4.1 Pfam Example Flat File

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 //


Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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