaccctagccttc
        R  E  L  I  E  I  G  C  E  D  K  T  L  A  F 
    742 aaaatgaatggttacatatccaatgcaaactactcagtgaagaag
        K  M  N  G  Y  I  S  N  A  N  Y  S  V  K  K 
    787 tgcatcttcttactcttcatcaaccatcgtctggtagaatcaact
        C  I  F  L  L  F  I  N  H  R  L  V  E  S  T 
    832 tccttgagaaaagccatagaaacagtgtatgcagcctatttgccc
        S  L  R  K  A  I  E  T  V  Y  A  A  Y  L  P 
    877 aaaaacacacacccattcctgtacctcagtttagaaatcagtccc
        K  N  T  H  P  F  L  Y  L  S  L  E  I  S  P 
    922 cagaatgtggatgttaatgtgcaccccacaaagcatgaagttcac
        Q  N  V  D  V  N  V  H  P  T  K  H  E  V  H 
    967 ttcctgcacgaggagagcatcctggagcgggtgcagcagcacatc
        F  L  H  E  E  S  I  L  E  R  V  Q  Q  H  I 
   1012 gagagcaagctcctgggctccaattcctccaggatgtacttcacc
        E  S  K  L  L  G  S  N  S  S  R  M  Y  F  T 
   1057 cagactttgctaccaggacttgctggcccctctggggagatggtt
        Q  T  L  L  P  G  L  A  G  P  S  G  E  M  V 
   1102 aaatccacaacaagtctgacctcgtcttctacttctggaagtagt
        K  S  T  T  S  L  T  S  S  S  T  S  G  S  S 
   1147 gataaggtctatgcccaccagatggttcgtacagattcccgggaa
        D  K  V  Y  A  H  Q  M  V  R  T  D  S  R  E 
   1192 cagaagcttgatgcatttctgcagcctctgagcaaacccctgtcc
        Q  K  L  D  A  F  L  Q  P  L  S  K  P  L  S 
   1237 agtcagccccaggccattgtcacagaggataagacagatatttct
        S  Q  P  Q  A  I  V  T  E  D  K  T  D  I  S 
   1282 agtggcagggctaggcagcaagatgaggagatgcttgaactccca
        S  G  R  A  R  Q  Q  D  E  E  M  L  E  L  P 
   1327 gcccctgctgaagtggctgccaaaaatcagagcttggagggggat
        A  P  A  E  V  A  A  K  N  Q  S  L  E  G  D 
   1372 acaacaaaggggacttcagaaatgtcagagaagagaggacctact
        T  T  K  G  T  S  E  M  S  E  K  R  G  P  T 
   1417 tccagcaaccccagaaagagacatcgggaagattctgatgtggaa
        S  S  N  P  R  K  R  H  R  E  D  S  D  V  E 
   1462 atggtggaagatgattcccgaaaggaaatgactgcagcttgtacc
        M  V  E  D  D  S  R  K  E  M  T  A  A  C  T 
   1507 ccccggagaaggatcattaacctcactagtgttttgagtctccag
        P  R  R  R  I  I  N  L  T  S  V  L  S  L  Q 
   1552 gaagaaattaatgagcagggacatgaggttctccgggagatgttg
        E  E  I  N  E  Q  G  H  E  V  L  R  E  M  L 
   1597 cataaccactccttcgtgggctgtgtgaatcctcagtgggccttg
        H  N  H  S  F  V  G  C  V  N  P  Q  W  A  L 
   1642 gcacagcatcaaaccaagttataccttctcaacaccaccaagctt
        A  Q  H  Q  T  K  L  Y  L  L  N  T  T  K  L 
   1687 agtgaagaactgttctaccagatactcatttatgattttgccaat
        S  E  E  L  F  Y  Q  I  L  I  Y  D  F  A  N 
   1732 tttggtgttctcaggttatcggagccagcaccgctctttgacctt
        F  G  V  L  R  L  S  E  P  A  P  L  F  D  L 
   1777 gccatgcttgccttagatagtccagagagtggctggacagaggaa
        A  M  L  A  L  D  S  P  E  S  G  W  T  E  E 
   1822 gatggtcccaaagaaggacttgctgaatacattgttgagtttctg
        D  G  P  K  E  G  L  A  E  Y  I  V  E  F  L 
   1867 aagaagaaggctgagatgcttgcagactatttctctttggaaatt
        K  K  K  A  E  M  L  A  D  Y  F  S  L  E  I 
   1912 gatgaggaagggaacctgattggattaccccttctgattgacaac
        D  E  E  G  N  L  I  G  L  P  L  L  I  D  N 
   1957 tatgtgccccctttggagggactgcctatcttcattcttcgacta
        Y  V  P  P  L  E  G  L  P  I  F  I  L  R  L 
   2002 gccactgaggtgaattgggacgaagaaaaggaatgttttgaaagc
        A  T  E  V  N  W  D  E  E  K  E  C  F  E  S 
   2047 ctcagtaaagaatgcgctatgttctattccatccggaagcagtac
        L  S  K  E  C  A  M  F  Y  S  I  R  K  Q  Y 
   2092 atatctgaggagtcgaccctctcaggccagcagagtgaagtgcct
        I  S  E  E  S  T  L  S  G  Q  Q  S  E  V  P 
   2137 ggctccattccaaactcctggaagtggactgtggaacacattgtc
        G  S  I  P  N  S  W  K  W  T  V  E  H  I  V 
   2182 tataaagccttgcgctcacacattctgcctcctaaacatttcaca
        Y  K  A  L  R  S  H  I  L  P  P  K  H  F  T 
   2227 gaagatggaaatatcctgcagcttgctaacctgcctgatctatac
        E  D  G  N  I  L  Q  L  A  N  L  P  D  L  Y 
   2272 aaagtctttgagaggtgttaa 2292   
        K  V  F  E  R  C  * 
     
