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
//