Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins

Table 5.

Examples of Superfamilies Present in Both Single- and Multi-Domain Proteins, Carrying out Different Functions

Table 5A. Single-Domain Proteins
Sfam Funct # SWISS-PROT ID SWISS-PROT function
352# FTN2_HAEIN Ferritin-like Protein 2
1.25.1 183# NIGY_DESVH Nigerythrin
E1.17.4 RIR4_YEAST (Ribonucleotide Reductase) (1.17.4.1)
192# NLP_HAEIN Ner-like Protein Homolog
1.4.3 196# H1A_PLADU Histone H1A, Sperm
1.81.2 E2.5.1 PFTB_PEA Farnesyltransferase Beta Su (2.5.1.–)
226# ERBP_RAT Epididymal-Tetinoic Acid Binding Protein
227# FAB3_CAEEL Fatty Acid-Binding Protein Homolog 3
2.45.1 228#412# NGAL_MOUSE Neutrophil Gelatinase-Assoc. Lipocalin
229# NP4_RHOPR Nitrophorin 4 Precursor
E5.3.99 PGHD_HUMAN Prostaglandin-H2 D-Isomerase (5.3.99.2)
230#421# VNS1_MOUSE Vesomeral Secretory Protein I
2.5.1 231# MPA3_AMBEL Pollen Allergen AMB A 3 (AMB A Iii)
232#427# SOXE_SULAC Sulfocyanin (Blue Copper Protein)
3.14.2 373# RRF1_DESVH Rrf1 Protein
E6.3.4 PURA_CAEEL Adenylosuccinate Synthetase (6.3.4.4)
3.29.1 E2.7.4 KTHY_YEAST Thymidylate Kinase (2.7.4.9)
D259# VA57_VACCV Guanylate Kinase Homolog
E2.7.1 KITH_VZVW Thymidine Kinase (2.7.1.21)
3.47.1 275# MBL_BACSU MBL Protein
276# MREB_BACSU Rod Shape-determining Protein Mreb
3.48.1 E3.1.3 PPA5_YEAST Repressible Acid Phosphatase (3.1.3.2)
3.81.1 D281# AMIC_PSEAE Aliphatic Amidase Expression-Regulator
282# LUXP_VIBHA LUXP Protein Precursor
4.103.1 E2/4/2 TOX1_BORPE Pertussis Toxin Su 1 (2.4.2.–)
4.105.1 291# LECC_POLMI Lectin–Polyandrocarpa Misakiensis
4.11.5 295# TERP_PSESP Terpredoxin
4.19.1 E5.2.1 FKB1_METJA Pept-ProlylCis-Trans Isomerase (5.2.1.8)
6.5.1 E3.6.1 ATPL_VIBAL ATP Synthase (3.6.1.34) (Lipid-binding)
540#325# BACT_HALVA Sensory Rhodopsin II (Sr-Ii)
7.35.4 E1.9.3 COXB_RAT Cytochrome C Oxidase (1.9.3.1) (Via*)
345# DESR_DESBI Desulforedoxin (Dx)
7.7.1 349# TAP_ORNMO Tick Anticoagulant Peptide
Table 5B. Multi-Domain Proteins
Sfam Comb. Funct# SWISS-PROT ID SWISS-PROT function
1.25.1/7.35.4 104# RUBY_METJA Putative Rubrerythrin
11# PURR_HAEIN Purine Nucleotide Synthesis Repressor
1.32.1/3.81.1 12# DEGA_BACSU Degradation Activator
581#11# SCRR_STRMU Sucrose Operon Repressor
582#11# REGA_CLOAB Transcription Regulatory Protein Rega
10# SKN7_YEAST Transcription Factor Skn7 (Pos9 Protein)
11# VIRG_AGRT5 Virg Regulatory Protein
1.4.3/3.14.2 13# RGX3_MYCTU Sensory Transduction Protein REGX3
190# PFER_PSEAE Transcriptional Activator Protein Pfer
366# PETR_RHOCA Petr Protein
2.45.1/7.7.1 203#153# HC_RAT Alpha-1-Microglobulin/Trypsin Inhibitor
2.5.1/6.5.1 E1.9.3 COX2_ZOOAN Cytochrome C Oxidase Ii (1.9.3.1)
3.29.1/3.48.1 E2.7.1 F26_RANCA 6-Phosphofructo-2-Kinase (2.7.1.105)
3.47.1/5.17.1 1# YED0_YEAST Heat Shock Protein 70 Homolog YEL030w
1#83# GR73_MAIZE Ig-Binding Protein

This Article

  1. Genome Res. 11: 1632-1640

Preprint Server