   b.muts
    679 atgagtgcaatagaaaatttcgacgcccatacgcccatgatgcag
        M  S  A  I  E  N  F  D  A  H  T  P  M  M  Q 
    724 cagtatctcaggctgaaagcccagcatcccgagatcctgctgttt
        Q  Y  L  R  L  K  A  Q  H  P  E  I  L  L  F 
    769 taccggatgggtgatttttatgaactgttttatgacgacgcaaaa
        Y  R  M  G  D  F  Y  E  L  F  Y  D  D  A  K 
    814 cgcgcgtcgcaactgctggatatttcactgaccaaacgcggtgct
        R  A  S  Q  L  L  D  I  S  L  T  K  R  G  A 
    859 tcggcgggagagccgatcccgatggcggggattccctaccatgcg
        S  A  G  E  P  I  P  M  A  G  I  P  Y  H  A 
    904 gtggaaaactatctcgccaaactggtgaatcagggagagtccgtt
        V  E  N  Y  L  A  K  L  V  N  Q  G  E  S  V 
    949 gccatctgcgaacaaattggcgatccggcgaccagcaaaggtccg
        A  I  C  E  Q  I  G  D  P  A  T  S  K  G  P 
    994 gttgagcgcaaagttgtgcgtatcgttacgccaggcaccatcagc
        V  E  R  K  V  V  R  I  V  T  P  G  T  I  S 
   1039 gatgaagccctgttgcaggagcgtcaggacaacctgctggcggct
        D  E  A  L  L  Q  E  R  Q  D  N  L  L  A  A 
   1084 atctggcaggacagcaaaggtttcggctacgcgacgctggatatc
        I  W  Q  D  S  K  G  F  G  Y  A  T  L  D  I 
   1129 agttccgggcgttttcgcctgagcgaaccggctgaccgcgaaacg
        S  S  G  R  F  R  L  S  E  P  A  D  R  E  T 
   1174 atggcggcagaactgcaacgcactaatcctgcggaactgctgtat
        M  A  A  E  L  Q  R  T  N  P  A  E  L  L  Y 
   1219 gcagaagattttgctgaaatgtcgttaattgaaggccgtcgcggc
        A  E  D  F  A  E  M  S  L  I  E  G  R  R  G 
   1264 ctgcgccgtcgcccgctgtgggagtttgaaatcgacaccgcgcgc
        L  R  R  R  P  L  W  E  F  E  I  D  T  A  R 
   1309 cagcagttgaatctgcaatttgggacccgcgatctggtcggtttt
        Q  Q  L  N  L  Q  F  G  T  R  D  L  V  G  F 
   1354 ggcgtcgagaacgcgccgcgcggactttgtgctgccggttgtctg
        G  V  E  N  A  P  R  G  L  C  A  A  G  C  L 
   1399 ttgcagtatgcgaaagatacccaacgtacgactctgccgcatatt
        L  Q  Y  A  K  D  T  Q  R  T  T  L  P  H  I 
   1444 cgttccatcaccatggaacgtgagcaggacagcatcattatggat
        R  S  I  T  M  E  R  E  Q  D  S  I  I  M  D 
   1489 gccgcgacgcgtcgtaatctggaaatcacccagaacctggcgggt
        A  A  T  R  R  N  L  E  I  T  Q  N  L  A  G 
   1534 ggtgcggaaaatacgctggcttctgtgctcgactgcaccgtcacg
        G  A  E  N  T  L  A  S  V  L  D  C  T  V  T 
   1579 ccgatgggcagccgtatgctgaaacgctggctgcatatgccagtg
        P  M  G  S  R  M  L  K  R  W  L  H  M  P  V 
   1624 cgcgatacccgcgtgttgcttgagcgccagcaaactattggcgca
        R  D  T  R  V  L  L  E  R  Q  Q  T  I  G  A 
   1669 ttgcaggatttcaccgccgggctacagccggtactgcgtcaggtc
        L  Q  D  F  T  A  G  L  Q  P  V  L  R  Q  V 
   1714 ggcgacctggaacgtattctggcacgtctggctttacgaactgct
        G  D  L  E  R  I  L  A  R  L  A  L  R  T  A 
   1759 cgcccacgcgatctggcccgtatgcgccacgctttccagcaactg
        R  P  R  D  L  A  R  M  R  H  A  F  Q  Q  L 
   1804 ccggagctgcgtgcgcagttagaaactgtcgatagtgcaccggta
        P  E  L  R  A  Q  L  E  T  V  D  S  A  P  V 
   1849 caggcgctacgtgagaagatgggcgagtttgccgagctgcgcgat
        Q  A  L  R  E  K  M  G  E  F  A  E  L  R  D 
   1894 ctgctggagcgagcaatcatcgacacaccgccggtgctggtacgc
        L  L  E  R  A  I  I  D  T  P  P  V  L  V  R 
   1939 gacggtggtgttatcgcatcgggctataacgaagagctggatgag
