A1

Name

Gene

Subgroup

Finger arrangement

YPR186c

TFC2

unique

1-2-3-4-5-6-7-8u..9i

YJL056c

 

unique

1i..2i..3-4-5-6-7-8d

YGL254w

FZF1

unique

1-2-3..4i..5iu

YOR113w

AZF1

unique

1-2-3-4

YHL027w

RIM101

unique

1..2-3

YDR146c

SWI5

SWI5

1-2-3

YLR131c

ACE2

SWI5

1-2-3

YNL027w

 

SWI5*

1-2-3u

A2

DNA recognition

 

Helixposition

Name

Gene

Sub-

Fing.

Finger1

Finger2

 

 

group

arr.

-1123$56

-1123$56

YDR216w

ADR1

ADR

1-2

RQEH$KR

RRDL$IR

YGR067c

 

ADR

1-2

....$..

....$L.

YJR127c

ZMS1

ADR

1-2

....$..

....$L.

YML081w

 

ADR

1-2

.S..$I.

....$Q.

YPR022c

 

ADR*

1-2u

....$S.

.K..$L.

YMR037c

MSN2

MSN

1-2

RSEH$KR

RSDN$SQ

YKL062w

MSN4

MSN

1-2

....$..

....$..

YER130c

 

MSN

1-2

.Q..$..

....$N.

YGL035c

MIG1

MIG

1-2

RLEH$TR

RSDE$TR

YGL209w

MIG2

MIG

1-2

....$K.

....$K.

YER028c

 

MIG

1-2

....$K.

....$K.

YMR182c

RGM1

RGM

1-2

RTEH$AR

RIDN$RQ

YPL230w

 

RGM

1-2

.A..$..

.V..$K.

YBR066c

 

NEW1

1-2

TSGH$SR

RHDN$NQ

YDR043c

 

NEW1

1-2

....$A.

....$..

YMR070w

HMS1

unique

1-2

RKSW$KR

RKDN$LQ

YDR096w

GIS1

NEW2

1-2

SGHH$TR

RRDH$LR

YER169w

 

NEW2

1-2

....$..

....$..

YDR253c

MET32

NEW3

1-2

RSSD$RR

RKDA$KR

YPL038w

MET31

NEW3

1-2

....$..

....$..

YPR013c

 

NEW4

1-2

RPST$KT

VKSN$LR

YPR015c

 

NEW4

1-2

....$R.

....$..

B

Name

Gene

Subgroup

Finger arrangement

YDR463w

STP1

STP

1-2u...3iu

YHR006w

STP2

STP

1-2u...3iu

YLR375w

STP3

NEW5

1u-2...3iu

YDL048c

STP4

NEW5

1u-2...3iu

YGR044c

RME1

unique

1d-2u..3i

YHR207c

 

unique

1u-2

C1

YLR387c

 

unique

1i..2i..3i

YLR403w

SFP1

unique

1i..2i..3i

YDL030w

PRP9

unique

1i..2iu

YNL227c

 

unique

1i..2i

C2

YMR127c

SAS2

SAS

1i

YBL052c

SAS3

SAS

1i

YBR267w

 

unique

1i

YDL043c

PRP11

unique

1i

YDL098c

 

unique

1i

YDR049w

 

unique

1i

YDR323c

PEP7

unique

1i

YFL044c

 

unique

1i

YLR074c

 

unique

1i

YOR077w

RTS2

unique

1i

YCR066w

RAD18

unique

1i*

YDL231c

 

unique

1i*

YDR112w

 

unique

1i*

 

Figure legend: Complete set of classified zinc finger proteins in the yeast genome

The zinc finger proteins (Zfp) are classified into three subsets (A-C) according to the number, kind and arrangements of their fingers : A, Zfp with tandem arrays of fingers in a cluster, with A1 containing proteins with three or more fingers and A2 containing proteins with a finger pair; B, Zfp with one canonical and two unusual fingers in unusual arrangements; C, Zfp with dispersed fingers (C1) or with a single finger (C2).

The first two columns contain systematic yeast ORF names and gene names (where known). The next column describes the yeast subgroups defined by Zfp with identical numbers, patterns and arrangements of their fingers as well as homologous finger sequences. A subgroup name marked by * indicates a less closely related member in the considered subgroup. Subgroup names are coined as a rule from the experimentally best-characterized member of a subgroup. The subgroups NEW1-5 contain exclusively new ORFs not yet experimentally investigated. Unique Zfp have no homologous proteins in the yeast genome. In the column describing finger arrangement additional fingers detected with the C2H2can or C2H2new motifs (see reference) are underlined, fingers with unusual patterns found only by visual inspection are indicated by u and underlined, d means a degenerate finger with one mutated zinc ligand, and i stands for isolated (dispersed) fingers. 1* indicates a questionable finger. The linker sequence in finger tandem repeats with a consensus lenght of five residues (in few cases with two, three or six residues) is given by (-), fingers linked by 10 or more residues are considered as dispersed or single fingers and connected by (.. or ...). In the last columns of subset A2 the sequences of the finger DNA recognition helices in positions -1 to 6 are given, except for conserved hydrophobic residues inposition 4 (marked by $), for both fingers of the proteins in subset A2. The helix positions are numbered relative to the beginning of the finger helix. A dot indicates an identical amino acid compared with the sequence of the first member of a subgroup. Key amino acid residues that are known or predicted to be essential for the specific DNA base recognition are coloured, with Arg in red, His in blue , Asn in green and Asp in purple. However, we cannot exclude that some other amino acids (not boxed and coloured) in the given sequences also participate in base recognition.