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Table 3 A summary of CoBaltDB integrated databases and tools features.

From: CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

Databases

Reference

Features predicted

Genome(s)

Protein numbers

EchoLOCATION

[124]

Subcellular-location (EXP)

E. coli K-12

4330 (506 exp)

Ecce

_

Subcellular-location

E. coli K-12

306

LocateP DataBase

[89]

Subcellular-location

178 MD

542788

cPSORTdb

[91]

Subcellular-location

140 BA

1634278

ePSORTdb

[91]

Subcellular-location (EXP)

 

2165

THGS

[125]

Transmembrane Helices

689 PROK

465411

Augur

[88]

Subcellular-location

126 MD

111223

CW-PRED

[126]

Cell-anchored (surface)

94 MD

954

PROFtmb

[78]

Beta-barrel (OM)

78 DD/19 MD

2152

HHomp

[127]

Beta-barrel (OM)

 

12495

PRED-LIPO

[58]

Lipoprotein SPs

179 MD

895

SPdb

[90]

Signal peptides (SPs)

855 PROK

7062

ExProt

[128]

Signal peptides (SPs)

23 AR/61 MD/115DD

 

Signal Peptide Website

_

Signal peptides (SPs)

384 BA

1161 (EXP)

PRED-SIGNAL

[129]

Signal peptides (SPs)

48 AR

9437

TMPDB

[130]

Alpha Helices & Beta-barrel

 

188

DTTSS

Shandong Univ.

Type III secretion system

 

1035

TOPDB

[131]

Transmembrane Proteins

755 BA/16 AR

 

TMBC-Database

Andrew Garrow

Transmembrane Beta-barrel

 

1219

Swissprot signal testset

[132]

Signal peptides (SPs) (EXP)

176 SP+/122 SP-

 
  1. MD = monoderm, DD = diderm. AR (Archeae), BA (Bacteria), PROK (Prokaryotes) include both bacteria and Archaee, EXP = Experimental database