        D  G  G  V  I  A  S  G  Y  N  E  E  L  D  E 
   1984 tggcgcgcgctggctgacggcgcgaccgattatctggagcgtctg
        W  R  A  L  A  D  G  A  T  D  Y  L  E  R  L 
   2029 gaagtccgcgagcgtgaacgtaccggcctggacacgctgaaagtt
        E  V  R  E  R  E  R  T  G  L  D  T  L  K  V 
   2074 ggctttaatgcggtgcacggctactacattcaaatcagccgtggg
        G  F  N  A  V  H  G  Y  Y  I  Q  I  S  R  G 
   2119 caaagccatctggcacccatcaactacatgcgtcgccagacgctg
        Q  S  H  L  A  P  I  N  Y  M  R  R  Q  T  L 
   2164 aaaaacgccgagcgctacatcattccagagctaaaagagtacgaa
        K  N  A  E  R  Y  I  I  P  E  L  K  E  Y  E 
   2209 gataaagttctcacctcaaaaggcaaagcactggcactggaaaaa
        D  K  V  L  T  S  K  G  K  A  L  A  L  E  K 
   2254 cagctttatgaagagctgttcgacctgctgttgccgcatctggaa
        Q  L  Y  E  E  L  F  D  L  L  L  P  H  L  E 
   2299 gcgttgcaacagagcgcgagcgcgctggcggaactcgacgtgctg
        A  L  Q  Q  S  A  S  A  L  A  E  L  D  V  L 
   2344 gttaacctggcggaacgggcctataccctgaactacacctgcccg
        V  N  L  A  E  R  A  Y  T  L  N  Y  T  C  P 
   2389 accttcattgataaaccgggcattcgcattaccgaaggtcgccat
        T  F  I  D  K  P  G  I  R  I  T  E  G  R  H 
   2434 ccggtagttgaacaagtactgaatgagccatttatcgccaacccg
        P  V  V  E  Q  V  L  N  E  P  F  I  A  N  P 
   2479 ctgaatctgtcgccgcagcgccgcatgttgatcatcaccggtccg
        L  N  L  S  P  Q  R  R  M  L  I  I  T  G  P 
   2524 aacatgggcggtaaaagtacctatatgcgccagaccgcactgatt
        N  M  G  G  K  S  T  Y  M  R  Q  T  A  L  I 
   2569 gcgctgatggcctacatcggcagctatgtaccggcacaaaaagtc
        A  L  M  A  Y  I  G  S  Y  V  P  A  Q  K  V 
   2614 gagattggacctatcgatcgcatctttacccgcgtaggcgcggca
        E  I  G  P  I  D  R  I  F  T  R  V  G  A  A 
   2659 gatgacctggcgtccgggcgctcaacctttatggtggagatgact
        D  D  L  A  S  G  R  S  T  F  M  V  E  M  T 
   2704 gaaaccgccaatattttacataacgccaccgaatacagtctggtg
        E  T  A  N  I  L  H  N  A  T  E  Y  S  L  V 
   2749 ttaatggatgagatcgggcgtggaacgtccacctacgatggtctg
        L  M  D  E  I  G  R  G  T  S  T  Y  D  G  L 
   2794 tcgctggcgtgggcgtgcgcggaaaatctggcgaataagattaag
        S  L  A  W  A  C  A  E  N  L  A  N  K  I  K 
   2839 gcattgacgttatttgctacccactatttcgagctgacccagtta
        A  L  T  L  F  A  T  H  Y  F  E  L  T  Q  L 
   2884 ccggagaaaatggaaggcgtcgctaacgtgcatctcgatgcactg
        P  E  K  M  E  G  V  A  N  V  H  L  D  A  L 
   2929 gagcacggcgacaccattgcctttatgcacagcgtgcaggatggc
        E  H  G  D  T  I  A  F  M  H  S  V  Q  D  G 
   2974 gcggcgagcaaaagctacggcctggcggttgcagctctggcaggc
        A  A  S  K  S  Y  G  L  A  V  A  A  L  A  G 
   3019 gtgccaaaagaggttattaagcgcgcacggcaaaagctgcgtgag
        V  P  K  E  V  I  K  R  A  R  Q  K  L  R  E 
   3064 ctggaaagcatttcgccgaacgccgccgctacgcaagtggatggt
        L  E  S  I  S  P  N  A  A  A  T  Q  V  D  G 
   3109 acgcaaatgtctttgctgtcagtaccagaagaaacttcgcctgcg
        T  Q  M  S  L  L  S  V  P  E  E  T  S  P  A 
   3154 gtcgaagctctggaaaatcttgatccggattcactcaccccgcgt
        V  E  A  L  E  N  L  D  P  D  S  L  T  P  R 
   3199 caggcgctggagtggatttatcgcttgaagagcctggtgtaa 3240   
        Q  A  L  E  W  I  Y  R  L  K  S  L  V  * 

