| 3.3 | Class: Fork head / winged helix factors (FKH), Alignment |
| Note: The three families of this class do not share significant sequence similarities. Therefore, the sequence aligments of their DNA-binding domains will be listed separately for the FOX family (3.3.1), the E2F family (3.3.2), and the RFX family (3.3.3). | |
| Aligned FOX sequences (Family 3.3.1): | |
KPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQ-----RWQNSIRHSLSFNDCFVKVARSPDKP----GKGSYWTLHPDSGNMFENGCYLRRQKR FOXA1 KPPYSYISLITMAIQQSPNKMLTLSEIYQWIMDLFPFYRQNQQ-----RWQNSIRHSLSFNDCFLKVPRSPDKP----GKGSFWTLHPDSGNMFENGCYLRRQKR FOXA2 KPPYSYISLITMAIQQAPGKMLTLSEIYQWIMDLFPYYRENQQ-----RWQNSIRHSLSFNDCFVKVARSPDKP----GKGSYWALHPSSGNMFENGCYLRRQKR FOXA3 KPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPYYRENTQ-----RWQNSLRHNLSFNDCFIKIPRRPDQP----GKGSFWALHPSCGDMFENGSFLRRQKR FOXB1 KPPYSYISLTAMAIQHSAEKMLPLSDIYKFIMERFPYYREHTQ-----RWQNSLRHNLSFNDCFIKIPRRPDQP----GKGSFWALHPDCGDMFENGSFLRRRKR FOXB2 KPPYSYIALITMAIQNAPDKKITLNGIYQFIMDRFPFYRDNKQ-----GWQNSIRHNLSLNECFVKVPRDDKKP----GKGSYWTLDPDSYNMFENGSFLRRRRR FOXC1 KPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQ-----GWQNSIRHNLSLNECFVKVPRDDKKP----GKGSYWTLDPDSYNMFENGSFLRRRRR FOXC2 KPPYSYIALITMAILQSPKKRLTLSEICEFISGRFPYYREKFP-----AWQNSIRHNLSLNDCFVKIPREPGNP----GKGNYWTLDPESADMFDNGSFLRRRKR FOXD1 KPPYSYIALITMAILQSPKKRLTLSEICEFISGRFPYYREKFP-----AWQNSIRHNLSLNDCFVKIPREPGNP----GKGNYWTLDPESADMFDNGSFLRRRKR FOXD2 KPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFP-----AWQNSIRHNLSLNDCFVKIPREPGNP----GKGNYWTLDPQSEDMFDNGSFLRRRKR FOXD3 KPPSSYIALITMAILQSPHKRLTLSGICAFISDRFPYYRRKFP-----AWQNSIRHNLSLNDCFVKIPREPGRP----GKGNYWSLDPASQDMFDNGSFLRRRKR FOXD4 KPPYSYIALITMAILQSPHKRLTLSGICAFISGRFPYYRRKFP-----AWQNSIRHNLSLNDCFVKIPREPGHP----GKGTYWSLDPASQDMFDNGSFLRRRKR FOXD4L1 KPPYSYIALITMAILQNPHKRLTLSGICAFISGRFPYYRRKFP-----AWQNSIRHNLSLNDCFVKIPREPGHP----GKGNYWSLDPASQDMFDNGSFLRRRKR FOXD4L2 KPPYSYIALITMAILQNPHKRLTLSGICAFISGRFPYYRRKFP-----AWQNSIRHNLSLNDCFVKIPREPGHP----GKGNYWSLDPASQDMFDNGSFLRRRKR FOXD4L3 KPPYSYIALITMAILQNPHKRLTLSGICAFISGRFPYYRRKFP-----AWQNSIRHNLSLNDCFVKIPREPGHP----GKGNYWSLDPASQDMFDNGSFLRRRKR