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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.
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BMC Research Notes

ISSN: 1756-0500

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