Measuring the functional sequence complexity of proteins

Table 1 FSC of Selected Proteins

	length (aa)	Number of Sequences	Null State (Bits)	FSC (Fits)	FSC Density Fits/aa
Ankyrin	33	1,171	143	46	1.4
HTH 8	41	1,610	177	76	1.9
HTH 7	45	503	194	83	1.8
HTH 5	47	1,317	203	80	1.7
HTH 11	53	663	229	80	1.5
HTH 3	55	3,319	238	80	1.5
Insulin	65	419	281	156	2.4
Ubiquitin	65	2,442	281	174	2.7
Kringle domain	75	601	324	173	2.3
Phage Integr N-dom	80	785	346	123	1.5
VPR	82	2,372	359	308	3.7
RVP	95	51	411	172	1.8
Acyl-Coa dh N-dom	103	1,684	445	174	1.7
MMR HSR1	119	792	514	179	1.5
Ribosomal S12	121	603	523	359	3.0
FtsH	133	456	575	216	1.6
Ribosomal S7	149	535	644	359	2.4
P53 DNA domain	157	156	679	525	3.3
Vif	190	1,982	821	675	3.6
SRP54	196	835	847	445	2.3
Ribosomal S2	197	605	851	462	2.4
Viral helicase1	229	904	990	335	1.5
Beta-lactamase	239	1,785	1,033	336	1.4
RecA	240	1,553	1,037	832	3.5
Bac luciferase	272	1,900	1,176	357	1.3
tRNA-synt 1b	280	865	1,210	438	1.6
SecY	342	469	1,478	688	2.0
EPSP Synthase	372	1,001	1,608	688	1.9
FTHFS	390	658	1,686	1,144	2.9
DctM	407	682	1,759	724	1.8
Corona S2	445	836	1,923	1,285	2.9
Flu PB2	608	1,692	2,628	2,416	4.0
Usher	724	316	3,129	1,296	1.8
Paramyx RNA Pol	887	389	3,834	1,886	2.1
ACR Tran	949	1,141	4,102	1,650	1.7
Random sequences	1000	500	4,321	0	0
50-mer polyadenosine	50	1	0	0	0

Results for 35 protein families Shown above are the 35 protein families analyzed, their sequence length (column 1), the number of sequences analyzed for each family (column 2), the Shannon uncertainty of the Null State H_ø (Eqn. 4) for each protein (column 3), the FSC value ζ in Fits for each protein (column 4), and the average Fit value/site (FSC/length, column 5). For comparison, the results for a set of uniformly random amino acid sequences (RSC) are shown in the second from last row, and a highly ordered, 50-mer polyadenosine sequence (OSC) in the last row. All values, except for the OSC example, which was calculated from the constrained ground state required to produce OSC, were computed from the null state. The Fit values obtained can be discussed as the measure of the change in functional uncertainty required to specify any functional sequence that falls into the given family being analyzed.

ISSN: 1742-4682