a GAG - zinc finger
REAL KTKRAPLTCYSCGKPGHIARDCQSTTRVRR
Skippy KRDKSKVTCYNCGKKGHYERECKNPVKTNQ
MpSaci11 QDYMKKGLCFYCSKTGHRVRDCPLKGGNSA
MpSaci13 QDYMKKGLCFYCSKTGHRVRDCPLKGGNSA
MpSaci14 QDYMKKGLCFYCSKTGHRVRDCPLKGGNSA
MpSaci4 QEYMKKGLCFYCSKTGHRVRDCPLKGSNSA
MpSaci9 QEYMQRGQCFRCSKTGHRARDCPSKGPTNT
grh QRRRETGACLRCGNSGHQVADCTYAAALRP
MAGGY HNRKENMLCYRCGSQEHFVAKCPEPDTRRT
marY1 SRARKLDLCYRCGEPGHRAGACPHRQDIRM
MpSaci6 NGGHEREICGHCTRAGHREAVCFDKWAGKP
* * * *
b Pol - protease
MpSaci1 IKALIDSGAGGR-FISPDFAKTLGKRWNKLRKPIKVYNIDGTP--NKTA-MITHSVLFEYSSGTKTFC-EEFMIS-GLGKEKLILGLPWLQNH
MpSaci15 IKALIDSGAGGR-FISLDFAKTLGKQWNKLRKPIKVYNVDGTP--NKTA-MITHSVLFEYSSGTKTFC-EEFMIS-GLGKEKLILGLPWLQNH
MpSaci9 KEALIDSGAGGK-FISHSAAK--GLKWKKLLKPIEVFNVDQTP--NKKG-MITHTVEVPLTIAGRQIR-EELYIS-GLGNKEIILGLPWLRKY
MpSaci12 KEALIDSGAGGK-FISHSAAR--GLKWKKLPKPIEVFNVDQTP--NKKG-MITHTVEVPLTIAGRQIR-EELYIS-GLGNEEIILGLPWLRKH
MpSaci6 IVAMIDSGATG-LFISRSWVTENQVWRHRLKREIPLYNIDGTK--NRAG-SISEFVRLELTIGEYVEV-IELLVT-DLGPEEVILGLPWLKKV
marY1 VSALLDSGATGL-FIDSHLVQQHRLNTRSLSRPIPVYNVDGSP--NEAG-AIREVADLVLRYKDHSER-ALFAVT-QLGKQKAILGYPWLRDH
MAGGY TYALTDCGAEGKCFLDQGWAEERQLQMYPLRNPFDIEVFDGRT--AESG-KCTHYVRGQLRIKDHIQKNALFFVT-QLAHYPIVLGMPWLKQH
grh VNAQVDSGCECYAAMSDKCAT--RLRIERIPLPQ-ARHVGTAV--GRAQPMIRELAKCEMDVDGWVTPMLFYIVP-GLA-RDVILGLPWMTHR
REAL AQALVDSGCLCYSLVNKKFAY--RHRLERFQIP--VRIIEGVN--GKLS-EINEVARFSFKLHGHEETAYAYVMDLSFG-EDIYLGRGWMNHN
Skippy LSALVDSGADMN-FISPTTVNELRLPWKDKNDPYTVHDGQGETYLYENGNITREIDHLKVFVNGKNQG-IDFDII-PVWRYDLVLGYPWLLRY
* * * ** *
c Pol - reverse transcriptase
1 2 3
------
marY1 LASGRIRPSKSPMASPFFFVKKKD-GSLRPVQDYRRLNNITVKNRYPLPLISELVNQLHGARYFTKLDVRWGYNNVRIKEGDEWKAAFRTNRG
MpSaci6 LRKGYIVPSKSPLASPVFFVKKKD-GKLRFVQDYRKLNEFTIKNRYPLPLASDIINRLKGARYFTKLDVRWGYNNIRIKEGDEWKAAFVTNRG
MpSaci1 LRKKYIRPSVSPIAAPFFFVSKKEKGALRPCQDYRDLNSGTVKNAYPLPLVGNLLDKLKGATIFSKLDLRNGYNNIRIKDGDQWKAAFRTEKG
MpSaci15 LRKKYIRPSVSPIAAPFFFVSKKEKGALRPCQDYRDLNSGTIKNAYPLPLVGNLLDKLKGATIFSKLDLRNRYNNIRIKDGDQWKVAFRTEKG
MpSaci9 LRKGYIQESKSPMASPFFFVSKKEKGALRPCQDYRHLNLGTVKNAFPLPLVTDLIDKLNEATIFTKMDLRNGYNNIRIKEGDEWKAAFRTPDG