FOXD4L4 KPPYSYIALITMAILQNPHKRLTLSGICAFISGRFPYYRRKFP-----AWQNSIRHNLSLNDCFVKIPREPGHP----GKGNYWSLDPASQDMFDNGSFLRRRKR FOXD4L5 KPPYSYIALITMAILQNPHKRLTLSGICAFISGRFPYYRRKFP-----AWQNSIRHNLSLNDCFVKIPREPGHP----GKGNYWSLDPASQDMFDNGSFLRRRKR FOXD4L6 KPPYSYIALIAMAIAHAPERRLTLGGIYKFITERFPFYRDNPK-----KWQNSIRHNLTLNDCFLKIPREAGRP----GKGNYWALDPNAEDMFESGSFLRRRKR FOXE1 KPPYSYIALIAMALAHAPGRRLTLAAIYRFITERFAFYRDSPR-----KWQNSIRHNLTLNDCFVKVPREPGNP----GKGNYWTLDPAAADMFDNGSFLRRRKR FOXE3 KPPYSYIALIVMAIQSSPTKRLTLSEIYQFLQSRFPFFRGSYQ-----GWKNSVRHNLSLNECFIKLPKGLGRP----GKGHYWTIDPASEFMFEEGSFRRRPRG FOXF1 KPPYSYIALIVMAIQSSPSKRLTLSEIYQFLQARFPFFRGAYQ-----GWKNSVRHNLSLNECFIKLPKGLGRP----GKGHYWTIDPASEFMFEEGSFRRRPRG FOXF2 KPPFSYNALIMMAIRQSPEKRLTLNGIYEFIMKNFPYYRENKQ-----GWQNSIRHNLSLNKCFVKVPRHYDDP----GKGNYWMLDPSSDDVFIGGTTGKLRRR FOXG1 KPPYTYLAMIALVIQAAPSRRLKLAQIIRQVQAVFPFFREDYE-----GWKDSIRHNLSSNRCFRKVPKDPAKPQ---AKGNFWAVDVSLIPAEALRLQNTALCR FOXH1 RPPYSYSALIAMAIHGAPDKRLTLSQIYQYVADNFPFYNKSKA-----GWQNSIRHNLSLNDCFKKVPRDEDDP----GKGNYWTLDPNCEKMFDNGNFRRKRKR FOXI1 RPPYSYSALIAMAIQSAPLRKLTLSQIYQYVAGNFPFYKRSKA-----GWQNSIRHNLSLNDCFKKVPRDEDDP----GKGNYWTLDPNCEKMFDNGNFRRKRKR FOXI2 RPPYSYSALIAMAIQSAPERKLTLSHIYQFVADSFPFYQRSKA-----GWQNSIRHNLSLNDCFKKVPRDEDDP----GKGNYWTLDPNCEKMFDNGNFRRKRKR FOXI3 KPPYSYATLICMAMQASKATKITLSAIYKWITDNFCYFRHADP-----TWQNSIRHNLSLNKCFIKVPREKDEP----GKGGFWRIDPQYAERLLSGAFKKRRLP FOXJ1 KPRYSYATLITYAINSSPAKKMTLSEIYRWICDNFPYYKNAGI-----GWKNSIRHNLSLNKCFRKVPRPRDDP----GKGSYWTIDTCPDISRKRRHPPDDDLS FOXJ2 KPPYSYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGS-----GWKNSIRHNLSLNKCFLKVPRSKDDP----GKGSYWAIDTNPKEDVLPTRPKKRARS FOXJ3 KPPFSYAQLIVQAISSAQDRQLTLSGIYAHITKHYPYYRTADK-----GWQNSIRHNLSLNRYFIKVPRSQEEP----GKGSFWRIDPASEAKLVEQAFRKRRQR FOXK1 KPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADK-----GWQNSIRHNLSLNRYFIKVPRSQEEP----GKGSFWRIDPASESKLIEQAFRKRRPR FOXK2 KPPYSYIALIAMAIQDAPEQRVTLNGIYQFIMDRFPFYHDNRQ-----GWQNSIRHNLSLNDCFVKVPREKGRP----GKGSYWTLDPRCLDMFENGNYRRRKRK FOXL1 KPPYSYVALIAMAIRESAEKRLTLSGIYQYIIAKFPFYEKNKK-----GWQNSIRHNLSLNECFIKVPREGGGE----RKGNYWTLDPACEDMFEKGNYRRRRRM