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Table 1 Examples of validated false hits from 5 Pfam domains (PF01298.13 Lipoprotein5, PF04814.8 HNF-1 N, PF05134.8 T2SL, PF09110.6 HAND, PF10390.4 ELL) and validated true hits from 3 Pfam domains (PF00004.24 AAA, PF00106.20 adh_short, PF01226.12 Form_Nir_trans)

From: On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

Domain name

Hit name

HMMER version

Total score (E-value)

Fold-critical score (E-value1)

Remnant score (E-value2)

Ratio of E-value1: E-value2

PF01298.13 Lipoprotein5

1.sp|O60841|IF2P_HUMAN (Eukaryotic translational initialization factor 5B)

HMMER2

−183.8 (3.1)

−164.6 (7.6e-1)

−7.6 (6.7e-6)

1.1e + 5

  

HMMER3

30.1 (6.7e-8)

−2.9 (5.8e + 4)

22.8 (1.0e-3)

5.8e + 7

Domain length: 979

2.sp|Q05D44|IF2P_MOUSE (Eukaryotic translational initialization factor 5B)

HMMER2

−184.6 (3.3)

−150.5 (2.7e-1)

−24.9 (2.4e-5)

1.1e + 4

  

HMMER3

26.5 (8e-7)

4.4 (3.9e + 2)

33.9 (4.6e-7)

8.5e + 8

PDB:3V8U|B

3.sp|Q5RDE1|IF2P_PONAB (Eukaryotic translational initialization factor 5B)

HMMER2

−185.0 (3.4)

−137.5 (1.0e-1)

−33.2 (4.5e-5)

2.2e + 3

  

HMMER3

28.6 (1.8e-7)

−2.9 (5.8e + 4)

22.2 (1.5e-3)

3.9e + 7

 

4.sp|Q7XTT4|NUCL2_ORYSJ (Nucleolin 2)

HMMER2

−190.8 (5.2)

−130.5 (6.1e-2)

−50.2 (1.6e-4)

3.8e + 2

  

HMMER3

13.2 (8.2e-3)

−5.0 (2.0e + 5)

14.5 (3.3e-1)

6.1e + 5

PF04814.8 HNF-1_N (Hepatocyte nuclear factor 1)

5.sp|Q6PDK2|MLL2_MOUSE (Histone-lysine N-methyltransferase 2D)

HMMER2

−70.2 (1.5)

−45.6 (1.1e-2)

−15.4 (2.5e-5)

4.4e + 2

  

HMMER3

24.5 (5.1e-6)

0.0 (2.9e + 4)

32.3 (4.1e-6)

7.1e + 9

Domain length: 250

6.sp|P41046|CORTO_DROME (Centrosomal/chromosomal factor)

HMMER2

−75.5 (4.4)

−55.3 (7.6e-2)

−6.1 (3.9e-6)

2.0e + 4

  

HMMER3

23.0 (1.6e-5)

0.0 (2.9e + 4)

32.9 (2.8e-6)

1.0e + 10

PDB:1IC8|B

7.sp|Q54RP6|DHKL_DICDI (Hybrid signal transduction histidine kinase L)

HMMER2

−75.6 (4.5)

−52.5 (4.3e-2)

−6.9 (4.5e-6)

9.6e + 3

  

HMMER3

32.6 (1.7e-8)

0.0 (2.9e + 4)

47.7 (8.3e-11)

3.5e + 14

PF05134.8 T2SL (Type II secretion system protein L)

8.sp|Q8VHG2|AMOT_MOUSE (Angiomotin)

HMMER2

−81.4 (4.5)

−69.3 (7.6e-1)

10.5 (6.1e-6)

1.3e + 5

Domain length: 321

 

HMMER3

18.2 (1.8e-5)

8.4 (3.6e + 1)

28.2 (3.5e-5)

1.0e + 6

PDB:1 W97|L

      

PF09110.6 HAND (Chromatin remodeling factor ISW1a)

9.sp|P19338|NUCL_HUMAN (Nucleolin)

HMMER2

−39.7 (2.1)

−40.8 (2.6)

16.7 (3.6e-5)

7.2e + 4

PDB:2Y9Z|A

 

HMMER3

23.3 (2.7e-5)

3.7 (2.3e + 3)

22.1 (5.0e-3)

4.6e + 5

PF10390.4 ELL (RNA polymerase II elongation factor)

10.sp|P34103|PK4_DICDI (Protein kinase 4)

HMMER2

−70.7(3.7e-2)

−49.4 (2.9e-3)

−13.0 (3.9e-5)

7.4e + 1

Domain length: 139

 

HMMER3

94.5 (2.5e-27)

0.0 (9.2e + 3)

99.8 (5.5e-27)

1.7e + 30

PDB:2E5N|A

      

PF00004.24 AAA (ATPase family associated with various cellular activities)

11.sp|P51394|CHLI_PORPU (Magnesium-chelatase subunit ChII)

HMMER2

−27.2 (1.8)

38.5 (2.2e-6)

−48.2 (1.4e + 2)

1.6e-8

Domain Length: 252

 

HMMER3

11.3 (1.1e-1)

22.4 (3.1e-3)

6.0 (3.1e + 2)

1.0e-5

PDB:1LV7|A

 

HMMER3

5.6 (5.9)

26.4 (1.9e-4)

−2.9 (1.4e + 5)

1.4e-9

PF00106.20 adh_short (Short chain dehydrogenase)

12.sp|Q9UXR8|HEM1_METKA (Glutamyl-tRNA reductase)

HMMER2

−49.7 (1.7e-1)

13.7 (1.1e-5)

−54.6 (9.0e-1)

1.2e-5

Domain length: 230

 

HMMER3

23.0 (7.9e-6)

43.1 (1.5e-9)

−6.4 (5.3e + 5)

2.8e-15

PDB:3MJC|B

      

PF01226.12 Form_Nir_trans (Formate/nitrate transporter)

13.sp|Q9ATM0|TIP12_MAIZE (Aquaporin TIP 1–2)

HMMER2

−109.7 (1.3e-1)

−47.5 (1.2e-4)

−45.3 (9.4e-5)

1.3

Domain length: 366

      

PDB:3KCU|E

      
  1. The segmentation of domain models is based on PDB/DSSP information.
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BMC Bioinformatics

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