MpSaci12 LRKGYIQESKSPMASPFFFVSKKEKGALRPCQDYRHLNLGTVKNAFPLPLVTDLIDKLNEATIFTKMDLRNGYNNIRIKEGDEWKAAFRTPNG
grh MDKGWIRASSSSAAAPVLMVRKASGG-WRLCVDYRALNSITMQDRYPLPLIKETIRSLTGARWFTKVDVRAAFHKLRIAEGDEHLTAFRTRFG
REAL LEKGFIRVSSSPAAAPVLFAKKPGGG-LRLCIDYRALNAITKKDRYPLPLIRETLNNLSKAKWFTKLDVIAAFHKIRVAEGDEWKTAFRTRFG
MAGGY LKKGFIRPSSSSVASPVLFVKKQGGG-LRFCVDYRALNNITVKDRYPLPLVRETLNNLAGMKFFSKIDIVSAFNNIRIKKGEEYLTAFRTRFG
Skippy IRKGYIRPSKSSAGFPVMFVPKPNSNKLRLVVDYRQLNEITEKDRTSLPLITELKDRLFGKKWFTALDLKSAYNLIRIKEADEWKTAFRTKYG
* * * * * * *** ** * *** * * * * ** * *
4 5 6 7
------
marY1 LFELLVMFFGLTNSPATFQTMMNDIFHDLILEGVVCIYLDDILIFTR-MVEEHRRITRLVLERLRRYKLYLHQDKCEFERTKIEYLGLII
MpSaci6 LFEPQVMFFGLTNSPATFQALMNSIFADLIAKGKVAVYLDDILIYST-TLEEHHQTTHEVLKRLQENDLYLRPEKCEFDQQQVEYLGMVI
MpSaci1 LFEPMVMFFGLANSPATFQVFMDDALSDFIAEGWCCVYMDDILIFSQ-NKEEHRTRTHQLLKRLADRDLFLKPEKCEFDVTEVNFLGMII
MpSaci15 LFEPMVMFFGLANSPATFQAFMDDTLSDFITEGWCCVYMDNILIFSR-NKEEHRTQTRRLLKRLADRDLFLKPEKCEFDVTEVNFLGMII
MpSaci9 LYEPLVMFFGLTNSPATFQAFMNDVFSDMIAEGWIVIYMDDILIFSK-DKEQHKERTRQVLQRLKKHDLFLKPEKCFFDVTEVEFLGMII
MpSaci12 LYEPLVMFFGLTNSPATFQAFMNDVFSDMIAEGWIVIYMDDILIFSK-DKEQHKERTRQVLQRLKEHDLFLKPEKCFFDVTEVEFLGMII
grh LFEWLVCPFGLAGAPATFQRYVNGVLGDTLGD-YASAYLDDILIYSSGSKSDHWSKVTRVLDKLAAAGLNLDLDKSAFAVKEVKYLGFIV
REAL LFEWLVTPFGMANSPSTFQRYINWTLREFLDD-FCSAYLDDVLIYTDGSLKQHQEHVRKVLRKLQDAGLQVDIKKCEFEVKSTKYLGFII
MAGGY LYESLVMPFGLTGAPATFQRYINDSLREYLDV-FCTAYLDDILIYSR-TRTEHEEHLKLVLEALRKAGLYANAAKCEFFVTETKFLGLLV
Skippy LFEYLVMPFGLTNAPAVFQRMITNVLREYLDI-FVVCYLDDILIFSD-TEEEHTEHVHKVLKALQDANMLVEPTKSHFHQSQVTYLGHEI
* * * ** * ** * * ** * * * * * **
Supplementary Fig. 2 Alignment of GAG and POL domains from different MpSaci elements and retrotransposons from other filamentous fungi. Amino acids highlighted in gray are conserved. Numbers 1 to 7 represent the reverse transcriptase domains described by Xiong Eickbush (1990). Conserved motifs in GAG, protease and reverse transcriptase are underlined. Inverted black triangles indicate the DDE motif at the integrase domain.
