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Table 4 Filtered dissectHMMER results from the analysis of the 11-TM Q9K8K1_BACHD

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

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 (2CFP|A:pdb)

Function description of representative pdb

PF05684

10–388/

5.30e–244/

1.00/0.00

0.00

-

Unknown function

DUF819

1

3.50e–162

1.00/0.00

length:400

pdb:-

PF07690.11

13–382/

7.72e–02/

0.845/0.00

0.00

0.0/

12-TM lactose permease (symporter) of E.coli that facilitates lactose and H+ translocation [57].

MFS_1

1

9.98e–05

0.815/0.00

100/

length:793

1–417:

pdb:2CFP|A

1–417

PF00999.16

10–387/

8.25e–03/-

0.415/0.15

0.18

4.99/

12-TM sodium/proton (Na(+)/H(+)) antiporters [58].

Na_H_Exchanger

1

0.490/0.03

6.7/

length:593

33–180:

pdb:4BWZ|A

75–238

PF13347.1

36–382/

8.31e–02/-

0.415/0.15

0.18

3.62/

12-TM glucose/H(+) symporter of Staphylococcus epidermidis [59]

MFS_2

1

0.490/0.03

9.4/

length:847

11–401:

pdb:4LDS|A

7–423

PF00083.19

6–385/

5.20e–02/-

0.225/0.50

0.54

4.79/

12-TM D-xylose or d-glucose transporter [60]

Sugar_tr

1

0.485/0.04

6.5/

length:605

4–388:

pdb:4GC0|A

5–428

PF00115.15

22–381/

7.88e–02/-

0.120/0.70

0.76

7.4/

12-TM mitochondrial cytochrome c oxidase that contains two proton pumps and a water channel [61].

COX1

1

0.475/0.06

1.7/

length:591

9–417:

pdb:1 V55|A

9–501

PF03611.9

7–379/

1.28e–03/-

0.035/0.90

0.94

-

10-TM 3-keto-L-gulonate sugar-specific permease [62].

EIIC-GAT

1

0.485/0.04

length:642

pdb:-

PF03169.10

3–388/

3.73e–02/-

0.050/0.88

0.98

-

12–14 TM oligopeptide transporter protein [63].

OPT

1

0.450/0.10

length:1010

pdb:-

PF02028.12

7–330/

1.18e–02/-

0.005/1.00

1.01

7.73/

12-TM carnitine/butyrobetaine antiporter [56]

BCCT

1

0.500/0.01

3.1/

length:722

8–212:

pdb:2WSW|A

48–404

  1. 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, coverageratio and coveragefold ‐ 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 2CFP|A and the representative structures of the domain models. The last column gives the biological function of the representative structures.
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