dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Table 3 Filtered dissectHMMER results from the analysis of the 6-TM TIP12_MAIZE

Domain description	Sequence range/Domain coverage	Original E-values [HMMER2/HMMER3]	[coverage/FPR]^ratio [coverage/FPR]^{fc E-value}	Total FPR	RMSD/%Id/Structural alignment range (1YMG\|A:pdb)	Function description of representative pdb
PF00230.15	13–234/	1.46e–127/	1.00/0.00	0.00	0.00/	6-TM water/glycerol channel of malarial parasite Plasmodium falciparum [52]
MIP	1	8.50e–73	1.00/0.00		100/
length:296					6–239:
pdb:1YMG\|A					6–239
PF00654.15	1–236/	3.89e–01/	0.345/0.28	0.29	4.99/	12-TM chloride channel; 3 Cl⁻ bind sites, each a “pore-like” trajectory transverse to the membrane plane [53]
Voltage_CLC	1	6.52e–05	0.550/0.01		6.6/
length:730					78–228:
pdb:2HLF\|A					254–383
PF01226.12	17–238/	3.54e–03/-	0.325/0.32	0.35	3.51/	6-TM nitrite anion channel of bacteria for cytoplasmic detoxification [54]
Form_Nir_trans	1		0.490/0.03		9.5/
length:366					10–223:
pdb:4FC4\|A					25–249
PF07155.7	57–190/	8.10e–02/-	0.235/0.48	0.61	3.52/	5-TM pore that transport riboflavin molecules across the lipid bilayer [55]
ECF-ribofla_trS	1		0.435/0.13		6.4/
ength:196					131–226:
pdb:4HZU\|S					35:162
PF02028.12	28–242/	7.24e–02/-	0.010/0.98	1.01	9.73/	12-TM carnitine/butyrobetaine antiporter [56]
BCCT	1		0.495/0.03		3.8/
length:722					6-198:
pdb:2WSW\|A					86–373

For each domain hit, the Pfam accession, domain name, domain length and representative PDB (if any) are given in column 1. Column 2 gives the sequence range (i.e. sequence stretch covered by the domain) and the domain coverage where 1 indicates full coverage while <1 implies partial coverage by the domain model. Column 3 gives the original (or undissected) HMMER2 and HMMER3 E-values of the sequence-to-domain alignments. Column 4 gives the coverage score, coverage^ratio and coverage^{fold ‐ critical E ‐ value} (see Eq. 5) which is the corrected domain coverage score of the HMMER2/HMMER3 sequence-to-domain hit. The expected FPRs (false-positive rates) for the coverage scores are also provided and they were estimated from the relevant dissectHMMER ROC plots in Fig. 6. Column 5 gives the sorted total FPR in ascending order, where the latter is the sum of the two independent FPRs as given in column 3. Column 6 gives the RMSD/%Id and alignment range derived from the structure alignments between 1YMG|A and the representative structures of the domain models. The last column gives the biological function of the representative structures.

ISSN: 1745-6150