d Pol - RNase H
grh DAKDTRMETDCSGAALGGCLSQKGT-DGLWRPVAFHSAKLTDAQRNYTIHDKELLAVIACLKAWDAELRSVRRPFLILTDHKALEYFSKPREV
REAL PERETVLETDSSGFAVGGVLSQYGD-DGVLRPCAYFSRKNNAHECNYEIHDKELLAVVRCLEEWDSELRSVER-FKVITDHKNLEYFMKPRML
MAGGY WEKDVILETDASDYVSAGILSQYGD-DGILRPVAFFSKKHTATECNYEIYDKELLAIIRCFEEWRPELEGTSSPVQIITDHRNLEYFTTTKML
MpSaci1 LDKPFLLETDASKWASGGILRQKGP-DGEWHPCGYISHSFNQAERNYQIYDRELLAMIRALKEWRHYLMGGKFPFVILSDHDNLRYFRKPQDL
MpSaci15 LDKPFLLETDASKWASGGVLRQKGP-DGEWHLCGYISHSFNQAERNYQIYDRELLAMIRALKEWRHYLMGGKFPFVILSDHNNLRYFRKPQDL
MpSaci9 --KPFLIESDASKWATGAVLRQKGT-DNEWHPCGYLSHSFNATERNYEIYDRELLGIVRALEAWRHYLQGGPHPVTILSDHKNLEYFRSAQKL
MpSaci12 ISKPFLIESDASKWATGAVLRQKGT-DNEWHPCGYLSHSFNTTERNYEIYDRELLGIVRALEAWRHYLQGGPHPVTILSDHKNLEYFRSAQKL
MpSaci6 PERPTRLEVDASGYATGGVILQQLE-DGLWHPVAYRSESMAPAERNYEIYDREMLAIIRALEDWRHYLEGLPESFEIITDHQNLEYWRTAQDL
marY1 DLRPFRVEADSSDFAMGAVLSQQSPEDQKWHPVAFYSKSLSAVERNYEIHDKEMLAIMRALEEWRHFLEGAQHKVEIWTDHKNLEYFMTAKKL
Skippy PDRQVELETDASDFALGGQIGQRDD-NGVLHPIAFYSHKMHGAELNYPIYDKEFLAIVNCFKEFRHYLRGSKHPVKVFTDHKNIAYFATTQEL
* * * * * ** * * * *. * ** *
grh SERQMRWAETLSKFNYNLRFRPGRLAGVPDALSRREQDECTT
REAL NERQIRWSLLLGRYNMELLYRPGKQNVRADALSRREQDLPVG
MAGGY NRRQARWAEFLSRFNFRITYRPGKQGAKPDALTRRSEDMPEE
MpSaci1 NPRQARWLLFLSDFNFKMVHTPGKQLIQADALSRRP-DHVTD
MpSaci15 NPRQARWLLFLSEFNFKMVHTPGKQLIQADALSRRP-DHVTD
MpSaci9 NRRQARWSLFLSEFDLHLIHVPGPRMVQSDALSRRE-DHVLE
MpSaci12 NRRQARWSLFLSEFDLHLIHVPGPRMVQSDALSRRD-DHVLE
MpSaci6 SRRQARWSLWLSRFDFRLTHKPGKTNTQADPLSRIPALQVTD
marY1 NRRQARWSLYLSRFDFSLHHRPGRSMGKTDALSRRA-DHGDG
Skippy NRRQLRYAEYLCEFDFTIAHCKGTDNGRADAISRRP-DFDTG
** * * * * *
e Pol - Integrase
grh RGRLWLPNWEPLTTAVLQRTHESPMVGHSGRDGTFAILARDYHWDGMAEHVRRFVRNCDICRRTKPSRRARQGLLQPLPIPDR--FWKQISID
REAL RGRKWVPDSEKLRTQIISGAHDSLATGHPGREVTYKILARDYFWPGMTQTIRRYVRNCSTCGRSKSWREGKQGLLKPLPIPAQ--IWKEISMD
Skippy QSLTDQDEQERVEQEFIYEIHAHPLHGHQGVTKTMKRLQELGYRHFKKGQVEKVIKQCDLCAKTKAQRHKPYGQLQPLPVAQR--PWDSITMD
MAGGY RNRLYVPDSNNLKAEILRRCHDSPVAGHPGKAKTYDLLSREYYWPGMLHYVSLWVKKCQTCRRINPSREGHQGLLRPLPTPER--SWQHLSMD
MpSaci1 RGKTYVPDDLETRRRVVKEIHESFRTEHPGQYLTQELVQRSYWWPGLAKFVKNFVDGCVPCQQMKINTHPTRTPLIPIPGTTNALPFQICTMD
MpSaci15 KGKTYVPDDLETRRRIVKEIHKSFGTGHPGQYLTQELVQRSYWWPGLAKFVKNFVDGCVPCQQMKINTHPTRTPLIPIPRTANALPFQVCTMD