3.Perform protein sequence homology searching for MLH1 in GenBank. Give the 10 highest hits.
ans:
gi|16130640|ref|NP_417213.1|  methyl-directed mismatch repai...  1576  0.0
gi|15832843|ref|NP_311616.1|  MutS protein [Escherichia coli...  1571  0.0
gi|15803252|ref|NP_289284.1|  methyl-directed mismatch repai...  1569  0.0
gi|1592569|gb|AAB97931.1|  (U69873) DNA mismatch repair prot...  1564  0.0
gi|16421457|gb|AAL21789.1|  (AE008832) methyl-directed misma...  1500  0.0
gi|417330|sp|P10339|MUTS_SALTY  DNA MISMATCH REPAIR PROTEIN ...  1473  0.0
gi|11514100|pdb|1E3M|A  Chain A, The Crystal Structure Of E....  1419  0.0
gi|79102|pir||A28668  DNA mismatch repair protein mutS - Sal...  1406  0.0
gi|16123504|ref|NP_406817.1|  DNA mismatch repair protein Mu...  1340  0.0
gi|16272647|ref|NP_438865.1|  DNA mismatch repair protein (m...  1130  0.0

4. Compare human MLH1 protein with MLH1 in M. musculus, R. norvegicus and D. melanogaster. Give the pairwise alignment and % of sequence smility.
ans: a.M. musculus
    Score =  608 bits (1569), Expect = e-173
 Identities = 309/385 (80%), Positives = 335/385 (86%), Gaps = 4/385 (1%)
 Frame = +2
Query: 959  DKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQ--AIVTEDKTDISSGRARQQDEEMLE 1132
            DKVYA+QMVRTDSREQKLDAFLQP+S    SQPQ  A V   +T+ S  RA ++DEEML 
Sbjct: 100  DKVYAYQMVRTDSREQKLDAFLQPVSSLGPSQPQDPAPVRGARTEGSPERATREDEEMLA 159

