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Table 2 DissectHMMER results for the analysis of HEM1_METKA for the middle sequence stretch from positions 168–265

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 (1GPJ|A:pdb)

Function description of representative pdb

PF01488.15

156–292/

1.90e–67/

0.995/0.00

0.00

3.12/

Synthesis of aromatic amino-acids in shikimate pathway [39]; NADP+ driven

Shikimate_DH

1

3.21e–40

0.995/0.00

14.0/

length:170

149–304:

pdb:1NVT|A

110–270

PF03807.12

169–268/

8.73e–06/

0.975/0.00

0.00

3.75/

Conversion of insoluble ferrin (Fe3+) to soluble ferrin(Fe2+) [40]; NADP+ driven

F420_oxidored

1

2.93e–07

0.980/0.00

14.0/

length:123

168–281:

pdb:2VNS|A

29–150

PF02882.14

131–258/

5.34e–01/

0.780/0.00

0.00

3.29/

Interconversion of 1-carbon derivatives of tetrahydrofolate; substrates for methione, thymidylate and purine syntheses [41]; NADP+ driven

THF_DHG_CYH_C

1

8.87e–03

0.795/0.00

10.7/

length:205

149–307:

pdb:1A4I|A

147–296

PF03446.10

167–321/1

3.00e–01/

0.700/0.00

0.00

3.57/

Decarboxylating reduction of 6-phosphogluconate to ribose 5-phosphate [42]; NADP+ driven

NAD_binding_2

1.27e–03

0.710/0.00

11.4/

length:235

167–288:

pdb:1PGQ|A

2–129

PF02826.14

127–269/

8.79e–03/

0.645/0.00

0.00

3.05/

Purine biosynthesis [43]; NADP+ driven

2-Hacid_dh_C

1

5.29e–09

0.670/0.00

11.8/

length:260

161–264:

pdb:3ORQ|A

3–101

PF00106.20

168–305/

1.10e–02/

0.640/0.00

0.00

3.00/

Synthesis of tripinone from pseudotropine [44]; NADP+ driven

adh_short

1

5.53e–05

0.645/0.00

9.2/

length:225

164–265:

pdb:1IPE|A

6–145

PF08659.5

169–281/1

4.86e + 00/

0.57/0.01

0.01

3.62/

Mammalian fatty acid synthase; a large multienzyme that catalyzes all steps of fatty acid synthesis [45]; NADP+ driven

KR

6.51e–03

0.725/0.00

9.0/

length:257

150–291:

pdb:2VZ9|A

1651–1802

PF13241.1

162–275/

9.13e–02/

0.535/0.01

0.02

4.17/

Siroheme synthesis from uro’gen III in tetrapyrrole biosynthesis [46]; NADP+ driven

NAD_binding_7

1

7.38e–03

0.535/0.01

12.0/

length:379

160–304:

pdb:1PJQ|A

5–150

PF13460.1

170–344/

2.40e–02/-

0.495/0.03

0.06

3.26/

Synthesis of bilverdin from bilirubin [47]; NADP+ driven

NAD_binding_10

1

0.490/0.03

11.5/

Length:362

168–288:

pdb:1HDO|A

4–152

PF01408.17

168–265/1

8.97e–02/-

0.445/0.11

0.20

3.73/

Cleavage of non-reducing N-acetylgactosamine from blood group ABO antigens [48]; NAD+ driven

GFO_IDH_MocA

0.450/0.10

9.4/

length:188

167–303:

pdb:2IXB|A

20–164

PF02254.13

170–285/

3.55e–02/-

0.400/0.18

0.33

3.31/

NAD-mediated conformation switch for K+ influx control [49]; NAD+ driven

TrkA_N

1

0.420/0.15

10.5/

length:195

168–300:

pdb:1LSS|A

1–132

PF03949.10

146–323/

3.44e–02/-

0.140/0.66

0.70

3.22/

Oxidation of malate to pyruvate [50]; NAD+ driven

Malic_M

1

0.485/0.04

6.4/

length:324

149–305:

pdb:1DO8|A

298–494

PF07991.7

165–233/

-/1.65e–04

0.205/0.53

1.07

3.49/

Synthesis of branched side of valine and isoleucine [51]; NADP+ driven

IlvN

0.42

0.205/0.54

9.7/

length:177

163–288:

pdb:1YVE|A

121–252

  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 1GPJ|A and the representative structures of the domain models. The last column gives the biological function of the representative structures.