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Table 1 Skate and lamprey gene homology determined with GnRH receptor type-specific HMM profiles of protein motifs using HMMER[34]

From: Dynamic evolution of the GnRH receptor gene family in vertebrates

  Little skate genome
Sequence ID AESE012567234.1 AESE011658775.1 AESE011105720.1 AESE010056425.1 AESE011520245.1 AESE012567234.1
Domain Homology‡ TM1 to TM4 TM1 to TM4 TM1 to TM4 TM6 to TM7 TM6 to TM7 TM6 to TM7
HMM-Type I 4.7E-28 (107.9) 1.1E-34 (129.2) 3.4E-48 (173.2) 1.3E-19 (79,9) 9.3E-29 (109.2) 1.8E-38 (140.4)
HMM-Type IIa-1 7.1E-50 (178.5) 2.4E-60 (212.4) 3.9E-43 (127.5) 5.5E-33 (122.6) 3.5E-33 (123.2) 6.73E-3 (119.1)
HMM-Type IIa-2 1.7E-47 (107.7) 8.5E-68 (236.5) 1.5E-31 (199.1) 1.0E-25 (99.5) 1.3E-40 (147.3) 1.4E-30 (115.1)
HMM-Type IIa-3 5.0E-41 (149.8) 7.2E-64 (223.8) 2.2E-32 (121.8) 3.6E-25 (97.7) 5.1E-39 (142.1) 9.3E-28 (106.0)
HMM-Type IIb 8.1E-41 (149.0) 2.1E-50 (180.0) 2.9E-35 (131.0) 1.6E-23 (92.2) 2.5E-21 (117.2) 2.1E-32 (120.6)
  Lamprey genome
Contig ID 22569.4_6 (586) 42790.2_1 (476) 31731.1_3 (265) 30359.1_1 (909) 36401.1_5 (1441)
Domain Homology‡ Tm1 to Tm4 Tm1 to Tm4 Tm1 to Tm4 Tm6 to Tm7 Tm6 to Tm7
HMM-Type I 1.2E-44 (138) 1.0E-33 (103) 1.9E-23 (69) 3.7E-36 (110) 7.2E-30 (90)
HMM-Type IIa-1 3.4E-75 (237) 2.5E-59 (186) 1.7E-41 (128) 6.7E-48 (138) 3.6E-45 (138)
HMM-Type IIa-2 7.3E-61 (191) 1.2E-49 (154) 7.3E-34 (103) 4.5E-39 (119) 1.2E-32 (98)
HMM-Type IIa-3 2.9E-59 (185) 6.9E-47 (145) 3.0E-32 (97) 4.9E-38 (116) 1.3E-32 (98)
HMM-Type IIb 2.5E-54 (169) 9.7E-46 (141) 2.5E-31 (95) 9.5E-37 (111) 3.0E-33 (100)
  1. Numbers represent e-values (with bit scores shown in parentheses) resulting from each HMMER search, in which the HMM profile was constructed with sequence input limited to GnRH receptors from each respective subclade; boldface font indicates the best e-value within each column. The HMM profiles were then used as queries against either the little skate (Leucoraja erinacea) or lamprey (Petromyzon marinus) genome. Reciprocal searches in which each sequence was used as a query against all HMM profiles (those constructed in this work in addition to all HMM models in the Pfam database) were congruent (Additional file 2: Table S2).
  2. ‡ Domain homology indicates the approximate physical position of the HMM with respect to the transmembrane (TM) domains in Figure 10.