MpSaci9 KGKCYVPNNEKLRREVTKRIHESIHAGHPRRYNTEEQVKREYWWPGMAKFIKTFVDGCALCQQMKVNTHPTDAPLLPISGEKGTLPFTRITMD
MpSaci12 KGKCYVPNDEKLRREVTKRIHESIHAGHPGRYNTEEQVKREYWWPGMAKFIKTFVDGCALCQQMKVNTHPTDAPLLPISGEKGTLPFTRITMD
MpSaci6 RGKLYIPGDKGLRTDVLKQCHDAPTAGHLGEHGTLEQVSRYYWWPGMSSFVKKYVQGCEKCQRVKPAAHP-DATLHPHDVPEG--PWNVVGVD
marY1 RDRIYVPNDPDLRRRIISQHHDSQIAGHPGRWKTLELTSRNYWWPQMSRLIGQYCRTCDLCLCTKVPRRKPIGELHPLPVPES--RWDVVSVD
* * * . * * * * *
▼ ▼
grh FMTDLPGNGEVTP----RYLMVITDRLS-KYVQLEAMHS-MKAEDCAARFLSSWWRFRGFPSQIISDRGSDWVGGFWTELCRQTGVEQLLSTS
REAL FVEGLPESEGMTN------LMVITDRLS-KGTIFVPLPN-IKTDTVVQKFIERVVAYHWLPDAITSDRGRQFVSVLWTKLCELLKINRRLSTA
Skippy FITKLPLSEEPSTGIFYDSIMVIVDRLT-KFSYYLPYREATDAEELSYVFYRHIVSIHGLPTEILSDRGPTFAATFWQSLMARLGLNHRLTTA
MAGGY FITHLPQSNGHDA------ILVVVDRLT-KMRHFVPCKGTCNAEDTANLYLHHVWKLHGLPLTIVSDRGTQFVSKFWKHLTTRLKIDSLLSTA
MpSaci1 LITDLPEIDGFDS------IMVVVDHSSTKGVIFTPCTKTLNAEGAAKLLLDNLYRRFGLPDKLISDRDPRFAAEVFQEMGRLLGIKHSMTTA
MpSaci15 LITDLPEVDGFDS------IMVVVDHSSTKGVIFTPCTKTLNAEGAAKLLLDNLYRRFGLPDKLISDRDPRFAAEVFQEMGRLLGIKHSMTTA
MpSaci9 LITDLPESDGFDS------ILVVVDHSSTKGVILTPCNKTITTEGVANLILNNVYRRFGLPDNIISDRDPRFAANVFQELGRLLGIKLSMSTA
MpSaci12 LITDLPESDGFDS------ILVVVDHSSTKGVILTPCNKTITAEGVANLILNNVYRRFGLPDNIISDRDPRFAANVFQELGRLLGIKLSMSTA
MpSaci6 LITGFPESQGYDA------IITYVDLYS-KQVHVLPTVTTLDAKGVADLHYREIFRLHGIPHKFVSDRGPQFAAQVTRALYKRLGIQAGLTTA
marY1 FVVELPESNGFDA------VMCTVDSVG-KRAHFIPTHTTVSALGAARLYLHHVWKLHGLPGAFLSDRGPQFMAEFTRELYRLLGIKLLASTA
* * * * *** *
▼
grh YHPETDGGTERANQEVQQYLRAYIAFDQGDWPDHLGAAQLALNNRNSSVTGTSPNKLLLGFDIEAV
REAL YHPQTDGATERMNSVWETYIRSFTNWAQNDWALLCPMAQIAINGRTATSTSMSPFFLQHGYEVNPL
Skippy FRPQVDGQTERMNQVLEQYLRCYINYEQNDWVEKLPIAQLAYNTAYNESTKLTPAYANFGFTPNAY
MAGGY HHPETDGQTERFNASLEQYLRAYVAYLQDDWESWLPLAEFTANSHKSETTGTSPFYATYGFHPRMG
MpSaci1 YHPQSDGETKRVNQEIEVFLRMFCAREQTMWKDFLGFAEFAHNNRTHSTMKLSPFHMMMGYDPRPL
MpSaci15 YHPQSDGETERVNQEIEVFLRMFCAKEQTMWKDFLGFAEFAHNNRTHSTMKLSPFHMMMGYDPRPL
MpSaci9 YHPQTDRETERVNQEIETFLKMFCAKKQTQWNEYLPMAEFAHNNREHSTMKKSPFYLMYGYNPRPL
MpSaci12 YHPQTDGETERVNQEIETFLKMFCAKKQTQWNEYLPMAEFAHNNREHSTMKKSPFYLMYGYNPRPL
MpSaci6 YHPSANGQTERANQEIEQFLRLFVSKRQDDWVDWLPTAEFVLNSRVHTAHDKSPFEVVYGYRPDFT
marY1 YHPQTDGQTERVNQELEQYIRLFVNERQDDWDDLLPLAEFGYNNHVHASTQQTPFLLDTGRHPRMG
* * * * * * * * * *
Supplementary Fig. 2 Continued.