FOXL2 RPPYSYMAMIQFAINSTERKRMTLKDIYTWIEDHFPYFKHIAKP----GWKNSIRHNLSLHDMFV---RETSAN----GKVSFWTIHPSANRYLTLDQVFKPLDP FOXM1 KPIYSYSILIFMALKNSKTGSLPVSEIYNFMTEHFPYFKTAPD-----GWKNSVRHNLSLNKCFEKVENKSGSSS---RKGCLWALNPAKIDKMQEELQKWKRKD FOXN1 KPPYSFSLLIYMAIEHSPNKCLPVKEIYSWILDHFPYFATAPT-----GWKNSVRHNLSLNKCFQKVERSHGKVN---GKGSLWCVDPEYKPNLIQALKKQPFSS FOXN2 KPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPT-----GWKNSVRHNLSLNKCFKKVDKERSQSI---GKGSLWCIDPEYRQNLIQALKKTPYHP FOXN3 KPIYSYSCLIAMALKNSKTGSLPVSEIYSFMKEHFPYFKTAPD-----GWKNSVRHNLSLNKCFEKVENKMSGSS---RKGCLWALNLARIDKMEEEMHKWKRKD FOXN4 WGNLSYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIRVQNEGT------GKSSWWMLNPEGGKSGKSPRRRAASMD FOXO1 WGNLSYADLITRAIESSPDKRLTLSQIYEWMVRCVPYFKDKGDSNSSAGWKNSIRHNLSLHSRFMRVQNEGT------GKSSWWIINPDGGKSGKAPRRRAVSMD FOXO3 WGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNEAT------GKSSWWMLNPEGGKSGKAPRRRAASMD FOXO4 WGNLSYADLITKAIESAPDKRLTLSQIYDWMVRYVPYFKDKGDSNSSAGWKNSIRHNLSLHTRFIRVQNEGT------GKSSWWMLNPEGGKTGKTPRRRAVSMD FOXO6 RPPFTYASLIRQAILESPEKQLTLNEIYNWFTRMFAYFRRNAA-----TWKNAVRHNLSLHKCFVRVEN---------VKGAVWTVDEVEFQKRRPQKISGNPSL FOXP1 RPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAA-----TWKNAVRHNLSLHKCFVRVEN---------VKGAVWTVDEVEYQKRRSQKITGSPTL FOXP2 RPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPA-----TWKNAIRHNLSLHKCFVRVES---------EKGAVWTVDELEFRKKRSQRPSRCSNP FOXP3 RPPFTYASLIRQAILETPDRQLTLNEIYNWFTRMFAYFRRNTA-----TWKNAVRHNLSLHKCFVRVEN---------VKGAVWTVDEREYQKRRPPKMTGSPTL FOXP4 KPPYSYIALIAMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYT-----GWRNSVRHNLSLNDCFVKVLRDPSRPW---GKDNYWMLNPNSEYTFADGVFRRRRKR FOXQ1 RPPLNYFHLIALALRNSSPCGLNVQQIYSFTRKHFPFFRTAPE-----GWKNTVRHNLCFRDSFEKVPVSMQGGASTRPRSCLWKLTEEGHRRFAEEARALASTR FOXR1 RPPLNCSHLIALALRNNPHCGLSVQEIYNFTRQHFPFFWTAPD-----GWKSTIHYNLCFLDSFEKVPDSLKDEDNARPRSCLWKLTKEGHRRFWEETRVLAFAQ FOXR2 KPPYSYIALIAMAIQSSPGQRATLSGIYRYIMGRFAFYRHNRP-----GWQNSIRHNLSLNECFVKVPRDDRKP----GKGSYWTLDPDCHDMFEHGSFLRRRRR FOXS1
| Aligned E2F sequences (Family 3.3.2): | |
| Note that E2F-7 and E2F-8 have two (potential) DBDs of FKH type, denoted E2F-7(or 8)-1 and E2F-7(or 8)-2, resp. |
