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Table 2 Comparison of IC, GGSEARCH, HMMER and SAM: Results for Homologous Proteins in Four Superfamilies1.

From: Animal Ca2+ release-activated Ca2+ (CRAC) channels appear to be homologous to and derived from the ubiquitous cation diffusion facilitators

Superfamily Family TC# Profile Database IC/GAP score (S.D.) GGSEARCH (FASTA) e-value HMMER e-value SAM e-value
   Protein-12 Acc# Protein-22 Acc#     
CDF Vs Orai 2.A.4.1 PfuCDF AAL80682 CelOrai NP_497230 14.6 0.0049 0.09 0.72
Orai Vs CDF 1.A.52.1 CelOrai NP_497230 PfuCDF AAL80682   5.4 e-5 0.22 0.29
CDF 3-4 TMSs Vs Orai 1-2 TMSs 2.A.4.1 PfuCDF AAL80682 CelOrai NP_497230 14.6 1.6 e-18 0.11 0.18
Orai 1-2 TMSs Vs CDF 3-4 TMSs 1.A.52.1 CelOrai NP_497230 PfuCDF AAL80682   4.7 e-6 0.11 0.02
DMT 2.A.7.20 PfCRT Q86M68 AthCRT Q8RWL5 16 0 9.2 e-226 0
DMT 2.A.7.20 AthCRT Q8RWL5 PfCRT Q86M68   0 2.6 e-149 3.26 e-163
DMT 2.A.7.12 SLC35A1 Q8BRW7 PfCRT Q86M68 9 6.9 e-10 3.2 e-6 8.55 e-9
DMT 2.A.7.20 PfCRT Q86M68 SLC35A1 Q8BRW7   3.8 e-8 9.5 e-6 2.17 e-6
BART 2.A.87.2 (P-RFT) YpaA NP_390186 Ade1 YP_464235 9 0.0002 0.007 5.4
BART 2.A.59.1 (Acr3) Ade1 YP_464235 YpaA NP_390186   0.02 0.11 0.2
BART 9.B.33 (SHK) LytS NP_847838 Rba2 NP_868846 8 0.04 0.08 0.03
BART 2.A.93 (UNK) Rba2 NP_868846 LytS NP_847838   0.09 0.007 0.28
BART 9.B.34 (KPSH) Dge1 YP_604037 Rba2 NP_868846 9 0.004 2.2 0.3
BART 2.A.93 (UNK) Rba2 NP_868846 Dge1 YP_604037   0.024 0.06 7.2
OPT ABvsCD 2.A.67.3 Spr1 YP_001477255.1 Lsa1 YP_394932.1 13 3.5 e-8 4 e-4 0.1
OPT CDvsAB 2.A.67.4 Lsa1 YP_394932.1 Spr1 YP_001477255.1   2.3 e-6 0.004 0.004
OPT AvsB 2.A.67.4 Ngo1 YP_208927.1 Sde1 YP_526125.1 11 7.1 e-6 0.06 0.5
OPT BvsA 2.A.67.4 Sde1 YP_526125.1 Ngo1 YP_208927.1   5.9 e-5 0.2 0.09
OPT AvsC 2.A.67.2 Zma1 NP_001104952.1 Chy1 YP_361078.1 12 5.9 e-5 0.03 0.002
OPT CvsA 2.A.67.4 Chy1 YP_361078.1 Zma1 NP_001104952.1   0.0015 0.03 0.02
OPT AvsD 2.A.67.1 Gze4 XP_389463.1 Sus1 YP_822933.1 12 0.0008 0.09 2
OPT DvsA 2.A.67.4 Sus1 YP_822933.1 Gze4 XP_389463.1   0.0001 0.03 0.2
OPT BvsC 2.A.67.1 Sco1 AAF26618.1 Mtu1 NP_216911.1 12 0.007 0.07 0.01
OPT CvsB 2.A.67.4 Mtu1 NP_216911.1 Sco1 AAF26618.1   0.003 0.08 0.003
OPT BvsD 2.A.67.2 Osa28 CAE02279.2 Asu1 YP_001343430.1 14 2.2 e-8 0.006 0.02
OPT DvsB 2.A.67.4 Asu1 YP_001343430.1 Osa28 CAE02279.2   7 e-5 0.007 0.001
OPT CvsD 2.A.67.4 Pgi1 NP_904744.1 Ani11 XP_658304.1 10 0.0002 0.2 2
OPT DvsC 2.A.67.2 Ani11 XP_658304.1 Pgi1 NP_904744.1   9.2 e-6 0.05 0.5
  1. 1The comparison scores obtained with the IC and GAP programs, other than the CRAC/CDF comparisons, are published as follows: DMT superfamily: Tran & Saier, 2004; see also Jack et al., 2001; BART superfamily: Mansour et al., 2007. The HMMER and IC/GAP values for comparison of the CRAC (Orai) and CDF families, as well as the OPT family, have not been published previously.
  2. 2Top entry in each set of comparisons: Protein-2 was used as the Blast query sequence to generate the target sequences; Protein-1 was used as the query sequence to generate the HMM profile. The opposite was used for the bottom entry in each set of comparisons.