Table of Novel Domains
| Domain | Description | Length (AS) | Sec.struct.pred. | Pred.function | No. of proteins | Associated domains | Species | Acc. no. of a representative sequence (domain borders) |
| Part A.—Domains Present in Different Species | ||||||||
| JmjC[ii] | Jumonji related family | 100 | β | Metallo-enzymes | 140 | BRIGHT, jmjN PHD, FBOX, LRR, C2, TPR PLAc, CXXC†, ZnF_C2H2 | Eu, y, a, c, d, h | O14607 [iv] (1042–1205) |
| CSZ | Domain in chromatin remodeling S1 domain containing and Zinc finger proteins | 750 | α/β | DNA-binding, Chromatin modulation | 35 | S1, SH2, C2HC, HhH | Eu y, a, c, d, h | P34703 (389–1120) |
| RPR | Proteins involved in regulation of nuclear pre-mRNA | 120 | α | Protein-interaction | 40 | RRM, PWWP, SURP†, G-Patch | y, a, c, d, h | Q9SJQ7 (88–225) |
| DDT[ii] | Different transcription and chromosome remodeling factors | 60 | α | DNA-binding | 30 | AT_Hook, PHD, HOX, BROMO, MBD | y, a, c, d, h | Q9UIG2[iv] (102–161) |
| TLDc | TBC, LysM and other proteins | 220 | α/β+β | Enzyme | 30 | TBC, LysM, R3H, FBOX | y, a, c, d, h | Q9VNA1[iv] (1163–1325) |
| PUG | Protein knases, UBA or UBX domain containing proteins and glycanases | 60 | α/β | RNA-binding | 25 | C2H2, UBA, TGc, UBX, S_TKc, STYKc | y, a, c, d, h | Q9MAT3 (323–386) |
| HSA | Helicases and SANT domains | 70 | α | DNA-binding | 20 | SANT, BROMO DEXDc, HELlc | y, a, c, d, h | P25439 [iv] (501–573) |
| PSP | Proline-rich, in spliceosome associated proteins | 60 | α | RNA- or snRNP-binding | 15 | SAP, C2HC | y, a, c, d, h | O16997 (200–357) |
| FYRN | Trithorax and X-chromosome inactivating proteins | 40 | α/β | Unknown | 25 | PHD, SET, PWWP | a, c, d, h | Q24742 [iv] (1869–1914) |
| FYRC | Trithorax and X-chromosome inactivating proteins | 90 | α/β | Unknown | 25 | PHD, SET, PWWP | a, c, d, h | Q24742 [iv] (3495–3583) |
| RUN[ii] | TBC, PH, FYVE and other proteins | 65 | α | GTPase signalling | 40 | DENN†, TBC, PLAT, PH, C1, FYVE, GST, SH3 | c, d, h | BAB14033 (115–178) |
| TCH | Transcription factors and CHROMO domain helicases | 50 | α/β | Unknown | 20 | CHROMO, PHD, TFSM2, DEXDc, HELIc, SANT, BROMO | c, d, h | O15025 [iv] (882–931) |
| DZF | DSRM or ZnF_C2H2 domain containing proteins | 250 | α/β | Unknown | 40 | C2H2, DSRM | c, d, h | O88531 (762–1016) |
| NEUZ | Domain in neuralized-like proteins | 120 | β | Unknown | 10 | SOCS, RING, SPRY, SH2 | c, d, h | Q19299 (199–321) |
| ZnF_TTF | Domain in transposases and transcription factors | 100 | α + β | Metal-binding | 20 | KRAB, BTB | a, d, h | Q9ZWT4 (100–199) |
| Part B.—Domains Species–Specific | ||||||||
| FBD | Domain in FBOX and other domain containing plant proteins | 80 | α/β | Unknown | 160 | FBOX, LRRcap, BRCT, AAA | a | Q9LXJ7[iv] (304–382) |
| ZnF_PMZ | Plant mutator transposase zinc finger domain | 27 | α/β | Metal-binding | 125 | AT_Hook, ZnF_C2HC, PHD | a | Q9SH73 (3212–3239) |
| SPK | SET and PHD domain containing proteins and protein kinases | 120 | α/β | Protein-interaction | 40 | SET, ICE_p10†, ICE_p20†, ZnF_C2HC, PHD, STYKc | c | Q9XU06 (139–250) |
| Part C.—Domains, Newly Recognized Divergent Subfamilies | ||||||||
| ZnF_BED[ii] | BED zinc finger, Related to C2H2/C2H2 zinc fingers (based on pattern similarity) | 60 | β | Metal binding | 50 | AT_Hook, PTPc_DSPc | y, a, c, d, h | Q9LWM2 (169–224) |