SRYETSLNLTTKRFLELLS----HSADGVVDLNWAAEVLKV-Q--------------------KRRIYDITNVLEGIQLIAKKSKNHIQWLG E2F-1 TRYDTSLGLLTKKFIYLLS----ESEDGVLDLNWAAEVLDVQ---------------------KRRIYDITNVLEGIQLIRKKAKNNIQWVG E2F-2 TRYDTSLGLLTKKFIQLLS----QSPDGVLDLNKAAEVLKVQ---------------------KRRIYDITNVLEGIHLIKKKSKNNVQWMG E2F-3 SRHEKSLGLLTTKFVSLLQ----EAKDGVLDLKLAADTLAVRQ--------------------KRRIYDITNVLEGIGLIEKKSKNSIQWKG E2F-4 SRHEKSLGLLTTKFVSLLQ----EAKDGVLDLKAAADTLAVRQ--------------------KRRIYDITNVLEGIDLIEKKSKNSIQWKG E2F-5 PRFDVSLVYLTRKFMDLVR----SAPGGILDLNKVATKLGVR---------------------KRRVYDITNVLDGIDLVEKKSKNHIRWIG E2F-6 SRKQKSLGLLCQKFLARYPSYPLSTEKTTISLDEVAVSLGVE---------------------RRRIYDIVNVLESLHLVSRVAKNQYGWHG E2F-7-1 SRKDKSLRIMSQKFVMLFL----VSKTKIVTLDVAAKILIEE-SQDAPDHSKFKTKVRRLYDIANVLTSLALIKKVHVTEERGRKPAFKWIG E2F-7-2 SRKEKSLGLLCHKFLARYPNYPNPAVNNDICLDEVAEELNVE---------------------RRRIYDIVNVLESLHMVSRLAKNRYTWHG E2F-8-1 SRKDKSLRVMSQKFVMLFL----VSTPQIVSLEVAAKILIGEDHVEDLDKSKFKTKIRRLYDIANVLSSLDLIKKVHVTEERGRKPAFKWTG E2F-8-2 EKNGKGLRHFSMKVCEKVQ------RKGTTSYNEVADELVAEFSAADNHILPNESAYDQK-NIRRRVYDALNVLMAMNIISKEKKE-IKWIG Dp-1 DKNGKGLRHFSMKVCEKVQ------RKGTTSYNEVADELVSEFTNSNNH-LAADSAYDQK-NIRRRVYDALNVLMAMNIISKEKKE-IKWIG Dp-2
| Aligned RFX sequences (Family 3.3.3): |
TVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKL-EPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA RFX1 HLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKL-DPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGIRLKP RFX2 HLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKL-DPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKP RFX3 TLQWLEENYEIAEGVCIPRSALYMHYLDFCEKNDT-QPVNAASFGKIIRQQFPQLTTRRLGTRGQSKYHYYGIAVKE RFX4 AYRWIRNHLEEHTDTCLPKQSVYDAYRKYCESLACCRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT RFX5 TLQWLEENYIVCEGVCLPRCILYAHYLDFCRKEKL-EPACAATFGKTIRQKFPLLTTRRLGTRGHSKYHYYGIGIKE RFX6 AFSWIRNTLEEHPETSLPKQEVYDEYKSYCDNLGY-HPLSAADFGKIMKNVFPNMKARRLGTRGKSKYCYSGLRKKA RFX7 VIQWLVDNFCICEECSVPRCLMYEIYVETCGQNTE-NQVNPATFGKLVRLVFPDLGTRRLGTRGSARYHYDGICIKK RFX8