Query: 1133 LPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSS--NPRKRHRXXXXXXXXXXXXRKEMT 1306
            LPAPAE AA++++LE ++   TS+ ++K  PTSS  + RKRHR             KEMT
Sbjct: 160  LPAPAEAAAESENLERESLMETSDAAQKAAPTSSPGSSRKRHREDSDVEMVENASGKEMT 219

Query: 1307 AACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLN 1486
            AAC PRRRIINLTSVLSLQEEI+E+ HE LREML NHSFVGCVNPQWALAQHQTKLYLLN
Sbjct: 220  AACYPRRRIINLTSVLSLQEEISERCHETLREMLRNHSFVGCVNPQWALAQHQTKLYLLN 279

Query: 1487 TTKLSEELFYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYI 1666
            TTKLSEELFYQILIYDFANFGVLRLSEPAPLFD AMLALDSPESGWTE+DGPKEGLAEYI
Sbjct: 280  TTKLSEELFYQILIYDFANFGVLRLSEPAPLFDRAMLALDSPESGWTEDDGPKEGLAEYI 339

Query: 1667 VEFLKKKAEMLADYFSLEIDEEGNLIGLPLLIDNYVPPLEGLPIFILRLATEVNWDEEKE 1846
            VEFLKKKAEMLADYFS+EIDEEGNLIGLPLLID+YVPPLEGLPIFILRLATEVNWDEEKE
Sbjct: 340  VEFLKKKAEMLADYFSVEIDEEGNLIGLPLLIDSYVPPLEGLPIFILRLATEVNWDEEKE 399

Query: 1847 CFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIVYKALRSHILPP 2026
            CFESLSKECAMFYSIRKQYI EESTLSGQQS++PGS    WKWTVEHI+YKA RSH+LPP
Sbjct: 400  CFESLSKECAMFYSIRKQYILEESTLSGQQSDMPGSTSKPWKWTVEHIIYKAFRSHLLPP 459