| CPDc | Catalytic domain of ctd-like phosphatases, related to phosphatase superfamily (based on pattern similarity) | 120 | α/β | Phosphatase | 70 | BRCT, DSRM, UBQ | y, a, c, d, h | Q9PTJ8 (93–236) |
| RWD | RING finger and WD repeat containing proteins and DEXDc helicases, related to the UBCc domain (revealed by hmm searches) | 110 | α/β | Protein-interaction | 60 | S_TKc, RING, WD, UPF29†, DEXDc, HELIc | y, a, c, d, h | Q9QZ05[iv] (25–137) |
| BTP | Bromodomain transcription factors and PHD domain containing Proteins, related to archaeal histone-like transcription factors, defined by PFAM (revealed by PSI-Blast results with less significance (E = 0.041)) | 90 | α | DNA-binding | 25 | AT_Hook, BROMO, PHD | y, a, c, d, h | Q9S7R9 (41–131) |
| MADF | Zinc finger, PHD domain and WD repeats containing proteins, related to SANT domain (after the second iteration Q9SR68 bridges to SANT domains (E = 0.002)) | 90 | α | DNA- or Potein-binding | 60 | C2H2, PHD, WD | Virus, a, c, d | Q9V5Y9 (22–110) |
| Znf_DBF | Zinc finger in DBF-like proteins, related to C2H2 zinc fingers (revealed by pattern similarity and hmm searches, E value = 1.4) | 50 | α | Metal-binding | 10 | BRCT, AT_Hook | y, d, h | O93843 (590–638) |
| CHK | C4-zinc finger and HLH domain containing kinase subfamily of choline kinases (after the second iteration P35790 bridges to choline kinases, defined by PFAM (E = 0.003)) | 200 | α/β | Enzyme | 70 | ZnF_C4, HLH, i.c† | Eu, c, d | Q9VBT6 (129–321) |
| Part D.—Family Specific Extensions of Known Domains | ||||||||
| AWS | Associated with SET domain, subdomain of PRESET[iii] (hmm searches, E value = 0.52) | 50 | α/β | Histone modification | 25 | SET, PWWP, AT_Hook, WW, PHD, POSTSET, BAH | y, a, c, d, h | P46995 (63–119) |
| POX | Domain associated with HOX-domains | 50 | α | Unknown | 20 | HOX | a | Q38897 (199–337) |
| PRE_C2HC | Associated with zinc fingers | 70 | α/β | Unknown | 15 | ZnF_C2HC | d | O44939 [iv] (546–616) |
[i] First column, domain name; second column, domain description (e.g., associated domains or well-described proteins); third column, approximate domain length (number of amino acids); fourth column, secondary structure prediction (Rost et al. 1994) (α: domain consists of α-helices; β: domain consists of β-strands; α/β: domain consists of α-helices and β-strands); fifth column, predicted function of novel domain; sixth column, number of proteins containing the novel domain; seventh column, names of associated domains (domain names are according to the Simple Modular Architecture Research Tool (http://smart.embl-heidelberg.de) (Schultz et al. 1998, 2000) or the domain is defined by Pfam (Bateman et al. 2000)†; eighth column, species representives containing the novel domain. Abbreviations: eu, eubacteria; virus, viruses; y, yeast; a, Arabidopsis thaliana; c, Caenorhabditis elegans; d,Drosophila melanogaster; h, Homo sapiens. The ninth column, gives the accession number of representative protein and region of the detected domain in amino acids.
[ii] Novel domain is accepted, in press, or published recently.
[iii] Unpublished domain.
[iv] Additional HMM searches are needed to define all novel domain-containing proteins.
[v] +The more conserved parts of the domains FYRN andFYRC were called ATA1 and ATA2 in human ALR protein (Prasad et al. 1997) and FYR (merged in one domain) in plant proteins (Balciunas and Ronne 2000), respectively.