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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.