Query: 2027 KHFTEDGNILQLANLPDLYKVFERC 2101
            KHFTEDGN+LQLANLPDLYKVFERC
Sbjct: 460  KHFTEDGNVLQLANLPDLYKVFERC 484

b.R. norvegicus
Score =  588 bits (1517), Expect = e-167
 Identities = 298/383 (77%), Positives = 331/383 (85%), Gaps = 2/383 (0%)
 Frame = +2

Query: 959  DKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELP 1138
            DKV+A+QMVRTDSR+QKLDAF+QP+S+ L SQPQ  V  ++T+ S  +A Q+D+E+ ELP
Sbjct: 376  DKVHAYQMVRTDSRDQKLDAFMQPVSRRLPSQPQDPVPGNRTEGSPEKAMQKDQEISELP 435

Query: 1139 APAEVAAKNQSLEGDTTKGTSEM-SEKRGPTS-SNPRKRHRXXXXXXXXXXXXRKEMTAA 1312
            AP E AA + SLE ++  G SE+ + +R P+S  + RKRH             RKEMTAA
Sbjct: 436  APMEAAADSASLERESVIGASEVVAPQRHPSSPGSSRKRHPEDSDVEMMENDSRKEMTAA 495

Query: 1313 CTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTT 1492
            C PRRRIINLTSVLSLQEEIN++GHE LREML NH+FVGCVNPQWALAQHQTKLYLLNTT
Sbjct: 496  CYPRRRIINLTSVLSLQEEINDRGHETLREMLRNHTFVGCVNPQWALAQHQTKLYLLNTT 555

Query: 1493 KLSEELFYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVE 1672
            KLSEELFYQILIYDFANFGVLRL EPAPLFD AMLALDSPESGWTEEDGPKEGLAEYIVE
Sbjct: 556  KLSEELFYQILIYDFANFGVLRLPEPAPLFDFAMLALDSPESGWTEEDGPKEGLAEYIVE 615

Query: 1673 FLKKKAEMLADYFSLEIDEEGNLIGLPLLIDNYVPPLEGLPIFILRLATEVNWDEEKECF 1852
            FLKKKA+MLADYFS+EIDEEGNLIGLPLLID+YVPPLEGLPIFILRLATEVNWDEE ECF
Sbjct: 616  FLKKKAKMLADYFSVEIDEEGNLIGLPLLIDSYVPPLEGLPIFILRLATEVNWDEE-ECF 674

Query: 1853 ESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIVYKALRSHILPPKH 2032
            ESLSKECA+FYSIRKQYI EES LSGQQS++PGS    WKWTVEHI+YKA RSH+LPPKH
Sbjct: 675  ESLSKECAVFYSIRKQYILEESALSGQQSDMPGSPSKPWKWTVEHIIYKAFRSHLLPPKH 734

Query: 2033 FTEDGNILQLANLPDLYKVFERC 2101
            FTEDGN+LQLANLPDL KVFERC
Sbjct: 735  FTEDGNVLQLANLPDLCKVFERC 757

c.D. melanogaster
Score =  208 bits (529), Expect = 2e-52
 Identities = 107/260 (41%), Positives = 158/260 (60%)
 Frame = +2

Query: 1322 RRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLS 1501
            + R + L+SVL +++ +  Q    LR  L N  +VGCV+ + AL QH+T+LY+ NT   S
Sbjct: 421  KSREVRLSSVLDMRKRVERQCSVQLRSTLKNLVYVGCVDERRALFQHETRLYMCNTRSFS 480

Query: 1502 EELFYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLK 1681
            EELFYQ +IY+F N   + +S P PL +L +L+L+S  +GWT EDG K  LA+   + L 
Sbjct: 481  EELFYQRMIYEFQNCSEITISPPLPLKELLILSLESEAAGWTPEDGDKAELADGAADILL 540

Query: 1682 KKAEMLADYFSLEIDEEGNLIGLPLLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESL 1861
            KKA ++ +YF L I E+G L  LP L+  + P +  LP+++LRLATEV+W++E  CFE+ 
Sbjct: 541  KKAPIMREYFGLRISEDGMLESLPSLLHQHRPCVAHLPVYLLRLATEVDWEQETRCFETF 600

