# STOCKHOLM 1.0
#=GF ID   Caudal_act
#=GF AC   PF04731.3
#=GF DE   Caudal like protein activation region
#=GF AU   Kerrison ND
#=GF SE   DOMO:DM04892;
#=GF GA   25.00 25.00; 15.30 15.30;
#=GF TC   46.20 46.20; 21.30 21.30;
#=GF NC   -6.30 -6.30; 13.20 11.50;
#=GF TP   Family
#=GF BM   hmmbuild -F HMM_ls SEED
#=GF BM   hmmcalibrate --seed 0 HMM_ls
#=GF BM   hmmbuild -f -F HMM_fs SEED
#=GF BM   hmmcalibrate --seed 0 HMM_fs
#=GF AM   globalfirst
#=GF RN   [1]
#=GF RM   11729123
#=GF RT   Phosphorylation of the serine 60 residue within the Cdx2
#=GF RT   activation domain mediates its transactivation capacity. 
#=GF RA   Rings EH, Boudreau F, Taylor JK, Moffett J, Suh ER, Traber
#=GF RA   PG; 
#=GF RL   Gastroenterology 2001;121:1437-1450.
#=GF DC   The following Pfam-B family may contain sequences that according to Prodom
#=GF DC   are members of this Pfam-A family.
#=GF DR   PFAMB; PB179679;
#=GF DR   INTERPRO; IPR006820;
#=GF CC   This family consists of the amino termini of proteins belonging to the
#=GF CC   caudal-related homeobox protein family.  This region is thought to mediate
#=GF CC   transcription activation.  The level of activation caused by mouse Cdx2 
#=GF CC   (Swiss:P43241) is affected by phosphorylation at serine 60 via the
#=GF CC   mitogen-activated protein kinase pathway [1]. 
#=GF CC   Caudal family proteins are involved in the transcriptional regulation of
#=GF CC   multiple genes expressed in the intestinal epithelium, and are important in
#=GF CC   differentiation and maintenance of the intestinal epithelial lining.
#=GF CC   Caudal proteins always have a homeobox DNA binding domain (Pfam:PF00046).
#=GF SQ   9
#=GS P79788_CHICK/13-172  AC P79788.1
#=GS CDX2_HUMAN/13-180    AC Q99626.2
#=GS HMD1_CHICK/1-132     AC P46692.1
#=GS CDX1_XENLA/13-142    AC Q91622.1
#=GS Q90262_BRARE/13-147  AC Q90262.1
#=GS CDX1_MOUSE/13-147    AC P18111.2
#=GS CDX4_HUMAN/13-171    AC O14627.1
#=GS CDX4_MOUSE/13-169    AC Q07424.1
#=GS Q91542_XENLA/16-147  AC Q91542.1
P79788_CHICK/13-172             MY.PGPVRHSGG.............LNLAAQNFV......GAAQYADYGGYH.........VNLDGA.QSPG....PVWAAPYAAPLRDDW.GAYGQGAPPPAAAAAVHGLNGGSPAAAMAYS.PVDFHHHHHHHPHAHHHVGPETHCSAGGMQTLGAAPAAAAASAAPEPLSPGGQRRGLCEWVRKPAQAPLGSQ
CDX2_HUMAN/13-180               MY.PSSVRHSGG.............LNLAPQNFV......SPPQYPDYGGYH.VAAAAAAAANLDSA.QSPG....PSWPAAYGAPLREDW.NGYAPGGAAAAANAVAHGLNGGSPAAAMGYSSPADYHPHHHPHHHPHHPAAAPS.CASGLLQTLNPGPPGPAATAAAEQLSPGGQRRNLCEWMRKPAQQSLGSQ
HMD1_CHICK/1-132                MY.PSPVRHPG..............LNLNPQNYV.....PGPPQYSDFASYHHVPGI.....NNDPHHGQPA....AAWGSPY.TPAKEDW.HSYGT...AAASAATNPGQFGF.........SPPDFNPMQPH.............AGSGLL........PPAISSSVPQLSPNAQRRTPYEWMRRSIPSTSSSG
CDX1_XENLA/13-142               MY.PNPVRHPG..............LNLNPQNYV.....PAPPQYSDFPSYHHVPGI.....NSDPHHGQPG....GTWSS.Y.TPSREDW.HPYGPGPGASSANPTQIA............FSPSDYNPVQPP..............GSGLL........PPSINSSVPPLSPSAQRADPYEWMRRTGVPTTTTT
Q90262_BRARE/13-147             MYHQGAVRRSG..............ISLPPQNFV......STPQYSDFTGYHHVP.......NMET.HAQSA....GAWGAPYGAP.REDW.GAYSLGPP....NSISAPMSNSSPGP.VSYCSP.DYNTMHGP..............GSAVL.......PPPPENIPVAQLSPERERRNSYQWMSKTVQSSSTGK
CDX1_MOUSE/13-147               VY.PGPARPSS..............LGLGPPTYAPPGPAPAPPQYPDFAGYTHV..........EPA.PAPP....PTWAAPFPAP.KDDWAAAYGPGPTA......SAA....SPAP.LAFGPPPDFSPV..P........APPG.PGPGIL........AQSLGAPGAPSSPGAPRRTPYEWMRRSVAAAGGGG
CDX4_HUMAN/13-171               MY.PGTLMSPGGDGTAGTGGTGGGGSPMPASNFA......AAPAFSHYMGYPHMP.......SMDP.HWPSL....GVWGSPYSPP.REDW.SVY.PGPSSTMGTVPVNDVTS.SPAA...FCS.TDYSNL.GPVGGGTSGSSLPGQAGGSLV.........PTDAGAAKASSPSRSRHSPYAWMRKTVQVTGKTR
CDX4_MOUSE/13-169               MY.PGTLRSPGGSSTAGVGTSGGSGSPLPASNFT......AAPVYPHYVGYPHM.......SNMDP.HGPSL....GAWSSPYSPP.REDW.STY.PGPPSTMGTVPMNDMT..SPV....FGSP.DYSTL.GPTSGASNGGSLPDAASESLVS.........LDSGTSGATSPSRSRHSPYAWMRKTVQVTGKTR
Q91542_XENLA/16-147             MY.PLSVRSTS..............NNHTAQNYV......SNQPYFNYVAYHHVP.......PMDDQ.GQPMEFGDSVWITEGGMELL..W.SWT.L.......TQIWHKSSDLSPNQ.FAYNS.SGYSSP.HP.............SGTGILH........SVDLTHAAANSPSALSQNSYEWMGKTVQSTSTGK
#=GC seq_cons                   MY.PusVRpsG..............lsLssQNaV......usPQYsDasGYHHVs.......NhDst.spPs....usWuuPYusP.REDW.usYusGssus.ussssts.ss.SPs....asSPsDYssh.tP.............sGuGlL........ssstsusssshSPuupR+ssYEWMRKolQsousop
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