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Table 1 List of all domains identified by described methods, as well as their likely function and number in S. coelicolor.

From: New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor

Pfam Accession No

Family Name

Pfam Type

Basic Function

No of copies in S. coelicolor

Antibiotic biosynthesis

Cell Wall Biosynth

Cell Wall/Periplasm

Replication

Secreted

A) Novel Families

PF03457

HA

Domain

Putative RNA binding domain

21

   

X

 

PF03621

MbtH

Domain

Possibly involved in antibiotic biosynthesis

2

X

    

PF03625

DUF302

Domain

Unknown function

3

  

X

 

X

PF03640

Lipoprotein_15

Repeat

Unknown function

6

  

X

 

X

PF03703

DUF304

Domain

Unknown function

4

  

X

 

X

PF03704

BTAD

Family

Bacterial transcriptional activator domain

12

X

    

PF03710

GlnE

Domain

Glutamate-ammonia ligase adenylyltransferase

2

     

PF03713

DUF305

Domain

Unknown function

6

  

X

 

X

PF03714

PUD

Domain

Putative carbohydrate binding domain

2

  

X

 

X

PF03724

DUF306

Domain

Unknown function

2

    

X

PF03729

DUF308

Repeat

Unknown function

6

  

X

 

X

PF03733

DUF307

Domain

Unknown function

2

  

X

 

X

PF03752

ALF

Repeat

Putative signal transduction domains

16

    

X

PF03756

AfsA_repeat

Repeat

A-factor biosynthesis

2

X

    

PF03771

SPDB

Domain

(Probably) mobile element replication

16

     

PF03777

DUF320

Domain

Unknown function

11

  

X

 

X

PF03779

SPW

Repeat

Unknown function

2

  

X

  

PF03793

PASTA

Domain

Cell wall peptidoglycan sensor domain

9

 

X

X

X

X

PF03794

HHE

Domain

Unknown function

7

 

X

   

PF03795

YCII

Domain

Probably enzymatic domain

3

     

PF03860

DUF326

Domain

Unknown function

6

  

X

  

PF03984

DUF346

Repeat

Unknown function (β-propeller)

7

  

X

 

X

PF03988

DUF347

Repeat

Unknown function

4

  

X

  

PF03990

DUF348

Domain

Unknown function

3

  

X

 

X

PF03992

ABM

Domain

Antibiotic biosynthesis monooxygenase

3

X

    

PF03993

DUF349

Domain

Unknown function

3

     

PF03994

DUF350

Domain

Unknown function

2

  

X

 

X

PF03995

DUF351

Domain

Unknown function

4

    

X

PF04151

PPC

Domain

PKD-like peptidase C-terminal domain

3

    

X

PF04205

FMN_bind

Domain

FMN-binding domain

2

  

X

 

X

PF05120

GvpG

Domain

Gas vesicle protein G

2

    

X

PF05121

GvpK

Domain

Gas vesicle protein K

2

     

PF05122

SpdB

Domain

Mobile element transfer proteins

2

     

B) Previously Described New Pfam Families

PF03458

UPF01261

Domain

Unknown function

4

  

X

 

X

PF03459

TOBE2

Domain

Transport-associated OB fold domain

9

  

X

  

PF03707

MHYT3

Repeat

Putative ligand receptor

6

  

X

 

X

PF03989

DNA_gyraseA_C4

Repeat

DNA-binding β-propeller

8

   

X

 

C) Significantly Extended Families

PF00188

SCP

Domain

Unknown function

4

  

X

 

X

PF01839

FG-GAP

Repeat

Putative β-propeller

57

  

X

 

X

  1. This table shows all new Pfam families added during this investigation. Part A shows entirely novel families. Part B shows families that are new to Pfam but have been previously described in the literature: (1) SWISS-PROT; (2) [54]; (3) [55]; (4) [56]. Part C shows families that have had significant extensions to them – for instance SCP was previously thought to be present only in eukaryotes. Domains highlighted in blue are discussed in further detail in section 3.2.
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BMC Microbiology

ISSN: 1471-2180

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