Example 4-1 shows a Pfam flat file. This entry contains terms from the Pfam Field Definitions, discussed later in this chapter. Example 4-1. Sample Pfam example# STOCKHOLM 1.0 #=GF ID 14-3-3 #=GF AC PF00244 #=GF DE 14-3-3 proteins #=GF AU Finn RD #=GF AL Clustalw #=GF SE Prosite #=GF GA 25 25 #=GF TC 35.40 35.40 #=GF NC 19.10 19.10 #=GF BM hmmbuild -f HMM SEED #=GF BM hmmcalibrate --seed 0 HMM #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken #=GF RA A, Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 #=GF RT protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF RN [3] #=GF RM 96182649 #=GF RT Interaction of 14-3-3 with signaling proteins is mediated #=GF RT by the recognition of phosphoserine. #=GF RA Muslin AJ, Tanner JW, Allen PM, Shaw AS; #=GF RL Cell 1996;84:889-897. #=GF RN [4] #=GF RM 97424374 #=GF RT The 14-3-3 protein binds its target proteins with a common #=GF RT site located towards the C-terminus. #=GF RA Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, #=GF RA Omata S, Ohno S, Isobe T #=GF RL FEBS Lett 1997;413:273-276. #=GF RN [5] #=GF RM 96394689 #=GF RT Molecular evolution of the 14-3-3 protein family. #=GF RA Wang W, Shakes DC #=GF RL J Mol Evol 1996;43:384-398. #=GF RN [6] #=GF RM 96300316 #=GF RT Function of 14-3-3 proteins. #=GF RA Jin DY, Lyu MS, Kozak CA, Jeang KT #=GF RL Nature 1996;382:308-308. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF DR SCOP; 1a4o; fa; #=GF DR PDB; 1a37 A; 3; 228; #=GF DR PDB; 1a37 B; 3; 228; #=GF DR PDB; 1a38 A; 3; 228; #=GF DR PDB; 1a38 B; 3; 228; #=GF DR PDB; 1a4o A; 3; 228; #=GF DR PDB; 1a4o B; 3; 228; #=GF DR PDB; 1a4o C; 3; 228; #=GF DR PDB; 1a4o D; 3; 228; #=GF DR PDB; 1qja B; 3; 229; #=GF DR PDB; 1qja A; 3; 230; #=GF DR PDB; 1qjb A; 3; 232; #=GF DR PDB; 1qjb B; 3; 232; #=GF DR INTERPRO; IPR000308; #=GF SQ 148 #=GS O61131/11-251 AC O61131 <deleted for brevity> #=GS 143Z_HUMAN/3-236 DR PDB; 1qjb B; 3; 232; O61131/11-251 RSDCTYRSKLAEQAERYDEMADAMRTLVEQCVnn....... dkdELTVEERNLLSVAYKNAVGARRASWRIISSVEQKEMSKA.NVHNKNIAATYRKKVEEELNNIC.QDILN. LLTKKLIPNT..SESESKVFYYKMKGDYYRYISEFS.CDE. GKKEASNFAQEAYQKATDIAENELPSTHPIRLGLALNYSVFFY..EILNQPHQACEMAKRAF...DDAITEFDNV.. SEDS..YKDSTLI.MQLLRDNLTLWTSDLQGDQ <deleted for brevity> Q9XZV0/2-235 KEELLNRCKLNDLIENYGEMFEYLKELSHIKI............ DLQPDELDLITRCTKCYIGHKRGQYRKILTLIDKDKIVD.NQKNSALLEILRKKLSEEILLLC.NSTIE.LSQNFLNNNV. .FPKKTQLFFTKIIADHYRYIYEIN.GKE.DIKLKAKEYYE--KGLQTIKTCKYNSTETAYLTFYLNYSVFLH.. DTMRNTEESIKVSKACL...YEALKDTEDI..VDNS..QKDIVLL.CQMLKDNISLWKTETNEDN #=GC SS_cons HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSC............ CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTT--.CCHHHHHHHHHHHHHHHHHHHHH.HHHHH.HHHHTTTTCC. .CSCHHHHHHHHHHHHHHHHHHHHC.CSC.HHHHHHHHHHHHHHHHHHHHHCHCCTTCHCHHHHHHHHHHHHC.. HTSCCHHHCHHHHHHHH...HHHHTTCGGC..CTTT..HHHHHHH.HHHHHHHHHHCTCCCXXXX #=GC SA_cons 26310320300350512510050022003352............ 4045500400120033002310402420152179179--.38752510440144014203510.43002.0035201642. .754403000010100011100201.867.7465125302500340252067635113122100001001127.. 31372485135106412...5415867932..3994..6651462.142043126627759XXXX // |