Query: 1862 SKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIVYKALRSHILPPKHFTE 2041
             +E A FY+              Q     G+     +WT+EH+++ A + ++LPP    +
Sbjct: 601  CRETARFYA--------------QLDWREGATAGFSRWTMEHVLFPAFKKYLLPPPRIKD 646

Query: 2042 DGNILQLANLPDLYKVFERC 2101
               I +L NLP LYKVFERC
Sbjct: 647  --QIYELTNLPTLYKVFERC 664

5. Search the conserve domain (CD) for MLH1. Give the position of the CD, name of CD and Pfam ID number.
ans:gnl|Pfam|pfam01119, DNA_mis_repair, DNA mismatch repair protein. Also known as the mutL/hexB/PMS1 family
Query:  147  GTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRT  206
Sbjct:  1    GTTVEVRDLFYNLPVRRKFLKSPKKEFRKILDLLQRYALIHPNVSFSLTKEGKALLQLKT  60

Query:  207  LPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAFKMNGYISNANYSV-KKCIFLLFINHR  265
Sbjct:  61   SPS-SLKERIRSVFGTAVLKNLIPF--EEKDGDFRIEGFISSPNVSRSSRDRQFLFINGR  117

Query:  266  LVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILER  325
Sbjct:  118  PVEDKLLLKAIREVYATYLPRGRYPVFVLNLELPPELVDVNVHPDKKEVRLLKEEEILDL  177

Query:  326  VQ  327
Sbjct:  178  IK  179

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 GTTVEVRDLFYNLPVRRKFLKSPKKEFRKILDLLQRYALIHPNVSFSLTKEG--KALLQL 58
query      147 GTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQG--ETVADV 204
1B63_A     144 GTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNG--KIVRQY 201
gi 8039787 159 GTVVRVEQLFENFPARKRFLGRQSAETTLCRSALIDVSLAHHPVEFRFTVDGthKLTLLS 218
gi 8928214 141 GTIVDVTKIFHNFPARKRFLKQEPIETKMCLKVLEEKIITHPEINFEIN-LN--QKLRKI 197

 
                       70        80        90       100       110       120
               ....*....|....*....|....*....|....*....|....*....|....*....|
consensus   59 KTSP--S-SLKERIRSVFGTAVLKNLIPF--EEKDGDFRIEG-FISSPNVSR-SSRDRQF 111
query      205 RTLP--NaSTVDNIRSIFGNAVSRELIEIgcEDKTLAFKMNG-YISNANYSV--KKCIFL 259
1B63_A     202 RAVPegG-QKERRLGAICGTAFLEQALAI--EWQHGDLTLRG-WVADPNHTTpALAEIQY 257
gi 8039787 219 QQTR--K-DRCLETQMLKGDPALFHTIEG--G--DCSFHFHLvLSEPAICRR--ERRGIF 269
gi 8928214 198 YFK---E-SLIDRVQNVYGNVIENNKFRV--LKKEHDNIKIEiFLAPDNFSK-KSKRHIK 250

 
                      130       140       150       160       170       180
               ....*....|....*....|....*....|....*....|....*....|....*....|
consensus  112 LFINGRPVEDKLLLKAIREVYATYLPRGRYPVFVLNLELPPELVDVNVHPDKKEVRLLKE 171
query      260 LFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHE 319
1B63_A     258 CYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQS 317
gi 8039787 270 TFVNGRRIFDYGLVQALVLGSEGYFPNGTFPVACLFLTVNSERIDFNIHPAKKEVHLQDY 329
gi 8928214 251 TFVNRRPIDQKDLLEAITNGHSRILSPGNFPICYLFLEINPEYIDFNVHPQKKEVRFYNL 310

 

               ....*...
consensus  172 EEILDLIK 179
query      320 ESILERVQ 327
1B63_A     318 RLVHDFIY 325
gi 8039787 330 AHIRHTLS 337
gi 8928214 311 PFLFKLIS 318